14 ERA-CAPS_Simultaneous manipulation of source and sink metabolism for improved crop yield
Lead Research Organisation:
University of Oxford
Department Name: Plant Sciences
Abstract
The capacity of the metabolic networks of different plant tissues is a key determinant of the yield of crop plants. Of particular importance is the capacity to assimilate environmental carbon (CO2) and nitrogen (NO3), the capacity to transport the resultant sugars and amino acids to the sink tissues (such as tubers, fruits and seeds) and the capacity of the sink tissues to convert the incoming sugars and amino acids into storage compounds. There is a great deal of interest in increasing the capacity or efficiency of these metabolic and transport processes by genetic engineering. Many of the current research consortia working in this area are focussing on the initial processes responsible for carbon and nitrogen assimilation in the source tissues. However, it is clear both on theoretical grounds and from experimental evidence that whole plant fluxes of carbon and nitrogen are co-limited by the metabolic capacities of both source and sink tissues. This is especially true if the source capacity is increased: control will inevitably shift to the sink tissues, the metabolism of which will therefore severely limit the yield potential of an engineered crop.
In this project, we will implement a metabolic engineering strategy of unprecedented scale in plants. Not only will we engineer both source and sink tissues, but we will target multiple metabolic and transport processes in each in an attempt to remove flux bottlenecks from across the metabolic network. The project will exploit the new technique of biolistic combinatorial co-transformation which allows the stable integration of an unlimited number of transgenes into a single locus in any plant amenable to biolistic transformation of the nuclear genome. Based on prior knowledge, we have identified 18 transgene targets which will be introduced into tomato plants. We will generate a large library of up to 200 transgenic lines and these will be screened for fruit yield, with the expectation of achieving a step-change in yield in comparison to the introduction of small numbers of transgenes modifying just source or sink. In addition, the project will undertake extensive research to identify additional metabolic bottlenecks (by comparison of metabolic network fluxes and enzyme activities), to identify transporters involved in fruit nitrogen allocationand to identify strong genetic alleles for harvest index and fruit nitrogen content (based on analysis of tomato introgression populations). This research will provide additional targets which will be super-transformed into the best performing transgenic line to assess the scope for even further yield increases.
In this project, we will implement a metabolic engineering strategy of unprecedented scale in plants. Not only will we engineer both source and sink tissues, but we will target multiple metabolic and transport processes in each in an attempt to remove flux bottlenecks from across the metabolic network. The project will exploit the new technique of biolistic combinatorial co-transformation which allows the stable integration of an unlimited number of transgenes into a single locus in any plant amenable to biolistic transformation of the nuclear genome. Based on prior knowledge, we have identified 18 transgene targets which will be introduced into tomato plants. We will generate a large library of up to 200 transgenic lines and these will be screened for fruit yield, with the expectation of achieving a step-change in yield in comparison to the introduction of small numbers of transgenes modifying just source or sink. In addition, the project will undertake extensive research to identify additional metabolic bottlenecks (by comparison of metabolic network fluxes and enzyme activities), to identify transporters involved in fruit nitrogen allocationand to identify strong genetic alleles for harvest index and fruit nitrogen content (based on analysis of tomato introgression populations). This research will provide additional targets which will be super-transformed into the best performing transgenic line to assess the scope for even further yield increases.
Technical Summary
The capacity of the metabolic networks of different plant tissues is a key determinant of the yield of crop plants. Of particular importance is the capacity to assimilate environmental carbon (CO2) and nitrogen (NO3), the capacity to transport the resultant sugars and amino acids to the sink tissues (such as tubers, fruits and seeds) and the capacity of the sink tissues to convert the incoming sugars and amino acids into storage compounds. In this project, we will implement a metabolic engineering strategy of unprecedented scale in plants. Not only will we engineer both source and sink tissues, but we will target multiple metabolic and transport processes in each in an attempt to remove flux bottlenecks from across the metabolic network. The project will exploit the new technique of biolistic combinatorial co-transformation which allows the stable integration of an unlimited number of transgenes into a single locus in any plant amenable to biolistic transformation of the nuclear genome. Based on prior knowledge, we have identified 18 transgene targets which will be introduced into tomato plants. We will generate a large library of up to 200 transgenic lines and these will be screened for fruit yield, with the expectation of achieving a step-change in yield in comparison to the introduction of small numbers of transgenes modifying just source or sink. In addition, the project will undertake extensive research to identify additional metabolic bottlenecks (by comparison of metabolic network fluxes and enzyme activities), to identify transporters involved in fruit nitrogen allocation and to identify strong genetic alleles for harvest index and fruit nitrogen content (based on analysis of tomato introgression populations). This research will provide additional targets which will be super-transformed into the best performing transgenic line to assess the scope for even further yield increases.
Planned Impact
All knowledge generated in this project will be disseminated by timely publication in high profile peer-review journals and once published, all data will be made available in complete form, both through journal websites (supplemental files) and via a dedicated project website. The website will serve two purposes: to facilitate data and information exchange between the partners and to provide a publically accessible data and information portal. The preference will be to publish in journals with an open access policy. In addition, all members of the consortium will be active in presenting the work at international conferences.
A consortium agreement (CA) will be drawn up and signed by all partner institutions prior to the start of the project using the template provided through the ERA-CAPS call, subject to modifications by the legal offices of the partner institutions. The consortium will manage intellectual property rights (IPR) following the principle that a result shall be owned by a partner generating the result. Results may be shared if generated by more than one partner and this will lead to co-ownership wherein a separate joint ownership agreement will set out allocation and terms. All partners will endeavour to exploit any IP arising from the work. All three institutions have exceptional track records of exploitation and translation of their research and have dedicated personnel and departments for this purpose. All partners will be required to check with the project coordinator prior to any public dissemination of results (includes conference presentations and posters as well as published manuscripts) and a 3 month delay may be requested to allow protection of IPR.
Improving crop yield is of crucial importance to the European agro-economy and for food security. Tomato is a valuable crop (as reflected by the involvement of Syngenta in this project) and, after China, Europe is the most important market for tomatoes, with an annual production of around 16 million tonnes for both the fresh and processed fruit markets. This project has the potential to dramatically and rapidly increase the yield of the crop and is a timely exploration of the potential of new genetic-engineering technologies. Ultimately, the immediate economic benefit of this research is limited by current GM legislation, but it is possible that current European regulatory requirements will have been relaxed by the time this project is completed. Even were this not to be the case, Syngenta routinely uses transgenic experiments to rapidly assess the effect of specific genes and alleles and then introduces these genetic changes into their elite varieties using molecular breeding techniques to provide new seed varieties for the non-GM markets. This route to exploitation would be slower because most of our transgenic changes are gain-of-function and this is more difficult to introduce with molecular breeding or mutational approaches. Most likely, additional work would be required to find negative regulators of the target genes which could be modified by mutation. Ultimately, it would be desirable to translate this research into the main broad-acre field crops such as wheat and rice. We view the current project as a means of demonstrating the potential for multi-point manipulation of source-to-sink nutrient flows for increasing yield in an experimentally tractable and commercially important crop as well as providing gene targets that may be used to apply the same approach in cereals.
A consortium agreement (CA) will be drawn up and signed by all partner institutions prior to the start of the project using the template provided through the ERA-CAPS call, subject to modifications by the legal offices of the partner institutions. The consortium will manage intellectual property rights (IPR) following the principle that a result shall be owned by a partner generating the result. Results may be shared if generated by more than one partner and this will lead to co-ownership wherein a separate joint ownership agreement will set out allocation and terms. All partners will endeavour to exploit any IP arising from the work. All three institutions have exceptional track records of exploitation and translation of their research and have dedicated personnel and departments for this purpose. All partners will be required to check with the project coordinator prior to any public dissemination of results (includes conference presentations and posters as well as published manuscripts) and a 3 month delay may be requested to allow protection of IPR.
Improving crop yield is of crucial importance to the European agro-economy and for food security. Tomato is a valuable crop (as reflected by the involvement of Syngenta in this project) and, after China, Europe is the most important market for tomatoes, with an annual production of around 16 million tonnes for both the fresh and processed fruit markets. This project has the potential to dramatically and rapidly increase the yield of the crop and is a timely exploration of the potential of new genetic-engineering technologies. Ultimately, the immediate economic benefit of this research is limited by current GM legislation, but it is possible that current European regulatory requirements will have been relaxed by the time this project is completed. Even were this not to be the case, Syngenta routinely uses transgenic experiments to rapidly assess the effect of specific genes and alleles and then introduces these genetic changes into their elite varieties using molecular breeding techniques to provide new seed varieties for the non-GM markets. This route to exploitation would be slower because most of our transgenic changes are gain-of-function and this is more difficult to introduce with molecular breeding or mutational approaches. Most likely, additional work would be required to find negative regulators of the target genes which could be modified by mutation. Ultimately, it would be desirable to translate this research into the main broad-acre field crops such as wheat and rice. We view the current project as a means of demonstrating the potential for multi-point manipulation of source-to-sink nutrient flows for increasing yield in an experimentally tractable and commercially important crop as well as providing gene targets that may be used to apply the same approach in cereals.
Organisations
Publications
Brog YM
(2019)
A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population.
in The Plant journal : for cell and molecular biology
Fernie AR
(2020)
Synchronization of developmental, molecular and metabolic aspects of source-sink interactions.
in Nature plants
Shameer S
(2018)
Computational analysis of the productivity potential of CAM.
in Nature plants
Shameer S
(2019)
Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light.
in Plant physiology
Shameer S
(2020)
Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits.
in The Plant journal : for cell and molecular biology
Sweetlove LJ
(2017)
Engineering central metabolism - a grand challenge for plant biologists.
in The Plant journal : for cell and molecular biology
Vallarino JG
(2020)
Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%.
in Scientific reports
Description | We have developed a model for tomato leaf metabolism and one for tomato fruit metabolism and have used these to predict ways to engineer increased productivity of the plant. We have identified a number of unexpected targets (e.g. mitochondrial glutamine synthetase, plastidial alkaline pyrophosphatase and the tonoplast PPi- and ATP-dependent proton pumps. One of these targets, mitochondrial glutamine synthetase has been tested by the project partners at the Max Planck Institute for Molecular Plant Physiology and has been proven to yield substantial benefits for tomato fruit productivity. |
Exploitation Route | The models will provide a useful platform for plant metabolism engineering and research. We have shown that the core model is a generic representation of plant primary metabolism and can be used, with species-specific and tissue-specific constraints, for any species, not just tomato. To model metabolism during fruit growth we had to develop a new computational framework that allowed for the main mechanism of growth of fruit - osmotic cell expansion - to be accounted for. The models are freely available for others to use via the Sweetlove lab GitHub repository. |
Sectors | Agriculture, Food and Drink |
URL | https://github.com/ljs1002 |
Description | The findings and general principles of coordinated manipulation of source and sink metabolism and model-guided plant engineering have been taken up by the company BASF who have funded a follow-on research project to look at the specific role of phloem transport in crop yield. This funded a postdoc in the Sweetlove lab for 3 years to do computational modelling, and 2 experimental postdocs for 3 years each in the labs of Alisdair Fernie (Max-Planck Institute for Molecular Plant Physiology) and Uwe Sonnewald, University of Erlangen. |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink |
Title | GrOE-FBA (Growth by Osmotic Expansion - Flux Balance Analysis) computational framework for modelling metabolism in expanding cells |
Description | Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and transport, but the main computational approach for predicting metabolic network fluxes, flux balance analysis (FBA), often uses biomass composition as the main output constraint and ignores potential changes in cell volume. Here we present GrOE-FBA (Growth by Osmotic Expansion - Flux Balance Analysis), a framework that accounts for both the metabolic and ionic contributions to the osmotica that drive cell expansion, as well as the synthesis of protein, cell wall and cell membrane components required for cell enlargement. Using GrOE-FBA, the metabolic fluxes in dividing and expanding cell were analyzed, and the energetic costs for metabolite biosynthesis and accumulation in the two scenarios were found to be surprisingly similar. The expansion phase of tomato fruit growth was also modelled using a multi-phase single optimization GrOE-FBA model and this approach gave accurate predictions of the major metabolite levels throughout fruit development as well as revealing a role for transitory starch accumulation in ensuring optimal fruit development. |
Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | only just released. |
URL | https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14707 |
Title | Core model of primary metabolism in plants |
Description | A charge and atom-balanced model of the stoichiometry and subcellular compartmentation of all reactions required by plants to synthesise the main components of their biomass from inorganic or organic precursors. |
Type Of Material | Computer model/algorithm |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | In addition to its use in this project, we have used this model in two other significant research projects that have led to a novel metabolic pathway for CAM (leading to enhanced water saving and metabolic efficiency) and an explanation of the metabolic component of guard cell function during stomatal dynamics. Both pieces of research are currently under consideration for publication. |
URL | https://github.com/ljs1002 |
Description | Fascination of Plants Day |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Exhibition stand at the Oxford University Arboretum as part of their annual Fascination of Plants Day event |
Year(s) Of Engagement Activity | 2012,2013 |
Description | Oxford Botanic Gardens Masterclass lecture |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | 20 A-level and GCSE-level pupils attended this talk, which was held as an after-school evening series. After the talk, the students worked with an advisor (PhD students from my department) to discuss the talk and this then led to a question and answer session with me. |
Year(s) Of Engagement Activity | 2017 |