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Thomas Dobrenel (middle) received the UPSC Agrisera prize 2024. It was presented to him by the chair of the UPSC Board Catherine Bellini (left) and by Conny Hiljanen (right) from Agrisera (photo: Anne Honsel).At today’s UPSC Christmas lunch, the UPSC Board awarded Thomas Dobrenel with this year’s UPSC Agrisera Prize. The award acknowledged his contribution to facilitating scientific discourse at UPSC and his dedication to making UPSC a good and collaborative place to work.
Thomas Dobrenel came to UPSC in 2013 as a postdoc in Johannes Hanson’s group, where he studied carbon starvation in Arabidopsis cell cultures. In 2019, he transitioned to Ove Nilsson’s group and the UPSC Spruce Transformation Facility. There, he started to work on a project to optimise methods for genetically engineering Norway spruce and propagating it via somatic embryogenesis.
The nominations for Thomas Dobrenel highlight his contributions to organising journal clubs, seminars, and PhD and Postdoc retreats, all of which stimulate scientific discussions and knowledge exchange at UPSC. He also organises social activities that strengthen the UPSC community, and nominations pointed out his approachability and willingness to assist others.
“We believe that a good and supportive work environment is essential for good research, and dedicated people like Thomas are important. With the UPSC Agrisera Prize, we show our appreciation for such commitment,” says Catherine Bellini, chairperson of the UPSC Board. She and Conny Hiljanen from Agrisera presented the prize today to Thomas Dobrenel.
About the UPSC Agrisera Prize
Each year, UPSC awards the UPSC Agrisera Prize, sponsored by Agrisera, to recognise outstanding scientific achievements and significant contributions to improving the work environment at UPSC. Everyone working at UPSC can nominate and be nominated. The recipient is chosen by the members of the UPSC Board and announced during the traditional UPSC Christmas lunch in December. The prize includes a diploma and a travel voucher.
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Stéphanie Robert (left; photo: Erik Abel) and Stephan Wenkel (right: photo Mattias Pettersson) are part of the two research consortia STARMORPH and RESYDE that are awarded an ERC Synergy Grant.
Two research consortia, including UPSC researchers Stéphanie Robert from the Swedish University of Agricultural Sciences and Stephan Wenkel from Umeå University, have been awarded prestigious ERC Synergy Grants. They aim to investigate fundamental aspects of plant development from diverse angles, paving the way for advancements in biotechnology and plant engineering.
The highly competitive ERC Synergy grants are designed to support collaborative research efforts that address complex, ambitious scientific challenges beyond the scope of individual researchers. Stéphanie Robert and Stephan Wenkel are part of the STARMORPH and RESYDE projects, which have each received €10 million in funding over six years.
STARMORPH - Creating a spatio-temporal map for auxin dynamics
The STARMORPH project, led by Stéphanie Robert from SLU, will focus on auxin - a plant hormone crucial to various aspects of plant development. For example, auxin plays a key role in promoting root and stem growth and is essential for organ formation.
Over the next six years, Stéphanie Robert will collaborate with Ondřej Novák from the Institute of Experimental Botany, Czech Academy of Sciences (Czech Republic), Jürgen Kleine-Vehn from the University of Freiburg (Germany), and Alexander Jones from the Sainsbury Laboratory, University of Cambridge (UK). Together, they aim to address the fundamental question of how auxin contributes to so many aspects of plant development.
STARMORPH introduces the innovative concept of an “auxin signature” which reflects auxin levels not only in organs, tissues, or cells but also within specific cellular compartments integrating cellular responses to developmental and external signals.
“The subcellular compartmentalization of auxin is still poorly understood,” explains Stéphanie Robert. “We believe that auxin’s specific effects are not solely determined by its overall concentration but rather by its unique subcellular distribution and how it is perceived at the different sites within the cell, creating an ‘auxin perception signature.’”
By combining their expertise in a multidisciplinary synergy, the project partners aim to map auxin dynamics with high temporal and spatial resolution. They will apply a wide range of different methods including advanced microscopy techniques, highly sensitive quantification methods of auxin and the usage of biosensors.
Their focus will be on the model plant Arabidopsis thaliana, specifically its apical hook - a structure essential for seedling survival during soil emergence. While growing in the soil, the seedling bends forming a hook to protect the delicate apex from mechanical damage. Once reaching the light, the hook is abolished, and the plant opens its leaves toward the sun.
“The hook is an excellent model for studying growth transition and plant development in general,” explains Stéphanie Robert. “Our findings could lead to a paradigm shift in understanding how auxin influences plant growth and organ formation at the cellular and subcellular levels, potentially driving advancements in plant engineering and biotechnology.”
RESYDE – Building a virtual flower
RESYDE, the project in which Stephan Wenkel is involved in, will tackle the question how multicellular organisms generate their intricate forms. The focus of the RESYDE project is on symmetry breaking during flower development – a process by which two initially identical cells adopt different cell fates – leading to diverse forms and functions. This fundamental phenomenon is crucial in all multicellular organisms and starts with an asymmetric cell division.
The research consortium comprises beside Stephan Wenkel, Kerstin Kaufmann from Humboldt-Universität zu Berlin (Germany), the coordinator of the project, Marcus Heisler from the University of Sydney (Australia) and Henrik Jönsson from Sainsbury Laboratory, University of Cambridge (UK).
Together they have an ambitious goal: they want to build a virtual flower meristem, the stem cell containing structure from which flowers originate. It will be based on data from the model plant Arabidopsis and integrate a detailed set of parameters that define how the final flower will look like.
“Flower structures are very complex and can look very different between species. We want to understand at the single cell level how such a variety of structures develops and then use this information to model and re-engineer different floral structures”, explained Stephan Wenkel.
The four project partners bring multidisciplinary expertise to the project. They plan to exploit genetic, molecular, experimental, live imaging, computational and synthetic biology techniques to better understand how floral symmetry breaking processes that occur at the single cell level have been changed during evolution to create the wealth of floral architectures.
“Our part will be to identify microProteins and other novel protein isoforms that play critical roles in flower development. Such small proteins can regulate large protein complexes and thereby affect symmetry breaking processes during flower development”, said Stephan Wenkel.
The research consortium plans among other things to apply engineered microProteins to alter floral symmetry breaking processes and change flower architecture. One of their goals is to engineer the tomato flower structure into Arabidopsis plants and vice versa.
“Flowers are not only beautiful. They must be fertilised and develop into fruits and grains. Understanding the specifics of the flower function and structure are critical for future plant breeding and agriculture”, added Stephan Wenkel.
About ERC Synergy Grants
ERC Synergy Grants are prestigious awards given by the European Research Council (ERC) to small teams of two to four Principal Investigators. The ambition is to foster collaborative research efforts aimed at addressing complex and ambitious scientific challenges that cannot be tackled by individual researchers alone. Emphasis is put on interdisciplinary collaborations that enable pushing the boundaries of scientific knowledge through innovative and synergistic approaches.
56 grants were awarded in 2024, and the research groups will share €570 million in total. The ERC Synergy Grant scheme is part of the research and innovation programme, Horizon Europe, of the European Union.
Link to the press release from the European Research Council
Short facts about the two projects:
STARMORPH - Unravelling Spatio-temporal Auxin intracellular Redistribution for Morphogenesis
The project partners:
- Stéphanie Robert (coordinator), Swedish University of Agricultural Sciences (SLU), Sweden
- Ondřej Novák (co-applicant), Institute of Experimental Botany of the Czech Academy of Sciences, Czech Republic
- Jürgen Kleine-Vehn (co-applicant), University of Freiburg, Germany
- Alexander Jones (co-applicant), Sainsbury Laboratory, University of Cambridge, United Kingdom
RESYDE - Re-engineering symmetry breaking in development and evolution
The project partners:
- Kerstin Kaufmann (coordinator), Humboldt-Universität zu Berlin, Germany
- Marcus Heisler (co-applicant), University of Sydney, Australia
- Henrik Jönsson (co-applicant), Sainsbury Laboratory, University of Cambridge, UK
- Stephan Wenkel (co-applicant), Umeå University, Sweden
For questions, please contact:
Stéphanie Robert
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/stephanie_robert
Stephan Wenkel
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/stephan_wenkel
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The five UPSC researchers who received a grant from the Swedish Research Council: Laura Bacete Cano (top left; photo: Mattias Pettersson), Johannes Messinger (middle top; photo: Felizitas Messinger), Ove Nilsson (top right; photo: Fredrik Larsson), Stéphanie Robert (bottom left; photo: Erik Abel) and Stephan Wenkel (bottom right; photo: Stephan Wenkel).
This year’s call from the Swedish Research Council for projects in natural and engineering sciences went very well for UPSC. Five researchers received funding. Laura Bacete Cano was awarded a starting grant, while Johannes Messinger, Ove Nilsson, Stéphanie Robert and Stephan Wenkel received a research project grant. This high number of granted projects was only reached in 2020 before.
The five researchers will receive together a total of about 22 million Swedish krona over a four-year period. They will use this funding to work on very different biological questions covering structural biology and biophysics, cell and developmental biology, plant physiology and adaptation.
Laura Bacete Cano wants to investigate how the plant cell wall maintains its functionality under stress. Cell walls provide stability to the plant and serve as first barrier against external attacks. What makes it difficult to study them is that they are not static, permanent structures but rather react dynamically to stress and can trigger plant immune responses. By using advanced microscopy techniques, Laura Bacete Cano wants to advance technologies to study the dynamic nature of the cell wall and investigate the nature and functioning of the cell wall signals.
Johannes Messinger and his team have recently published the, to date, highest-resolution structure of photosystem II, one of the two light-conversion units of photosynthesis. The photosystem II protein complex harbors metal ions that form the water-splitting cofactor and uses the released electrons during photosynthesis. In the new project, Johannes Messinger will employ photosystem II as a model system to understand how protein-water-cofactor interactions, protein dynamics and charge fields allow the activation of abundant metals for performing complex chemistry.
Ove Nilsson’s project will focus on the regulation of phenology in trees concentrating on aspen, poplar and birch. He and his group have identified genes in aspen and poplar that are similar to flowering-promoting genes of the model plant Arabidopsis but have diverse functions in trees. Now, he wants to study how these genes are involved in seasonal growth and growth adaptation at different latitudes. His long-term goal is to understand how climate change affects the regulation of these genes and thus the ability of trees to adjust to new climates.
The fundamental question that stands behind Stéphanie Robert’s research project is how cell shape contributes to multicellularity and the proper structure and function of tissues. She and her team will study the outermost cell layer of the leaf – the epidermal pavement cells - which often form very characteristic puzzle-like patterns. Her goal is to create a geometrical map of a leaf that integrates mechanical interactions between cells, cell layers and tissues to identify key molecular players that determine the shape of a cell, tissue and organ.
Stephan Wenkel investigates microProteins, small proteins that have been often ignored because of their size but that play important roles in regulating larger protein complexes. His new project will focus on a certain subgroup of microProteins that seem to be involved in DNA methylation, a process that affects the activity of genes. By using protein biochemistry, genetics and live imaging techniques, Stephan Wenkel will study how this special group of microProteins is involved in DNA methylation during development.
The five UPSC projects awarded by the Swedish Research Council:
• Project: Watchers on the Wall: Decoding the Early Stages of Plant Cell Wall Integrity
Laura Bacete Cano
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/laura_bacete
• Project: Protein-water-cofactor interactions in biological water oxidation - a paradigm for base metal activation
Johannes Messinger
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.umu.se/personal/johannes-messinger/
• Project: Molecular Regulation of FT-like Genes in Latitudinal Climate Adaptation in Trees
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/ove_nilsson
• Project: Coordination of cell shape acquisition during plant morphogenesis
Stéphanie Robert
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/stephanie_robert
• Project: Decoding Tissue Patterning: The role of microProteins in epigenetic cell memory
Stephan Wenkel
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/stephan_wenkel
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Camilla Canovi showing the first aspen trees that she modified with the CRISPR-Cas9 technology to remove a putative long non-coding RNA. She successfully defended her PhD thesis last week (photo: Anne Honsel).Many things were not known when she started her PhD, but Camilla Canovi was not scared by the abyss. She developed a bioinformatics pipeline to identify and assign putative functions to long non-coding RNAs – RNA molecules that do not contain instructions for making proteins. Camilla Canovi applied this pipeline to spruce and aspen and also started to validate her predictions in aspen trees. In this interview, she explains what long non-coding RNAs are and tells more about her research.
You worked already during your master’s thesis together with Nathaniel Street on a bioinformatics project. What convinced you to continue with a PhD in his group?
Camilla Canovi: Yes, I was doing an Erasmus traineeship together with Nathaniel Street. I did my Master’s in Italy. My professor there knew Nathaniel and send me here. We worked well together and to know him and his group made it very easy for me to say yes when he offered me the PhD project. It made it also easier for me to tell him that I do not want to spend all my days in front of a computer but would like to do also things in the lab. I know myself and that I need some variety to keep my motivation up. So, we adjusted the study plan accordingly. I really appreciate that Nathaniel gave me this freedom and the possibility to take my own choices during my PhD.
You studied long non-coding RNAs in Norway spruce and aspen. What are long non-coding RNAs?
Camilla Canovi: There is a lot of DNA that is transcribed into RNA but does not contain information for a protein. All such RNA is called non-coding RNA. Some of them are more known such as microRNAs and small interfering RNAs because they have been discovered earlier. Those ones usually have a length of below 200 base pairs and some of their functions are well studied already. All non-coding RNAs that are longer than 200 base pairs are defined as long non-coding RNAs. This group is much more diverse. The sequences often differ a lot even between relatively close related species such as spruce and pine. Sometimes only the location in the genome is conserved between species but not the DNA sequence itself which made it very difficult to study them.
Why is it important to study long non-coding RNAs and what are their functions?
Camilla Canovi: Not only the structure but also the functions of long non-coding RNAs can be very different. They can regulate gene activity in many different ways, or they can influence how accessible a certain gene is by modifying the packing of the DNA double strand. They can also serve as decoys that fish out microRNAs so that those ones are not interfering with the expression of a gene anymore. In plants, they seem to be mostly activated when the plants are exposed to stress. In humans, they are a bit better studied because they can serve as marker for cancer. However, the high diversity in function and appearance makes it difficult to study long non-coding RNAs and there is not much done yet with respect to trees like spruce and aspen.
What do you consider as the major outcome of your thesis?
Camilla Canovi: To identify long non-coding RNAs with bioinformatics analyses, we need to first define parameters which is a challenge with such a diversity in appearance. I focused on a certain group of long non-coding RNAs that do not overlap with any gene but are located only in regions between genes and developed a bioinformatics pipeline to identify them in plants. I have applied this pipeline on spruce and aspen to look for this subgroup of long non-coding RNAs, but it can be also used on other plants and to search for other types of long non-coding RNAs by modifying some parameters.
In a next step, I constructed a co-expression network to see which genes are active at the same time as the identified long non-coding RNAs. Then, I checked in which biological processes those genes were involved and assumed that the long non-coding RNA is involved in the same processes as the genes, like for example photosynthesis or leaf development. And finally, I wanted to check if our predictions were correct and modified aspen trees using the CRISPR-Cas9 technology to remove a putative long non-coding RNA. This work is still in process, but I managed to get the first modified trees and some of them are really promising. That is very exciting!
Where there any results that you did not expect?
Camilla Canovi: Many things were unknown when I started, and it was not clear what to expect, especially when trying to modify long non-coding RNAs in aspen with CRISPR-Cas9. There are a few studies in Arabidopsis but not for aspen or spruce as far as I know. I focused on long non-coding RNAs that are involved in leaf development and tried to cut them out. We did not expect that this would work right away but when I tested the first modified aspen trees, it looked like our strategy worked out. There are still many more tests to do but I was very happy to see that.
Your title starts with “Tackling a genomic abyss”. Did you face any other than the “genomic abyss” during your PhD?
Camilla Canovi: When I was about to start the functional validation of some of the identified long non-coding RNAs, I discovered that we had an error in the pipeline. The programme that should make sure to choose only regions in between genes did not work properly. So, we had to fix that which costed me quite some time. However, I was very glad that I realized it before starting with modifying aspen trees which takes even more time.
And then, there was of course the Covid-19 pandemic, and I was somehow stuck here for one year and nine months which was a bit too long. I did not want to go home where my grandmothers were waiting to see me and risk that they get infected. That felt quite long but luckily, I had good friends here.
What are you planning to do now?
Camilla Canovi: My contract lasts until January which gives me time to finish the last things. But first, I will go to Namibia for vacation for ten days to see a desert. I have never seen one before and I am curious about that. Then, I would like to change air and go back to Italy and move away from academia. I would like to try working in industry and have started to look for companies in Northern Italy now. I will see how it goes.
About the public defence:
Camilla Canovi, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, defended her PhD thesis on Thursday, 24th of October 2024. Faculty opponent was Tanja Susanna Pyhäjärvi, Department of Forest Sciences, Viikki Plant Science Centre (ViPS), Helsinki, Finland. The thesis was supervised by Nathaniel Street.
Title of the thesis: Tackling a genomic abyss: Approaches to link long non-coding RNAs to potential biological function in Norway spruce and aspen
Link to Camilla Canovi’s PhD thesis
For more information, please contact:
Camilla Canovi
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
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The project led by Olivier Keech from UPSC will develop sustainable methods to produce shrimp and fish in circular aquaculture systems. Photo: Sergio Zimmermann
The Swedish Agricultural Agency has granted SEK 10 million for a project on sustainable food production, led by Olivier Keech, group leader at UPSC and Associate Professor at Umeå University. The project aims to establish and optimize sustainable production of shrimp and fish in a circular aquaculture system.
“In the project we use bio-RAS, a technology where the water contains particles which are then filtered by a mixture of microorganisms such as bacteria, microalgae and zooplankton. These convert leftover nutrients into natural feed for the fish and shrimp. In addition, it acts as a probiotic for the animals. Overall, it creates a much more sustainable loop,” says Olivier Keech.
The project is interdisciplinary and involves researchers from Umeå University, the Swedish University of Agriculture in Ultuna (SLU) as well as the newly started company Cresponix AB and Brazilian partners. Together, they will apply cutting-edge research to develop and optimize the use of bio-RAS. The technology, originally developed by professor Anders Kiessling (SLU) and Sergio Zimmerman (Zimmermann Aqua Solutions) is a tropical alternative to cold water recirculating aquaculture systems (RAS) that allows for the recapture of organic resources.
The team will create an innovative, sustainable production of feed, as well as evaluate various aspects of shrimp physiology with professor Johan Dicksved and associate professor Kartik Baruah at SLU Ultuna. Furthermore, in collaboration with professor Stefan Bertilsson SLU Ultuna, a metagenomic analysis will also be carried out to assess how the microorganisms in the shrimp's gastrointestinal system develop depending on different compositions of feed and water.
Another part of the project is to develop a mathematical model that can help control and optimize energy conversion, nutrient storage, biomass production and economic viability for the pilot plant the researchers will establish.
“This is a key component for the expansion of such facilities and municipalities, industries and future investors need to know the efficiency and return on investment of such a food production platform,” explains Olivier Keech.
For this, Olivier Keech can also count on his colleagues at Umeå University, Professor Sebastian Diehl, Department of Ecology and Environmental Science, and Associate Professor Jonas Westin, Department of Mathematics and Mathematical Statistics.
The project is part of a larger project that Anders Kiessling, professor at SLU Ultuna, and Olivier Keech initiated several years ago. In a joint venture with both academics and companies, they are establishing a pilot platform for research and development at Östersjöfabriken in Västervik.
The aim is to develop a completely circular food production system that includes both fish, shrimp, vegetables, fruit, insects, mushrooms. Such platforms should ideally be placed strategically downstream of industries, such as server halls and metallurgical companies, which emit large amounts of low-grade heat, i.e. 30-60 degrees Celsius.
“Low-grade heat has no real value in itself and is currently simply cooled down to a certain threshold and released as warm air or lukewarm water into the environment. Instead, channeling the heat into greenhouses and fixing the remaining energy into biomass is a much better way to reduce the environmental impact of human activities,” says Olivier Keech.
The idea of the research is to contribute to food security and reduce dependency on imported food. Today, close to 70 percent of the fresh produce consumed in Sweden is imported.
“By producing more "tropical" products locally, you logically lower the carbon dioxide emissions related to imports from distant countries,” says Olivier Keech.
For more information, please contact:
Olivier Keech, associate professor, Department of Physiological Botany, Umeå University Phone: +46 90 786 53 88
Email:
Anders Kiessling, professor, Swedish University of Agriculture, Ultuna
Email:
Text: Anna-Lena Lindskog, Umeå University
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Thale cress in the snow. DNA previously thought to be “junk” has now been shown to help plants to cope better with cold stress (photo: Vaughan Hurry).
A vast amount of DNA contains no genetic information and was long thought to be junk. Recent research has shown that much of this “junk” DNA is in fact activated but it was not known why. Researchers from Umeå Plant Science Centre have now shown that this activation of “junk”-DNA plays a key role in promoting plant survival during stress.
The study from Peter Kindgren’s research group from Umeå Plant Science Centre and SLU was published recently in the journal The Plant Cell.
Our genetic code is stored in the DNA. When a gene is activated, the double-stranded DNA helix is unwound to make the two individual strands and the gene that is located on one of the two strands accessible. The gene, which contains the building description for a protein, is then rewritten into RNA, which is used as a template to synthesise the protein.
In humans, only one or two percent of the DNA contains genes and thus information for proteins. The rest was believed to be junk. However, new sequencing techniques have revealed that a lot of this “junk”-DNA is activated and rewritten into RNA-templates, even though it is not used for protein synthesis.
Is there a common mechanism behind the activation of so much "junk"-DNA?
“We want to understand why so much of this “junk”-DNA is activated. This is a big question among scientists. It does not only occur in plants but also in other organisms and it is quite an investment”, explains Peter Kindgren, group leader at UPSC and researcher at SLU. “We think that there must be a common reason for this activation.”
Peter Kindgren and his research team focussed on “junk”-DNA that is located on the opposite DNA strand facing a gene. Such DNA segments are called “antisense” and are complementary to the opposite “sense” DNA segment (the gene), similarly like the two different strands of a zipper. The researchers have shown earlier that this type of antisense “junk”-DNA is often activated and rewritten to RNA in the model plant thale cress, but so far only a few examples have been further characterised in plants.
By looking through the known examples, Peter Kindgren and his group tried to identify a general function of this antisense DNA activation. They hypothesised that it might play a role in the regulation of the gene on the opposite sense DNA strand. The challenge was to devise a way to test this hypothesis. They wanted to inhibit the activation of the antisense DNA without affecting the activity of the gene on the opposite DNA strand.
Great potential to make plants grow better in more stressful environments
“We used the gene scissor CRISPR-Cas9 to manipulate the region of the antisense strand where the rewriting of the DNA into RNA is initiated. Like this, the gene on the sense DNA strand could be rewritten normally into RNA and the corresponding protein could be synthesised, but less RNA was produced from the antisense strand,” says Shiv Meena, first author of the article. He was working as postdoc in Peter Kindgren’s group but has recently started to set up his independent research group in India at the National Institute of Plant Genome Research in New Delhi.
The researchers concentrated on genes that are switched on in thale cress during cold and that help the plant to adapt. When the activity of these genes was switched off, the plants were less tolerant to cold. The researchers observed a similar response in the plants that produced less antisense RNA. They concluded that the activation of the antisense DNA increases the gene activity on the opposite sense DNA strand and think that this might be a common mechanism in plants, especially important under stress.
“We are just beginning to understand why so much of this antisense “junk”-DNA is activated in plants, but we see great potential to use this knowledge to make plants grow better in more stressful environments,” says Peter Kindgren. “This story has been brewing in the lab since my postdoc. It is amazing that we finally were able to publish it. None of the people involved are actually working in my lab anymore. One moved to India, one to France, one to Spain, one to the US, and one to Uppsala. But we pulled it off!”
The article
Shiv Kumar Meena, Marti Quevedo, Sarah Muniz Nardeli, Clément Verez, Susheel Sagar Bhat, Vasiliki Zacharaki, Peter Kindgren. Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis. The Plant Cell, 2024; koae160, https://doi.org/10.1093/plcell/koae160
For questions, please contact:
Peter Kindgren
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
Phone: 0046 738400272
https://www.upsc.se/peter_kindgren
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PhD student Johan Sjölander discovered that modifying the internal clock in hybrid aspen can increase growth (photo: Anne Honsel).
The internal clock coordinates the plant growth and adaptation to daily and seasonal changes. It is among others acting via plant hormones. These small molecules are present in low concentrations in plants and control plant growth. Johan Sjölander focussed his PhD studies on the connection between the clock and plant hormones, particularly gibberellin. He discovered that modifying clock components altered the levels of this plant hormone and increased growth in hybrid aspen.
Environmental conditions during day and night, as well across different seasons, vary significantly. Without light, photosynthesis is impossible, and extreme temperatures such as those in winter can harm plants. The plant’s internal clock helps coordinate growth and adaptation to these recurring changes. It is regulated by a complex molecular network and interacts with many other developmental and growth processes like those ones controlled by plant hormones.
“Plant hormones play important roles in regulating almost every aspect of plant development”, says Johan Sjölander, PhD student in Maria E. Eriksson’s group at Umeå Plant Science Centre and Umeå University. “The clock acts as a master regulator, ensuring optimal timing and hormone balance throughout the day and seasons, which ultimately increases the fitness and adaptation of the plant.”
To investigate how the internal clock interacts with plant hormones, Johan Sjölander and his colleagues created hybrid aspen with reduced activity in one clock component. When measuring plant hormone levels, they observed that the levels of the plant hormone gibberellin were altered, along with increased growth. While gibberellin is known to stimulate cell elongation and promote plant height, seeing this effect when perturbing the internal clock was unusual.
“Generally, these kinds of alterations of the internal clock led to trees that are out-of-sync with their environment, which ultimately hamper their ability to grow”, explains Johan Sjölander. “Our research indicates that targeting specific clock components can have the opposite effect. This illustrates how complex the relationship between the internal clock and plant hormones such as gibberellin is.”
Johan Sjölander’s supervisor Maria E. Eriksson previously demonstrated that trees producing more gibberellins struggled to adjust their growth to seasonal changes. The trees did not stop to grow when the days became short. Johan Sjölander and colleagues now used an adjusted strategy. He created hybrid aspen in which the increase of gibberellins was controlled by the internal clock. These trees grew better, produced more biomass and did not lose their ability to stop growth under short days.
“These findings imply that the internal clock is a promising target for enhancing tree productivity without sacrificing seasonal adaptability”, says Johan Sjölander. “When starting my PhD, one of the selling points for me was that my findings might help improve efficiency and sustainability in agriculture and forestry. There is of course still a lot to do but it is rewarding to see the potential of this research for improving future breeding strategies.”
About the public defence:
Johan Sjölander, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, defended his PhD thesis on Friday, 14th of June 2024. Faculty opponent was Anthony Hall, Head of Plant Genomics, Earlham Institute, Norwich Research Park, Norwich, UK. The thesis was supervised by Maria E. Eriksson.
Title of the thesis: Timing is everything: Exploring the role of the circadian clock in plant growth and adaptation
Link to Johan Sjölander’s PhD thesis
For more information, please contact:
Johan Sjölander
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
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Stylistic image of how an electron beam from the cryo-microscope hits frozen PSII particles, whereby a reflection is formed that enables the reconstruction of how the atoms are situated (image: Wolfgang Schröder).
By generating extremely high-resolution images in a cryo-electron microscope, at a level never achieved before for comparable complexes, researchers at Umeå University have revealed the positions of hydrogen atoms and water molecules in photosynthesis. This breakthrough provides a new avenue towards uncovering how water is split – a process crucial for life on Earth as well as for scaling up renewable energy systems.
In photosynthesis, a protein complex called Photosystem II uses the energy of sunlight to oxidize water into molecular oxygen, releasing electrons and protons necessary for converting carbon dioxide into organic compounds in plants. This process is vital for the gas conversion reactions that shape our biosphere and atmosphere: the evolution of oxygen and the reduction of carbon dioxide.
By utilizing a cryo-electron microscope, researchers have generated a 1.7 Å resolution three-dimensional structural map of Photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus. The study is published in the scientific journal Science.
“This resolution is a new record for a membrane protein complex, regardless of method or species. At this resolution a large fraction of the hydrogen atoms of the protein can be detected. This is the first time this has been achieved for such a huge protein complex”, says Wolfgang Schröder, Professor Emeritus at the Department of Plant Physiology at Umeå University which is part of Umeå Plant Science Centre.
The high-resolution structure also allowed the identification of water molecules that were missed in previous structures. The knowledge of both hydrogen and water positions are required for understanding how water enters the catalytic site through extended channels and how protons are guided out.
“These processes are crucial for efficient water oxidation with cheap and abundant metals that presently cannot be mimicked adequately in artificial systems”, says Wolfgang Schröder.
Splitting water with cheap metals instead of rare and expensive ones found in present day electrolysers will allow more readily to scale up water electrolysis as a means of producing hydrogen (H2), a much discussed future energy carrier and base chemical for many processes in industry, including CO2-free ammonia production.
Splitting water to make hydrogen is a promising area of research into sustainable fuels. Currently, the most efficient catalysts require rare and expensive metals. This research into the structure of Photosystem II, shows how cheap and abundant metals can be used to efficiently split water, which may provide new insights into energy production in the future.
About the study
Rana Hussein, André Graça, Jack Forsman, A Orkun Aydin, Michael Hall, Julia Gaetcke, Petko Chernev, Petra Wendler, Holger Dobbek, Johannes Messinger, Athina Zouni, Wolfgang Schröder, Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II, Science, 2024, DOI: 10.1126/science.adn6541
Read the article in Science: https://www.science.org/doi/10.1126/science.adn6541
Link to the Swedish press release from Umeå University
For more information, please contact:
André Graça, Doctoral student, Department of Chemistry, Umeå University
Email:
Phone: +46 72 205 68 16
Wolfgang Schröder, professor emeritus, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University
Email:
Phone: +46 70 589 97 29
Johannes Messinger, professor, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University
Email:
Phone: +46 70 167 984 32
Text: Anna-Lena Lindskog, Umeå University
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PhD student Félix Barbut has studied the function and development of secondary cell walls (photo: Christine Pottier).
Secondary cell walls provide the plant with stability and protection against damage and pathogens. PhD student Félix Barbut from Ewa Mellerowicz’s group at UPSC and SLU has been studying the role of xylan, a long-chain carbohydrate, that is part of the secondary cell wall. He not only identified new molecular players involved in maintaining the integrity of the cell wall, but also interesting target points for bioengineering. Read more about Félix Barbut’s research in this interview with him.
You studied secondary cell walls in Arabidopsis and aspen. What motivated you to choose this PhD project in Ewa Mellerowicz’s research group?
Félix Barbut: I was particularly drawn to pursue my PhD at UPSC due to my profound interest in the complexities of plant science and my specific fascination with how trees adapt to their environment. Reading the PhD proposal, I immediately recognized how well it aligned with my prior research on hormonal interplay, abiotic stress, and the regulation of reactive oxygen species. Moreover, I was thrilled by the broad approach of the project and its ambitious goals.
What is the role of secondary cell walls and why is it important to better understand their structure and function?
Félix Barbut: Secondary cell walls are crucial structures in various aspects of plant development, particularly in trees. They help plants resist numerous challenges such as pathogen attack or strong winds and enable trees to live for thousands of years and grow up to one hundred meters tall. Understanding the structure and dynamics of secondary cell walls could help us develop more resilient crops to withstand climate change and promote more sustainable agricultural practices. Additionally, wood, which is composed of secondary cell walls, is a major sink of atmospheric carbon dioxide. Biofuels derived from wood could serve as an alternative to fossil fuels, potentially achieving net-zero carbon emissions.
What do you consider as the major outcome of your thesis?
Félix Barbut: In my thesis, we identified several molecular players potentially involved in maintaining the integrity of secondary cell walls, a system that allows plants to sense external stresses and adjust wood development accordingly. We also created hybrid aspen trees and Arabidopsis plants that are more drought-resistant and easier to convert to biofuel. However, these plants exhibited slower growth, indicating a need to further optimize secondary cell wall integrity for creating more promising crops and trees. Additionally, we discovered that lipids, fatty compounds that are for example part of cell membranes, may play a more significant role in wood than previously understood.
Did your results match your expectations or working hypotheses?
Félix Barbut: Given the exploratory nature of our research, we did not set much specific expectations for the outcomes. However, we observed many consistent responses to drought and cell wall defects in herbaceous plants and perennial trees. Notably, unexpected findings - such as the presence of lipids in the wood and the drought resistance of cell wall-impaired lines - have paved the way for further research on the secondary cell wall integrity maintenance.
Did you had to overcome any challenges during your PhD?
Félix Barbut: Yes, I faced several challenges during my PhD. First, I had to adapt to a new country, which was a significant transition. Additionally, the onset of the COVID-19 pandemic in the middle of my studies presented considerable difficulties. Overall, the PhD journey is filled with ups and downs, and I am grateful for the resilience I developed during these tough times, from which I learned a great deal.
What are you planning to do now? Do you like to continue in Academia?
Félix Barbut: I am committed to pursuing a career in academia and hope to secure a permanent position in the future. Currently, I have one more paper to publish at UPSC. After that, I plan to seek a position abroad, which I believe will give me more chances of building a successful career.
About the public defence:
Félix Barbut, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, has defended his PhD thesis on Friday, 14th of June 2024. Faculty opponent was Professor Thorsten Hamann, Professor at the Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. The thesis was supervised by Ewa Mellerowicz.
Title of the thesis: Unraveling the Role of Xylan in the Integrity of Secondary Cell Walls: Insights from Arabidopsis and Aspen
Link to Félix Barbut’s PhD thesis
Link to a news about one of Félix Barbut's research projects: Aspen trees exposed to repetitive flexing grew faster
For more information, please contact:
Félix Barbut
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
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Petra Marhava is awarded the SPPS Early Career Prize (photo: Andreas Palmén)
The Scandinavian Plant Physiology Society (SPPS) awards Petra Marhava with the SPPS Early Career Prize. The prize recognises her progress and contributions to plant biology over the past few years and will be awarded to her at the SPPS2024 Conference in Copenhagen in August this year.
Petra Marhava started to establish her research group at UPSC in 2022 when she became Assistant Professor at SLU. Her research focuses on plant acclimation to temperature stress. Right at the beginning, she secured starting grants from the Swedish and the European Research Councils. With the Early Career Prize, SPPS acknowledges Petra Marhava’s achievements over the past years and aims to further support her career.
The motivation for the prize highlights Petra Marhava’s “excellent track record with publications in top tier journals such as Nature and Cell” and that she “has been able to quickly secure funding from important sources”. This is reflected in the size of Petra Marhava’s research group, which currently comprises four postdoctoral researchers and one PhD student, as well as project students.
The SPPS Early Career Prize is awarded every second year to an early career plant scientist based in a Nordic country if nominations of sufficient quality are received. It is a monetary award and will be officially presented to Petra Marhava during the SPPS2024 Conference in Copenhagen in August this year where she will also present her research. This is the fourth time that the SPPS Early Career Prize has been awarded to a UPSC researcher.
More information about the SPPS Early Career Prize and other prizes awarded by SPPS
For more information, please contact:
Petra Marhava
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
Twitter: @MarhavaPetra
https://www.upsc.se/petra_marhava