Charting the protein modifications systems that underpin submergence tolerance in rice

Climate change models predict that large areas of Northern Europe and Asia is likely to experience flooding in the next 50 years. Currently flooding affects rice cultivation across 20 million hectares in Asia. To stabilize crop yields it is imperative to increase the capacity of cereal and vegetable crops to endure partial to complete submergence. This has been feasible for rice, due to the identification of the SUBMERGENCE 1A gene (SUB1A, (encoding a group VII ETHYLENE RESPONSE FACTOR [ERFVII] transcription factor) providing tolerance to complete submergence for over 7 days. The molecular characterization of SUB1A has begun to provide new insights into molecular, physiological and developmental processes that underlie an effective submergence survival strategy in plants. While SUB1A is important to ensure rice productivity in vast flood prone areas of the world, recent increases in frequency and magnitude of submergence due to extreme flooding events across Asia has negatively impacted SUB1A efficacy. New knowledge and resources are urgently needed that can boost SUB1A efficacy in mediating flooding tolerance. Recent evidence indicates that a difference in levels of flooding tolerance of SUB1A introgressed lines may be due to either transcriptional or post-transcriptional mechanisms that affect SUB1A activity. Our preliminary evidence suggests that the stability of the SUB1A protein is likely to be critical in mediated prolonged submergence tolerance in rice.

The project partners have discovered that SUB1A protein stability (and therefore activity) is affected by two major post-translational mechanisms, ubiquitylation and SUMOylation. By exploiting this new knowledge we aim to pave the way to develop new rice varieties in which the SUB1A protein is more stable and active during prolonged flooding, generates enhanced submergence tolerance and therefore greater stability of yield.

This proposal also aims to exploit the project partners unique insight and world leads into post-translational mechanisms (PTMs), including N-end rule based Ubiquitylation and SUMOylation, to identify new molecular regulators that control submergence response in plants. This could lead the development of a new generation of flooding tolerant crop varieties.

Overarching hypotheses of the proposal:
1. Manipulating protein modifications that govern SUB1A stability can lead to extended flooding tolerance in rice.
2. Protein modification systems can be exploited to identify new regulators of submergence tolerance in rice.

These 2 hypotheses will be tested by 3 main objectives within the 3 year project.
1. To investigate the interaction between the molecular and environmental factors that affect SUB1A stability and posttranslational state.

2. To test for submergence tolerance and (time permitting) cross-tolerance to multiple abiotic stresses in transgenic rice plants that manipulate the regulatory components of SUB1A stability.

3. Discover novel regulators of flooding tolerance by exploiting preliminary data that indicates the presence of new targets that affects plant survival and undergo both N-end rule mediated Ubiquitylation and SUMOylation during submergence induced hypoxia.

Timeliness: Our preliminary observations demonstrating that posttranslational modifications are essential for SUB1A function provide a highly novel molecular explanation and conduit to enhanced flooding tolerance in rice. Characterization of the role of the PTMs in controlling SUB1A and definition of new regulators of submergence with solved molecular mechanisms will offer novel approaches for delivery of plants with robust flooding and wider abiotic stress tolerance.

Rice typically induce elongation in the stems and leaves in an attempt to escape flooding, but varieties containing the SUB1A gene switch to a quiescent state restricting elongation and conserve energy until the flood recedes then induce tillering thereby positively impacting yield. While SUB1A is important to ensure rice productivity in vast flood prone areas of the world, recent increases in frequency and magnitude of submergence due to extreme flooding events across Asia has negatively impacted SUB1A efficacy. New knowledge and resources are urgently needed that can boost SUB1A efficacy in mediating flooding tolerance. Recent evidence indicates that a difference in levels of flooding tolerance of SUB1A introgressed lines may be due to either transcriptional or post-transcriptional mechanisms that affect SUB1A activity. The project partners have previously shown the importance of post-translational mechanisms (PTMs) such as Ubiquitylation and SUMOylation in regulating the flooding response. These observations demonstrate that molecular components that affect SUB1A protein stability are still not understood, but could be key for boosting submergence tolerance in rice.
This 3-year project aims to
1. Determine how flooding affects SUB1A ubiquitination and SUMOylation and its stability in rice.
2. To test for submergence tolerance and (time permitting) cross-tolerance to multiple abiotic stresses in rice plants that manipulate the regulatory components of SUB1A stability.
3. Discover novel regulators of flooding tolerance by exploiting preliminary data that indicates the presence of new targets that undergo both N-end rule mediated Ubiquitylation and SUMOylation during submergence induced hypoxia.

The knowledge gleaned in this study could lead to the identity of new molecular regulators, establish tools that provide novel insights into molecular, physiological and developmental processes that underpin an effective submergence survival strategy in plants.

Economic and Societal Impact: The project aims to provide greater resilience to submergence in rice production systems with climatic variability. Our research will have direct academic and ODA-related impacts. It will produce new knowledge and scientific advancements which will be published and therefore enhance UK and global knowledge economies. Development of stress adapted high yielding flood resistant rice varieties not only enhances food security and boosts local economy but also reduces the expenditure on rice imports in case of crop failure. A surety of crop safety leads to better adaptation of technology and directly contributes to poverty alleviation. Development of rice varieties with tolerance to extended flooding will expand rice production into new areas and will provide additional sources of work and income to the rural poor in flood prone areas of the world.

The UK PIs have developed a collaboration with International Rice Research Institute (IRRI) to begin the process of translating new knowledge gleaned from this study into the field. IRRI, targets countries such as India, Bangladesh, Nepal, and Sri Lanka in South Asia, countries such as Lao PDR, Vietnam, Cambodia, Myanmar and Philippines in South East Asia; and Tanzania, Mozambique and Burundi in East Africa through several of its large scale variety development and dissemination projects. IRRI works with a number of partners from these countries to deliver large scale impact. Previously, varieties with SUB1 have been deployed all over Asia on large scale through these channels. Apart from this, regional hubs of IRRI in South Asia and Africa are also engaged in development and distribution of stress tolerant varieties.

Collaborations to enhance the knowledge economy: The project will strengthen a successful existing collaboration between the PIs in Durham, Nottingham. The PI at Durham is active in the new HEFC funded N8 Agrifood Resilience Programme, and we will use this network of academic and commercial partners to enhance the impact of the project and consolidate and extend collaborative research interactions between the participating organisations. Such interactions will generate additional opportunities to expand and develop this area of research.

Training: The project creates an opportunity to train the next generation of scientists to continue the development of submergence tolerance research activities. The PDRAs will have the opportunity of giving Guest Lectures at corresponding partner academic institutions. For example, the PDRA at Nottingham will have the opportunities to give guest lectures in the 'Gene Technology' module, which forms part of an Crops for the Future programme at Durham. Similar opportunities will be made available for the Durham PDRA. This experience will provide the PDRAs and with valuable insights into how crop varieties can be developed from initial molecular discoveries at the fundamental level. This exchange of staff will ensure that capacity building and knowledge sharing will be effective. The synergy that is generated within the consortium is likely to generate new strategies that can add significantly to the yield potential of rice during flooding stress.

Communication and Engagement: A set of deliverables at specific timepoints within the project lifetime is provided in the detailed impact statement, however we provide a summary of it below;
Dissemination to the wider scientific community: The research will be published in relevant peer-reviewed international journals and presented at appropriate meetings.
Outreach and public engagement activities: To communicate directly with the relevant commercial and stakeholder audience, PI at Durham and co-Is at Nottingham will showcase the data in a variety of outreach events in through their institutions to maximize knowledge transfer and public engagement.