14 ERA-CAPS PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

For plants, light is a signal that carries information about the environment, and a source of energy for photosynthesis. PHYTOCAL focuses on the interaction between phytochrome signalling and photosynthesis, and seeks to understand fundamental processes that make carbon (C) and nitrogen (N) resources available for plant growth. These unexplored connections underlie plasticity, which contributes significantly to yield variability in the field. Phytochrome photochemistry is exquisitely tuned to detect spectral changes indicative of nearby vegetation. This light-activated surveillance mechanism initiates changes in plant architecture, biomass formation and the timing of reproduction: traits that are strongly linked to crop yield. These changes in growth strategy require corresponding adjustments in resource deployment, yet we have no understanding of how this is accomplished.
PHYTOCAL builds on new research from the partner labs showing that cross talk between phytochrome and carbon signalling is central to C resource use efficiency and resource conservation. A principal aim will be to determine the role of phytochrome in C resource management. PHYTOCAL will also delineate the genetic basis and impact of shading-induced N re-allocation in canopies. This trait strongly impacts on N use efficiency and stand photosynthesis, and in many crops is closely linked to yield.
PHYTOCAL will conduct a systematic study across scales, delivering mechanistic information about signal integration, time-resolved transcriptome and metabolite profiles, and quantitative information about biomass accumulation, defined as the flux of carbon to protein and cell wall components, and growth dynamics. The experimental findings will be integrated into models to test hypotheses and to gain understanding at a system level. An aim will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production. PHYTOCAL will run parallel work programmes in the reference species, Arabidopsis and the closely related crop Brassica rapa. The rapid life cycle and larger resource pool of the reference species will enable us to accelerate knowledge acquisition. B. rapa brings the advantage of larger size, and allows new insights to be directly applied to a food crop.

Technical Summary

PHYTOCAL builds on new research from the partner labs showing that cross talk between phytochrome and carbon signalling is central to C resource use efficiency and resource conservation. It will test the following hypotheses: (i) phytochrome plays an influential role in coupling C resources to growth; (ii) phytochrome and photosynthesis signals cooperate to conserve night time C reserves, preventing starvation and growth arrest; and (iii) phytochrome and photosynthesis interact at dawn to delay the activation of energy costly processes until the light intensity is high enough to drive photosynthesis. PHYTOCAL will also delineate the impact and genetic basis of shading-induced N re-allocation in canopies. This trait strongly impacts on N use efficiency, and yield in many crops.
PHYTOCAL will conduct a systematic study across scales, delivering mechanistic information about signal integration, time-resolved transcriptome and metabolite profiles, and quantitative information about biomass accumulation, defined as the flux of carbon to protein and cell wall components, and growth dynamics. The experimental findings will be integrated into models to test hypotheses and to gain understanding at a system level. PHYTOCAL benefits from prior investment in modelling from partner labs: (i) a Phytochrome Signalling Model that regulates growth; and (ii) a modular Framework Model where environmental inputs (incl. light) control resource production and allocation to leaves and growth. These models will be amalgamated to produce models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.
PHYTOCAL will work in the reference species, Arabidopsis and the closely related crop Brassica rapa. The rapid life cycle and larger resource pool of the reference species will to enable us to accelerate knowledge acquisition. B. rapa brings the advantage of larger size, and allows new insights to be directly applied to a food crop.

Planned Impact

Confronted by the competing pressures of a rapidly-increasing human population, decreasing available arable land, and a climate in flux, there has perhaps never been a time where increasing crop yields has been more urgent for the global economy and the environment. This project is squarely focused on the connection between C metabolism and allocation and growth, a link that has been largely overlooked in previous efforts for yield improvement. Moreover, global increases in CO2 levels will have highly variable impacts on plants, depending on their genetics and their environment, and FACE experiments point to the allocation of C for growth and N use efficiency as a feature that will limit plant productivity in these future conditions. The data and models proposed as major milestones for this project may aid in planning for plants in both agricultural and natural settings. Seen in terms of the main focus areas of ERA-CAPS 2014, thus PHYTOCAL will provide basic insights into adaptation to a changing climate and plant responses to biotic/abiotic stress, and will establish a pipeline to accelerate the transfer of findings from a model system to a crop plant grown in the countries of all three partners, thus contributing to food security. Existing connections to biotechnology companies by the partners will be leveraged to facilitate technology transfer and new product development.

Publications


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Halliday KJ (2016) Light-sensing phytochromes feel the heat. in Science (New York, N.Y.)


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Yang D (2016) Photoreceptor effects on plant biomass, resource allocation, and metabolic state. in Proceedings of the National Academy of Sciences of the United States of America

 
Description Plants sense the light environment through an ensemble of photoreceptors. Members of the phytochrome class of light receptors are known to play a critical role in seedling establishment, and are among the best-characterized plant signaling components. Phytochromes also regulate adult plant growth; however, our knowledge of this process is rather fragmented. This study demonstrates that phytochrome controls carbon allocation and biomass production in the developing plant. Phytochrome mutants have a reduced CO2 uptake, yet overaccumulate daytime sucrose and starch. This finding suggests that even though carbon fixation is impeded, the available carbon resources are not fully used for growth during the day. Supporting this notion, phytochrome depletion alters the proportion of day:night growth. In addition, phytochrome loss leads to sizeable reductions in overall growth, dry weight, total protein levels, and the expression of CELLULOSE SYNTHASE-LIKE genes. Because cellulose and protein are major constituents of plant biomass, our data point to an important role for phytochrome in regulating these fundamental components of plant productivity. We show that phytochrome loss impacts core metabolism, leading to elevated levels of tricarboxylic acid cycle intermediates, amino acids, sugar derivatives, and notably the stress metabolites proline and raffinose. Furthermore, the already growth-retarded phytochrome mutants are less responsive to growth-inhibiting abiotic stresses and have elevated expression of stress marker genes. This coordinated response appears to divert resources from energetically costly biomass production to improve resilience. In nature, this strategy may be activated in phytochrome-disabling, vegetation-dense habitats to enhance survival in potentially resource-limiting conditions.
Exploitation Route Our findings provide a basic strategy to maximise plant/crop biomass and to improve resilience to abiotic stresses.
Sectors Agriculture, Food and Drink
 
Description Photoperiod model 
Organisation University of Washington
Department Department of Biochemistry
Country United States of America 
Sector Academic/University 
PI Contribution Building on our earlier joint publication (Seaton et al., Mol Syst Biol. 2015 Jan 19;11(1):776), we have continued to expand our understanding of photoperiodic mechanisms. We have contributed data, plus expertise in light signalling and modelling.
Collaborator Contribution The Imaizumi lab have contributed data and expertise on the circadian oscillator.
Impact An earlier collaboration led to the publication of Seaton et al., Mol Syst Biol. 2015 Jan 19;11(1):776. This more recent collaboration has culminated in a manuscript that we are in the final stages of preparation.
Start Year 2015
 
Description Toledo-Ortiz Collaboration 
Organisation Lancaster University
Department Department of Physics
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution We sought and were awarded funding from the Leverhulme Trust to support this joint venture
Collaborator Contribution new research findings and expertise
Impact We are preparing a research manuscript that describes our joint findings
Start Year 2015
 
Description ERA-CAPs Award holders meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Sharing project aims and objectives with the other ERA-CAPs awardees and the funding agencies.
Year(s) Of Engagement Activity 2015
 
Description Edinburgh Plant Science Network- Meeting series 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact I am Director of Edinburgh Plant Science (EPS), a body that aims to bring plant scientists and social together to participate in strategic research. EPS is committed to delivering fundamental and translational research, education and outreach to ensure that new discoveries bring benefits for human health, society and the environment.

Edinburgh Plant Science assembles over 600 plant scientists and social scientists that collectively provide wide-ranging expertise and capability in food security, environmental sustainability and related policy. Since the launch in June 2015 EPS activities have brought in >£2M in joint grant funding.
Year(s) Of Engagement Activity 2015,2016,2017
URL http://www.edinburghplantscience.com/
 
Description Equate Scotland - Gender Equality Event, Playfair Library Old College University of Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact Equate Scotland event to discuss gender equality in the workplace. Broad audience- academics, students, general public.
Year(s) Of Engagement Activity 2017
URL http://www.equatescotland.org.uk/
 
Description GCRF Impact Accelerator Award meeting, Niarobi 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact GCRF-inspired meeting in Nairobi, 2017 to build collaborations based on translating our research findings to crops. The meeting focuses on how we can utilise genetic / imaging / surveillance and modelling methods to improve crop yield in arid or changeable environments in sub-Saharan Africa.
Year(s) Of Engagement Activity 2017
 
Description Royal Society London- Parent Carer Scientist Launch 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact The Royal Society Parent-Carer-Scientist Launch aimed to raise awareness that science drives huge benefits from a diverse workforce. The event, was attended by scientists, their families and friends. It celebrated the best UK science, while highlighting the challenges that many scientists have in managing other matters such as disability and/or caring responsibilities. Several of the attendees were interviewed by the BBC and other press outlets.
Year(s) Of Engagement Activity 2016
URL https://royalsociety.org/topics-policy/diversity-in-science/parent-carer-scientist/
 
Description Scientific Conference - Barcelona, Spain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk delivered on project findings and future directions. The talk stimulated discussion on several novel lines of research that we are pursuing on project. The aim was to open dialogue around our new hypotheses and new ways of thinking in the scientific field of plant light signalling.
Year(s) Of Engagement Activity 2016
 
Description Scientific Conference - Gelveston, Texas USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Scientific conference where project findings were presented to an audience that mainly comprised scientists in the field
Year(s) Of Engagement Activity 2016
URL https://www.grc.org/programs.aspx?id=14420
 
Description Scientific Conference - Halle, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk delivered on using mathematical modelling approaches to understand complex signalling pathway behaviour. The talk stimulated discussion on the utility of modelling methods in testing hypotheses and predicting pathway and whole plant responses. In this conference the focus was on the influence of temperature on plant signalling, metabolism and development.
Year(s) Of Engagement Activity 2016
 
Description Scientific workshop - Dundee, UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Local Plant Science meeting. Plant scientists from around Scotland delivered talks with a view to sharing ideas and initiating new collaborations.
Year(s) Of Engagement Activity 2016