Publications 2022

@article{morales_heritable_2022,
	title = {Heritable and {Climatic} {Sources} of {Variation} in {Juvenile} {Tree} {Growth} in an {Austrian} {Common} {Garden} {Experiment} of {Central} {European} {Norway} {Spruce} {Populations}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/13/5/809},
	doi = {10.3390/f13050809},
	abstract = {We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.},
	language = {en},
	number = {5},
	urldate = {2024-03-22},
	journal = {Forests},
	author = {Morales, Laura and Swarts, Kelly},
	month = may,
	year = {2022},
	note = {Number: 5
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {Norway spruce, climate, genotype-by-environment, prediction, tree height},
	pages = {809},
}

We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.

@article{korolyova_last_2022,
	title = {The {Last} {Trees} {Standing}: {Climate} modulates tree survival factors during a prolonged bark beetle outbreak in {Europe}},
	volume = {322},
	issn = {0168-1923},
	shorttitle = {The {Last} {Trees} {Standing}},
	url = {https://www.sciencedirect.com/science/article/pii/S0168192322002143},
	doi = {10.1016/j.agrformet.2022.109025},
	abstract = {Plant traits are an expression of strategic tradeoffs in plant performance that determine variation in allocation of finite resources to alternate physiological functions. Climate factors interact with plant traits to mediate tree survival. This study investigated survival dynamics in Norway spruce (Picea abies) in relation to tree-level morphological traits during a prolonged multi-year outbreak of the bark beetle, Ips typographus, in Central Europe. We acquired datasets describing the trait attributes of individual spruce using remote sensing and field surveys. We used nonlinear regression in a hypothesis-driven framework to quantify survival probability as a function of tree size, crown morphology, intraspecific competition and a growing season water balance. Extant spruce trees that persisted through the outbreak were spatially clustered, suggesting that survival was a non-random process. Larger diameter trees were more susceptible to bark beetles, reflecting either life history tradeoffs or a dynamic interaction between defense capacity and insect aggregation behavior. Competition had a strong negative effect on survival, presumably through resource limitation. Trees with more extensive crowns were buffered against bark beetles, ostensibly by a more robust photosynthetic capability and greater carbon reserves. The outbreak spanned a warming trend and conditions of anomalous aridity. Sustained water limitation during this period amplified the consequences of other factors, rendering even smaller trees vulnerable to colonization by insects. Our results are in agreement with prior research indicating that climate change has the potential to intensify bark beetle activity. However, forest outcomes will depend on complex cross-scale interactions between global climate trends and tree-level trait factors, as well as feedback effects associated with landscape patterns of stand structural diversity.},
	urldate = {2024-03-22},
	journal = {Agricultural and Forest Meteorology},
	author = {Korolyova, Nataliya and Buechling, Arne and Ďuračiová, Renata and Zabihi, Khodabakhsh and Turčáni, Marek and Svoboda, Miroslav and Bláha, Jaromír and Swarts, Kelly and Poláček, Miroslav and Hradecký, Jaromir and Červenka, Jaroslav and Němčák, Pavel and Schlyter, Fredrik and Jakuš, Rastislav},
	month = jul,
	year = {2022},
	keywords = {Carbon, Climate change, Competition, Crown shading, Drought, Tree survival},
	pages = {109025},
}

Plant traits are an expression of strategic tradeoffs in plant performance that determine variation in allocation of finite resources to alternate physiological functions. Climate factors interact with plant traits to mediate tree survival. This study investigated survival dynamics in Norway spruce (Picea abies) in relation to tree-level morphological traits during a prolonged multi-year outbreak of the bark beetle, Ips typographus, in Central Europe. We acquired datasets describing the trait attributes of individual spruce using remote sensing and field surveys. We used nonlinear regression in a hypothesis-driven framework to quantify survival probability as a function of tree size, crown morphology, intraspecific competition and a growing season water balance. Extant spruce trees that persisted through the outbreak were spatially clustered, suggesting that survival was a non-random process. Larger diameter trees were more susceptible to bark beetles, reflecting either life history tradeoffs or a dynamic interaction between defense capacity and insect aggregation behavior. Competition had a strong negative effect on survival, presumably through resource limitation. Trees with more extensive crowns were buffered against bark beetles, ostensibly by a more robust photosynthetic capability and greater carbon reserves. The outbreak spanned a warming trend and conditions of anomalous aridity. Sustained water limitation during this period amplified the consequences of other factors, rendering even smaller trees vulnerable to colonization by insects. Our results are in agreement with prior research indicating that climate change has the potential to intensify bark beetle activity. However, forest outcomes will depend on complex cross-scale interactions between global climate trends and tree-level trait factors, as well as feedback effects associated with landscape patterns of stand structural diversity.

@incollection{anjam_rna_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {{RNA} {Isolation} from {Nematode}-{Induced} {Feeding} {Sites} in {Arabidopsis} {RootsRoots} {Using} {Laser} {Capture} {Microdissection}},
	isbn = {978-1-07-162297-1},
	url = {https://doi.org/10.1007/978-1-0716-2297-1_22},
	abstract = {Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.},
	language = {en},
	urldate = {2022-04-29},
	booktitle = {Environmental {Responses} in {Plants}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Anjam, Muhammad Shahzad and Siddique, Shahid and Marhavý, Peter},
	editor = {Duque, Paula and Szakonyi, Dóra},
	year = {2022},
	keywords = {Arabidopsis root dissection, Laser capture dissection, Plant-nematode infection, RNA extraction, Syncytial cell isolation},
	pages = {313--324},
}

Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.

@article{kolbeck_casp_2022,
	title = {{CASP} microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of {LOTR1}},
	volume = {11},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.69602},
	doi = {10/gpjfdm},
	abstract = {Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.},
	urldate = {2022-02-17},
	journal = {eLife},
	author = {Kolbeck, Andreas and Marhavý, Peter and De Bellis, Damien and Li, Baohai and Kamiya, Takehiro and Fujiwara, Toru and Kalmbach, Lothar and Geldner, Niko},
	editor = {Benitez-Alfonso, Yoselin and Kleine-Vehn, Jürgen and Jallais, Yvon and Somssich, Marc},
	month = jan,
	year = {2022},
	keywords = {arabidopsis, casparian strip, endodermis, microdomains, neprosin, network},
	pages = {e69602},
}

Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.

@article{de_bellis_extracellular_2022,
	title = {Extracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-29110-0},
	doi = {10.1038/s41467-022-29110-0},
	abstract = {Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots. Suberin is deposited in most suberizing cells in the form of lamellae just outside of the plasma membrane, below the primary cell wall. How monomeric suberin precursors, thought to be synthesized at the endoplasmic reticulum, are transported outside of the cell, for polymerization into suberin lamellae has remained obscure. Using electron-microscopy, we observed large numbers of extracellular vesiculo-tubular structures (EVs) to accumulate specifically in suberizing cells, in both chemically and cryo-fixed samples. EV presence correlates perfectly with root suberization and we could block suberin deposition and vesicle accumulation by affecting early, as well as late steps in the secretory pathway. Whereas many previous reports have described EVs in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in the formation of a major cell wall polymer.},
	language = {en},
	number = {1},
	urldate = {2024-02-08},
	journal = {Nature Communications},
	author = {De Bellis, Damien and Kalmbach, Lothar and Marhavý, Peter and Daraspe, Jean and Geldner, Niko and Barberon, Marie},
	month = mar,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Plant cell biology, Plant development},
	pages = {1489},
}

Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots. Suberin is deposited in most suberizing cells in the form of lamellae just outside of the plasma membrane, below the primary cell wall. How monomeric suberin precursors, thought to be synthesized at the endoplasmic reticulum, are transported outside of the cell, for polymerization into suberin lamellae has remained obscure. Using electron-microscopy, we observed large numbers of extracellular vesiculo-tubular structures (EVs) to accumulate specifically in suberizing cells, in both chemically and cryo-fixed samples. EV presence correlates perfectly with root suberization and we could block suberin deposition and vesicle accumulation by affecting early, as well as late steps in the secretory pathway. Whereas many previous reports have described EVs in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in the formation of a major cell wall polymer.

@article{nookaraju_understanding_2022,
	title = {Understanding the {Modus} {Operandi} of {Class} {II} {KNOX} {Transcription} {Factors} in {Secondary} {Cell} {Wall} {Biosynthesis}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/4/493},
	doi = {10.3390/plants11040493},
	abstract = {Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.},
	language = {en},
	number = {4},
	urldate = {2023-11-14},
	journal = {Plants},
	author = {Nookaraju, Akula and Pandey, Shashank K. and Ahlawat, Yogesh K. and Joshi, Chandrashekhar P.},
	month = jan,
	year = {2022},
	note = {Number: 4
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {KNOX II transcription factors, bioethanol, saccharification, secondary cell walls, xylan, xylem and fiber development},
	pages = {493},
}

Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.

@article{liu_repetitive_2022,
	title = {Repetitive {Elements}, {Sequence} {Turnover} and {Cyto}-{Nuclear} {Gene} {Transfer} in {Gymnosperm} {Mitogenomes}},
	volume = {13},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2022.867736},
	abstract = {Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of Platycladus orientalis (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23\% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion (r = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time (r = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8–12 protein-coding genes, of which 4–7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Liu, Hui and Zhao, Wei and Zhang, Ren-Gang and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2022},
	keywords = {⛔ No DOI found},
}

Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of Platycladus orientalis (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion (r = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time (r = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8–12 protein-coding genes, of which 4–7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.

@article{nakano_enhancement_2022,
	title = {Enhancement of {Secondary} {Cell} {Wall} {Formation} in {Poplar} {Xylem} {Using} a {Self}-{Reinforced} {System} of {Secondary} {Cell} {Wall}-{Related} {Transcription} {Factors}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.819360},
	abstract = {The secondary cell wall (SCW) in the xylem is one of the largest sink organs of carbon in woody plants, and is considered a promising sustainable bioresource for biofuels and biomaterials. To enhance SCW formation in poplar (Populus sp.) xylem, we developed a self-reinforced system of SCW-related transcription factors from Arabidopsis thaliana, involving VASCULAR-RELATED NAC-DOMAIN7 (VND7), SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN 1/NAC SECONDARY WALL THICKENING-PROMOTING FACTOR3 (SND1/NST3), and MYB46. In this system, these transcription factors were fused with the transactivation domain VP16 and expressed under the control of the Populus trichocarpa CesA18 (PtCesA18) gene promoter, creating the chimeric genes PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16. The PtCesA18 promoter is active in tissues generating SCWs, and can be regulated by AtVND7, AtSND1, and AtMYB46; thus, the expression levels of PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16 are expected to be boosted in SCW-generating tissues. In the transgenic hybrid aspens (Populus tremula × tremuloides T89) expressing PtCesA18pro::AtSND1:VP16 or PtCesA18pro::AtMYB46:VP16 grown in sterile half-strength Murashige and Skoog growth medium, SCW thickening was significantly enhanced in the secondary xylem cells, while the PtCesA18pro::AtVND7:VP16 plants showed stunted xylem formation, possibly because of the enhanced programmed cell death (PCD) in the xylem regions. After acclimation, the transgenic plants were transferred from the sterile growth medium to pots of soil in the greenhouse, where only the PtCesA18pro::AtMYB46:VP16 aspens survived. A nuclear magnetic resonance footprinting cell wall analysis and enzymatic saccharification analysis demonstrated that PtCesA18pro::AtMYB46:VP16 influences cell wall properties such as the ratio of syringyl (S) and guaiacyl (G) units of lignin, the abundance of the lignin β-aryl ether and resinol bonds, and hemicellulose acetylation levels. Together, these data indicate that we have created a self-reinforced system using SCW-related transcription factors to enhance SCW accumulation.},
	urldate = {2023-03-27},
	journal = {Frontiers in Plant Science},
	author = {Nakano, Yoshimi and Endo, Hitoshi and Gerber, Lorenz and Hori, Chiaki and Ihara, Ayumi and Sekimoto, Masayo and Matsumoto, Tomoko and Kikuchi, Jun and Ohtani, Misato and Demura, Taku},
	month = mar,
	year = {2022},
	keywords = {⛔ No DOI found},
}

The secondary cell wall (SCW) in the xylem is one of the largest sink organs of carbon in woody plants, and is considered a promising sustainable bioresource for biofuels and biomaterials. To enhance SCW formation in poplar (Populus sp.) xylem, we developed a self-reinforced system of SCW-related transcription factors from Arabidopsis thaliana, involving VASCULAR-RELATED NAC-DOMAIN7 (VND7), SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN 1/NAC SECONDARY WALL THICKENING-PROMOTING FACTOR3 (SND1/NST3), and MYB46. In this system, these transcription factors were fused with the transactivation domain VP16 and expressed under the control of the Populus trichocarpa CesA18 (PtCesA18) gene promoter, creating the chimeric genes PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16. The PtCesA18 promoter is active in tissues generating SCWs, and can be regulated by AtVND7, AtSND1, and AtMYB46; thus, the expression levels of PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16 are expected to be boosted in SCW-generating tissues. In the transgenic hybrid aspens (Populus tremula × tremuloides T89) expressing PtCesA18pro::AtSND1:VP16 or PtCesA18pro::AtMYB46:VP16 grown in sterile half-strength Murashige and Skoog growth medium, SCW thickening was significantly enhanced in the secondary xylem cells, while the PtCesA18pro::AtVND7:VP16 plants showed stunted xylem formation, possibly because of the enhanced programmed cell death (PCD) in the xylem regions. After acclimation, the transgenic plants were transferred from the sterile growth medium to pots of soil in the greenhouse, where only the PtCesA18pro::AtMYB46:VP16 aspens survived. A nuclear magnetic resonance footprinting cell wall analysis and enzymatic saccharification analysis demonstrated that PtCesA18pro::AtMYB46:VP16 influences cell wall properties such as the ratio of syringyl (S) and guaiacyl (G) units of lignin, the abundance of the lignin β-aryl ether and resinol bonds, and hemicellulose acetylation levels. Together, these data indicate that we have created a self-reinforced system using SCW-related transcription factors to enhance SCW accumulation.

@article{nie_potential_2022,
	title = {Potential allopolyploid origin of {Ericales} revealed with gene-tree reconciliation},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1006904},
	abstract = {Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from {\textasciitilde} 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.},
	urldate = {2023-03-27},
	journal = {Frontiers in Plant Science},
	author = {Nie, Shuai and Tian, Xue-Chan and Kong, Lei and Zhao, Shi-Wei and Chen, Zhao-Yang and Jiao, Si-Qian and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Zhao, Wei and Mao, Jian-Feng},
	month = nov,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.

@article{an_high_2022,
	title = {High quality haplotype-resolved genome assemblies of {Populus} tomentosa {Carr}., a stabilized interspecific hybrid species widespread in {Asia}},
	volume = {22},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13507},
	doi = {10.1111/1755-0998.13507},
	abstract = {Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {An, Xinmin and Gao, Kai and Chen, Zhong and Li, Juan and Yang, Xiong and Yang, Xiaoyu and Zhou, Jing and Guo, Ting and Zhao, Tianyun and Huang, Sai and Miao, Deyu and Ullah Khan, Wasif and Rao, Pian and Ye, Meixia and Lei, Bingqi and Liao, Weihua and Wang, Jia and Ji, Lexiang and Li, Ying and Guo, Bin and Siddig Mustafa, Nada and Li, Shanwen and Yun, Quanzheng and Keller, Stephen R. and Mao, Jian-Feng and Zhang, Ren-Gang and Strauss, Steven H.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13507},
	keywords = {PacBio long-read sequencing, Populus tomentosa, forest biotechnology, haplotype-resolved genome assembly, hybridization},
	pages = {786--802},
}

Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.

@article{xu_uv-b_2022,
	title = {{UV}-{B} and {UV}-{C} radiation trigger both common and distinctive signal perceptions and transmissions in {Pinus} tabuliformis {Carr}.},
	volume = {42},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpac021},
	doi = {10.1093/treephys/tpac021},
	abstract = {In plants, ultraviolet (UV)-light is an important driver for growth and natural distribution, and is also a valuable tool for manipulating productivity as well as biotic interactions. Understanding of plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene coexpression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis, and conversely, the improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C radiation. From these subnetworks, we further identified phototropins as potentially important elements in both UV-B and UV-C signaling and, for the first time, suggesting peptide hormones to be involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in the defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a nonmodel plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.},
	number = {8},
	urldate = {2023-04-27},
	journal = {Tree Physiology},
	author = {Xu, Jie and Luo, Hang and Zhou, Shan-Shan and Jiao, Si-Qian and Jia, Kai-Hua and Nie, Shuai and Liu, Hui and Zhao, Wei and Wang, Xiao-Ru and El-Kassaby, Yousry A and Porth, Ilga and Mao, Jian-Feng},
	month = aug,
	year = {2022},
	pages = {1587--1600},
}

In plants, ultraviolet (UV)-light is an important driver for growth and natural distribution, and is also a valuable tool for manipulating productivity as well as biotic interactions. Understanding of plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene coexpression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis, and conversely, the improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C radiation. From these subnetworks, we further identified phototropins as potentially important elements in both UV-B and UV-C signaling and, for the first time, suggesting peptide hormones to be involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in the defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a nonmodel plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.

@article{ma_lilac_2022,
	title = {Lilac ({Syringa} oblata) genome provides insights into its evolution and molecular mechanism of petal color change},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03646-9},
	doi = {10.1038/s42003-022-03646-9},
	abstract = {Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6\%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Communications Biology},
	author = {Ma, Bo and Wu, Jing and Shi, Tian-Le and Yang, Yun-Yao and Wang, Wen-Bo and Zheng, Yi and Su, Shu-Chai and Yao, Yun-Cong and Xue, Wen-Bo and Porth, Ilga and El-Kassaby, Yousry A. and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
	month = jul,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Gene regulatory networks, Genomics, Metabolomics, Secondary metabolism, Transcriptomics},
	pages = {1--13},
}

Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac.

@article{jia_subphaser_2022,
	title = {{SubPhaser}: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers},
	volume = {235},
	issn = {1469-8137},
	shorttitle = {{SubPhaser}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18173},
	doi = {10.1111/nph.18173},
	abstract = {With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {New Phytologist},
	author = {Jia, Kai-Hua and Wang, Zhao-Xuan and Wang, Longxin and Li, Guang-Yuan and Zhang, Wei and Wang, Xiao-Ling and Xu, Fang-Ji and Jiao, Si-Qian and Zhou, Shan-Shan and Liu, Hui and Ma, Yongpeng and Bi, Guiqi and Zhao, Wei and El-Kassaby, Yousry A. and Porth, Ilga and Li, Guowei and Zhang, Ren-Gang and Mao, Jian-Feng},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18173},
	keywords = {SubPhaser, allopolyploids, k-mer, phasing, subgenome},
	pages = {801--809},
}

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

@article{priebe_transformative_2022,
	title = {Transformative change in context—stakeholders’ understandings of leverage at the forest–climate nexus},
	volume = {17},
	issn = {1862-4057},
	url = {https://doi.org/10.1007/s11625-022-01090-6},
	doi = {10.1007/s11625-022-01090-6},
	abstract = {Transformation acquires its meaning within contexts and particular settings where transformative change is experienced, and where people engage in meaning-making. We used the forest–climate nexus in Sweden as an empirical case study, and the leverage-points perspective as an analytical lens. The aim was to investigate contextual leverage for transformative change, and how our use of context and relations shapes our understanding of transformation and leverage for change. The empirical basis was a whole-day workshop, held in both northern and southern Sweden, for local forest stakeholders. To detract from current conflict and barriers to change, we asked the stakeholders to reflect on transformative change in the past and in the future, and the spatio-temporal relations that form the forest–climate nexus. Our analysis suggests that leverage associated with a transformative change in the future is commonly seen as universal and detached from context, reflecting, for example, national and global discourses on forests and climate change. Regarding transformative changes in the past, however, contextual leverage is linked to the community values and pluralism that drove the change in particular situations. Focusing on the complex spatio-temporal relations and meaning-making helps identify how leverage emerges from context, and how leverage also acquires a richer meaning for people experiencing transformative change.},
	language = {en},
	number = {5},
	urldate = {2023-03-27},
	journal = {Sustainability Science},
	author = {Priebe, Janina and Reimerson, Elsa and Hallberg-Sramek, Isabella and Sténs, Anna and Sandström, Camilla and Mårald, Erland},
	month = sep,
	year = {2022},
	keywords = {Community, Leverage points, Stakeholders, Sweden, Transdisciplinary, Transformation},
	pages = {1921--1938},
}

Transformation acquires its meaning within contexts and particular settings where transformative change is experienced, and where people engage in meaning-making. We used the forest–climate nexus in Sweden as an empirical case study, and the leverage-points perspective as an analytical lens. The aim was to investigate contextual leverage for transformative change, and how our use of context and relations shapes our understanding of transformation and leverage for change. The empirical basis was a whole-day workshop, held in both northern and southern Sweden, for local forest stakeholders. To detract from current conflict and barriers to change, we asked the stakeholders to reflect on transformative change in the past and in the future, and the spatio-temporal relations that form the forest–climate nexus. Our analysis suggests that leverage associated with a transformative change in the future is commonly seen as universal and detached from context, reflecting, for example, national and global discourses on forests and climate change. Regarding transformative changes in the past, however, contextual leverage is linked to the community values and pluralism that drove the change in particular situations. Focusing on the complex spatio-temporal relations and meaning-making helps identify how leverage emerges from context, and how leverage also acquires a richer meaning for people experiencing transformative change.

@article{colesie_longest_2022,
	title = {The {Longest} {Baseline} {Record} of {Vegetation} {Dynamics} in {Antarctica} {Reveals} {Acute} {Sensitivity} to {Water} {Availability}},
	volume = {10},
	issn = {2328-4277},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2022EF002823},
	doi = {10.1029/2022EF002823},
	abstract = {Against a changing climate, the development of evidence-based and progressive conservation policies depends on robust and quantitative baseline studies to resolve habitat natural variability and rate of change. Despite Antarctica's significant role in global climate regulation, climate trend estimates for continental Antarctica are ambiguous due to sparse long-term in situ records. Here, we present the longest, spatially explicit survey of Antarctic vegetation by harmonizing historic vegetation mapping with modern remote sensing techniques. In 1961, E. D. Rudolph established a permanent survey plot at Cape Hallett, one of the most botanically diverse areas along the Ross Sea coastline, harboring all known types of non-vascular Antarctic vegetation. Following a survey in 2004 using ground-based photography, we conducted the third survey of Rudolph's Plot in 2018 using near-ground remote sensing and methodologies closely mirroring the two historic surveys to identify long-term changes and trends. Our results revealed that the vegetation at Cape Hallett remained stable over the past six decades with no evidence of transformation related to a changing climate. Instead, the local vegetation shows strong seasonal phenology, distribution patterns that are driven by water availability, and steady perennial growth of moss. Given that East Antarctica is at the tipping point of drastic change in the near future, with biological change having been reported at certain locations, this record represents a unique and potentially the last opportunity to establish a meaningful biological sentinel that will allow us to track subtle yet impactful environmental change in terrestrial Antarctica in the 21st century.},
	language = {en},
	number = {8},
	urldate = {2023-03-27},
	journal = {Earth's Future},
	author = {Colesie, Claudia and Pan, Yueming and Cary, S. Craig and Gemal, Emma and Brabyn, Lars and Kim, Jeong-Hoon and Green, T. G. Allan and Lee, Charles K.},
	month = aug,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2022EF002823},
	keywords = {Antarctica, baseline environment, climate change, moss, remote sensing, terrestrial ecosystem},
	pages = {e2022EF002823},
}

Against a changing climate, the development of evidence-based and progressive conservation policies depends on robust and quantitative baseline studies to resolve habitat natural variability and rate of change. Despite Antarctica's significant role in global climate regulation, climate trend estimates for continental Antarctica are ambiguous due to sparse long-term in situ records. Here, we present the longest, spatially explicit survey of Antarctic vegetation by harmonizing historic vegetation mapping with modern remote sensing techniques. In 1961, E. D. Rudolph established a permanent survey plot at Cape Hallett, one of the most botanically diverse areas along the Ross Sea coastline, harboring all known types of non-vascular Antarctic vegetation. Following a survey in 2004 using ground-based photography, we conducted the third survey of Rudolph's Plot in 2018 using near-ground remote sensing and methodologies closely mirroring the two historic surveys to identify long-term changes and trends. Our results revealed that the vegetation at Cape Hallett remained stable over the past six decades with no evidence of transformation related to a changing climate. Instead, the local vegetation shows strong seasonal phenology, distribution patterns that are driven by water availability, and steady perennial growth of moss. Given that East Antarctica is at the tipping point of drastic change in the near future, with biological change having been reported at certain locations, this record represents a unique and potentially the last opportunity to establish a meaningful biological sentinel that will allow us to track subtle yet impactful environmental change in terrestrial Antarctica in the 21st century.

@article{tan_integrating_2022,
	title = {Integrating genome-wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in {Eucalyptus}},
	volume = {15},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tpg2.20208},
	doi = {10.1002/tpg2.20208},
	abstract = {Genome-wide association studies (GWAS) is a powerful and widely used approach to decipher the genetic control of complex traits. Still, a significant challenge for dissecting quantitative traits in forest trees is statistical power. This study uses a population consisting of 1,123 samples derived from two successive generations of crosses between Eucalyptus grandis (W. Hill) and E. urophylla (S.T. Blake). All samples have been phenotyped for growth and wood property traits and genotyped using the EuChip60K chip, yielding 37,832 informative single nucleotide polymorphisms (SNPs). We use multi-locus GWAS models to assess additive and dominance effects to identify markers associated with growth and wood property traits in the eucalypt hybrids. Additive and dominance association models identified 78 and 82 significant SNPs across all traits, respectively, which captured between 39 and 86\% of the genomic-based heritability. We also used SNPs identified from the GWAS and SNPs using less stringent significance thresholds to evaluate predictive abilities in a genomic selection framework. Genomic selection models based on the top 1\% SNPs captured a substantially greater proportion of the genetic variance of traits compared with when we used all SNPs for model training. The prediction ability of estimated breeding values improved significantly for all traits when using either the top 1\% SNPs or SNPs identified using a relaxed p value threshold (p {\textless} 10–3). This study also highlights the added value of incorporating dominance effects for identifying genomic regions controlling growth traits in trees. Moreover, integrating GWAS results into genomic selection method provides enhanced power relative to discrete associations for identifying genomic variation potentially valuable for forest tree breeding.},
	language = {en},
	number = {2},
	urldate = {2023-03-27},
	journal = {The Plant Genome},
	author = {Tan, Biyue and Ingvarsson, Pär K.},
	month = apr,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.20208},
	pages = {e20208},
}

Genome-wide association studies (GWAS) is a powerful and widely used approach to decipher the genetic control of complex traits. Still, a significant challenge for dissecting quantitative traits in forest trees is statistical power. This study uses a population consisting of 1,123 samples derived from two successive generations of crosses between Eucalyptus grandis (W. Hill) and E. urophylla (S.T. Blake). All samples have been phenotyped for growth and wood property traits and genotyped using the EuChip60K chip, yielding 37,832 informative single nucleotide polymorphisms (SNPs). We use multi-locus GWAS models to assess additive and dominance effects to identify markers associated with growth and wood property traits in the eucalypt hybrids. Additive and dominance association models identified 78 and 82 significant SNPs across all traits, respectively, which captured between 39 and 86% of the genomic-based heritability. We also used SNPs identified from the GWAS and SNPs using less stringent significance thresholds to evaluate predictive abilities in a genomic selection framework. Genomic selection models based on the top 1% SNPs captured a substantially greater proportion of the genetic variance of traits compared with when we used all SNPs for model training. The prediction ability of estimated breeding values improved significantly for all traits when using either the top 1% SNPs or SNPs identified using a relaxed p value threshold (p \textless 10–3). This study also highlights the added value of incorporating dominance effects for identifying genomic regions controlling growth traits in trees. Moreover, integrating GWAS results into genomic selection method provides enhanced power relative to discrete associations for identifying genomic variation potentially valuable for forest tree breeding.

@article{bacete_theseus1_2022,
	title = {{THESEUS1} modulates cell wall stiffness and abscisic acid production in {Arabidopsis} thaliana},
	volume = {119},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2119258119},
	doi = {10.1073/pnas.2119258119},
	abstract = {Plant cells can be distinguished from animal cells by their cell walls and high-turgor pressure. Although changes in turgor and the stiffness of cell walls seem coordinated, we know little about the mechanism responsible for coordination. Evidence has accumulated that plants, like yeast, have a dedicated cell wall integrity maintenance mechanism. It monitors the functional integrity of the wall and maintains integrity through adaptive responses induced by cell wall damage arising during growth, development, and interactions with the environment. These adaptive responses include osmosensitive induction of phytohormone production, defense responses, as well as changes in cell wall composition and structure. Here, we investigate how the cell wall integrity maintenance mechanism coordinates changes in cell wall stiffness and turgor in Arabidopsis thaliana. We show that the production of abscisic acid (ABA), the phytohormone-modulating turgor pressure, and responses to drought depend on the presence of a functional cell wall. We find that the cell wall integrity sensor THESEUS1 modulates mechanical properties of walls, turgor loss point, ABA biosynthesis, and ABA-controlled processes. We identify RECEPTOR-LIKE PROTEIN 12 as a component of cell wall integrity maintenance–controlling, cell wall damage–induced jasmonic acid (JA) production. We propose that THE1 is responsible for coordinating changes in turgor pressure and cell wall stiffness.},
	number = {1},
	urldate = {2023-03-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Bacete, Laura and Schulz, Julia and Engelsdorf, Timo and Bartosova, Zdenka and Vaahtera, Lauri and Yan, Guqi and Gerhold, Joachim Matthias and Tichá, Tereza and Øvstebø, Camilla and Gigli-Bisceglia, Nora and Johannessen-Starheim, Svanhild and Margueritat, Jeremie and Kollist, Hannes and Dehoux, Thomas and McAdam, Scott A. M. and Hamann, Thorsten},
	month = jan,
	year = {2022},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2119258119},
}

Plant cells can be distinguished from animal cells by their cell walls and high-turgor pressure. Although changes in turgor and the stiffness of cell walls seem coordinated, we know little about the mechanism responsible for coordination. Evidence has accumulated that plants, like yeast, have a dedicated cell wall integrity maintenance mechanism. It monitors the functional integrity of the wall and maintains integrity through adaptive responses induced by cell wall damage arising during growth, development, and interactions with the environment. These adaptive responses include osmosensitive induction of phytohormone production, defense responses, as well as changes in cell wall composition and structure. Here, we investigate how the cell wall integrity maintenance mechanism coordinates changes in cell wall stiffness and turgor in Arabidopsis thaliana. We show that the production of abscisic acid (ABA), the phytohormone-modulating turgor pressure, and responses to drought depend on the presence of a functional cell wall. We find that the cell wall integrity sensor THESEUS1 modulates mechanical properties of walls, turgor loss point, ABA biosynthesis, and ABA-controlled processes. We identify RECEPTOR-LIKE PROTEIN 12 as a component of cell wall integrity maintenance–controlling, cell wall damage–induced jasmonic acid (JA) production. We propose that THE1 is responsible for coordinating changes in turgor pressure and cell wall stiffness.

@article{boussardon_rpn12a_2022,
	title = {The {RPN12a} proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03998-2},
	doi = {10.1038/s42003-022-03998-2},
	abstract = {The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.},
	language = {en},
	number = {1},
	urldate = {2022-10-03},
	journal = {Communications Biology},
	author = {Boussardon, Clément and Bag, Pushan and Juvany, Marta and Šimura, Jan and Ljung, Karin and Jansson, Stefan and Keech, Olivier},
	month = sep,
	year = {2022},
	keywords = {Leaf development, Senescence},
	pages = {1--14},
}

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

@article{castro_soil_2022,
	title = {Soil {Microbiome} {Influences} on {Seedling} {Establishment} and {Growth} of {Prosopis} chilensis and {Prosopis} tamarugo from {Northern} {Chile}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/20/2717},
	doi = {10.3390/plants11202717},
	abstract = {Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.},
	language = {en},
	number = {20},
	urldate = {2022-10-18},
	journal = {Plants},
	author = {Castro, David and Concha, Christopher and Jamett, Fabiola and Ibáñez, Cristian and Hurry, Vaughan},
	month = oct,
	year = {2022},
	keywords = {\textit{Prosopis chilensis}, \textit{Prosopis tamarugo}, Atacama desert, northern Chile, plant–microbe interactions, soil microbiome},
	pages = {2717},
}

Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.

@article{chowdhury_laccaria_2022,
	title = {Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with {Populus} tremula × {Populus} tremuloides},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18358},
	doi = {10.1111/nph.18358},
	abstract = {The development of ectomycorrhizal (ECM) symbioses between soil fungi and tree roots requires modification of root cell walls. The pectin-mediated adhesion between adjacent root cells loosens to accommodate fungal hyphae in the Hartig net, facilitating nutrient exchange between partners. We investigated the role of fungal pectin modifying enzymes in Laccaria bicolor for ECM formation with Populus tremula × Populus tremuloides. We combine transcriptomics of cell-wall-related enzymes in both partners during ECM formation, immunolocalisation of pectin (Homogalacturonan, HG) epitopes in different methylesterification states, pectin methylesterase (PME) activity assays and functional analyses of transgenic L. bicolor to uncover pectin modification mechanisms and the requirement of fungal pectin methylesterases (LbPMEs) for ECM formation. Immunolocalisation identified remodelling of pectin towards de-esterified HG during ECM formation, which was accompanied by increased LbPME1 expression and PME activity. Overexpression or RNAi of the ECM-induced LbPME1 in transgenic L. bicolor lines led to reduced ECM formation. Hartig Nets formed with LbPME1 RNAi lines were shallower, whereas those formed with LbPME1 overexpressors were deeper. This suggests that LbPME1 plays a role in ECM formation potentially through HG de-esterification, which initiates loosening of adjacent root cells to facilitate Hartig net formation.},
	language = {en},
	number = {2},
	urldate = {2022-10-03},
	journal = {New Phytologist},
	author = {Chowdhury, Jamil and Kemppainen, Minna and Delhomme, Nicolas and Shutava, Iryna and Zhou, Jingjing and Takahashi, Junko and Pardo, Alejandro G. and Lundberg-Felten, Judith},
	month = oct,
	year = {2022},
	keywords = {Laccaria bicolor, Populus, cell wall, cell-wall, cell-wall remodelling, cell-wall-modifying enzymes, ectomycorrhiza, pectin, pectin methylesterase},
	pages = {639--655},
}

The development of ectomycorrhizal (ECM) symbioses between soil fungi and tree roots requires modification of root cell walls. The pectin-mediated adhesion between adjacent root cells loosens to accommodate fungal hyphae in the Hartig net, facilitating nutrient exchange between partners. We investigated the role of fungal pectin modifying enzymes in Laccaria bicolor for ECM formation with Populus tremula × Populus tremuloides. We combine transcriptomics of cell-wall-related enzymes in both partners during ECM formation, immunolocalisation of pectin (Homogalacturonan, HG) epitopes in different methylesterification states, pectin methylesterase (PME) activity assays and functional analyses of transgenic L. bicolor to uncover pectin modification mechanisms and the requirement of fungal pectin methylesterases (LbPMEs) for ECM formation. Immunolocalisation identified remodelling of pectin towards de-esterified HG during ECM formation, which was accompanied by increased LbPME1 expression and PME activity. Overexpression or RNAi of the ECM-induced LbPME1 in transgenic L. bicolor lines led to reduced ECM formation. Hartig Nets formed with LbPME1 RNAi lines were shallower, whereas those formed with LbPME1 overexpressors were deeper. This suggests that LbPME1 plays a role in ECM formation potentially through HG de-esterification, which initiates loosening of adjacent root cells to facilitate Hartig net formation.

@article{jonasson_characteristics_2022,
	title = {Characteristics of {Cellulose} {Nanofibrils} from {Transgenic} {Trees} with {Reduced} {Expression} of {Cellulose} {Synthase} {Interacting} 1},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-4991},
	url = {https://www.mdpi.com/2079-4991/12/19/3448},
	doi = {10.3390/nano12193448},
	abstract = {Cellulose nanofibrils can be derived from the native load-bearing cellulose microfibrils in wood. These microfibrils are synthesized by a cellulose synthase enzyme complex that resides in the plasma membrane of developing wood cells. It was previously shown that transgenic hybrid aspen trees with reduced expression of CSI1 have different wood mechanics and cellulose microfibril properties. We hypothesized that these changes in the native cellulose may affect the quality of the corresponding nanofibrils. To test this hypothesis, wood from wild-type and transgenic trees with reduced expression of CSI1 was subjected to oxidative nanofibril isolation. The transgenic wood-extracted nanofibrils exhibited a significantly lower suspension viscosity and estimated surface area than the wild-type nanofibrils. Furthermore, the nanofibril networks manufactured from the transgenics exhibited high stiffness, as well as reduced water uptake, tensile strength, strain-to-break, and degree of polymerization. Presumably, the difference in wood properties caused by the decreased expression of CSI1 resulted in nanofibrils with distinctive qualities. The observed changes in the physicochemical properties suggest that the differences were caused by changes in the apparent nanofibril aspect ratio and surface accessibility. This study demonstrates the possibility of influencing wood-derived nanofibril quality through the genetic engineering of trees.},
	language = {en},
	number = {19},
	urldate = {2022-10-04},
	journal = {Nanomaterials},
	author = {Jonasson, Simon and Bünder, Anne and Berglund, Linn and Niittylä, Totte and Oksman, Kristiina},
	month = oct,
	year = {2022},
	keywords = {cellulose nanofibrils, fibrillation, network properties, transgenic wood},
	pages = {3448},
}

Cellulose nanofibrils can be derived from the native load-bearing cellulose microfibrils in wood. These microfibrils are synthesized by a cellulose synthase enzyme complex that resides in the plasma membrane of developing wood cells. It was previously shown that transgenic hybrid aspen trees with reduced expression of CSI1 have different wood mechanics and cellulose microfibril properties. We hypothesized that these changes in the native cellulose may affect the quality of the corresponding nanofibrils. To test this hypothesis, wood from wild-type and transgenic trees with reduced expression of CSI1 was subjected to oxidative nanofibril isolation. The transgenic wood-extracted nanofibrils exhibited a significantly lower suspension viscosity and estimated surface area than the wild-type nanofibrils. Furthermore, the nanofibril networks manufactured from the transgenics exhibited high stiffness, as well as reduced water uptake, tensile strength, strain-to-break, and degree of polymerization. Presumably, the difference in wood properties caused by the decreased expression of CSI1 resulted in nanofibrils with distinctive qualities. The observed changes in the physicochemical properties suggest that the differences were caused by changes in the apparent nanofibril aspect ratio and surface accessibility. This study demonstrates the possibility of influencing wood-derived nanofibril quality through the genetic engineering of trees.

@article{ma_endoreplication_2022,
	title = {Endoreplication mediates cell size control via mechanochemical signaling from cell wall},
	volume = {8},
	url = {https://www.science.org/doi/10.1126/sciadv.abq2047},
	doi = {10.1126/sciadv.abq2047},
	abstract = {Endoreplication is an evolutionarily conserved mechanism for increasing nuclear DNA content (ploidy). Ploidy frequently scales with final cell and organ size, suggesting a key role for endoreplication in these processes. However, exceptions exist, and, consequently, the endoreplication-size nexus remains enigmatic. Here, we show that prolonged tissue folding at the apical hook in Arabidopsis requires endoreplication asymmetry under the control of an auxin gradient. We identify a molecular pathway linking endoreplication levels to cell size through cell wall remodeling and stiffness modulation. We find that endoreplication is not only permissive for growth: Endoreplication reduction enhances wall stiffening, actively reducing cell size. The cell wall integrity kinase THESEUS plays a key role in this feedback loop. Our data thus explain the nonlinearity between ploidy levels and size while also providing a molecular mechanism linking mechanochemical signaling with endoreplication-mediated dynamic control of cell growth.},
	number = {49},
	urldate = {2022-12-16},
	journal = {Science Advances},
	author = {Ma, Yuan and Jonsson, Kristoffer and Aryal, Bibek and De Veylder, Lieven and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = dec,
	year = {2022},
	pages = {eabq2047},
}

Endoreplication is an evolutionarily conserved mechanism for increasing nuclear DNA content (ploidy). Ploidy frequently scales with final cell and organ size, suggesting a key role for endoreplication in these processes. However, exceptions exist, and, consequently, the endoreplication-size nexus remains enigmatic. Here, we show that prolonged tissue folding at the apical hook in Arabidopsis requires endoreplication asymmetry under the control of an auxin gradient. We identify a molecular pathway linking endoreplication levels to cell size through cell wall remodeling and stiffness modulation. We find that endoreplication is not only permissive for growth: Endoreplication reduction enhances wall stiffening, actively reducing cell size. The cell wall integrity kinase THESEUS plays a key role in this feedback loop. Our data thus explain the nonlinearity between ploidy levels and size while also providing a molecular mechanism linking mechanochemical signaling with endoreplication-mediated dynamic control of cell growth.

@article{mehra_hydraulic_2022,
	title = {Hydraulic flux–responsive hormone redistribution determines root branching},
	volume = {378},
	url = {https://www.science.org/doi/10.1126/science.add3771},
	doi = {10.1126/science.add3771},
	abstract = {Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.},
	number = {6621},
	urldate = {2022-11-24},
	journal = {Science},
	author = {Mehra, Poonam and Pandey, Bipin K. and Melebari, Dalia and Banda, Jason and Leftley, Nicola and Couvreur, Valentin and Rowe, James and Anfang, Moran and De Gernier, Hugues and Morris, Emily and Sturrock, Craig J. and Mooney, Sacha J. and Swarup, Ranjan and Faulkner, Christine and Beeckman, Tom and Bhalerao, Rishikesh P. and Shani, Eilon and Jones, Alexander M. and Dodd, Ian C. and Sharp, Robert E. and Sadanandom, Ari and Draye, Xavier and Bennett, Malcolm J.},
	month = nov,
	year = {2022},
	pages = {762--768},
}

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.

@article{singh_when_2022,
	title = {When to branch: seasonal control of shoot architecture in trees},
	volume = {289},
	issn = {1742-4658},
	shorttitle = {When to branch},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.16227},
	doi = {10.1111/febs.16227},
	abstract = {Long-lived perennial plants optimize their shoot architecture by responding to seasonal cues. The main strategy used by plants of temperate and boreal regions with respect to surviving the extremely unfavourable conditions of winter comprises the protection of their apical and lateral meristematic tissues. This involves myriads of transcriptional, translational and metabolic changes in the plants because shoot architecture is controlled by multiple pathways that regulate processes such as bud formation and flowering, small RNAs, environmental factors (especially light quality, photoperiod and temperature), hormones, and sugars. Recent studies have begun to reveal how these pathways are recruited for the seasonal adaptation and regulation of shoot architecture in perennial plants, including the role of a regulatory module consisting of antagonistic players terminal flower 1 (TFL1) and like-ap1 (LAP1) in the hybrid aspen. Here, we review recent progress in our understanding of the genetic control of shoot architecture in perennials compared to in annuals.},
	language = {en},
	number = {24},
	urldate = {2022-12-30},
	journal = {The FEBS Journal},
	author = {Singh, Rajesh Kumar and Bhalerao, Rishikesh P. and Maurya, Jay P.},
	month = oct,
	year = {2022},
	keywords = {Axillary buds, Branching, Photoperiod, Seasonal growth, Shoot Architecture, axillary buds, branching, photoperiod, seasonal growth, shoot architecture, temperature},
	pages = {8062--8070},
}

Long-lived perennial plants optimize their shoot architecture by responding to seasonal cues. The main strategy used by plants of temperate and boreal regions with respect to surviving the extremely unfavourable conditions of winter comprises the protection of their apical and lateral meristematic tissues. This involves myriads of transcriptional, translational and metabolic changes in the plants because shoot architecture is controlled by multiple pathways that regulate processes such as bud formation and flowering, small RNAs, environmental factors (especially light quality, photoperiod and temperature), hormones, and sugars. Recent studies have begun to reveal how these pathways are recruited for the seasonal adaptation and regulation of shoot architecture in perennial plants, including the role of a regulatory module consisting of antagonistic players terminal flower 1 (TFL1) and like-ap1 (LAP1) in the hybrid aspen. Here, we review recent progress in our understanding of the genetic control of shoot architecture in perennials compared to in annuals.

@article{cataldo_human_2022,
	title = {The human batokine {EPDR1} regulates β-cell metabolism and function},
	volume = {66},
	issn = {2212-8778},
	url = {https://www.sciencedirect.com/science/article/pii/S2212877822001983},
	doi = {10.1016/j.molmet.2022.101629},
	abstract = {Objective
Ependymin-Related Protein 1 (EPDR1) was recently identified as a secreted human batokine regulating mitochondrial respiration linked to thermogenesis in brown fat. Despite that EPDR1 is expressed in human pancreatic β-cells and that glucose-stimulated mitochondrial metabolism is critical for stimulus-secretion coupling in β-cells, the role of EPDR1 in β-cell metabolism and function has not been investigated.
Methods
EPDR1 mRNA levels in human pancreatic islets from non-diabetic (ND) and type 2 diabetes (T2D) subjects were assessed. Human islets, EndoC-βH1 and INS1 832/13 cells were transfected with scramble (control) and EPDR1 siRNAs (EPDR1-KD) or treated with human EPDR1 protein, and glucose-stimulated insulin secretion (GSIS) assessed by ELISA. Mitochondrial metabolism was investigated by extracellular flux analyzer, confocal microscopy and mass spectrometry-based metabolomics analysis.
Results
EPDR1 mRNA expression was upregulated in human islets from T2D and obese donors and positively correlated to BMI of donors. In T2D donors, EPDR1 mRNA levels negatively correlated with HbA1c and positively correlated with GSIS. EPDR1 silencing in human islets and β-cell lines reduced GSIS whereas treatment with human EPDR1 protein increased GSIS. Epdr1 silencing in INS1 832/13 cells reduced glucose- and pyruvate- but not K+-stimulated insulin secretion. Metabolomics analysis in Epdr1-KD INS1 832/13 cells suggests diversion of glucose-derived pyruvate to lactate production and decreased malate-aspartate shuttle and the tricarboxylic acid (TCA) cycle activity. The glucose-stimulated rise in mitochondrial respiration and ATP/ADP-ratio was impaired in Epdr1-deficient cells.
Conclusion
These results suggests that to maintain glucose homeostasis in obese people, upregulation of EPDR1 may improve β-cell function via channelling glycolysis-derived pyruvate to the mitochondrial TCA cycle.},
	language = {en},
	urldate = {2022-12-22},
	journal = {Molecular Metabolism},
	author = {Cataldo, Luis Rodrigo and Gao, Qian and Argemi-Muntadas, Lidia and Hodek, Ondrej and Cowan, Elaine and Hladkou, Sergey and Gheibi, Sevda and Spégel, Peter and Prasad, Rashmi B. and Eliasson, Lena and Scheele, Camilla and Fex, Malin and Mulder, Hindrik and Moritz, Thomas},
	month = dec,
	year = {2022},
	keywords = {Beta cells, Insulin secretion, Lactate, Mitochondrial metabolism, TCA cycle, Type 2 diabetes},
	pages = {101629},
}

Objective Ependymin-Related Protein 1 (EPDR1) was recently identified as a secreted human batokine regulating mitochondrial respiration linked to thermogenesis in brown fat. Despite that EPDR1 is expressed in human pancreatic β-cells and that glucose-stimulated mitochondrial metabolism is critical for stimulus-secretion coupling in β-cells, the role of EPDR1 in β-cell metabolism and function has not been investigated. Methods EPDR1 mRNA levels in human pancreatic islets from non-diabetic (ND) and type 2 diabetes (T2D) subjects were assessed. Human islets, EndoC-βH1 and INS1 832/13 cells were transfected with scramble (control) and EPDR1 siRNAs (EPDR1-KD) or treated with human EPDR1 protein, and glucose-stimulated insulin secretion (GSIS) assessed by ELISA. Mitochondrial metabolism was investigated by extracellular flux analyzer, confocal microscopy and mass spectrometry-based metabolomics analysis. Results EPDR1 mRNA expression was upregulated in human islets from T2D and obese donors and positively correlated to BMI of donors. In T2D donors, EPDR1 mRNA levels negatively correlated with HbA1c and positively correlated with GSIS. EPDR1 silencing in human islets and β-cell lines reduced GSIS whereas treatment with human EPDR1 protein increased GSIS. Epdr1 silencing in INS1 832/13 cells reduced glucose- and pyruvate- but not K+-stimulated insulin secretion. Metabolomics analysis in Epdr1-KD INS1 832/13 cells suggests diversion of glucose-derived pyruvate to lactate production and decreased malate-aspartate shuttle and the tricarboxylic acid (TCA) cycle activity. The glucose-stimulated rise in mitochondrial respiration and ATP/ADP-ratio was impaired in Epdr1-deficient cells. Conclusion These results suggests that to maintain glucose homeostasis in obese people, upregulation of EPDR1 may improve β-cell function via channelling glycolysis-derived pyruvate to the mitochondrial TCA cycle.

@article{jobert_auxin_2022,
	title = {Auxin triggers pectin modification during rootlet emergence in white lupin},
	volume = {112},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15993},
	doi = {10.1111/tpj.15993},
	abstract = {Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.},
	language = {en},
	number = {5},
	urldate = {2022-12-09},
	journal = {The Plant Journal},
	author = {Jobert, François and Soriano, Alexandre and Brottier, Laurent and Casset, Célia and Divol, Fanchon and Safran, Josip and Lefebvre, Valérie and Pelloux, Jérôme and Robert, Stéphanie and Péret, Benjamin},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.15993},
	keywords = {Auxin, Cell wall, Lupinus albus (white lupin), Pectin, Root development, auxin, cell wall, pectin, root development},
	pages = {1127--1140},
}

Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.

@article{curci_identification_2022,
	title = {Identification of growth regulators using cross-species network analysis in plants},
	volume = {190},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac374},
	doi = {10.1093/plphys/kiac374},
	abstract = {With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.},
	number = {4},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Curci, Pasquale Luca and Zhang, Jie and Mähler, Niklas and Seyfferth, Carolin and Mannapperuma, Chanaka and Diels, Tim and Van Hautegem, Tom and Jonsen, David and Street, Nathaniel and Hvidsten, Torgeir R and Hertzberg, Magnus and Nilsson, Ove and Inzé, Dirk and Nelissen, Hilde and Vandepoele, Klaas},
	month = dec,
	year = {2022},
	pages = {2350--2365},
}

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

@article{bru_major_2022,
	title = {The major trimeric antenna complexes serve as a site for {qH}-energy dissipation in plants},
	volume = {298},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925822009620},
	doi = {10.1016/j.jbc.2022.102519},
	abstract = {Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.},
	language = {en},
	number = {11},
	urldate = {2022-12-02},
	journal = {Journal of Biological Chemistry},
	author = {Bru, Pierrick and Steen, Collin J. and Park, Soomin and Amstutz, Cynthia L. and Sylak-Glassman, Emily J. and Lam, Lam and Fekete, Agnes and Mueller, Martin J. and Longoni, Fiamma and Fleming, Graham R. and Niyogi, Krishna K. and Malnoë, Alizée},
	month = nov,
	year = {2022},
	keywords = {CRISPR/Cas9, CRISPR–Cas9, abiotic stress, energy dissipation, light-harvesting complexes, non-photochemical quenching qH, nonphotochemical quenching qH, photosynthesis, time-resolved fluorescence},
	pages = {102519},
}

Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.

@article{borysiuk_glyoxalase_2022,
	title = {Glyoxalase {I} activity affects {Arabidopsis} sensitivity to ammonium nutrition},
	volume = {41},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-022-02931-5},
	doi = {10.1007/s00299-022-02931-5},
	abstract = {Elevated methylglyoxal levels contribute to ammonium-induced growth disorders in Arabidopsis thaliana. Methylglyoxal detoxification pathway limitation, mainly the glyoxalase I activity, leads to enhanced sensitivity of plants to ammonium nutrition.},
	language = {en},
	number = {12},
	urldate = {2022-12-02},
	journal = {Plant Cell Reports},
	author = {Borysiuk, Klaudia and Ostaszewska-Bugajska, Monika and Kryzheuskaya, Katsiaryna and Gardeström, Per and Szal, Bożena},
	month = dec,
	year = {2022},
	keywords = {Ammonium nutrition, D-Lactate dehydrogenase, Dicarbonyl stress, Glyoxalase, Methylglyoxal, Mitochondrial Complex I mutant},
	pages = {2393--2413},
}

Elevated methylglyoxal levels contribute to ammonium-induced growth disorders in Arabidopsis thaliana. Methylglyoxal detoxification pathway limitation, mainly the glyoxalase I activity, leads to enhanced sensitivity of plants to ammonium nutrition.

@article{mateos_picln_2022,
	title = {{PICLN} modulates alternative splicing and light/temperature responses in plants},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac527},
	doi = {10.1093/plphys/kiac527},
	abstract = {Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN-ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Mateos, Julieta L and Sanchez, Sabrina E and Legris, Martina and Esteve-Bruna, David and Torchio, Jeanette C and Petrillo, Ezequiel and Goretti, Daniela and Blanco-Touriñán, Noel and Seymour, Danelle K and Schmid, Markus and Weigel, Detlef and Alabadí, David and Yanovsky, Marcelo J},
	month = nov,
	year = {2022},
	pages = {kiac527},
}

Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN-ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

@article{aghbolaghi_stipagrostis_2022,
	title = {Stipagrostis pennata ({Trin}.) {De} {Winter} {Artificial} {Seed} {Production} and {Seedlings} {Multiplication} in {Temporary} {Immersion} {Bioreactors}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/22/3122},
	doi = {10.3390/plants11223122},
	abstract = {This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5\%, 2.5\%, and 3.5\%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5\% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.},
	language = {en},
	number = {22},
	urldate = {2022-12-02},
	journal = {Plants},
	author = {Aghbolaghi, Masoumeh Asadi and Dedicova, Beata and Sharifzadeh, Farzad and Omidi, Mansoor and Egertsdotter, Ulrika},
	month = jan,
	year = {2022},
	note = {Number: 22
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {in vitro cultures, protein analyses, somatic embryogenesis},
	pages = {3122},
}

This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5%, 2.5%, and 3.5%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.

@article{sun_fiona1-mediated_2022,
	title = {{FIONA1}-mediated methylation of the 3’{UTR} of {FLC} affects {FLC} transcript levels and flowering in {Arabidopsis}},
	volume = {18},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010386},
	doi = {10.1371/journal.pgen.1010386},
	abstract = {Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identify suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated RNAs. We provide evidence that FIO1 is the elusive methyltransferase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.},
	language = {en},
	number = {9},
	urldate = {2022-11-30},
	journal = {PLOS Genetics},
	author = {Sun, Bin and Bhati, Kaushal Kumar and Song, Peizhe and Edwards, Ashleigh and Petri, Louise and Kruusvee, Valdeko and Blaakmeer, Anko and Dolde, Ulla and Rodrigues, Vandasue and Straub, Daniel and Yang, Junbo and Jia, Guifang and Wenkel, Stephan},
	month = sep,
	year = {2022},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Leaves, Messenger RNA, Methylation, Phenotypes, RNA sequencing},
	pages = {e1010386},
}

Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identify suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated RNAs. We provide evidence that FIO1 is the elusive methyltransferase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.

@article{kruusvee_microproteins_2022,
	title = {Microproteins — lost in translation},
	volume = {18},
	copyright = {2022 Springer Nature America, Inc.},
	issn = {1552-4469},
	url = {https://www.nature.com/articles/s41589-022-01007-5},
	doi = {10.1038/s41589-022-01007-5},
	abstract = {Microproteins can be generated by a shift in the reading frame during translation. A chemoproteomics approach led to the identification of MINAS-60 as an alternative microprotein that regulates the assembly of the pre-60S ribosome.},
	language = {en},
	number = {6},
	urldate = {2022-11-30},
	journal = {Nature Chemical Biology},
	author = {Kruusvee, Valdeko and Wenkel, Stephan},
	month = jun,
	year = {2022},
	keywords = {Nuclear organization, Proteins, Proteomics},
	pages = {581--582},
}

Microproteins can be generated by a shift in the reading frame during translation. A chemoproteomics approach led to the identification of MINAS-60 as an alternative microprotein that regulates the assembly of the pre-60S ribosome.

@article{bresson_genetic_2022,
	title = {The genetic interaction of {REVOLUTA} and {WRKY53} links plant development, senescence, and immune responses},
	volume = {17},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0254741},
	doi = {10.1371/journal.pone.0254741},
	abstract = {In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate in the interplay between plant development and immunity.},
	language = {en},
	number = {3},
	urldate = {2022-11-30},
	journal = {PLOS ONE},
	author = {Bresson, Justine and Doll, Jasmin and Vasseur, François and Stahl, Mark and Roepenack-Lahaye, Edda von and Kilian, Joachim and Stadelhofer, Bettina and Kremer, James M. and Kolb, Dagmar and Wenkel, Stephan and Zentgraf, Ulrike},
	month = mar,
	year = {2022},
	keywords = {Arabidopsis thaliana, Flowering plants, Genetic interactions, Leaves, Metabolites, Plant development, Plant disease resistance, Plant pathogens},
	pages = {e0254741},
}

In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate in the interplay between plant development and immunity.

@article{chiurazzi_controlling_2022,
	title = {Controlling flowering of {Medicago} sativa (alfalfa) by inducing dominant mutations},
	volume = {64},
	issn = {1744-7909},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jipb.13186},
	doi = {10.1111/jipb.13186},
	abstract = {Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants. Medicago sativa is tetraploid and obligate outcrossing, which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit. Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy. Here we describe two complementary strategies to induce dominant mutations in the M. sativa genome and how they can be relevant in the control of flowering time. First, we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators. MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins. Genome-engineering allows us to retrace evolution and create microProtein-coding genes de novo. Second, we provide an inventory of genes regulated by microRNAs that control plant development. Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation. Finally, we investigated the recently published genomes of M. sativa and provide an inventory of breeding targets, some of which, when mutated, are likely to result in dominant traits.},
	language = {en},
	number = {2},
	urldate = {2022-11-30},
	journal = {Journal of Integrative Plant Biology},
	author = {Chiurazzi, Maurizio Junior and Nørrevang, Anton Frisgaard and García, Pedro and Cerdán, Pablo D. and Palmgren, Michael and Wenkel, Stephan},
	year = {2022},
	keywords = {Medicago sativa, flowering time, genome-engineering, microProtein, microRNA},
	pages = {205--214},
}

Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants. Medicago sativa is tetraploid and obligate outcrossing, which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit. Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy. Here we describe two complementary strategies to induce dominant mutations in the M. sativa genome and how they can be relevant in the control of flowering time. First, we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators. MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins. Genome-engineering allows us to retrace evolution and create microProtein-coding genes de novo. Second, we provide an inventory of genes regulated by microRNAs that control plant development. Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation. Finally, we investigated the recently published genomes of M. sativa and provide an inventory of breeding targets, some of which, when mutated, are likely to result in dominant traits.

@article{kruusvee_stop_2022,
	title = {Stop {CRYing}! {Inhibition} of cryptochrome function by small proteins},
	volume = {50},
	issn = {0300-5127},
	url = {https://doi.org/10.1042/BST20190062},
	doi = {10.1042/BST20190062},
	abstract = {Plants can detect the presence of light using specialised photoreceptor proteins. These photoreceptors measure the intensity of light, but they can also respond to different spectra of light and thus ‘see' different colours. Cryptochromes, which are also present in animals, are flavin-based photoreceptors that enable plants to detect blue and ultraviolet-A (UV-A) light. In Arabidopsis, there are two cryptochromes, CRYPTOCHROME 1 (CRY1) and CRYPTOCHROME 2 (CRY2) with known sensory roles. They function in various processes such as blue-light mediated inhibition of hypocotyl elongation, photoperiodic promotion of floral initiation, cotyledon expansion, anthocyanin production, and magnetoreception, to name a few. In the dark, the cryptochromes are in an inactive monomeric state and undergo photochemical and conformational change in response to illumination. This results in flavin reduction, oligomerisation, and the formation of the ‘cryptochrome complexome'. Mechanisms of cryptochrome activation and signalling have been extensively studied and found to be conserved across phylogenetic lines. In this review, we will therefore focus on a far lesser-known mechanism of regulation that is unique to plant cryptochromes. This involves inhibition of cryptochrome activity by small proteins that prevent its dimerisation in response to light. The resulting inhibition of function cause profound alterations in economically important traits such as plant growth, flowering, and fruit production. This review will describe the known mechanisms of cryptochrome activation and signalling in the context of their modulation by these endogenous and artificial small inhibitor proteins. Promising new applications for biotechnological and agricultural applications will be discussed.},
	number = {2},
	urldate = {2022-11-30},
	journal = {Biochemical Society Transactions},
	author = {Kruusvee, Valdeko and Toft, Arendse Maria and Aguida, Blanche and Ahmad, Margaret and Wenkel, Stephan},
	month = mar,
	year = {2022},
	pages = {773--782},
}

Plants can detect the presence of light using specialised photoreceptor proteins. These photoreceptors measure the intensity of light, but they can also respond to different spectra of light and thus ‘see' different colours. Cryptochromes, which are also present in animals, are flavin-based photoreceptors that enable plants to detect blue and ultraviolet-A (UV-A) light. In Arabidopsis, there are two cryptochromes, CRYPTOCHROME 1 (CRY1) and CRYPTOCHROME 2 (CRY2) with known sensory roles. They function in various processes such as blue-light mediated inhibition of hypocotyl elongation, photoperiodic promotion of floral initiation, cotyledon expansion, anthocyanin production, and magnetoreception, to name a few. In the dark, the cryptochromes are in an inactive monomeric state and undergo photochemical and conformational change in response to illumination. This results in flavin reduction, oligomerisation, and the formation of the ‘cryptochrome complexome'. Mechanisms of cryptochrome activation and signalling have been extensively studied and found to be conserved across phylogenetic lines. In this review, we will therefore focus on a far lesser-known mechanism of regulation that is unique to plant cryptochromes. This involves inhibition of cryptochrome activity by small proteins that prevent its dimerisation in response to light. The resulting inhibition of function cause profound alterations in economically important traits such as plant growth, flowering, and fruit production. This review will describe the known mechanisms of cryptochrome activation and signalling in the context of their modulation by these endogenous and artificial small inhibitor proteins. Promising new applications for biotechnological and agricultural applications will be discussed.

@article{heisler_context-specific_2022,
	title = {Context-specific functions of transcription factors controlling plant development: {From} leaves to flowers},
	volume = {69},
	issn = {1369-5266},
	shorttitle = {Context-specific functions of transcription factors controlling plant development},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526622000917},
	doi = {10.1016/j.pbi.2022.102262},
	abstract = {Plant development is regulated by transcription factors that often act in more than one process and stage of development. Yet the molecular mechanisms that govern the functional diversity and specificity of these proteins remains far from understood. Flower development provides an ideal context to study these mechanisms since the development of distinct floral organs depends on similar but distinct combinations of transcriptional regulators. Recent work also highlights the importance of leaf polarity regulators as additional key factors in flower initiation, floral organ morphogenesis, and possibly floral organ positioning. A detailed understanding of how these factors work in combination will enable us to address outstanding questions in flower development including how distinct shapes and positions of floral organs are generated. Experimental approaches and computer-based modeling will be required to characterize gene-regulatory networks at the level of single cells.},
	language = {en},
	urldate = {2022-11-30},
	journal = {Current Opinion in Plant Biology},
	author = {Heisler, Marcus G. and Jönsson, Henrik and Wenkel, Stephan and Kaufmann, Kerstin},
	month = oct,
	year = {2022},
	pages = {102262},
}

Plant development is regulated by transcription factors that often act in more than one process and stage of development. Yet the molecular mechanisms that govern the functional diversity and specificity of these proteins remains far from understood. Flower development provides an ideal context to study these mechanisms since the development of distinct floral organs depends on similar but distinct combinations of transcriptional regulators. Recent work also highlights the importance of leaf polarity regulators as additional key factors in flower initiation, floral organ morphogenesis, and possibly floral organ positioning. A detailed understanding of how these factors work in combination will enable us to address outstanding questions in flower development including how distinct shapes and positions of floral organs are generated. Experimental approaches and computer-based modeling will be required to characterize gene-regulatory networks at the level of single cells.

@article{akhter_cone-setting_2022,
	title = {Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18449},
	doi = {10.1111/nph.18449},
	abstract = {Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.},
	language = {en},
	number = {5},
	urldate = {2022-11-10},
	journal = {New Phytologist},
	author = {Akhter, Shirin and Westrin, Karl Johan and Zivi, Nathan and Nordal, Veronika and Kretzschmar, Warren W. and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = dec,
	year = {2022},
	keywords = {Cone-setting, Flowering, Gymnosperm, Picea abies, Reproductive development, SPL-gene family, Transcriptome, cone-setting, flowering, gymnosperm, reproductive development, transcriptome},
	pages = {1951--1963},
}

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

@article{li_teasing_2022,
	title = {Teasing apart the joint effect of demography and natural selection in the birth of a contact zone},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18480},
	doi = {10.1111/nph.18480},
	abstract = {Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.},
	language = {en},
	number = {5},
	urldate = {2022-11-10},
	journal = {New Phytologist},
	author = {Li, Lili and Milesi, Pascal and Tiret, Mathieu and Chen, Jun and Sendrowski, Janek and Baison, John and Chen, Zhi-qiang and Zhou, Linghua and Karlsson, Bo and Berlin, Mats and Westin, Johan and Garcia-Gil, Maria Rosario and Wu, Harry X. and Lascoux, Martin},
	month = dec,
	year = {2022},
	keywords = {Climate change, Contact zone, Demography, Last Glacial Maximum, Local adaptation, Natural selection, Picea abies, climate change, contact zone, demography, local adaptation, natural selection},
	pages = {1976--1987},
}

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.

@article{nickolov_regulation_2022,
	title = {Regulation of {PaRBOH1}-mediated {ROS} production in {Norway} spruce by {Ca2}+ binding and phosphorylation},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.978586},
	doi = {babia},
	abstract = {Plant respiratory burst oxidase homologs (RBOHs) are plasma membrane-localized NADPH oxidases that generate superoxide anion radicals, which then dismutate to H2O2, into the apoplast using cytoplasmic NADPH as an electron donor. PaRBOH1 is the most highly expressed RBOH gene in developing xylem as well as in a lignin-forming cell culture of Norway spruce (Picea abies L. Karst.). Since no previous information about regulation of gymnosperm RBOHs exist, our aim was to resolve how PaRBOH1 is regulated with a focus on phosphorylation. The N-terminal part of PaRBOH1 was found to contain several putative phosphorylation sites and a four-times repeated motif with similarities to the Botrytis-induced kinase 1 target site in Arabidopsis AtRBOHD. Phosphorylation was indicated for six of the sites in in vitro kinase assays using 15 amino-acid-long peptides for each of the predicted phosphotarget site in the presence of protein extracts of developing xylem. Serine and threonine residues showing positive response in the peptide assays were individually mutated to alanine (kinase-inactive) or to aspartate (phosphomimic), and the wild type PaRBOH1 and the mutated constructs transfected to human kidney embryogenic (HEK293T) cells with a low endogenous level of extracellular ROS production. ROS-producing assays with HEK cells showed that Ca2+ and phosphorylation synergistically activate the enzyme and identified several serine and threonine residues that are likely to be phosphorylated including a novel phosphorylation site not characterized in other plant species. These were further investigated with a phosphoproteomic study. Results of Norway spruce, the first gymnosperm species studied in relation to RBOH regulation, show that regulation of RBOH activity is conserved among seed plants.},
	urldate = {2022-11-03},
	journal = {Frontiers in Plant Science},
	author = {Nickolov, Kaloian and Gauthier, Adrien and Hashimoto, Kenji and Laitinen, Teresa and Väisänen, Enni and Paasela, Tanja and Soliymani, Rabah and Kurusu, Takamitsu and Himanen, Kristiina and Blokhina, Olga and Fagerstedt, Kurt V. and Jokipii-Lukkari, Soile and Tuominen, Hannele and Häggman, Hely and Wingsle, Gunnar and Teeri, Teemu H. and Kuchitsu, Kazuyuki and Kärkönen, Anna},
	month = oct,
	year = {2022},
}

Plant respiratory burst oxidase homologs (RBOHs) are plasma membrane-localized NADPH oxidases that generate superoxide anion radicals, which then dismutate to H2O2, into the apoplast using cytoplasmic NADPH as an electron donor. PaRBOH1 is the most highly expressed RBOH gene in developing xylem as well as in a lignin-forming cell culture of Norway spruce (Picea abies L. Karst.). Since no previous information about regulation of gymnosperm RBOHs exist, our aim was to resolve how PaRBOH1 is regulated with a focus on phosphorylation. The N-terminal part of PaRBOH1 was found to contain several putative phosphorylation sites and a four-times repeated motif with similarities to the Botrytis-induced kinase 1 target site in Arabidopsis AtRBOHD. Phosphorylation was indicated for six of the sites in in vitro kinase assays using 15 amino-acid-long peptides for each of the predicted phosphotarget site in the presence of protein extracts of developing xylem. Serine and threonine residues showing positive response in the peptide assays were individually mutated to alanine (kinase-inactive) or to aspartate (phosphomimic), and the wild type PaRBOH1 and the mutated constructs transfected to human kidney embryogenic (HEK293T) cells with a low endogenous level of extracellular ROS production. ROS-producing assays with HEK cells showed that Ca2+ and phosphorylation synergistically activate the enzyme and identified several serine and threonine residues that are likely to be phosphorylated including a novel phosphorylation site not characterized in other plant species. These were further investigated with a phosphoproteomic study. Results of Norway spruce, the first gymnosperm species studied in relation to RBOH regulation, show that regulation of RBOH activity is conserved among seed plants.

@article{navarro-quiles_arabidopsis_2022,
	title = {The {Arabidopsis} {ATP}-{Binding} {Cassette} {E} protein {ABCE2} is a conserved component of the translation machinery},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1009895},
	abstract = {ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.},
	urldate = {2022-11-10},
	journal = {Frontiers in Plant Science},
	author = {Navarro-Quiles, Carla and Mateo-Bonmatí, Eduardo and Candela, Héctor and Robles, Pedro and Martínez-Laborda, Antonio and Fernández, Yolanda and Šimura, Jan and Ljung, Karin and Rubio, Vicente and Ponce, María Rosa and Micol, José Luis},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.

@article{nielsen_accumulated_2022,
	title = {Accumulated effects of factors determining plant development from somatic embryos of {Abies} nordmanniana and {Abies} bornmuelleriana},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.989484},
	abstract = {Despite a much later inception of somatic embryogenesis (SE) propagation protocols for gymnosperms than for angiosperm species, SE is becoming increasingly important due to its applications for commercial forestry. For many conifers, there are however still major bottlenecks in the SE plant production process limiting the use of SE for forestry operations, Christmas tree production and research projects. In the present case study, the effects on plant growth from different cultural factors applied during the SE developmental process were studied in two conifer species of high value for Christmas tree production. Seven clones of Abies nordmanniana and two clones of Abies bornmuelleriana were included in the study. Accumulated effects from cultural treatments were recorded from the start of germination of mature embryos of different quality scores through development into plants in the third growing period. Experimental factors of the cultural treatments included were: germination temperature, germination time, light conditions, survival ex vitro and traits for plant growth and vitality. The results reveal that most of the studied experimental factors influenced plant growth during the first three years however their relative importance was different. Plant survival rate at end of the nursery stage was strongly impacted by germination temperature (p{\textless}0.001), initial embryo score (p=0.007), clone (p{\textless}0.001) and to a lesser extend week of germination (p=0.017). This case-study highlights and quantifies the strong interrelation between the developmental steps of somatic embryogenesis and show the importance of considering all cultural steps when optimizing SE plant production protocols.},
	urldate = {2022-11-03},
	journal = {Frontiers in Plant Science},
	author = {Nielsen, Ulrik Braüner and Hansen, Camilla Bülow and Hansen, Ulrich and Johansen, Vivian Kvist and Egertsdotter, Ulrika},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Despite a much later inception of somatic embryogenesis (SE) propagation protocols for gymnosperms than for angiosperm species, SE is becoming increasingly important due to its applications for commercial forestry. For many conifers, there are however still major bottlenecks in the SE plant production process limiting the use of SE for forestry operations, Christmas tree production and research projects. In the present case study, the effects on plant growth from different cultural factors applied during the SE developmental process were studied in two conifer species of high value for Christmas tree production. Seven clones of Abies nordmanniana and two clones of Abies bornmuelleriana were included in the study. Accumulated effects from cultural treatments were recorded from the start of germination of mature embryos of different quality scores through development into plants in the third growing period. Experimental factors of the cultural treatments included were: germination temperature, germination time, light conditions, survival ex vitro and traits for plant growth and vitality. The results reveal that most of the studied experimental factors influenced plant growth during the first three years however their relative importance was different. Plant survival rate at end of the nursery stage was strongly impacted by germination temperature (p\textless0.001), initial embryo score (p=0.007), clone (p\textless0.001) and to a lesser extend week of germination (p=0.017). This case-study highlights and quantifies the strong interrelation between the developmental steps of somatic embryogenesis and show the importance of considering all cultural steps when optimizing SE plant production protocols.

@article{ranade_adaptive_2022,
	title = {Adaptive strategies of {Scots} pine under shade: increase in lignin synthesis and ecotypic variation in defence-related gene expression},
	volume = {2022-10},
	issn = {1399-3054},
	shorttitle = {Adaptive strategies of {Scots} pine under shade},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13792},
	doi = {10.1111/ppl.13792},
	abstract = {Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	month = sep,
	year = {2022},
	pages = {e13792},
}

Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.

@article{antoniadi_ipt9_2022,
	title = {{IPT9}, a cis-zeatin cytokinin biosynthesis gene, promotes root growth},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.932008},
	abstract = {Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.},
	urldate = {2022-10-19},
	journal = {Frontiers in Plant Science},
	author = {Antoniadi, Ioanna and Mateo-Bonmatí, Eduardo and Pernisová, Markéta and Brunoni, Federica and Antoniadi, Mariana and Villalonga, Mauricio Garcia-Atance and Ament, Anita and Karády, Michal and Turnbull, Colin and Doležal, Karel and Pěnčík, Aleš and Ljung, Karin and Novák, Ondřej},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.

@article{velez_taxol_2022,
	title = {Taxol and β-tubulins from endophytic fungi isolated from the {Himalayan} {Yew}, {Taxus} wallichiana {Zucc}.},
	volume = {13},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.956855},
	abstract = {Paclitaxel, better known as the anticancer drug Taxol®, has been isolated from several plant species and has been shown to be produced by fungi, actinomycetes, and even bacteria isolated from marine macroalgae. Given its cytostatic effect, studies conducted in the 1990's showed that paclitaxel was toxic to many pathogenic fungi and oomycetes. Further studies led to the idea that the differences in paclitaxel sensitivity exhibited by different fungi were due to differences in the β-tubulin protein sequence. With the recent isolation of endophytic fungi from the leaves and bark of the Himalayan Yew, Taxus wallichiana Zucc., and the availability of genomes from paclitaxel-producing fungi, we decided to further explore the idea that endophytic fungi isolated from Yews should be well-adapted to their environment by encoding β-tubulin proteins that are insensitive to paclitaxel. Our results found evidence of episodic positive/diversifying selection at 10 sites (default p-value threshold of 0.1) in the β-tubulin sequences, corresponding to codon positions 33, 55, 172, 218, 279, 335, 359, 362, 379, and 406. Four of these positions (i.e., 172, 279, 359, and 362) have been implicated in the binding of paclitaxel by β-tubulin or formed part of the binding pocket. As expected, all the fungal endophytes grew in different media regardless of the paclitaxel concentration tested. Furthermore, our results also showed that Taxomyces andreanae CBS 279.92, the first fungus shown to produce paclitaxel, is a Basidiomycete fungus as the two beta tubulins encoded by the fungus clustered together with other Basidiomycete fungi.},
	urldate = {2022-10-21},
	journal = {Frontiers in Microbiology},
	author = {Vélëz, Heriberto and Gauchan, Dhurva Prasad and García-Gil, María del Rosario},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Paclitaxel, better known as the anticancer drug Taxol®, has been isolated from several plant species and has been shown to be produced by fungi, actinomycetes, and even bacteria isolated from marine macroalgae. Given its cytostatic effect, studies conducted in the 1990's showed that paclitaxel was toxic to many pathogenic fungi and oomycetes. Further studies led to the idea that the differences in paclitaxel sensitivity exhibited by different fungi were due to differences in the β-tubulin protein sequence. With the recent isolation of endophytic fungi from the leaves and bark of the Himalayan Yew, Taxus wallichiana Zucc., and the availability of genomes from paclitaxel-producing fungi, we decided to further explore the idea that endophytic fungi isolated from Yews should be well-adapted to their environment by encoding β-tubulin proteins that are insensitive to paclitaxel. Our results found evidence of episodic positive/diversifying selection at 10 sites (default p-value threshold of 0.1) in the β-tubulin sequences, corresponding to codon positions 33, 55, 172, 218, 279, 335, 359, 362, 379, and 406. Four of these positions (i.e., 172, 279, 359, and 362) have been implicated in the binding of paclitaxel by β-tubulin or formed part of the binding pocket. As expected, all the fungal endophytes grew in different media regardless of the paclitaxel concentration tested. Furthermore, our results also showed that Taxomyces andreanae CBS 279.92, the first fungus shown to produce paclitaxel, is a Basidiomycete fungus as the two beta tubulins encoded by the fungus clustered together with other Basidiomycete fungi.

@article{wang_aspen_2022,
	title = {Aspen growth is not limited by starch reserves},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222010181},
	doi = {10.1016/j.cub.2022.06.056},
	abstract = {All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30\% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.},
	language = {en},
	number = {16},
	urldate = {2022-10-10},
	journal = {Current Biology},
	author = {Wang, Wei and Talide, Loic and Viljamaa, Sonja and Niittylä, Totte},
	month = aug,
	year = {2022},
	keywords = {Populus, carbon partitioning, phosphoglucomutase, starch},
	pages = {3619--3627.e4},
}

All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.

@article{andre_flowering_2022,
	title = {{FLOWERING} {LOCUS} {T} paralogs control the annual growth cycle in {Populus} trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(22)00782-5},
	doi = {10.1016/j.cub.2022.05.023},
	abstract = {In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1, 2, 3, 4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.},
	language = {English},
	number = {13},
	urldate = {2022-08-12},
	journal = {Current Biology},
	author = {André, Domenique and Marcon, Alice and Lee, Keh Chien and Goretti, Daniela and Zhang, Bo and Delhomme, Nicolas and Schmid, Markus and Nilsson, Ove},
	month = jul,
	year = {2022},
	pmid = {35660141},
	note = {Publisher: Elsevier},
	keywords = {FLOWERING LOCUS T, Populus, annual growth cycle, bud flush, dormancy, paralogs},
	pages = {2988--2996.e4},
}

In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1, 2, 3, 4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.

@article{antoniadi_fluorescence_2022,
	title = {Fluorescence activated cell sorting—{A} selective tool for plant cell isolation and analysis},
	volume = {101},
	issn = {1552-4930},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cyto.a.24461},
	doi = {10.1002/cyto.a.24461},
	abstract = {Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.},
	language = {en},
	number = {9},
	urldate = {2022-09-16},
	journal = {Cytometry Part A},
	author = {Antoniadi, Ioanna and Skalický, Vladimír and Sun, Guiling and Ma, Wen and Galbraith, David W. and Novák, Ondřej and Ljung, Karin},
	month = may,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cyto.a.24461},
	keywords = {autofluorescence, best practices, plant flow cytometry and sorting, protoplasts, viability and integrity},
	pages = {725--736},
}

Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.

@article{chen_genetic_2022,
	title = {Genetic architecture behind developmental and seasonal control of tree growth and wood properties in {Norway} spruce},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.927673},
	abstract = {Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover {\textasciitilde}130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.},
	urldate = {2022-09-01},
	journal = {Frontiers in Plant Science},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Zhou, Linghua and Karlsson, Bo and Tuominen, Hannele and García-Gil, Maria Rosario and Wu, Harry X.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

@article{linden_circum-arctic_2022,
	title = {Circum-{Arctic} distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in {Arctic} shrubs},
	issn = {1600-0587},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.06166},
	doi = {10.1111/ecog.06166},
	abstract = {Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.},
	language = {en},
	urldate = {2022-09-08},
	journal = {Ecography},
	author = {Lindén, Elin and te Beest, Mariska and Aubreu, Ilka and Moritz, Thomas and Sundqvist, Maja K. and Barrio, Isabel C. and Boike, Julia and Bryant, John P. and Bråthen, Kari Anne and Buchwal, Agata and Bueno, C. Guillermo and Currier, Alain and Egelkraut, Dagmar D. and Forbes, Bruce C. and Hallinger, Martin and Heijmans, Monique and Hermanutz, Luise and Hik, David S. and Hofgaard, Annika and Holmgren, Milena and Huebner, Diane C. and Høye, Toke T. and Jónsdóttir, Ingibjörg S. and Kaarlejärvi, Elina and Kissler, Emilie and Kumpula, Timo and Limpens, Juul and Myers-Smith, Isla H. and Normand, Signe and Post, Eric and Rocha, Adrian V. and Schmidt, Niels Martin and Skarin, Anna and Soininen, Eeva M. and Sokolov, Aleksandr and Sokolova, Natalia and Speed, James D. M. and Street, Lorna and Tananaev, Nikita and Tremblay, Jean-Pierre and Urbanowicz, Christine and Watts, David A. and Zimmermann, Heike and Olofsson, Johan},
	month = aug,
	year = {2022},
	keywords = {Arctic, Betula, birch, herbivory, metabolomics, plant chemical defence, shrubs, tundra},
	pages = {e06166},
}

Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.

@article{rodriguez_effects_2022,
	title = {Effects of condensed tannins on behavior and performance of a specialist aphid on aspen},
	volume = {12},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.9229},
	doi = {10.1002/ece3.9229},
	abstract = {Genes involved in plant defences against herbivores and pathogens are often highly polymorphic. This is a putative sign that balancing selection may have operated reciprocally on the hosts and their herbivores. Spatial and temporal variations (for example, in soil nutrients and the plants' ontogenetic development) may also modulate resistance traits, and thus selection pressures, but have been largely overlooked in theories of plant defences. Important elements of defences in Populus tremula (hereafter aspen) are phenolic compounds, including condensed tannins (CTs). Concentrations of CTs vary considerably with both variations in external factors and time, but they are also believed to provide genotype-dependent resistance, mainly against chewing herbivores and pathogens. However, evidence of their contributions to resistance is sparse. Detailed studies of co-evolved plant–herbivore associations could provide valuable insights into these contributions. Therefore, we examined correlations between CT levels in aspen leaves and both the feeding behavior and reproduction of the specialist aspen leaf aphid (Chaitophorus tremulae) in varied conditions. We found that xylem sap intake and probing difficulties were higher on genotypes with high-CT concentrations. However, aphids engaged in more nonprobing activities on low-CT genotypes, indicating that CTs were not the only defence traits involved. Thus, high-CT genotypes were not necessarily more resistant than low-CT genotypes, but aphid reproduction was generally negatively correlated with local CT accumulation. Genotype-specific resistance ranking also depended on the experimental conditions. These results support the hypothesis that growth conditions may affect selection pressures mediated by aphids in accordance with balancing selection theory.},
	language = {en},
	number = {8},
	urldate = {2022-09-01},
	journal = {Ecology and Evolution},
	author = {Rodríguez, Bárbara Díez and Kloth, Karen J. and Albrectsen, Benedicte Riber},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.9229},
	keywords = {Chaitophorus tremulae, Populus tremula, condensed tannins, electric penetration graph (EPG), xylem feeding},
	pages = {e9229},
}

Genes involved in plant defences against herbivores and pathogens are often highly polymorphic. This is a putative sign that balancing selection may have operated reciprocally on the hosts and their herbivores. Spatial and temporal variations (for example, in soil nutrients and the plants' ontogenetic development) may also modulate resistance traits, and thus selection pressures, but have been largely overlooked in theories of plant defences. Important elements of defences in Populus tremula (hereafter aspen) are phenolic compounds, including condensed tannins (CTs). Concentrations of CTs vary considerably with both variations in external factors and time, but they are also believed to provide genotype-dependent resistance, mainly against chewing herbivores and pathogens. However, evidence of their contributions to resistance is sparse. Detailed studies of co-evolved plant–herbivore associations could provide valuable insights into these contributions. Therefore, we examined correlations between CT levels in aspen leaves and both the feeding behavior and reproduction of the specialist aspen leaf aphid (Chaitophorus tremulae) in varied conditions. We found that xylem sap intake and probing difficulties were higher on genotypes with high-CT concentrations. However, aphids engaged in more nonprobing activities on low-CT genotypes, indicating that CTs were not the only defence traits involved. Thus, high-CT genotypes were not necessarily more resistant than low-CT genotypes, but aphid reproduction was generally negatively correlated with local CT accumulation. Genotype-specific resistance ranking also depended on the experimental conditions. These results support the hypothesis that growth conditions may affect selection pressures mediated by aphids in accordance with balancing selection theory.

@article{burko_pif7_2022,
	title = {{PIF7} is a master regulator of thermomorphogenesis in shade},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-32585-6},
	doi = {10.1038/s41467-022-32585-6},
	abstract = {The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.},
	language = {en},
	number = {1},
	urldate = {2022-09-01},
	journal = {Nature Communications},
	author = {Burko, Yogev and Willige, Björn Christopher and Seluzicki, Adam and Novák, Ondřej and Ljung, Karin and Chory, Joanne},
	month = aug,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Light responses, Plant development, Plant signalling},
	pages = {4942},
}

The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.

@article{ranade_enhanced_2022,
	title = {Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in {Norway} spruce},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14387},
	doi = {10.1111/pce.14387},
	abstract = {During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.},
	language = {en},
	number = {9},
	urldate = {2022-08-19},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14387},
	keywords = {Conifer, Defense, Ecotypic variation, Immunity, Light quality, Lignin, Local adaptation, Norway spruce, R:FR ratio, RNA sequencing, Response to shade, conifer, disease resistance, far-red light, immunity, latitudinal cline, light quality, local adaptation, red light},
	pages = {2671--2681},
}

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

@article{van_dijk_single_2022,
	title = {Single, but not dual, attack by a biotrophic pathogen and a sap-sucking insect affects the oak leaf metabolome},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.897186},
	abstract = {Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.},
	urldate = {2022-08-12},
	journal = {Frontiers in Plant Science},
	author = {van Dijk, Laura J. A. and Regazzoni, Emilia D. E. and Albrectsen, Benedicte R. and Ehrlén, Johan and Abdelfattah, Ahmed and Stenlund, Hans and Pawlowski, Katharina and Tack, Ayco J. M.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.

@article{liebsch_metabolic_2022,
	title = {Metabolic control of arginine and ornithine levels paces the progression of leaf senescence},
	volume = {189},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac244},
	doi = {10.1093/plphys/kiac244},
	abstract = {Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.},
	number = {4},
	urldate = {2022-08-08},
	journal = {Plant Physiology},
	author = {Liebsch, Daniela and Juvany, Marta and Li, Zhonghai and Wang, Hou-Ling and Ziolkowska, Agnieszka and Chrobok, Daria and Boussardon, Clément and Wen, Xing and Law, Simon R and Janečková, Helena and Brouwer, Bastiaan and Lindén, Pernilla and Delhomme, Nicolas and Stenlund, Hans and Moritz, Thomas and Gardeström, Per and Guo, Hongwei and Keech, Olivier},
	month = aug,
	year = {2022},
	pages = {1943--1960},
}

Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.

@article{biniaz_transcriptome_2022,
	title = {Transcriptome {Meta}-{Analysis} {Identifies} {Candidate} {Hub} {Genes} and {Pathways} of {Pathogen} {Stress} {Responses} in {Arabidopsis} thaliana},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-7737},
	url = {https://www.mdpi.com/2079-7737/11/8/1155},
	doi = {10.3390/biology11081155},
	abstract = {Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.},
	language = {en},
	number = {8},
	urldate = {2022-08-02},
	journal = {Biology},
	author = {Biniaz, Yaser and Tahmasebi, Ahmad and Tahmasebi, Aminallah and Albrectsen, Benedicte Riber and Poczai, Péter and Afsharifar, Alireza},
	month = aug,
	year = {2022},
	note = {Number: 8
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Arabidopsis thaliana}, biotic stress, plant–pathogen interaction, transcriptome data},
	pages = {1155},
}

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.

@article{yu_structure_2022,
	title = {Structure of {Arabidopsis} {SOQ1} lumenal region unveils {C}-terminal domain essential for negative regulation of photoprotective {qH}},
	volume = {8},
	copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01177-z},
	doi = {10.1038/s41477-022-01177-z},
	abstract = {Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.},
	language = {en},
	number = {7},
	urldate = {2022-07-22},
	journal = {Nature Plants},
	author = {Yu, Guimei and Hao, Jingfang and Pan, Xiaowei and Shi, Lifang and Zhang, Yong and Wang, Jifeng and Fan, Hongcheng and Xiao, Yang and Yang, Fuquan and Lou, Jizhong and Chang, Wenrui and Malnoë, Alizée and Li, Mei},
	month = jul,
	year = {2022},
	note = {Number: 7
Publisher: Nature Publishing Group},
	keywords = {Photosynthesis, Plant sciences},
	pages = {840--855},
}

Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.

@article{diamanti_comparative_2022,
	title = {Comparative structural analysis provides new insights into the function of {R2}-like ligand-binding oxidase},
	volume = {596},
	copyright = {© 2022 The Authors. FEBS Letters published by John Wiley \& Sons Ltd on behalf of Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.14319},
	doi = {10.1002/1873-3468.14319},
	abstract = {R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.},
	language = {en},
	number = {12},
	urldate = {2022-06-30},
	journal = {FEBS Letters},
	author = {Diamanti, Riccardo and Srinivas, Vivek and Johansson, Annika I. and Nordström, Anders and Griese, Julia J. and Lebrette, Hugo and Högbom, Martin},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/1873-3468.14319},
	keywords = {R2-like ligand-binding oxidase, R2lox, aldehyde deformylating oxygenase, ferritin-like protein, hydroxy fatty acids, long-chain fatty acids},
	pages = {1600--1610},
}

R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.

@article{ranjan_molecular_2022,
	title = {Molecular basis of differential adventitious rooting competence in poplar genotypes},
	volume = {73},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erac126},
	doi = {10.1093/jxb/erac126},
	abstract = {Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.},
	number = {12},
	urldate = {2022-06-30},
	journal = {Journal of Experimental Botany},
	author = {Ranjan, Alok and Perrone, Irene and Alallaq, Sanaria and Singh, Rajesh and Rigal, Adeline and Brunoni, Federica and Chitarra, Walter and Guinet, Frederic and Kohler, Annegret and Martin, Francis and Street, Nathaniel R and Bhalerao, Rishikesh and Legué, Valérie and Bellini, Catherine},
	month = jun,
	year = {2022},
	pages = {4046--4064},
}

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

@article{fataftah_nitrate_2022,
	title = {Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not},
	volume = {174},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13690},
	doi = {10.1111/ppl.13690},
	abstract = {Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.},
	language = {en},
	number = {3},
	urldate = {2022-06-30},
	journal = {Physiologia Plantarum},
	author = {Fataftah, Nazeer and Edlund, Erik and Lihavainen, Jenna and Bag, Pushan and Björkén, Lars and Näsholm, Torgny and Jansson, Stefan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13690},
	pages = {e13690},
}

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

@article{arshad_kaleidoscope_2022,
	title = {A kaleidoscope of photosynthetic antenna proteins and their emerging roles},
	volume = {189},
	issn = {1532-2548},
	doi = {10.1093/plphys/kiac175},
	abstract = {Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckaité, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J. and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kouřil, Roman and Michel, Sylvie and Mullineaux, Conrad W. and Panzarová, Klára and Robert, Bruno and Ruban, Alexander V. and van Stokkum, Ivo and Wientjes, Emilie and Büchel, Claudia},
	month = jun,
	year = {2022},
	pmid = {35512089},
	keywords = {Adaptation, Physiological, Light-Harvesting Protein Complexes, Photosynthesis, Plants, Thylakoids},
	pages = {1204--1219},
}

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

@article{blasko_carbon_2022,
	title = {The carbon sequestration response of aboveground biomass and soils to nutrient enrichment in boreal forests depends on baseline site productivity},
	volume = {838},
	issn = {0048-9697},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969722034246},
	doi = {10.1016/j.scitotenv.2022.156327},
	abstract = {Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95\% increase in tree biomass C stocks, 150\% increase in litter production, 67\% increase in organic layer C stocks, and a 46\% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.},
	language = {en},
	urldate = {2022-06-30},
	journal = {Science of The Total Environment},
	author = {Blaško, Róbert and Forsmark, Benjamin and Gundale, Michael J. and Lim, Hyungwoo and Lundmark, Tomas and Nordin, Annika},
	month = sep,
	year = {2022},
	keywords = {Ecosystem carbon stocks, Litterfall, Soil carbon, Soil microbial community, Soil nitrogen, Soil respiration},
	pages = {156327},
}

Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95% increase in tree biomass C stocks, 150% increase in litter production, 67% increase in organic layer C stocks, and a 46% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.

@article{kleczkowski_effects_2022,
	title = {Effects of {Magnesium}, {Pyrophosphate} and {Phosphonates} on {Pyrophosphorolytic} {Reaction} of {UDP}-{Glucose} {Pyrophosphorylase}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/12/1611},
	doi = {10.3390/plants11121611},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) carries a freely reversible reaction, using glucose-1-P and UTP to produce UDP-glucose (UDPG) and pyrophosphate (PPi), with UDPG being essential for glycosylation reactions in all organisms including, e.g., synthesis of sucrose, cellulose and glycoproteins. In the present study, we found that free magnesium (Mg2+) had profound effects on the reverse reaction of purified barley UGPase, and was absolutely required for its activity, with an apparent Km of 0.13 mM. More detailed analyses with varied concentrations of MgPPi allowed us to conclude that it is the MgPPi complex which serves as true substrate for UGPase in its reverse reaction, with an apparent Km of 0.06 mM. Free PPi was an inhibitor in this reaction. Given the key role of PPi in the UGPase reaction, we have also tested possible effects of phosphonates, which are analogs of PPi and phosphate (Pi). Clodronate and etidronate (PPi analogs) had little or no effect on UGPase activity, whereas fosetyl-Al (Pi analog), a known fungicide, acted as effective near-competitive inhibitor versus PPi, with Ki of 0.15 mM. The data are discussed with respect to the role of magnesium in the UGPase reaction and elucidating the use of inhibitors in studies on cellular function of UGPase and related enzymes.},
	language = {en},
	number = {12},
	urldate = {2022-06-30},
	journal = {Plants},
	author = {Kleczkowski, Leszek A. and Decker, Daniel},
	month = jun,
	year = {2022},
	note = {Number: 12
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Phytophthora}, Dixon plot, chemical genetics, fosetyl-Al, inhibitor kinetics, magnesium activation},
	pages = {1611},
}

UDP-glucose pyrophosphorylase (UGPase) carries a freely reversible reaction, using glucose-1-P and UTP to produce UDP-glucose (UDPG) and pyrophosphate (PPi), with UDPG being essential for glycosylation reactions in all organisms including, e.g., synthesis of sucrose, cellulose and glycoproteins. In the present study, we found that free magnesium (Mg2+) had profound effects on the reverse reaction of purified barley UGPase, and was absolutely required for its activity, with an apparent Km of 0.13 mM. More detailed analyses with varied concentrations of MgPPi allowed us to conclude that it is the MgPPi complex which serves as true substrate for UGPase in its reverse reaction, with an apparent Km of 0.06 mM. Free PPi was an inhibitor in this reaction. Given the key role of PPi in the UGPase reaction, we have also tested possible effects of phosphonates, which are analogs of PPi and phosphate (Pi). Clodronate and etidronate (PPi analogs) had little or no effect on UGPase activity, whereas fosetyl-Al (Pi analog), a known fungicide, acted as effective near-competitive inhibitor versus PPi, with Ki of 0.15 mM. The data are discussed with respect to the role of magnesium in the UGPase reaction and elucidating the use of inhibitors in studies on cellular function of UGPase and related enzymes.

@article{kauppi_managing_2022,
	title = {Managing existing forests can mitigate climate change},
	volume = {513},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112722001803},
	doi = {10.1016/j.foreco.2022.120186},
	abstract = {Planting new forests has received scientific and political attention as a measure to mitigate climate change. Large, new forests have been planted in places like China and Ethiopia and, over time, a billion hectares could become available globally for planting new forests. Sustainable management of forests, which are available to wood production, has received less attention despite these forests covering at least two billion hectares globally. Better management of existing forests would improve forest growth and help mitigate climate change by increasing the forest carbon (C) stock, by storing C in forest products, and by generating wood-based materials substituting fossil C based materials or other CO2-emission-intensive materials. Some published research assumes a trade-off between the timber harvested from existing forests and the stock of C in those forest ecosystems, asserting that both cannot increase simultaneously. We tested this assumption using the uniquely detailed forest inventory data available from Finland, Norway and Sweden, hereafter denoted northern Europe. We focused on the period 1960 – 2017, that saw little change in the total area covered by forests in northern Europe. At the start of the period, rotational forestry practices began to diffuse, eventually replacing selective felling management systems as the most common management practice. Looking at data over the period we find that despite significant increases in timber and pulp wood harvests, the growth of the forest C stock accelerated. Over the study period, the C stock of the forest ecosystems in northern Europe increased by nearly 70\%, while annual timber harvests increased at the about 40\% over the same period. This increase in the forest C stock was close to on par with the CO2-emissions from the region (other greenhouse gases not included). Our results suggest that the important effects of management on forest growth allows the forest C stock and timber harvests to increase simultaneously. The development in northern Europe raises the question of how better forest management can improve forest growth elsewhere around the globe while at the same time protecting biodiversity and preserving landscapes.},
	language = {en},
	urldate = {2022-06-27},
	journal = {Forest Ecology and Management},
	author = {Kauppi, Pekka E. and Stål, Gustav and Arnesson-Ceder, Lina and Hallberg Sramek, Isabella and Hoen, Hans Fredrik and Svensson, Arvid and Wernick, Iddo K. and Högberg, Peter and Lundmark, Tomas and Nordin, Annika},
	month = jun,
	year = {2022},
	keywords = {Boreal forests, Carbon cycle, Carbon mitigation, Forest ecosystems, Forest management, Global forests},
	pages = {120186},
}

Planting new forests has received scientific and political attention as a measure to mitigate climate change. Large, new forests have been planted in places like China and Ethiopia and, over time, a billion hectares could become available globally for planting new forests. Sustainable management of forests, which are available to wood production, has received less attention despite these forests covering at least two billion hectares globally. Better management of existing forests would improve forest growth and help mitigate climate change by increasing the forest carbon (C) stock, by storing C in forest products, and by generating wood-based materials substituting fossil C based materials or other CO2-emission-intensive materials. Some published research assumes a trade-off between the timber harvested from existing forests and the stock of C in those forest ecosystems, asserting that both cannot increase simultaneously. We tested this assumption using the uniquely detailed forest inventory data available from Finland, Norway and Sweden, hereafter denoted northern Europe. We focused on the period 1960 – 2017, that saw little change in the total area covered by forests in northern Europe. At the start of the period, rotational forestry practices began to diffuse, eventually replacing selective felling management systems as the most common management practice. Looking at data over the period we find that despite significant increases in timber and pulp wood harvests, the growth of the forest C stock accelerated. Over the study period, the C stock of the forest ecosystems in northern Europe increased by nearly 70%, while annual timber harvests increased at the about 40% over the same period. This increase in the forest C stock was close to on par with the CO2-emissions from the region (other greenhouse gases not included). Our results suggest that the important effects of management on forest growth allows the forest C stock and timber harvests to increase simultaneously. The development in northern Europe raises the question of how better forest management can improve forest growth elsewhere around the globe while at the same time protecting biodiversity and preserving landscapes.

@article{law_metatranscriptomics_2022,
	title = {Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests},
	volume = {119},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2118852119},
	doi = {10.1073/pnas.2118852119},
	abstract = {Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.},
	number = {26},
	urldate = {2022-06-22},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Law, Simon R. and Serrano, Alonso R. and Daguerre, Yohann and Sundh, John and Schneider, Andreas N. and Stangl, Zsofia R. and Castro, David and Grabherr, Manfred and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = jun,
	year = {2022},
	pages = {e2118852119},
}

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.

@article{lopez-lopez_maturation_2022,
	title = {Maturation and {Assembly} of {Iron}-{Sulfur} {Cluster}-{Containing} {Subunits} in the {Mitochondrial} {Complex} {I} {From} {Plants}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.916948},
	abstract = {In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.},
	urldate = {2022-06-07},
	journal = {Frontiers in Plant Science},
	author = {López-López, Alicia and Keech, Olivier and Rouhier, Nicolas},
	month = may,
	year = {2022},
	keywords = {⛔ No DOI found},
}

In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.

@article{nilsson_winter_2022,
	title = {Winter dormancy in trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222005802},
	doi = {10.1016/j.cub.2022.04.011},
	abstract = {Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.},
	language = {en},
	number = {12},
	urldate = {2022-06-21},
	journal = {Current Biology},
	author = {Nilsson, Ove},
	month = jun,
	year = {2022},
	pages = {R630--R634},
}

Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.

@article{zacharaki_impaired_2022,
	title = {Impaired {KIN10} function restores developmental defects in the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18104},
	doi = {10.1111/nph.18104},
	abstract = {Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Zacharaki, Vasiliki and Ponnu, Jathish and Crepin, Nathalie and Langenecker, Tobias and Hagmann, Jörg and Skorzinski, Noemi and Musialak-Lange, Magdalena and Wahl, Vanessa and Rolland, Filip and Schmid, Markus},
	year = {2022},
	keywords = {Arabidopsis thaliana, SnRK1 complex, T6P pathway, TPS1, embryogenesis, flowering time},
	pages = {220--233},
}

Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.

@article{wang_sucrose_2022,
	title = {Sucrose synthase activity is not required for cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15752},
	doi = {10.1111/tpj.15752},
	abstract = {Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20\% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Wang, Wei and Viljamaa, Sonja and Hodek, Ondrej and Moritz, Thomas and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis thaliana, UDP-glucose, cellulose, sucrose synthase},
	pages = {1493--1497},
}

Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.

@article{nibbering_cages_2022,
	title = {{CAGEs} are {Golgi}-localized {GT31} enzymes involved in cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15734},
	doi = {10.1111/tpj.15734},
	abstract = {Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30\% reduction in cellulose content, an approximately 50\% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Nibbering, Pieter and Castilleux, Romain and Wingsle, Gunnar and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis, Golgi, arabinogalactan protein, cell wall, cellulose, glycosyltransferase family 31},
	pages = {1271--1285},
}

Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30% reduction in cellulose content, an approximately 50% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.

@article{kokla_nitrogen_2022,
	title = {Nitrogen represses haustoria formation through abscisic acid in the parasitic plant {Phtheirospermum} japonicum},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-30550-x},
	doi = {10.1038/s41467-022-30550-x},
	abstract = {Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.},
	language = {en},
	number = {1},
	urldate = {2022-06-02},
	journal = {Nature Communications},
	author = {Kokla, Anna and Leso, Martina and Zhang, Xiang and Simura, Jan and Serivichyaswat, Phanu T. and Cui, Songkui and Ljung, Karin and Yoshida, Satoko and Melnyk, Charles W.},
	month = may,
	year = {2022},
	keywords = {Parasitism, Plant hormones, Plant physiology},
	pages = {2976},
}

Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.

@article{hoffmann_arabidopsis_2022,
	title = {Arabidopsis {RNA} processing body components {LSM1} and {DCP5} aid in the evasion of translational repression during {Cauliflower} mosaic virus infection},
	issn = {1532-298X},
	doi = {10.1093/plcell/koac132},
	abstract = {Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.},
	language = {eng},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and Mahboubi, Amir and Bente, Heinrich and Garcia, Damien and Hanson, Johannes and Hafrén, Anders},
	month = may,
	year = {2022},
	pages = {koac132},
}

Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.

@article{hernandez-verdeja_genomes_2022,
	title = {{GENOMES} {UNCOUPLED1} plays a key role during the de-etiolation process in {Arabidopsis}},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18115},
	doi = {10.1111/nph.18115},
	abstract = {One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Hernández-Verdeja, Tamara and Vuorijoki, Linda and Jin, Xu and Vergara, Alexander and Dubreuil, Carole and Strand, Åsa},
	year = {2022},
	keywords = {GUN1, chloroplast, greening, light signalling, plastid retrograde signalling, transcriptional regulation},
	pages = {188--203},
}

One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.

@article{hamon-josse_kai2_2022,
	title = {{KAI2} regulates seedling development by mediating light-induced remodelling of auxin transport},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18110},
	doi = {10.1111/nph.18110},
	abstract = {Photomorphogenic remodelling of seedling growth is a key developmental transition in the plant life cycle. The α/β-hydrolase signalling protein KARRIKIN-INSENSITIVE2 (KAI2), a close homologue of the strigolactone receptor DWARF14 (D14), is involved in this process, but it is unclear how the effects of KAI2 on development are mediated. Here, using a combination of physiological, pharmacological, genetic and imaging approaches in Arabidopsis thaliana (Heynh.) we show that kai2 phenotypes arise because of a failure to downregulate auxin transport from the seedling shoot apex towards the root system, rather than a failure to respond to light per se. We demonstrate that KAI2 controls the light-induced remodelling of the PIN-mediated auxin transport system in seedlings, promoting a reduction in PIN7 abundance in older tissues, and an increase of PIN1/PIN2 abundance in the root meristem. We show that removing PIN3, PIN4 and PIN7 from kai2 mutants, or pharmacological inhibition of auxin transport and synthesis, is sufficient to suppress most kai2 seedling phenotypes. We conclude that KAI2 regulates seedling morphogenesis by its effects on the auxin transport system. We propose that KAI2 is not required for the light-mediated changes in PIN gene expression but is required for the appropriate changes in PIN protein abundance within cells.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Hamon-Josse, Maxime and Villaécija-Aguilar, José Antonio and Ljung, Karin and Leyser, Ottoline and Gutjahr, Caroline and Bennett, Tom},
	year = {2022},
	keywords = {Arabidopsis, KAI2 signalling, PIN proteins, auxin, auxin transport, light signalling, seedling development},
	pages = {126--140},
}

Photomorphogenic remodelling of seedling growth is a key developmental transition in the plant life cycle. The α/β-hydrolase signalling protein KARRIKIN-INSENSITIVE2 (KAI2), a close homologue of the strigolactone receptor DWARF14 (D14), is involved in this process, but it is unclear how the effects of KAI2 on development are mediated. Here, using a combination of physiological, pharmacological, genetic and imaging approaches in Arabidopsis thaliana (Heynh.) we show that kai2 phenotypes arise because of a failure to downregulate auxin transport from the seedling shoot apex towards the root system, rather than a failure to respond to light per se. We demonstrate that KAI2 controls the light-induced remodelling of the PIN-mediated auxin transport system in seedlings, promoting a reduction in PIN7 abundance in older tissues, and an increase of PIN1/PIN2 abundance in the root meristem. We show that removing PIN3, PIN4 and PIN7 from kai2 mutants, or pharmacological inhibition of auxin transport and synthesis, is sufficient to suppress most kai2 seedling phenotypes. We conclude that KAI2 regulates seedling morphogenesis by its effects on the auxin transport system. We propose that KAI2 is not required for the light-mediated changes in PIN gene expression but is required for the appropriate changes in PIN protein abundance within cells.

@article{gaur_compensatory_2022,
	title = {Compensatory phenolic induction dynamics in aspen after aphid infestation},
	volume = {12},
	copyright = {2022 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-022-13225-x},
	doi = {10.1038/s41598-022-13225-x},
	abstract = {Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.},
	language = {en},
	number = {1},
	urldate = {2022-06-13},
	journal = {Scientific Reports},
	author = {Gaur, Rajarshi Kumar and de Abreu, Ilka Nacif and Albrectsen, Benedicte Riber},
	month = jun,
	year = {2022},
	keywords = {Biochemistry, Plant sciences},
	pages = {9582},
}

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.

@article{funfgeld_sucrose_2022,
	title = {Sucrose synthases are not involved in starch synthesis in {Arabidopsis} leaves},
	volume = {8},
	copyright = {2022 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01140-y},
	doi = {10.1038/s41477-022-01140-y},
	abstract = {Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.},
	language = {en},
	number = {5},
	urldate = {2022-05-30},
	journal = {Nature Plants},
	author = {Fünfgeld, Maximilian M. F. F. and Wang, Wei and Ishihara, Hirofumi and Arrivault, Stéphanie and Feil, Regina and Smith, Alison M. and Stitt, Mark and Lunn, John E. and Niittylä, Totte},
	month = may,
	year = {2022},
	keywords = {Plant molecular biology, Plant physiology},
	pages = {574--582},
}

Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.

@article{casanova-saez_inactivation_2022,
	title = {Inactivation of the entire {Arabidopsis} group {II} {GH3s} confers tolerance to salinity and water deficit},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18114},
	doi = {10.1111/nph.18114},
	abstract = {Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Casanova-Sáez, Rubén and Mateo-Bonmatí, Eduardo and Šimura, Jan and Pěnčík, Aleš and Novák, Ondřej and Ljung, Karin},
	year = {2022},
	keywords = {Arabidopsis, GH3, auxin, drought, salinity, stress tolerance},
	pages = {263--275},
}

Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.

@article{rabe_combining_2022,
	title = {Combining metabolic phenotype determination with metabolomics and transcriptional analyses to reveal pathways regulated by hydroxycarboxylic acid receptor 2},
	volume = {13},
	issn = {2730-6011},
	url = {https://doi.org/10.1007/s12672-022-00503-3},
	doi = {10.1007/s12672-022-00503-3},
	abstract = {The adaptation of cellular metabolism is considered a hallmark of cancer. Oncogenic signaling pathways support tumorigenesis and cancer progression through the induction of certain metabolic phenotypes associated with altered regulation of key metabolic enzymes. Hydroxycarboxylic acid receptor 2 (HCA2) is a G protein-coupled receptor previously shown to act as a tumor suppressor. Here, we aimed to unveil the connection between cellular metabolism and HCA2 in BT-474 cells. Moreover, we intend to clarify how well this metabolic phenotype is reflected in transcriptional changes and metabolite levels as determined by global metabolomics analyses.},
	language = {en},
	number = {1},
	urldate = {2022-06-17},
	journal = {Discover Oncology},
	author = {Rabe, Philipp and Gehmlich, Mareike and Peters, Anna and Krumbholz, Petra and Nordström, Anders and Stäubert, Claudia},
	month = jun,
	year = {2022},
	keywords = {Cancer metabolism, GPR109A, HCA2, LC-MS, Metabolite profile, Metabolite-sensing GPCR},
	pages = {47},
}

The adaptation of cellular metabolism is considered a hallmark of cancer. Oncogenic signaling pathways support tumorigenesis and cancer progression through the induction of certain metabolic phenotypes associated with altered regulation of key metabolic enzymes. Hydroxycarboxylic acid receptor 2 (HCA2) is a G protein-coupled receptor previously shown to act as a tumor suppressor. Here, we aimed to unveil the connection between cellular metabolism and HCA2 in BT-474 cells. Moreover, we intend to clarify how well this metabolic phenotype is reflected in transcriptional changes and metabolite levels as determined by global metabolomics analyses.

@article{heuchel_genetic_2022,
	title = {Genetic diversity and background pollen contamination in {Norway} spruce and {Scots} pine seed orchard crops},
	volume = {2},
	copyright = {2022 The Author(s)},
	issn = {2767-3812},
	url = {https://www.maxapress.com/rticle/doi/10.48130/FR-2022-0008},
	doi = {10.48130/FR-2022-0008},
	abstract = {Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85\% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (\textit{H}$_{\textrm{O}}$) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher \textit{H}$_{\textrm{O}}$ and BPC than spruce. BPC in pine crops varied from 87\% at young orchard age to 12\% at mature age, wherease this rate ranged between 27\%−4\% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30\%−50\% parents contibuting to 80\% of the progeny. Selfing was low (2\%−6\%) in all seed crops. Compared to natural stands, orchard crops had slightly lower \textit{H}$_{\textrm{O}}$ but no strong signal of inbreeding. Our results provide valuable references for orchard management.},
	language = {en},
	number = {1},
	urldate = {2022-06-03},
	journal = {Forestry Research},
	author = {Heuchel, Alisa and Hall, David and Zhao, Wei and Gao, Jie and Wennström, Ulfstand and Wang, Xiao-Ru and Heuchel, Alisa and Hall, David and Zhao, Wei and Gao, Jie and Wennström, Ulfstand and Wang, Xiao-Ru},
	month = jun,
	year = {2022},
	pages = {1--12},
}

Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (H$_{\textrm{O}}$) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher H$_{\textrm{O}}$ and BPC than spruce. BPC in pine crops varied from 87% at young orchard age to 12% at mature age, wherease this rate ranged between 27%−4% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30%−50% parents contibuting to 80% of the progeny. Selfing was low (2%−6%) in all seed crops. Compared to natural stands, orchard crops had slightly lower H$_{\textrm{O}}$ but no strong signal of inbreeding. Our results provide valuable references for orchard management.

@article{chardon_natural_2022,
	title = {Natural variation in the long-distance transport of nutrients and photoassimilates in response to {N} availability},
	volume = {273},
	issn = {0176-1617},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722000931},
	doi = {10.1016/j.jplph.2022.153707},
	abstract = {Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56\% carbohydrates, 27 or 45\% amino acids, and 5 or 13\% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86\% carbohydrates, 7 or 18\% amino acids, and 5 or 6\% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.},
	language = {en},
	urldate = {2022-05-30},
	journal = {Journal of Plant Physiology},
	author = {Chardon, Fabien and De Marco, Federica and Marmagne, Anne and Le Hir, Rozenn and Vilaine, Françoise and Bellini, Catherine and Dinant, Sylvie},
	month = jun,
	year = {2022},
	keywords = {Allocation, Pipecolate, Raffinose, Succinate, Sucrose, Transport},
	pages = {153707},
}

Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56% carbohydrates, 27 or 45% amino acids, and 5 or 13% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86% carbohydrates, 7 or 18% amino acids, and 5 or 6% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.

@article{long_dgat1_2022,
	title = {{DGAT1} activity synchronises with mitophagy to protect cells from metabolic rewiring by iron  depletion},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.2021109390},
	doi = {10.15252/embj.2021109390},
	abstract = {Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.},
	urldate = {2022-04-19},
	journal = {The EMBO Journal},
	author = {Long, Maeve and Sanchez-Martinez, Alvaro and Longo, Marianna and Suomi, Fumi and Stenlund, Hans and Johansson, Annika I. and Ehsan, Homa and Salo, Veijo T. and Montava-Garriga, Lambert and Naddafi, Seyedehshima and Ikonen, Elina and Ganley, Ian G. and Whitworth, Alexander J. and McWilliams, Thomas G.},
	month = apr,
	year = {2022},
	keywords = {DGAT1, iron, lipid droplet, metabolism, mitophagy},
	pages = {e109390},
}

Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.

@article{jonsson_plant_2022,
	title = {Plant cell walls as mechanical signaling hubs for morphogenesis},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222002585},
	doi = {10.1016/j.cub.2022.02.036},
	abstract = {The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.},
	language = {en},
	number = {7},
	urldate = {2022-05-20},
	journal = {Current Biology},
	author = {Jonsson, Kristoffer and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2022},
	pages = {R334--R340},
}

The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.

@article{domevscik_large-scale_2022,
	title = {Large-scale assessment of artificially coated seeds for forest regeneration across {Sweden}},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-022-09920-2},
	doi = {10.1007/s11056-022-09920-2},
	abstract = {We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4\% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.},
	language = {en},
	urldate = {2022-05-20},
	journal = {New Forests},
	author = {Domevscik, Matej and Häggström, Bodil and Lim, Hyungwoo and Öhlund, Jonas and Nordin, Annika},
	month = may,
	year = {2022},
	keywords = {Boreal forest, Coated seeds, Forest regeneration, Scots pine, SeedPAD, Seeding},
}

We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.

@article{hallberg-sramek_bringing_2022,
	title = {Bringing “{Climate}-{Smart} {Forestry}” {Down} to the {Local} {Level}—{Identifying} {Barriers}, {Pathways} and {Indicators} for {Its} {Implementation} in {Practice}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/13/1/98},
	doi = {10/gn3n2b},
	abstract = {The theoretical concept of “climate-smart forestry” aims to integrate climate change mitigation and adaptation to maintain and enhance forests’ contributions to people and global agendas. We carried out two local transdisciplinary collaboration processes with the aim of developing local articulations of climate-smart forestry and to identify barriers, pathways and indicators to applying it in practice. During workshops in northern and southern Sweden, local stakeholders described how they would like forests to be managed, considering their past experiences, future visions and climate change. As a result, the stakeholders framed climate-smart forestry as active and diverse management towards multiple goals. They identified several conditions that could act both as barriers and pathways for its implementation in practice, such as value chains for forest products and services, local knowledge and experiences of different management alternatives, and the management of ungulates. Based on the workshop material, a total of 39 indicators for climate-smart forestry were identified, of which six were novel indicators adding to the existing literature. Our results emphasize the importance of understanding the local perspectives to promote climate-smart forestry practices across Europe. We also suggest how the concept of climate-smart forestry can be further developed, through the interplay between theory and practice.},
	language = {en},
	number = {1},
	urldate = {2022-03-16},
	journal = {Forests},
	author = {Hallberg-Sramek, Isabella and Reimerson, Elsa and Priebe, Janina and Nordström, Eva-Maria and Mårald, Erland and Sandström, Camilla and Nordin, Annika},
	month = jan,
	year = {2022},
	keywords = {adaptation, climate change, forest policy, interdisciplinary research, mitigation, nature’s contributions to people, stakeholder participation, sustainable forest management, transdisciplinary collaboration},
	pages = {98},
}

The theoretical concept of “climate-smart forestry” aims to integrate climate change mitigation and adaptation to maintain and enhance forests’ contributions to people and global agendas. We carried out two local transdisciplinary collaboration processes with the aim of developing local articulations of climate-smart forestry and to identify barriers, pathways and indicators to applying it in practice. During workshops in northern and southern Sweden, local stakeholders described how they would like forests to be managed, considering their past experiences, future visions and climate change. As a result, the stakeholders framed climate-smart forestry as active and diverse management towards multiple goals. They identified several conditions that could act both as barriers and pathways for its implementation in practice, such as value chains for forest products and services, local knowledge and experiences of different management alternatives, and the management of ungulates. Based on the workshop material, a total of 39 indicators for climate-smart forestry were identified, of which six were novel indicators adding to the existing literature. Our results emphasize the importance of understanding the local perspectives to promote climate-smart forestry practices across Europe. We also suggest how the concept of climate-smart forestry can be further developed, through the interplay between theory and practice.

@article{miao_katanin-dependent_2022,
	title = {Katanin-{Dependent} {Microtubule} {Ordering} in {Association} with {ABA} {Is} {Important} for {Root} {Hydrotropism}},
	volume = {23},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/23/7/3846},
	doi = {10.3390/ijms23073846},
	abstract = {Root hydrotropism refers to root directional growth toward soil moisture. Cortical microtubule arrays are essential for determining the growth axis of the elongating cells in plants. However, the role of microtubule reorganization in root hydrotropism remains elusive. Here, we demonstrate that the well-ordered microtubule arrays and the microtubule-severing protein KATANIN (KTN) play important roles in regulating root hydrotropism in Arabidopsis. We found that the root hydrotropic bending of the ktn1 mutant was severely attenuated but not root gravitropism. After hydrostimulation, cortical microtubule arrays in cells of the elongation zone of wild-type (WT) Col-0 roots were reoriented from transverse into an oblique array along the axis of cell elongation, whereas the microtubule arrays in the ktn1 mutant remained in disorder. Moreover, we revealed that abscisic acid (ABA) signaling enhanced the root hydrotropism of WT and partially rescued the oryzalin (a microtubule destabilizer) alterative root hydrotropism of WT but not ktn1 mutants. These results suggest that katanin-dependent microtubule ordering is required for root hydrotropism, which might work downstream of ABA signaling pathways for plant roots to search for water.},
	language = {en},
	number = {7},
	urldate = {2022-04-19},
	journal = {International Journal of Molecular Sciences},
	author = {Miao, Rui and Siao, Wei and Zhang, Na and Lei, Zuliang and Lin, Deshu and Bhalerao, Rishikesh P. and Lu, Congming and Xu, Weifeng},
	month = jan,
	year = {2022},
	keywords = {KATANIN, abscisic acid, cortical microtubule arrays, oryzalin, root hydrotropism},
	pages = {3846},
}

Root hydrotropism refers to root directional growth toward soil moisture. Cortical microtubule arrays are essential for determining the growth axis of the elongating cells in plants. However, the role of microtubule reorganization in root hydrotropism remains elusive. Here, we demonstrate that the well-ordered microtubule arrays and the microtubule-severing protein KATANIN (KTN) play important roles in regulating root hydrotropism in Arabidopsis. We found that the root hydrotropic bending of the ktn1 mutant was severely attenuated but not root gravitropism. After hydrostimulation, cortical microtubule arrays in cells of the elongation zone of wild-type (WT) Col-0 roots were reoriented from transverse into an oblique array along the axis of cell elongation, whereas the microtubule arrays in the ktn1 mutant remained in disorder. Moreover, we revealed that abscisic acid (ABA) signaling enhanced the root hydrotropism of WT and partially rescued the oryzalin (a microtubule destabilizer) alterative root hydrotropism of WT but not ktn1 mutants. These results suggest that katanin-dependent microtubule ordering is required for root hydrotropism, which might work downstream of ABA signaling pathways for plant roots to search for water.

@article{niu_chinese_2022,
	title = {The {Chinese} pine genome and methylome unveil key features of conifer evolution},
	volume = {185},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(21)01428-8},
	doi = {10/gnw8q5},
	abstract = {Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2\% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.},
	language = {English},
	number = {1},
	urldate = {2022-02-04},
	journal = {Cell},
	author = {Niu, Shihui and Li, Jiang and Bo, Wenhao and Yang, Weifei and Zuccolo, Andrea and Giacomello, Stefania and Chen, Xi and Han, Fangxu and Yang, Junhe and Song, Yitong and Nie, Yumeng and Zhou, Biao and Wang, Peiyi and Zuo, Quan and Zhang, Hui and Ma, Jingjing and Wang, Jun and Wang, Lvji and Zhu, Qianya and Zhao, Huanhuan and Liu, Zhanmin and Zhang, Xuemei and Liu, Tao and Pei, Surui and Li, Zhimin and Hu, Yao and Yang, Yehui and Li, Wenzhao and Zan, Yanjun and Zhou, Linghua and Lin, Jinxing and Yuan, Tongqi and Li, Wei and Li, Yue and Wei, Hairong and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {Chinese pine, chromosome-level genome, climate adaptation, conifer evolution, conifer reproduction, gene expression, genome expansion, long intron, methylome},
	pages = {204--217.e14},
}

Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

@article{hodek_mixed-mode_2022,
	title = {Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples},
	volume = {14},
	issn = {1759-9679},
	url = {https://pubs.rsc.org/en/content/articlelanding/2022/ay/d1ay02143e},
	doi = {10/gpkx25},
	abstract = {Carboxylic acids are crucial metabolites in the tricarboxylic acid (TCA) cycle and thus participate in central carbon metabolism (CCM). Research dependent on the analysis of metabolites involved in central carbon metabolism requires fast separation and sensitive detection of carboxylic acids using liquid chromatography-mass spectrometry (LC-MS). However, successful separation of all carboxylic acids from the TCA cycle by liquid chromatography remains a challenging task because of their high polarity and thus low retention on the conventional reversed-phase columns. In this study, we tested a reversed-phase/anion exchange mixed-mode stationary phase (Waters BEH C18 AX) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We developed and optimized a method that enables a 10 minute separation of all carboxylic acids from the TCA cycle and lactic acid without prior derivatization or addition of ion-pair reagents in the mobile phase. The developed method was validated for quantification of 8 acids in murine brown preadipocytes, 5 acids in human plasma and 6 acids in Arabidopsis thaliana leaves with limits of quantification ranging from 0.1 μM for malic acid to 10 μM for isocitric acid. Moreover, the mixed-mode chromatography enabled untargeted screening of medium- to long-chain fatty acids in murine brown preadipocytes, Arabidopsis thaliana, and human plasma, where 23 fatty acids were identified by using liquid chromatography with high-resolution mass spectrometry (HRMS).},
	language = {en},
	number = {10},
	urldate = {2022-02-25},
	journal = {Analytical Methods},
	author = {Hodek, Ondřej and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = jan,
	year = {2022},
	pages = {1015--1022},
}

Carboxylic acids are crucial metabolites in the tricarboxylic acid (TCA) cycle and thus participate in central carbon metabolism (CCM). Research dependent on the analysis of metabolites involved in central carbon metabolism requires fast separation and sensitive detection of carboxylic acids using liquid chromatography-mass spectrometry (LC-MS). However, successful separation of all carboxylic acids from the TCA cycle by liquid chromatography remains a challenging task because of their high polarity and thus low retention on the conventional reversed-phase columns. In this study, we tested a reversed-phase/anion exchange mixed-mode stationary phase (Waters BEH C18 AX) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We developed and optimized a method that enables a 10 minute separation of all carboxylic acids from the TCA cycle and lactic acid without prior derivatization or addition of ion-pair reagents in the mobile phase. The developed method was validated for quantification of 8 acids in murine brown preadipocytes, 5 acids in human plasma and 6 acids in Arabidopsis thaliana leaves with limits of quantification ranging from 0.1 μM for malic acid to 10 μM for isocitric acid. Moreover, the mixed-mode chromatography enabled untargeted screening of medium- to long-chain fatty acids in murine brown preadipocytes, Arabidopsis thaliana, and human plasma, where 23 fatty acids were identified by using liquid chromatography with high-resolution mass spectrometry (HRMS).

@article{marabita_multiomics_2022,
	title = {Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health},
	volume = {13},
	issn = {2405-4712},
	url = {https://www.cell.com/cell-systems/abstract/S2405-4712(21)00451-8},
	doi = {10.1016/j.cels.2021.11.001},
	language = {English},
	number = {3},
	urldate = {2022-04-08},
	journal = {Cell Systems},
	author = {Marabita, Francesco and James, Tojo and Karhu, Anu and Virtanen, Heidi and Kettunen, Kaisa and Stenlund, Hans and Boulund, Fredrik and Hellström, Cecilia and Neiman, Maja and Mills, Robert and Perheentupa, Teemu and Laivuori, Hannele and Helkkula, Pyry and Byrne, Myles and Jokinen, Ilkka and Honko, Harri and Kallonen, Antti and Ermes, Miikka and Similä, Heidi and Lindholm, Mikko and Widén, Elisabeth and Ripatti, Samuli and Perälä-Heape, Maritta and Engstrand, Lars and Nilsson, Peter and Moritz, Thomas and Miettinen, Timo and Sallinen, Riitta and Kallioniemi, Olli},
	month = mar,
	year = {2022},
	keywords = {P4 medicine, lifestyle changes, multiomics data integration, personalized medicine, precision health, precision medicine, systems medicine},
	pages = {241--255.e7},
}

@incollection{chantreau_spatio-temporal_2022,
	title = {Spatio-temporal regulation of lignification},
	url = {https://www.sciencedirect.com/science/article/pii/S0065229622000398},
	abstract = {Lignin is a poly-aromatic polymer found in plant cell walls. This polymer, mainly composed of three phenylpropanoid units, confers exceptional properties to the cell wall such as hydrophobicity, mechanical strength, or resistance against stresses. Thereby the cell wall deposition of lignin represents often the main molecular event that defines the biological function(s) of the lignified cell or tissue. The time and localization of lignin deposition as well as the composition of the polymer can be considered as the three essential components of the polymer that will define the biological function of the lignified tissue. In this review, we will cover the localizations, types and functions of lignin found in various part of land plants. Then, for the various lignified tissues, the mechanisms controlling the developmental deposition of lignin such as transcriptional regulation, intercellular coordinated control of lignification or posttranslational modification of proteins will be discussed. Finally, a focus will be made on the environmental cues that influence the lignification during radial tree growth, as well as the plant responses that these signals trigger in the regulation of lignification.},
	language = {en},
	urldate = {2022-04-26},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Academic Press},
	author = {Chantreau, Maxime and Tuominen, Hannele},
	month = apr,
	year = {2022},
	keywords = {Lignification, Lignin, Non-cell autonomous lignification, Regulation},
}

Lignin is a poly-aromatic polymer found in plant cell walls. This polymer, mainly composed of three phenylpropanoid units, confers exceptional properties to the cell wall such as hydrophobicity, mechanical strength, or resistance against stresses. Thereby the cell wall deposition of lignin represents often the main molecular event that defines the biological function(s) of the lignified cell or tissue. The time and localization of lignin deposition as well as the composition of the polymer can be considered as the three essential components of the polymer that will define the biological function of the lignified tissue. In this review, we will cover the localizations, types and functions of lignin found in various part of land plants. Then, for the various lignified tissues, the mechanisms controlling the developmental deposition of lignin such as transcriptional regulation, intercellular coordinated control of lignification or posttranslational modification of proteins will be discussed. Finally, a focus will be made on the environmental cues that influence the lignification during radial tree growth, as well as the plant responses that these signals trigger in the regulation of lignification.

@article{parizkova_ip_2022,
	title = {{iP} \& {OEIP} – {Cytokinin} {Micro} {Application} {Modulates} {Root} {Development} with {High} {Spatial} {Resolution}},
	issn = {2365-709X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/admt.202101664},
	doi = {10.1002/admt.202101664},
	abstract = {State-of-the-art technology based on organic electronics can be used as a flow-free delivery method for organic substances with high spatial resolution. Such highly targeted drug micro applications can be used in plant research for the regulation of physiological processes on tissue and cellular levels. Here, for the first time, an organic electronic ion pump (OEIP) is reported that can transport an isoprenoid-type cytokinin, N6-isopentenyladenine (iP), to intact plants. Cytokinins (CKs) are plant hormones involved in many essential physiological processes, including primary root (PR) and lateral root (LR) development. Using the Arabidopsis thaliana root as a model system, efficient iP delivery is demonstrated with a biological output – cytokinin-related PR and LR growth inhibition. The spatial resolution of iP delivery, defined for the first time for an organic compound, is shown to be less than 1 mm, exclusively affecting the OEIP-targeted LR. Results from the application of the high-resolution OIEP treatment method confirm previously published findings showing that the influence of CKs may vary at different stages of LR development. Thus, OEIP-based technologies offer a novel, electronically controlled method for phytohormone delivery that could contribute to unraveling cytokinin functions during different developmental processes with high specificity.},
	language = {en},
	urldate = {2022-04-29},
	journal = {Advanced Materials Technologies},
	author = {Pařízková, Barbora and Antoniadi, Ioanna and Poxson, David J. and Karady, Michal and Simon, Daniel T. and Zatloukal, Marek and Strnad, Miroslav and Doležal, Karel and Novák, Ondřej and Ljung, Karin},
	month = apr,
	year = {2022},
	keywords = {arabidopsis, cytokinin, hormone delivery, lateral root, organic bioelectronics, root development, spatial resolution},
	pages = {2101664},
}

State-of-the-art technology based on organic electronics can be used as a flow-free delivery method for organic substances with high spatial resolution. Such highly targeted drug micro applications can be used in plant research for the regulation of physiological processes on tissue and cellular levels. Here, for the first time, an organic electronic ion pump (OEIP) is reported that can transport an isoprenoid-type cytokinin, N6-isopentenyladenine (iP), to intact plants. Cytokinins (CKs) are plant hormones involved in many essential physiological processes, including primary root (PR) and lateral root (LR) development. Using the Arabidopsis thaliana root as a model system, efficient iP delivery is demonstrated with a biological output – cytokinin-related PR and LR growth inhibition. The spatial resolution of iP delivery, defined for the first time for an organic compound, is shown to be less than 1 mm, exclusively affecting the OEIP-targeted LR. Results from the application of the high-resolution OIEP treatment method confirm previously published findings showing that the influence of CKs may vary at different stages of LR development. Thus, OEIP-based technologies offer a novel, electronically controlled method for phytohormone delivery that could contribute to unraveling cytokinin functions during different developmental processes with high specificity.

@article{amanda_auxin_2022,
	title = {Auxin boosts energy generation pathways to fuel pollen maturation in barley},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222003438},
	doi = {10.1016/j.cub.2022.02.073},
	abstract = {Pollen grains become increasingly independent of the mother plant as they reach maturity through poorly understood developmental programs. We report that the hormone auxin is essential during barley pollen maturation to boost the expression of genes encoding almost every step of heterotrophic energy production pathways. Accordingly, auxin is necessary for the flux of sucrose and hexoses into glycolysis and to increase the levels of pyruvate and two tricarboxylic (TCA) cycle metabolites (citrate and succinate). Moreover, bioactive auxin is synthesized by the pollen-localized enzyme HvYUCCA4, supporting that pollen grains autonomously produce auxin to stimulate a specific cellular output, energy generation, that fuels maturation processes such as starch accumulation. Our results demonstrate that auxin can shift central carbon metabolism to drive plant cell development, which suggests a direct mechanism for auxin’s ability to promote growth and differentiation.},
	language = {en},
	number = {8},
	urldate = {2022-05-06},
	journal = {Current Biology},
	author = {Amanda, Dhika and Frey, Felix P. and Neumann, Ulla and Przybyl, Marine and Šimura, Jan and Zhang, Youjun and Chen, Zongliang and Gallavotti, Andrea and Fernie, Alisdair R. and Ljung, Karin and Acosta, Iván F.},
	month = apr,
	year = {2022},
	keywords = {anther, auxin, barley, metabolism, plant male fertility, pollen, stamen maturation, starch},
	pages = {1798--1811.e8},
}

Pollen grains become increasingly independent of the mother plant as they reach maturity through poorly understood developmental programs. We report that the hormone auxin is essential during barley pollen maturation to boost the expression of genes encoding almost every step of heterotrophic energy production pathways. Accordingly, auxin is necessary for the flux of sucrose and hexoses into glycolysis and to increase the levels of pyruvate and two tricarboxylic (TCA) cycle metabolites (citrate and succinate). Moreover, bioactive auxin is synthesized by the pollen-localized enzyme HvYUCCA4, supporting that pollen grains autonomously produce auxin to stimulate a specific cellular output, energy generation, that fuels maturation processes such as starch accumulation. Our results demonstrate that auxin can shift central carbon metabolism to drive plant cell development, which suggests a direct mechanism for auxin’s ability to promote growth and differentiation.

@article{chen_lncrna_2022,
	title = {{LncRNA} {PMAT}–{PtoMYB46} module represses {PtoMATE} and {PtoARF2} promoting {Pb2}+ uptake and plant growth in poplar},
	volume = {433},
	issn = {0304-3894},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389422005581},
	doi = {10.1016/j.jhazmat.2022.128769},
	abstract = {Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.},
	language = {en},
	urldate = {2022-04-22},
	journal = {Journal of Hazardous Materials},
	author = {Chen, Panfei and Song, Yuepeng and Liu, Xin and Xiao, Liang and Bu, Chenhao and Liu, Peng and Zhao, Lei and Ingvarsson, Pär K. and Wu, Harry X. and El-Kassaby, Yousry A. and Zhang, Deqiang},
	month = jul,
	year = {2022},
	keywords = {Association genetics, Lead, Long non-coding RNAs, Phytoremediation},
	pages = {128769},
}

Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.

@article{dominguez_mobile_2022,
	title = {Mobile forms of carbon in trees: metabolism and transport},
	volume = {42},
	issn = {1758-4469},
	shorttitle = {Mobile forms of carbon in trees},
	url = {https://doi.org/10.1093/treephys/tpab123},
	doi = {10.1093/treephys/tpab123},
	abstract = {Plants constitute 80\% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.},
	number = {3},
	urldate = {2021-09-21},
	journal = {Tree Physiology},
	author = {Dominguez, Pia Guadalupe and Niittylä, Totte},
	month = mar,
	year = {2022},
	pages = {458--487},
}

Plants constitute 80% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.

@article{hasegawa_tgnee_2022,
	title = {The {TGN}/{EE} {SNARE} protein {SYP61} and the ubiquitin ligase {ATL31} cooperatively regulate plant responses to carbon/nitrogen conditions in {Arabidopsis}},
	volume = {34},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac014},
	doi = {10.1093/plcell/koac014},
	abstract = {Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.},
	number = {4},
	urldate = {2022-04-08},
	journal = {The Plant Cell},
	author = {Hasegawa, Yoko and Huarancca Reyes, Thais and Uemura, Tomohiro and Baral, Anirban and Fujimaki, Akari and Luo, Yongming and Morita, Yoshie and Saeki, Yasushi and Maekawa, Shugo and Yasuda, Shigetaka and Mukuta, Koki and Fukao, Yoichiro and Tanaka, Keiji and Nakano, Akihiko and Takagi, Junpei and Bhalerao, Rishikesh P and Yamaguchi, Junji and Sato, Takeo},
	month = apr,
	year = {2022},
	pages = {1354--1374},
}

Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.

@article{nie_genome-wide_2022,
	title = {Genome-wide {TCP} transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in {Pinus} tabuliformis},
	volume = {22},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-022-03554-4},
	doi = {10.1186/s12870-022-03554-4},
	abstract = {Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.},
	number = {1},
	urldate = {2022-04-08},
	journal = {BMC Plant Biology},
	author = {Nie, Yu-meng and Han, Fang-xu and Ma, Jing-jing and Chen, Xi and Song, Yi-tong and Niu, Shi-Hui and Wu, Harry X.},
	month = apr,
	year = {2022},
	keywords = {Diurnal, Gene family, Oscillation, Pinus tabuliformis, Seasonal, TCP},
	pages = {167},
}

Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.

@article{liu_demographic_2022,
	title = {Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across {Populus} genome},
	volume = {39},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msac008},
	doi = {10/gn9jc6},
	abstract = {Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.},
	number = {2},
	urldate = {2022-01-24},
	journal = {Molecular Biology and Evolution},
	author = {Liu, Shuyu and Zhang, Lei and Sang, Yupeng and Lai, Qiang and Zhang, Xinxin and Jia, Changfu and Long, Zhiqin and Wu, Jiali and Ma, Tao and Mao, Kangshan and Street, Nathaniel R and Ingvarsson, Pär K and Liu, Jianquan and Wang, Jing},
	month = jan,
	year = {2022},
	pages = {msac008},
}

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.

@article{aubry_vacuolar_2022,
	title = {A vacuolar hexose transport is required for xylem development in the inflorescence stem},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab551},
	doi = {10.1093/plphys/kiab551},
	abstract = {In Angiosperms, the development of the vascular system is controlled by a complex network of transcription factors. However, how nutrient availability in the vascular cells affects their development remains to be addressed. At the cellular level, cytosolic sugar availability is regulated mainly by sugar exchanges at the tonoplast through active and/or facilitated transport. In Arabidopsis (Arabidopsis thaliana), among the genes encoding tonoplastic transporters, SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 16 (SWEET16) and SWEET17 expression has been previously detected in the vascular system. Here, using a reverse genetics approach, we propose that sugar exchanges at the tonoplast, regulated by SWEET16, are important for xylem cell division as revealed in particular by the decreased number of xylem cells in the swt16 mutant and the accumulation of SWEET16 at the procambium–xylem boundary. In addition, we demonstrate that transport of hexoses mediated by SWEET16 and/or SWEET17 is required to sustain the formation of the xylem secondary cell wall. This result is in line with a defect in the xylem cell wall composition as measured by Fourier-transformed infrared spectroscopy in the swt16swt17 double mutant and by upregulation of several genes involved in secondary cell wall synthesis. Our work therefore supports a model in which xylem development partially depends on the exchange of hexoses at the tonoplast of xylem-forming cells.},
	number = {2},
	urldate = {2022-03-31},
	journal = {Plant Physiology},
	author = {Aubry, Emilie and Hoffmann, Beate and Vilaine, Françoise and Gilard, Françoise and Klemens, Patrick A W and Guérard, Florence and Gakière, Bertrand and Neuhaus, H Ekkehard and Bellini, Catherine and Dinant, Sylvie and Le Hir, Rozenn},
	month = feb,
	year = {2022},
	pages = {1229--1247},
}

In Angiosperms, the development of the vascular system is controlled by a complex network of transcription factors. However, how nutrient availability in the vascular cells affects their development remains to be addressed. At the cellular level, cytosolic sugar availability is regulated mainly by sugar exchanges at the tonoplast through active and/or facilitated transport. In Arabidopsis (Arabidopsis thaliana), among the genes encoding tonoplastic transporters, SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 16 (SWEET16) and SWEET17 expression has been previously detected in the vascular system. Here, using a reverse genetics approach, we propose that sugar exchanges at the tonoplast, regulated by SWEET16, are important for xylem cell division as revealed in particular by the decreased number of xylem cells in the swt16 mutant and the accumulation of SWEET16 at the procambium–xylem boundary. In addition, we demonstrate that transport of hexoses mediated by SWEET16 and/or SWEET17 is required to sustain the formation of the xylem secondary cell wall. This result is in line with a defect in the xylem cell wall composition as measured by Fourier-transformed infrared spectroscopy in the swt16swt17 double mutant and by upregulation of several genes involved in secondary cell wall synthesis. Our work therefore supports a model in which xylem development partially depends on the exchange of hexoses at the tonoplast of xylem-forming cells.

@article{przybyla-toscano_protein_2022,
	title = {Protein lipoylation in mitochondria requires {Fe}–{S} cluster assembly factors {NFU4} and {NFU5}},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab501},
	doi = {10.1093/plphys/kiab501},
	abstract = {Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.},
	number = {2},
	urldate = {2021-11-04},
	journal = {Plant Physiology},
	author = {Przybyla-Toscano, Jonathan and Maclean, Andrew E and Franceschetti, Marina and Liebsch, Daniela and Vignols, Florence and Keech, Olivier and Rouhier, Nicolas and Balk, Janneke},
	month = feb,
	year = {2022},
	pages = {997--1013},
}

Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.

@article{atakhani_characterising_2022,
	title = {Characterising the mechanics of cell–cell adhesion in plants},
	volume = {3},
	issn = {2632-8828},
	url = {https://www.cambridge.org/core/journals/quantitative-plant-biology/article/characterising-the-mechanics-of-cellcell-adhesion-in-plants/9D165A5D6EA6F2B1927B9F0F38F88AAC},
	doi = {10/gpjfdn},
	abstract = {, 

Cell–cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell–cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell–cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell–cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell–cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.},
	language = {en},
	urldate = {2022-02-16},
	journal = {Quantitative Plant Biology},
	author = {Atakhani, Asal and Bogdziewiez, Léa and Verger, Stéphane},
	month = feb,
	year = {2022},
	keywords = {adhesion strength, cell–cell adhesion, multicellularity, plant, single cell, tissue},
}

, Cell–cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell–cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell–cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell–cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell–cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.

@article{maqdasy_impaired_2022,
	title = {Impaired phosphocreatine metabolism in white adipocytes promotes inflammation},
	volume = {4},
	copyright = {2022 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-022-00525-9},
	doi = {10.1038/s42255-022-00525-9},
	abstract = {The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters adenosine monophosphate-activated protein kinase activity via effects on adenosine triphosphate/adenosine diphosphate levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased chemokine (C-C motif) ligand 2 (CCL2) production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.},
	language = {en},
	number = {2},
	urldate = {2022-02-17},
	journal = {Nature Metabolism},
	author = {Maqdasy, Salwan and Lecoutre, Simon and Renzi, Gianluca and Frendo-Cumbo, Scott and Rizo-Roca, David and Moritz, Thomas and Juvany, Marta and Hodek, Ondrej and Gao, Hui and Couchet, Morgane and Witting, Michael and Kerr, Alastair and Bergo, Martin O. and Choudhury, Robin P. and Aouadi, Myriam and Zierath, Juleen R. and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2022},
	keywords = {Fat metabolism, Mechanisms of disease, Obesity},
	pages = {1--13},
}

The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters adenosine monophosphate-activated protein kinase activity via effects on adenosine triphosphate/adenosine diphosphate levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased chemokine (C-C motif) ligand 2 (CCL2) production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.

@article{ding_transcriptome-based_2022,
	title = {A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population},
	volume = {18},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010017},
	doi = {10/gpn67c},
	abstract = {Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3\% to 21.8\% and from 10.6\% to 16.7\%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.},
	language = {en},
	number = {2},
	urldate = {2022-03-03},
	journal = {PLOS Genetics},
	author = {Ding, Xianyin and Diao, Shu and Luan, Qifu and Wu, Harry X. and Zhang, Yini and Jiang, Jingmin},
	month = feb,
	year = {2022},
	keywords = {Gene expression, Genetics, Genome-wide association studies, Phenotypes, Phylogenetic analysis, Pines, Single nucleotide polymorphisms, Transcriptome analysis},
	pages = {e1010017},
}

Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.

@article{pervaiz_microrna_2022,
	title = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}: {Advances} and {Prospects}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4395},
	shorttitle = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}},
	url = {https://www.mdpi.com/2073-4395/12/1/11},
	doi = {10/gpjfdp},
	abstract = {Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.},
	language = {en},
	number = {1},
	urldate = {2022-02-14},
	journal = {Agronomy},
	author = {Pervaiz, Tariq and Amjid, Muhammad Waqas and El-kereamy, Ashraf and Niu, Shi-Hui and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {abiotic stress tolerance, adaptation, cold stress, drought stress, miRNA target gene expression, salinity stress},
	pages = {11},
}

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.

@article{svennerstam_timing_2022,
	title = {Timing is everything – obtaining accurate measures of plant uptake of amino acids},
	volume = {234},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17964},
	doi = {10/gn9jc5},
	abstract = {Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data. This study compared bulk stable isotope analysis and compound-specific liquid chromatography-mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U-13C5-15N2-l-glutamine and axenically grown Arabidopsis thaliana. After 15–120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the 15N and 13C content increased over time, resulting in very different estimated uptake rates. The 13C : 15N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15\% within 120 min. The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post-uptake metabolism, compound-specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post-uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre-uptake metabolism by microbes that accounts for the 15N–13C mismatch reported in ecological studies, but also post-uptake metabolism in the plant.},
	language = {en},
	number = {1},
	urldate = {2022-02-14},
	journal = {New Phytologist},
	author = {Svennerstam, Henrik and Jämtgård, Sandra},
	month = jan,
	year = {2022},
	keywords = {Arabidopsis thaliana, EA-IRMS, LC-MS, amino acids, glutamine, isotopes, organic nitrogen, plant uptake},
	pages = {311--318},
}

Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data. This study compared bulk stable isotope analysis and compound-specific liquid chromatography-mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U-13C5-15N2-l-glutamine and axenically grown Arabidopsis thaliana. After 15–120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the 15N and 13C content increased over time, resulting in very different estimated uptake rates. The 13C : 15N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15% within 120 min. The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post-uptake metabolism, compound-specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post-uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre-uptake metabolism by microbes that accounts for the 15N–13C mismatch reported in ecological studies, but also post-uptake metabolism in the plant.

@article{cardoso_editorial_2022,
	title = {Editorial: {Advances} on the {Biological} {Mechanisms} {Involved} in {Adventitious} {Root} {Formation}: {From} {Signaling} to {Morphogenesis}},
	volume = {13},
	issn = {1664-462X},
	shorttitle = {Editorial},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.867651},
	doi = {10.3389/fpls.2022.867651},
	urldate = {2022-03-25},
	journal = {Frontiers in Plant Science},
	author = {Cardoso, Hélia and Peixe, Augusto and Bellini, Catherine and Porfírio, Sara and Druege, Uwe},
	year = {2022},
}

@article{templalexis_potassium_2022,
	title = {Potassium transporter {TRH1}/{KUP4} contributes to distinct auxin-mediated root system architecture responses},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab472},
	doi = {10.1093/plphys/kiab472},
	abstract = {In plants, auxin transport and development are tightly coupled, just as hormone and growth responses are intimately linked in multicellular systems. Here we provide insights into uncoupling this tight control by specifically targeting the expression of TINY ROOT HAIR 1 (TRH1), a member of plant high-affinity potassium (K+)/K+ uptake/K+ transporter (HAK/KUP/KT) transporters that facilitate K+ uptake by co-transporting protons, in Arabidopsis root cell files. Use of this system pinpointed specific root developmental responses to acropetal versus basipetal auxin transport. Loss of TRH1 function shows TRHs and defective root gravitropism, associated with auxin imbalance in the root apex. Cell file-specific expression of TRH1 in the central cylinder rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers, including epidermis and cortex, restored trh1 defects. Applying a system-level approach, the role of RAP2.11 and ROOT HAIR DEFECTIVE-LIKE 5 transcription factors (TFs) in root hair development was verified. Furthermore, ERF53 and WRKY51 TFs were overrepresented upon restoration of root gravitropism supporting involvement in gravitropic control. Auxin has a central role in shaping root system architecture by regulating multiple developmental processes. We reveal that TRH1 jointly modulates intracellular ionic gradients and cell-to-cell polar auxin transport to drive root epidermal cell differentiation and gravitropic response. Our results indicate the developmental importance of HAK/KUP/KT proton-coupled K+ transporters.},
	number = {2},
	urldate = {2022-03-24},
	journal = {Plant Physiology},
	author = {Templalexis, Dimitris and Tsitsekian, Dikran and Liu, Chen and Daras, Gerasimos and Šimura, Jan and Moschou, Panagiotis and Ljung, Karin and Hatzopoulos, Polydefkis and Rigas, Stamatis},
	month = feb,
	year = {2022},
	pages = {1043--1060},
}

In plants, auxin transport and development are tightly coupled, just as hormone and growth responses are intimately linked in multicellular systems. Here we provide insights into uncoupling this tight control by specifically targeting the expression of TINY ROOT HAIR 1 (TRH1), a member of plant high-affinity potassium (K+)/K+ uptake/K+ transporter (HAK/KUP/KT) transporters that facilitate K+ uptake by co-transporting protons, in Arabidopsis root cell files. Use of this system pinpointed specific root developmental responses to acropetal versus basipetal auxin transport. Loss of TRH1 function shows TRHs and defective root gravitropism, associated with auxin imbalance in the root apex. Cell file-specific expression of TRH1 in the central cylinder rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers, including epidermis and cortex, restored trh1 defects. Applying a system-level approach, the role of RAP2.11 and ROOT HAIR DEFECTIVE-LIKE 5 transcription factors (TFs) in root hair development was verified. Furthermore, ERF53 and WRKY51 TFs were overrepresented upon restoration of root gravitropism supporting involvement in gravitropic control. Auxin has a central role in shaping root system architecture by regulating multiple developmental processes. We reveal that TRH1 jointly modulates intracellular ionic gradients and cell-to-cell polar auxin transport to drive root epidermal cell differentiation and gravitropic response. Our results indicate the developmental importance of HAK/KUP/KT proton-coupled K+ transporters.

@article{andre_populus_2022,
	title = {Populus {SVL} {Acts} in {Leaves} to {Modulate} the {Timing} of {Growth} {Cessation} and {Bud} {Set}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.823019},
	doi = {10.3389/fpls.2022.823019},
	abstract = {SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.},
	urldate = {2022-02-17},
	journal = {Frontiers in Plant Science},
	author = {André, Domenique and Zambrano, José Alfredo and Zhang, Bo and Lee, Keh Chien and Rühl, Mark and Marcon, Alice and Nilsson, Ove},
	month = feb,
	year = {2022},
}

SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.

@article{zuch_cell_2022,
	title = {Cell biology of the leaf epidermis: {Fate} specification, morphogenesis, and coordination},
	volume = {34},
	issn = {1040-4651},
	shorttitle = {Cell biology of the leaf epidermis},
	url = {https://doi.org/10.1093/plcell/koab250},
	doi = {10/gpjfdq},
	abstract = {As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.},
	number = {1},
	urldate = {2022-02-14},
	journal = {The Plant Cell},
	author = {Zuch, Daniel T and Doyle, Siamsa M and Majda, Mateusz and Smith, Richard S and Robert, Stéphanie and Torii, Keiko U},
	month = jan,
	year = {2022},
	pages = {209--227},
}

As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.

@article{witzell_aspen_2022,
	title = {Aspen {Leaves} as a “{Chemical} {Landscape}” for {Fungal} {Endophyte} {Diversity}—{Effects} of {Nitrogen} {Addition}},
	volume = {13},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.846208},
	doi = {10/gpq8cc},
	abstract = {Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.},
	urldate = {2022-03-22},
	journal = {Frontiers in Microbiology},
	author = {Witzell, Johanna and Decker, Vicki Huizu Guo and Agostinelli, Marta and Romeralo, Carmen and Cleary, Michelle and Albrectsen, Benedicte Riber},
	month = mar,
	year = {2022},
}

Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.

@article{siddique_optimization_2022,
	title = {Optimization of {Protocol} for {Construction} of {Fungal} {ITS} {Amplicon} {Library} for {High}-{Throughput} {Illumina} {Sequencing} to {Study} the {Mycobiome} of {Aspen} {Leaves}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2076-3417},
	url = {https://www.mdpi.com/2076-3417/12/3/1136},
	doi = {10.3390/app12031136},
	abstract = {High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/\µL to 1526 ng/\µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63\–2.04 and 0.26\–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.},
	language = {en},
	number = {3},
	urldate = {2022-01-24},
	journal = {Applied Sciences},
	author = {Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ilbi, Hulya and Siddique, Abu Bakar},
	month = jan,
	year = {2022},
	keywords = {ITS, NGS, amplicon, aspen, eDNA, endophytes, metabarcoding, metagenomics, rDNA},
	pages = {1136},
}

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.

@article{jurca_zeitlupe_2022,
	title = {{ZEITLUPE} {Promotes} {ABA}-{Induced} {Stomatal} {Closure} in {Arabidopsis} and {Populus}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.829121},
	abstract = {Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins—which are expressed from dawn to dusk—interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.},
	urldate = {2022-03-02},
	journal = {Frontiers in Plant Science},
	author = {Jurca, Manuela and Sjölander, Johan and Ibáñez, Cristian and Matrosova, Anastasia and Johansson, Mikael and Kozarewa, Iwanka and Takata, Naoki and Bakó, Laszlo and Webb, Alex A. R. and Israelsson-Nordström, Maria and Eriksson, Maria E.},
	month = mar,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins—which are expressed from dawn to dusk—interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.

@article{vergara_norway_2022,
	title = {Norway spruce deploys tissue-specific responses during acclimation to cold},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241},
	doi = {10.1111/pce.14241},
	abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {2},
	urldate = {2021-12-09},
	journal = {Plant, Cell \& Environment},
	author = {Vergara, Alexander and Haas, Julia Christa and Aro, Tuuli and Stachula, Paulina and Street, Nathaniel Robert and Hurry, Vaughan},
	month = feb,
	year = {2022},
	keywords = {Norway spruce, cold, transcriptome},
}

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.

@article{tunnermann_have_2022,
	title = {To have or not to have: expression of amino acid transporters during pathogen infection},
	issn = {1573-5028},
	shorttitle = {To have or not to have},
	url = {https://doi.org/10.1007/s11103-022-01244-1},
	doi = {10/gpjfdr},
	abstract = {The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.},
	language = {en},
	urldate = {2022-02-14},
	journal = {Plant Molecular Biology},
	author = {Tünnermann, Laura and Colou, Justine and Näsholm, Torgny and Gratz, Regina},
	month = feb,
	year = {2022},
}

The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.

@article{ohlund_transcriptome_2022,
	title = {Transcriptome {Analysis} of an {Aedes} albopictus {Cell} {Line} {Single}- and {Dual}-{Infected} with {Lammi} {Virus} and {WNV}},
	volume = {23},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/23/2/875},
	doi = {10.3390/ijms23020875},
	abstract = {Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes' ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.},
	language = {eng},
	number = {2},
	journal = {International Journal of Molecular Sciences},
	author = {Öhlund, Pontus and Delhomme, Nicolas and Hayer, Juliette and Hesson, Jenny C. and Blomström, Anne-Lie},
	month = jan,
	year = {2022},
	keywords = {\textit{Aedes albopictus}, Aedes albopictus, West Nile virus, insect-specific flaviviruses, transcriptome, viral interference},
	pages = {875},
}

Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes' ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.

@incollection{johansson_perennial_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {The {Perennial} {Clock} {Is} an {Essential} {Timer} for {Seasonal} {Growth} {Events} and {Cold} {Hardiness}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_18},
	abstract = {Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Ibáñez, Cristian and Takata, Naoki and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	month = jan,
	year = {2022},
	keywords = {Bud burst, Bud set, Circadian clock, Cold tolerance, Growth, Perennial plants, Populus, Seasonal regulation},
	pages = {227--242},
}

Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.

@incollection{johansson_monitoring_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Monitoring {Seasonal} {Bud} {Set}, {Bud} {Burst}, and {Cold} {Hardiness} in {Populus}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_17},
	abstract = {Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Takata, Naoki and Ibáñez, Cristian and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	month = jan,
	year = {2022},
	keywords = {Bud burst, Bud set, Cold acclimation, Critical day length, Freezing tolerance, Perennial, Photoperiod, Populus},
	pages = {215--226},
}

Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.

@article{ivanov_decreased_2022,
	title = {The decreased {PG} content of pgp1 inhibits {PSI} photochemistry and limits reaction center and light-harvesting polypeptide accumulation in response to cold acclimation},
	volume = {255},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-022-03819-0},
	doi = {10/gn64qq},
	abstract = {Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.},
	language = {en},
	number = {2},
	urldate = {2022-01-17},
	journal = {Planta},
	author = {Ivanov, Alexander G. and Krol, Marianna and Savitch, Leonid V. and Szyszka-Mroz, Beth and Roche, Jessica and Sprott, D. P. and Selstam, Eva and Wilson, Kenneth W. and Gardiner, Richard and Öquist, Gunnar and Hurry, Vaughan M. and Hüner, Norman P. A.},
	month = jan,
	year = {2022},
	pages = {36},
}

Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.

@incollection{boussardon_cell_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Cell {Type}–{Specific} {Isolation} of {Mitochondria} in {Arabidopsis}},
	isbn = {978-1-07-161653-6},
	url = {https://doi.org/10.1007/978-1-0716-1653-6_2},
	abstract = {Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.},
	language = {en},
	urldate = {2021-09-23},
	booktitle = {Plant {Mitochondria}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Boussardon, Clément and Keech, Olivier},
	editor = {Van Aken, Olivier and Rasmusson, Allan G.},
	month = jan,
	year = {2022},
	keywords = {Biotin–streptavidin interaction, Editable Golden Gate plasmids, Mitochondria, Tagged outer membrane, Tissue-specific isolation},
	pages = {13--23},
}

Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.

@article{li_towards_2022,
	title = {Towards understanding the biological foundations of perenniality},
	volume = {27},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138521002181},
	doi = {10.1016/j.tplants.2021.08.007},
	abstract = {Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials’ physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.},
	language = {en},
	number = {1},
	urldate = {2021-09-30},
	journal = {Trends in Plant Science},
	author = {Li, Zheng and Lathe, Rahul S. and Li, Jinping and He, Hong and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2022},
	keywords = {perenniality, polycarpy, seasonal adaptation, sustainable agriculture},
	pages = {56--68},
}

Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials’ physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.

@article{marhava_recent_2022,
	title = {Recent developments in the understanding of {PIN} polarity},
	volume = {233},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17867},
	doi = {10/gnr3sd},
	abstract = {Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.},
	language = {en},
	number = {2},
	urldate = {2021-12-14},
	journal = {New Phytologist},
	author = {Marhava, Petra},
	month = jan,
	year = {2022},
	keywords = {PIN clustering, PIN polarity establishment, PIN polarity maintenance, auxin transport, self-reinforcing polarity},
	pages = {624--630},
}

Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.

@article{peters_hydroxycarboxylic_2022,
	title = {Hydroxycarboxylic acid receptor 3 and {GPR84} – {Two} metabolite-sensing {G} protein-coupled receptors with opposing functions in innate immune cells},
	volume = {176},
	issn = {1043-6618},
	url = {https://www.sciencedirect.com/science/article/pii/S1043661821006319},
	doi = {10/gn29gj},
	abstract = {G protein-coupled receptors (GPCRs) are key regulatory proteins of immune cell function inducing signaling in response to extracellular (pathogenic) stimuli. Although unrelated, hydroxycarboxylic acid receptor 3 (HCA3) and GPR84 share signaling via Gαi/o proteins and the agonist 3-hydroxydecanoic acid (3HDec). Both receptors are abundantly expressed in monocytes, macrophages and neutrophils but have opposing functions in these innate immune cells. Detailed insights into the molecular mechanisms and signaling components involved in immune cell regulation by GPR84 and HCA3 are still lacking. Here, we report that GPR84-mediated pro-inflammatory signaling depends on coupling to the hematopoietic cell-specific Gα15 protein in human macrophages, while HCA3 exclusively couples to Gαi protein. We show that activated GPR84 induces Gα15-dependent ERK activation, increases intracellular Ca2+ and IP3 levels as well as ROS production. In contrast, HCA3 activation shifts macrophage metabolism to a less glycolytic phenotype, which is associated with anti-inflammatory responses. This is supported by an increased release of anti-inflammatory IL-10 and a decreased secretion of pro-inflammatory IL-1β. In primary human neutrophils, stimulation with HCA3 agonists counteracts the GPR84-induced neutrophil activation. Our analyses reveal that 3HDec acts solely through GPR84 but not HCA3 activation in macrophages. In summary, this study shows that HCA3 mediates hyporesponsiveness in response to metabolites derived from dietary lactic acid bacteria and uncovers that GPR84, which is already targeted in clinical trials, promotes pro-inflammatory signaling via Gα15 protein in macrophages.},
	language = {en},
	urldate = {2022-01-10},
	journal = {Pharmacological Research},
	author = {Peters, Anna and Rabe, Philipp and Liebing, Aenne-Dorothea and Krumbholz, Petra and Nordström, Anders and Jäger, Elisabeth and Kraft, Robert and Stäubert, Claudia},
	month = feb,
	year = {2022},
	keywords = {D-phenyllactic acid, GPR84, Hydroxycarboxylic acid receptor 3, Lactic acid bacteria, Macrophages, Neutrophils},
	pages = {106047},
}

G protein-coupled receptors (GPCRs) are key regulatory proteins of immune cell function inducing signaling in response to extracellular (pathogenic) stimuli. Although unrelated, hydroxycarboxylic acid receptor 3 (HCA3) and GPR84 share signaling via Gαi/o proteins and the agonist 3-hydroxydecanoic acid (3HDec). Both receptors are abundantly expressed in monocytes, macrophages and neutrophils but have opposing functions in these innate immune cells. Detailed insights into the molecular mechanisms and signaling components involved in immune cell regulation by GPR84 and HCA3 are still lacking. Here, we report that GPR84-mediated pro-inflammatory signaling depends on coupling to the hematopoietic cell-specific Gα15 protein in human macrophages, while HCA3 exclusively couples to Gαi protein. We show that activated GPR84 induces Gα15-dependent ERK activation, increases intracellular Ca2+ and IP3 levels as well as ROS production. In contrast, HCA3 activation shifts macrophage metabolism to a less glycolytic phenotype, which is associated with anti-inflammatory responses. This is supported by an increased release of anti-inflammatory IL-10 and a decreased secretion of pro-inflammatory IL-1β. In primary human neutrophils, stimulation with HCA3 agonists counteracts the GPR84-induced neutrophil activation. Our analyses reveal that 3HDec acts solely through GPR84 but not HCA3 activation in macrophages. In summary, this study shows that HCA3 mediates hyporesponsiveness in response to metabolites derived from dietary lactic acid bacteria and uncovers that GPR84, which is already targeted in clinical trials, promotes pro-inflammatory signaling via Gα15 protein in macrophages.