@article{baral_typhon_2024,
	title = {{TYPHON} proteins are {RAB}-dependent mediators of the trans-{Golgi} network secretory pathway},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae280},
	doi = {10.1093/plcell/koae280},
	abstract = {The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.},
	urldate = {2024-11-08},
	journal = {The Plant Cell},
	author = {Baral, Anirban and Gendre, Delphine and Aryal, Bibek and Fougère, Louise and Di Fino, Luciano Martin and Ohori, Chihiro and Sztojka, Bernadette and Uemura, Tomohiro and Ueda, Takashi and Marhavý, Peter and Boutté, Yohann and Bhalerao, Rishikesh P},
	month = oct,
	year = {2024},
	pages = {koae280},
}

The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.

@article{hermida-carrera_cdk8_2024,
	title = {{CDK8} of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor {SPEECHLESS} ({SPCH})},
	volume = {47},
	copyright = {© 2024 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15102},
	doi = {10.1111/pce.15102},
	abstract = {The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.},
	language = {en},
	number = {12},
	urldate = {2024-11-08},
	journal = {Plant, Cell \& Environment},
	author = {Hermida-Carrera, Carmen and Vergara, Alexander and Cervela-Cardona, Luis and Jin, Xu and Björklund, Stefan and Strand, Åsa},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15102},
	keywords = {CO2 response, climate change, drought},
	pages = {5237--5251},
}

The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.

@article{lazaro-gimeno_circadian_2024,
	title = {The circadian clock participates in seasonal growth in {Norway} spruce ({Picea} abies)},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae139},
	doi = {10.1093/treephys/tpae139},
	abstract = {The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies (L.) H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be participating a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, evidences indicate that there is time for spruce.},
	urldate = {2024-11-08},
	journal = {Tree Physiology},
	author = {Lázaro-Gimeno, David and Ferrari, Camilla and Delhomme, Nico and Johansson, Mikael and Sjölander, Johan and Singh, Rajesh K and Mutwil, Marek and Eriksson, Maria E},
	month = nov,
	year = {2024},
	pages = {tpae139},
}

The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies (L.) H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be participating a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, evidences indicate that there is time for spruce.

@article{pawlowski_frankia_2024,
	title = {Frankia [{NiFe}] uptake hydrogenases and genome reduction: different lineages of loss},
	issn = {0168-6496},
	shorttitle = {Frankia [{NiFe}] uptake hydrogenases and genome reduction},
	url = {https://doi.org/10.1093/femsec/fiae147},
	doi = {10.1093/femsec/fiae147},
	abstract = {Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup−, while only one Hup−  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a and 3b according to Søndergaard et al. (2016); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1h and group 3b are not.},
	urldate = {2024-11-01},
	journal = {FEMS Microbiology Ecology},
	author = {Pawlowski, Katharina and Wibberg, Daniel and Mehrabi, Sara and Obaid, Nadia Binte and Patyi, András and Berckx, Fede and Nguyen, Han and Hagen, Michelle and Lundin, Daniel and Brachmann, Andreas and Blom, Jochen and Herrera-Belaroussi, Aude and Abrouk, Danis and Pujic, Petar and Hahlin, Ann-Sofi and Kalinowski, Jörn and Normand, Philippe and Sellstedt, Anita},
	month = oct,
	year = {2024},
	pages = {fiae147},
}

Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup−, while only one Hup−  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a and 3b according to Søndergaard et al. (2016); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1h and group 3b are not.

@article{el_arbi_arabidopsis_2024,
	title = {The {Arabidopsis} splicing factor {PORCUPINE}/{SmE1} orchestrates temperature-dependent root development via auxin homeostasis maintenance},
	volume = {244},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20153},
	doi = {10.1111/nph.20153},
	abstract = {Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.},
	language = {en},
	number = {4},
	urldate = {2024-10-25},
	journal = {New Phytologist},
	author = {El Arbi, Nabila and Nardeli, Sarah Muniz and Šimura, Jan and Ljung, Karin and Schmid, Markus},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20153},
	keywords = {Arabidopsis thaliana, SmE, alternative RNA splicing, auxin signaling, root apical meristem, root development, temperature signaling},
	pages = {1408--1421},
}

Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.