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From left to right: Carolin Seyfferth, Nathaniel Street, Xiao-Ru Wang and Hannele Tuominen; photo: Anne HonselLink to the announcement from Formas:
http://www.formas.se/en/Press-News/News/Given-decisions-November-2018/
The projects:
Carolin Seyfferth (Mobility grant):
Title: Regulation of wood properties in aspen and birch through large-scale gene expression studies
Nathanial Street (Research and development project grants):
Title: Engineering specialised metabolism in aspen
Hannele Tuominen (Research and development project grants):
Title: Harnessing natural variation in aspen for forest feedstock improvement
Xiao-Ru Wang (Research and development project grants):
Title: Genetic diversity in Swedish conifer forests: are there reasons for concern?
For more information contact the project leader or have a look on their homepage:
Carolin Seyfferth
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
e-mail:
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: +46 (0)90 786 5473
e-mail:
www.upsc.se/nathaniel_street
Hannele Tuominen
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: +46 (0)90 786 9693
e-mail:
www.upsc.se/hannele_tuominen
Xiao-Ru Wang
Department of Ecology and Environmental Sciences
Umeå University
Phone: +46 90 786 99 55
Email:
https://www.upsc.se/xiao-ru_wang
http://www.emg.umu.se/english/about-the-department/staff/wang-xiao-ru/
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Two starting grants and two research project grants from researchers at UPSC were approved by the Swedish Research Council (Vetenskapsrådet). The four projects from Peter Kindgren, Karin Ljung, Alizée Malnoë and Ove Nilsson will examine how non-coding DNA can influence transcription of coding DNA, how nitrogen affects the formation of lateral roots, how plants protect themselves against too much light and how the annual growth cycle of trees is regulated.
Peter Kindgren and Alizée Malnoë received starting grants to establish their research groups at UPSC. Peter Kindgren is currently still working at the University of Copenhagen but he will move in the end of 2019 to Umeå and then start setting up his own research group. He wants to understand how DNA that does not contain protein information (non-coding DNA) affects the transcription of protein encoding DNA, especially under stress conditions like cold. Alizée Malnoë started her research group at UPSC in January 2018. She is working on molecular mechanisms of photoprotection in plants, i.e. molecular processes that prevent the damage of a plant by an excess of light.
Karin Ljung and Ove Nilsson, both professors at the Swedish University of Agricultural Sciences and group leaders at UPSC, got research project grants. Karin Ljung will examine how different sources of nitrogen affect the initiation and development of lateral roots and influence the structure of the root system. Ove Nilsson’s project addresses how bud set, bud break and flowering are regulated in trees like aspen. His focus is on the genetic mechanisms that control the annual growth cycle.
The projects:
Peter Kindgren:
ImPaCT – Implications of Polymerase Collision caused by Transcription
Karin Ljung:
Nitrogen modulation of lateral root initiation in Arabidopsis
Alizée Malnoë:
Molecular Mechanisms of Photoprotection in Plants
Ove Nilsson:
The Role of FT-like Genes in the Regulation of the Annual Growth Cycle in Trees
Link to the announcement from the Swedish Research Council:
https://www.vr.se/english/calls-and-decisions/grant-decisions/decisions/2018-09-06-natural-and-engineering-sciences.html
For more information contact the project leader or have a look on their homepage:
Peter Robert Kindgren
Section for Molecular Plant Biology
Department of Plant and Environmental Sciences
University of Copenhagen
Phone: +45 35 33 46 39
e-mail:
https://plen.ku.dk/english/employees/?pure=en%2Fpersons%2Fpeter-robert-kindgren(525289c6-db78-4032-8942-ade2c82c3792).html
Karin Ljung
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Phone: +46 (0)90 786 8355
e-mail:
www.upsc.se/karin_ljung
Alizée Malnoë
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: +46 (0)90 786 5459
e-mail:
www.upsc.se/alizee_malnoe
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Phone: +46 (0)90 786 8487
e-mail:
www.upsc.se/ove_nilsson
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Aspen tree which genome is now mapped; photo: Stefan Jansson
This week, a team of researchers from Sweden, Belgium, England, Italy, Norway and South Korea published the genomes of two species of aspen trees. The project has taken close to ten years to complete and proved to be more complicated than thought as well as significantly expanding in scope.
"At last! We really had a moving target as we wanted to develop a resource that will be of maximum use to all researchers in tree biology, which led us to expand the project and keep trying to improve the work", says Nathaniel Street, Umeå University, who has shifted from being a postdoctoral researcher at the start of the position to assistant professor and, currently, university lecturer, and who eventually led the project.
Charting the set of genes present in a species provides perhaps the most important piece of the puzzle for all kinds of biology studies that, once available, enables virtually any type of study. The mapping of the human genome (published in 2001) was the foundation for a broad range of breakthroughs in medicine in the 21st century. Swedish tree researchers were early comers to this area, with work starting in 1998 that provided a first mapping for a subset of the aspen genes as well as contributing to the first complete mapping of a tree genome – black cottonwood (Populus trichocarpa) in 2006. This was only the third plant genome to be published, with only thale cress (Arabidopsis) and rice being available earlier.
In 2008-2009, a small group of Swedish researchers at the Umeå Plant Science Centre took on the challenge of mapping the aspen (Populus tremula) genome. Despite the fact that no such extensive genome project had been carried out in Sweden, they were optimistic; new, cheaper and more powerful techniques had just become available and pilot studies using these had shown that, among other things, the genetic variation in aspen was enormous. Indeed, in some respects, two aspen trees are, on average, as genetically different as a human and a chimpanzee. The project received a total of one million kronor from the Centre for Metagenomic Sequence Analysis - a precursor to SciLife Lab, which was formed in 2010 - and the Kempe Foundation and Nathaniel Street, a postdoc at the Umeå Plant Science Centre, started the practical work.
The tree selected for mapping grows on the Umeå University / SLU campus and had been studied since 1999. The researchers rapidly generated promising results, but it also became clear that the genome of the closely related black cottonwood could not be used as a reference, which made the project substantially more challenging. The project expanded, and more people and research groups became involved, with 27 researchers from six countries contributing to the results that are now published in the journal Proceedings of the National Academy of Sciences, PNAS. As well as mapping the genome, 24 individuals of European trembling aspen, 22 of the American quaking aspen (Populus tremuloides) and, as a reference, 24 black cottonwood poplars were analysed, which made it possible to understand how the species have evolved and adapted to different environments.
"The biggest challenge for the work, apart from the project lacking a long-term budget, was to deal with those parts of the genome that do not contain genes" says Nathaniel Street.
The genes themselves were mapped very early in the project, but the DNA sequence between genes differs so extensively in aspen between the two copies of the genome that each individual has - one inherited from the mother and one from the father - that methods developed to study other genomes such as humans, which are very inbred compared to aspen, did not work.
"We have now been able to show, for example, which genes appear to be the most important for the adaptation of aspen to our Nordic climate. This and much of our other work in the last five years has been made possible by this project" says Pär Ingvarsson, who, during the long journey, moved to SLU in Uppsala. This is a real milestone, the huge variation in aspen is a great resource for understanding evolution and the genome sequence gives us the tools needed to unlock this information.
"While it took a long time to finally map the whole genome, the project has produced multiple spin-offs along the way. Without this project, the gigantic work of sequencing Norway spruce, published in 2013, would not have been started. The databases of plant genomes we have produced and updated are used worldwide today, says Stefan Jansson, professor at Umeå University, who started the project in 2009.
The article:
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen, Yao-Cheng Lin, Jing Wang, Nicolas Delhomme, Bastian Schiffthaler, Görel Sundström, Andrea Zuccolo, Björn Nystedt, Torgeir R. Hvidsten, Amanda de la Torre, Rosa M. Cossu, Marc P. Hoeppner, Henrik Lantz, Douglas G. Scofield, Neda Zamani, Anna Johansson, Chanaka Mannapperuma, Kathryn M. Robinson, Niklas Mähler, Ilia J. Leitch, Jaume Pellicer, Eung-Jun Park, Marc Van Montagu, Yves Van de Peer, Manfred Grabherr, Stefan Jansson, Pär K. Ingvarsson, and Nathaniel R. Street
Proceedings of the National Academy of Sciences (PNAS) October 29, 2018
Link to the publication: https://doi.org/10.1073/pnas.1801437115
For further information, please contact:
Nathaniel Street, UPSC, Fysiologisk botanik, Umeå universitet,
Pär K Ingvarsson, UPSC, Department of Plant Biology, Swedish University of Agricultural Sciences,
Stefan Jansson, UPSC, Department of Plant Physiology, Umeå universitet,
More information:
Link to the Swedish press release at Umeå University
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Live images of a plastid-localized ATP sensor in an Arabidopsis seedling. Read more
Photosynthesis generates adenosine triphosphate (ATP), which is the universal molecular fuel in living organisms. An international research team led by Dr Boon Leong Lim from the School of Biological Sciences of The University of Hong Kong could visualize ATP concentrations in chloroplasts and cytosol of living plants. The team included research groups from Sweden, USA and Germany. The Swedish participant was professor Per Gardeström from UPSC, Department of Plant Physiology at Umeå University. The results highlight how different parts of the photosynthetic cell are interconnected in order to optimize the efficiency of photosynthesis and is of interest for future crop breeding. The study is now presented by the journal PNAS.
All life on earth ultimately relies on energy from the sun and photosynthesis in plants is the vital link. The researchers around Boon Leong Lim showed that in mature plants the chloroplastic ATP pool is separated from the rest of the cell. A surplus of reducing equivalents can be exported from the chloroplast and used by mitochondria to supply ATP to the cytosol but the rate of ATP import into mature chloroplasts to support CO2 fixation was negligible. Only chloroplasts of very young developing leaves of Arabidopsis thaliana could import ATP from the cytosol to support their development. This developmental transition could be important in order to restrict futile ATP consumption at night when photosynthesis is not operating.
“We saw a significantly lower concentration of ATP in the chloroplast than in the cytosol of mature photosynthetic cells,” said study lead author Dr Boon Leong Lim. “Although the chloroplast is the key energy harvester and producer in a plant cell, its demand for ATP is also extremely high. Illumination increases chloroplast ATP concentration instantly, but it drops to a basal level very quickly after illumination stops. Our results suggest that there was a need to restrict ATP consumption in mature chloroplasts in the dark. A primary job of mature mesophyll chloroplasts is to harvest energy and export sugar to support plant growth in the light. Nevertheless, wasteful energy consumption must be avoided in the dark.”
Co-authors Dr Wayne K. Versaw and Abira Sahu of Texas A&M University stated: “Live imaging of intact plants provided the spatial and temporal resolution to reveal important changes in how different cell compartments collaborate to manage photosynthesis and overall cellular energy.”
The results also have important implications for the understanding of energy flow in plant cells. Using energy harvested from sunlight, water molecules are split into protons, oxygen and electrons. The electrons pass through photosystems to reduce NADP+ to NADPH that acts as a carrier for the electrons. Together with water splitting, this so called linear electron flow (LEF) also creates a pH gradient across the thylakoid membrane, the inner membrane of the chloroplast. This pH gradient is the driving force for ATP synthesis. To fix one CO2 molecule in a chloroplast, 3 ATP and 2 NADPH molecules are consumed. However, only 2.57 ATP molecules per 2 NADPH are generated by LEF. The shortfall of ATP must be met for photosynthesis to operate efficiently.
A paper published in Nature in 2015 (524:366–369) showed that chloroplasts in unicellular diatoms can import cytosolic ATP to support carbon fixation. Chiapao Voon, who joined the lab as a PhD student, explained: “Unlike unicellular diatoms, mature plant chloroplasts are unable to import ATP from the cytosol to supplement the demand for CO2 fixation. Rather, the export of reducing equivalents is the key to maintaining the optimal ATP/NADPH ratio required for photosynthesis. Otherwise, the build-up of NADPH in chloroplasts will impede photosynthesis”.
“The ability to study metabolism in the living cell with a spatial resolution between the different cellular compartments is a big step forward and will significantly increase our understanding on how the cell is operating. I have in particular been interested in the implications for mitochondrial contributions to photosynthetic metabolism” complements co-author Prof. Per Gardeström from Umeå University.
Co-author Prof. Markus Schwarzländer of Münster University added: “The study brings us a step closer to understanding how carefully cells optimize the operating conditions in their different organelles. I find it particularly intriguing how efficiency of plant energy metabolism can be maintained, and how this appears to be dynamically adjusted.”
The article:
ATP compartmentation in plastids and cytosol of Arabidopsis thaliana revealed by fluorescent protein sensing
Chia Pao Voon, Xiaoqian Guan, Yuzhe Sun, Abira Sahu, May Ngor Chan, Per Gardeström, Stephan Wagner, Philippe Fuchs, Thomas Nietzel, Wayne K. Versaw, Markus Schwarzländer, Boon Leong Lim
Proceedings of the National Academy of Sciences (PNAS) Oct 2018, 201711497; DOI: 10.1073/pnas.1711497115
Link to the publication
Photo description:
Live images of a plastid-localized ATP sensor in an Arabidopsis seedling. Red and green panels show the emission of the ATP sensor at 470 nm – 507 nm, and 526 nm – 545 nm, in a 3-day-old seedling. The ratio between both emission channels is represented in a rainbow color scale in the lower left panel, which corresponds to ATP concentration (higher levels in red and lower levels in green). The lower right panel shows a brightfield image of the same seedling.
For questions please contact:
Professor Per Gardeström
Department of Plant Physiology
e-mail:
Photo: Chia Pao Voon
Text: Boon Leong Lim, Chia Pao Voon, Wayne K. Versaw, Per Gardeström, Markus Schwarzländer
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Lifting response of hybrid aspen: Time-lapse video showing 28 days of the tension wood response of a wild type hybrid aspen (Populus tremula x P. tremuloides). Video created by Bernard Wessels.
Link to the thesis: urn:nbn:se:umu:diva-151724
| What is ethylene? |
| Did you ever experience that your green bananas ripened faster when you placed them next to an apple? This is caused by the plant hormone ethylene that is produced by the ripening apple. Ethylene is a colourless gas with a faint sweet odour that acts as a hormone in plants. It stimulates fruits to ripe but it is also involved in many other aspects of plant development, e.g. like germination of seeds, senescence, reaction to environmental stresses or mechanical wounding. Ethylene is of high commercial interest because it fastens the ripening process of fruits and vegetables and the senescence of cut flowers. |
About the thesis defence:
On Friday, the 5th of October, Bernard Wessels, Department of Plant Physiology, Umeå University, defended his thesis, entitled ’The significance of ethylene and ETHYLENE RESPONSE FACTORS in wood formation of hybrid aspen’. The public defence took place at 9:00 am in Lilla hörsalen ( KB.E3.01) in the KBC building, Umeå University. The faculty opponent was Prof. Kurt Fagerstedt, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland. Supervisor of the PhD thesis was Hannele Tuominen.
For more information, please contact:
Bernard Wessels, Department of Plant Physiology, Umeå University
Telephone +4670 0130923
E-mail:
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Two different stages of germinating somatic embryos from Norway Spruce; photos: Johanna Carlsson
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Christmas trees and jigsaw puzzles - Niklas Mähler won the UPSC flash-talk competition 2018; photo: Anne HonselThis year’s UPSC Days were organised by a committee representing one member of every staff category, i.e. PhD students, Postdocs, administration and technical personal and group leaders. Their aim was to compile a program that is interesting for everyone working at UPSC and that stimulates internal communication and interactions.
Link to the programme of the UPSC Days 2018
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"Fighting Swedish mosquitos" - UPSC Phd students and postdocs in Skeppsvik; photo: Niklas MählerText: Domenique André, Carolin Seyfferth, Anne Honsel
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Left photo: porcupine mutant (pcp-2) growing at low ambient temperature (16°C); right photo: close-up showing the malformed “spiky” leaves of a pcp mutant (photos: Giovanna Capovilla; arrangement: Markus Schmid)A research team led by Markus Schmid has identified a new player regulating plant development under low temperatures. The researchers searched for mutants that have strong growth defects when grown at low temperatures but look otherwise normal. They found the porcupine mutant and showed that the PORCUPINE gene is crucial for normal plant development at low temperatures. Their results are published as Brief Communication article in the journal Nature Plants.
Plants react to changing temperatures by adjusting their development and growth rate. The mutant, that lost the active PORCUPINE gene, grows very slowly at lower temperatures (16°C), displays sever developmental defects and is not able to produce seeds. However, it looks almost like non-mutated plants when growing at favourable temperatures (23°C). The researchers around Markus Schmid concluded that the PORCUPINE gene is required specifically at low temperatures and is crucial for adjusting the plant development and growth to low temperatures.
A recently suggested important mechanism that allows plants to adjust their growth and development to changes in temperature is the so-called alternative splicing (see also below). This process enables a single gene to produce different protein versions depending on which parts of the gene are spliced together and translated. The resulting proteins are altered in their structure and can have different functions. There are factors that regulate which protein variant is synthesised by alternative splicing. PORCUPINE appears to be one of those factors that regulates alternative splicing events under cold temperatures.
Many of the alternative splicing events that take place in the non-mutated plant at lower temperatures are missing in the mutant that lost the active PORCUPINE gene. “We think that PORCUPINE plays a crucial role for connecting plant responses to low temperature with plant development via alternative splicing”, explains Markus Schmid. “This is a new but very complex regulation pathway that we just now start to explore.”
The PORCUPINE gene got its name from the special look of the mutant that lost the functional PORCUPINE gene. The leaves of the mutant are radialised and the hairs (trichomes) on the surface of the mutant are often branched more frequently, giving the mutant a very “spiky” appearance – reminiscent of a porcupine.
| What is alternative splicing? |
|---|
| When a gene gets activated its DNA sequence is first transcribed into pre-mRNA (precursor messenger ribonucleic acid). Many pre-mRNAs in plants and animals are than spliced to remove parts (introns) that do not contain information for the encoded protein. The remaining “exons” are stitched together to form a mature mRNA, which is subsequently translated into a protein. Depending on which intros are spliced out and which exons are joined together, different mRNAs can be produced from a single gene, resulting in different protein versions. |
The article:
Giovanna Capovilla, Nicolas Delhomme, Silvio Collani, Iryna Shutava, Ilja Bezrukov, Efthymia Symeonidi, Marcella de Francisco Amorim, Sascha Laubinger & Markus Schmid (2018) Nature Plants, doi.org/10.1038/s41477-018-0176-z.
PORCUPINE regulates development in response to temperature through alternative splicing
Link to the publication: https://www.nature.com/articles/s41477-018-0176-z
For more information, please contact:
Markus Schmid, professor
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
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Daria Chrobok (middle) and her two supervisor Olivier Keech (right) and Per Gardeström (left); photo: Anne Honsel
Leaves turn yellow naturally, in autumn, when they get old or when the plant is exposed to stresses like darkness or drought. Daria Chrobok compared in her PhD thesis different scenarios of leaf yellowing and analysed what happens on the metabolic level. She showed that mitochondria, the respiratory power stations of the cell, are crucial for a coordinated adjustment of metabolism during leaf yellowing. Mitochondria stay active until the last stages of leaf yellowing to provide the energy that is needed for recycling nutrients from the dying leaf. Daria Chrobok successfully defended her thesis on the 8th of June.
The yellowing of a leaf, also called senescence, occurs naturally in for example deciduous trees in autumn or when annual plants get old and produce seeds. However, also stresses like a lack of nutrients, drought or pathogens can induce senescence. Daria Chrobok compared naturally aging plants with plants where senescence was induced by darkening a single leaf. She showed that in both cases the mitochondria remain intact until the last stages of leaf senescence to provide the energy needed for the mobilisation and transport of nutrients.
In addition, she showed that especially the amino acid glutamate, that can be easily transported within the plant, accumulates during leaf senescence. She hypothesized that this accumulation of glutamate in the mitochondria and its conversion to glutamine in the cytosol are essential steps for the reallocation of nitrogen rich compounds to other parts of the plant.
The export of amino acids with high nitrogen content into developing parts of the plant, e.g. seeds, is of high importance to ensure that those seeds contain enough nitrogen and the survival of the next generation is guaranteed. Nitrogen is often a limiting factor for plant growth and development and therefore the reallocation of nitrogen during senescence is important for plants.
Without light, plants cannot perform photosynthesis and produce energy-rich carbon compounds like sugars. If only one leaf is darkened, the covered leaf will rapidly turn yellow. In contrast, when the whole plant is darkened, the leaves are repressing this induction of senescence, i.e. they stay green. The plant keeps all components needed for photosynthesis alive and intact so that upon sudden light exposure, the plants are ready to start photosynthesis and continue growing.
Daria Chrobok and her colleagues analysed how plants adjust their metabolism to those two darkening conditions and they compared these results with the light-dependent “stay-green” mutant. When one leaf of a stay-green plant is darkened, it stays green, whereas the same treatment in a wild type plant leads to the yellowing of the darkened leaf. This darkened stay-green leaf, as well as the whole darkened plant accumulate amino acids, especially those with high nitrogen and low carbon content.
The understanding of how “stay-green” plants manage to stay green is interesting for the food industry to keep vegetables green for longer time and for agriculture, to ensure proper grain and nutrient filling as well as other improved traits for crop plants.
The public defence took place in Lilla hörsalen at KBC, Umeå University, on Friday, 8th of June 2018. Faculty opponent was David Macherel, IRHS-MitoStress, University of Angers, France. Supervisors were Olivier Keech and Per Gardeström.
Title of Daria Chrobok’s thesis: “To “leaf” or not to “leaf” - Understanding the metabolic adjustments associated with leaf senescence”
Link to the doctoral thesis: urn:nbn:se:umu:diva-147700
Are you interested to read more? Have a look on the comic strip made by Neil E. Robbins II. He illustrated the results from the article Law et al., 2018 (Plant Physiology) that is included in Daria Chrobok’s thesis. The comic explains very nicely the metabolic adjustments during the different dark treatments:
https://neilercomics.com/2018/05/18/are-plants-afraid-of-the-dark/
The article:
Simon R Law, Daria Chrobok, Marta Juvany, Nicolas Delhomme, Pernilla Lindén, Bastiaan Brouwer, Abdul Ahad, Thomas Moritz, Stefan Jansson, Per Gardestrom, Olivier Keech (Plant Physiology) 2018; DOI: https://doi.org/10.1104/pp.18.00062
Title: Darkened leaves use different metabolic strategies for senescence and survival