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.
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:
Link to the Swedish press release at Umeå University
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.”
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
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
Photo: Chia Pao Voon
Text: Boon Leong Lim, Chia Pao Voon, Wayne K. Versaw, Per Gardeström, Markus Schwarzländer
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
This 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
Text: Domenique André, Carolin Seyfferth, Anne Honsel
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.|
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
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:
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
The registration to the UPSC Days 2018 is now open! They will take place on September 6-7 at Sliperiet on the Konstnärlig Campus in Umeå.
The first day will start with a session about future visions for UPSC and continue after lunch with an update about the most recent changes of the UPSC infrastructures. We will also have a scientific session with 3 minutes flash talks and end the first day with a barbecue that will take place in front of UPSC.
On the second day, Anna-Karin Byström from DC Consulting AB will give a workshop on intercultural communications. This workshop will include seminars giving theoretical background about cultural understanding and the communication process as well as practical exercises and tools to handle and interpret actions and reactions that arise in meetings with people of different backgrounds. We will finish the second day with the lunch.
Location: White boxes, Sliperiet, Konstnärlig campus, Umeå (see on map)
|Day 1 - Thursday, 6th September 2018
|9:30 - 10:00||Registration and coffee|
|10.00 - 10.10||Welcome|
|The future UPSC|
|10.10 - 10.40||
Visions for UCMR (Umeå Centre for Microbial Research)
Bernt Eric Uhlin, UCMR & MIMS, Department of Molecular Biology, Umeå University
|10.40 - 11.35||
Visions for UPSC
Ove Nilsson (director of UPSC), Karin Ljung (prefect of the Department of Forest Genetics and Plant Physiology, SLU) and Stefan Jansson (prefect of the Department of Plant Physiology, Umeå University) will talk about their visions for UPSC.
|11.35 - 12.15||
Chair: Catherine Bellini, Chairmen of the UPSC board
|12.15 - 13.30||Lunch|
|13.30 - 13.50||
The new phenotyping platform at UPSC
Ove Nilsson (director of UPSC)
|13.50 - 14.10||
News from the Bioinformatics platform
Nicolas Delhomme (Manager of the UPSC Bioinformatics platform)
|14.10 - 14.40||Coffee break|
|14.40 - 15.10||
Scientific session with 3 min flash talks (max. 1 slide)
|15.10 - 15.20||
Voting and award presentation
|16.30||Barbecue at the Umeå Plant Science Centre (Please bring your own food and drinks)
|Day 2 - Friday, 7th September 2018|
Intercultural communications workshop
Anna-Karin Byström, Ph.Lic. Organisational Communication and CEO, DC Consulting AB
|9.00 - 9.10||
Brief introduction and presentations
|9.10 - 10.10||
Intercultural communication - introduction to cultural understanding and the communication process
|10.10 - 10.55||Coffee and workshop|
|10.55 - 11.45||
Practical tips concerning communication between people of different backgrounds including practical exercises
|11.45 - 12.00||
Concluding the workshop and shorter reflection
|12.00 - 12.10||
Final conclusion by the organisers
|12.10 - 13.10||Lunch|
On Friday, 18th of May, HalehHayatgheibi successfully defended her PhD thesis. She has worked on lodgepole pine (Pinus contorta), a fast-growing tree that was largely introduced into Sweden in the mid-1960s. One major problem of lodgepole pine trees is that their stems are often bending or even break and this lowers the economic value of the wood. Haleh Hayatgheibi designed breeding strategies to optimize both wood quantity and quality of lodgepole pine to reduce stem bending and breakage.
Haleh Hayatgheibi estimated genetic parameters which determine wood quality and quantity of lodgepole pine. She measured for example the diameter of the stem as parameter for wood quantity and the stiffness of the stem. A higher stiffness might prevent the breakage of the stem when it bends and decrease the economic loss. This feature is especially interesting for Northern Sweden.
Lodgepole pine trees from different origin in Canada were planted in different climatic regions in Northern Sweden, e.g. close to the coast or more inland. Haleh Hayatgheibi compared those trees with each other to see which are best suited for which region in Northern Sweden. Based on her results, she can now recommend tree breeders which lodgepole pine trees have the best prerequisites for which climatic region.
Title of the thesis: “Quantitative genetics of lodgepole pine (Pinus contorta) wood quality traits in Sweden”
Link to the doctoral thesis: http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4836
The public defence took place in Björken at SLU Umeå on Friday, 18thof May 2018. Faculty opponent was Yousry A. El-Kassaby from the Forest Sciences Centre, University of British Columbia, Canada. The supervisor was Harry Xiaming Wu.