Application of the plastidic E3 ligase SP1 in crop improvement, using tomato and rice as models

Lead Research Organisation: University of Oxford
Department Name: Plant Sciences

Abstract

The human population is growing rapidly and set to reach 9bn by 2050, and there are ever-increasing pressures on natural resources. Thus, the drivers for increased crop yields and productivity, and for resilience to climate change and sub-optimal growing conditions, are stronger than ever. To meet these demands it will be essential to develop new, improved crop varieties. Through research on the model plant Arabidopsis, we recently made a significant breakthrough that may have important implications for crop yields and food security. We discovered a gene called SP1 that controls many important aspects of plant development. More specifically, SP1 regulates the development of structures inside plant cells called chloroplasts, which are responsible for photosynthesis. By altering SP1 activity in crops, we believe that we will be able to exert control over diverse aspects of crop development, including fruit ripening, grain development, stress tolerance, leaf aging, and crop yield.
 
Description By manipulating expression of the chloroplast protein SP1, it is possible to manipulate important aspects of crop plant development and performance; for example, fruit ripening and abiotic stress tolerance.
Exploitation Route My manipulating SP1, we believe it will be possible to modify diverse aspects of chloroplast function, enabling novel crop improvement strategies; for example, improving the tolerance of crop plants to abiotic stress, or altering fruit ripening and fruit post-harvest properties.
Sectors Agriculture, Food and Drink,Environment
URL https://www.oxfordsparks.ox.ac.uk/content/hardy-crops-tackle-food-insecurity
 
Description The findings from this award have been used to support a US patent application on the potential applications of SP1 in novel crop improvement strategies. In addition to furthering our understanding of how the SP1 technology may be utilized, the new data will facilitate attempts to commercialize the technology, for example through licensing agreements.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Societal
 
Description BBSRC Follow-On Funding Pathfinder: "Manipulation of the chloroplast-associated protein degradation pathway (CHLORAD) - applications in plant breeding and biotechnology" (Jan - Jul 2019)
Amount £10,897 (GBP)
Funding ID BB/S013873/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 07/2019
 
Description China Scholarship Council (CSC) / British Council "China-British Joint Research Innovation Fund" scholarship to Ms Yuan Zhou (Jun 2018 - Jun 2019)
Amount £15,400 (GBP)
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2018 
End 06/2019
 
Description Developing CHLORAD as a technology for crop improvement using wheat as a model
Amount £50,000 (GBP)
Funding ID BB/S50676X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2020 
End 05/2021
 
Description Improving yields and stress tolerance in wheat by using CHLORAD as a technology
Amount £561,563 (GBP)
Funding ID BB/W017741/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2023 
End 12/2024
 
Description Manipulating CHLORAD in wheat: Altering expression of the plastid retrotranslocon SP2 in order to develop novel crop improvement strategies [OEX/RNAi]
Amount £1 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2019 
End 11/2020
 
Description Dr Enrique Lopez-Juez, Royal Holloway, University of London 
Organisation Royal Holloway, University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration on the import characteristics of newly identified mutant affecting the TIC machinery of chloroplasts
Collaborator Contribution Identification of the gene affected by the mutation
Impact Identification and characterization of a significant new mutant affecting the TIC machinery of chloroplasts; manuscript in preparation
Start Year 2012
 
Description Dr Gail Preston, Department of Plant Sciences, University of Oxford 
Organisation University of Oxford
Department Department of Experimental Psychology
Country United Kingdom 
Sector Academic/University 
PI Contribution We are collaborating on the role of SP1 in biotic stress responses in Arabidopsis and brassica, via a PhD studentship
Collaborator Contribution Expertise in plant pathology
Impact The project is on-going.
Start Year 2015
 
Description Dr Masanori Izumi 
Organisation Tohoku University
Department Graduate School of Life Sciences
Country Japan 
Sector Academic/University 
PI Contribution We are collaborating on the role of ubiquitination in chloroplast degradation by autophagy. Dr Izumi visited the group in Oxford for four months in 2015 on a Japanese government fellowship.
Collaborator Contribution Expertise in autophagy.
Impact The work is on-going.
Start Year 2015
 
Description Dr Mats Töpel, Department of Marine Sciences, University of Gothenburg, Sweden 
Organisation University of Gothenburg
Department Department of Marine Sciences
Country Sweden 
Sector Academic/University 
PI Contribution We have collaborated on the phylogenetic analysis of STIC2-related proteins, and other chloroplast proteins, as well as on the analysis of whole genome sequence data.
Collaborator Contribution Advanced expertise in bioinformatics and phylogenetic analysis.
Impact Ling, Q., Broad, W., Trösch, R., Töpel, M., Demiral Sert, T., Lymperopoulos, P., Baldwin, A. and Jarvis, R.P. (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science 363: eaav4467. Bédard, J., Trösch, R., Wu, F., Ling, Q., Flores-Pérez, Ú., Töpel, M., Nawaz, F. and Jarvis P. (2017) Suppressors of the chloroplast protein import mutant tic40 reveal a genetic link between protein import and thylakoid biogenesis. Plant Cell 29: 1726-1747. Trösch, R., Töpel, M., Flores-Pérez, Ú. and Jarvis, P. (2015) Genetic and physical interaction studies reveal functional similarities between ALBINO3 and ALBINO4 in Arabidopsis. Plant Physiol. 169: 1292-1306.
Start Year 2015
 
Description Dr Qihua Ling, Shanghai Institute of Plant Physiology and Ecology (SIPPE), China 
Organisation Chinese Academy of Sciences
Department Shanghai Institute of Plant Physiology and Ecology
Country China 
Sector Academic/University 
PI Contribution We are continuing our work together on the further characterization of the CHLORAD pathway, following the establishment of Dr Ling's own group in China.
Collaborator Contribution We are collaborating on the further characterization of the CHLORAD pathway.
Impact We are collaborating on the further characterization of the CHLORAD pathway. Outputs are expected to appear soon.
Start Year 2020
 
Description Prof. Matthew Terry, University of Southampton 
Organisation University of Southampton
Country United Kingdom 
Sector Academic/University 
PI Contribution We are providing expertise in the area of chloroplast protein import, as well as seeds of relevant mutant genotypes. We will be conducting analyses of the levels of components of the protein import machinery in a new mutant identified by our collaborators that displays defective plastid signalling.
Collaborator Contribution Our collaborators are supplying the new plastid signalling mutant to us, and are conducting detailed analyses on the mutant seed lines that we are providing.
Impact This collaboration is on-going and so has not yet generated any outputs.
Start Year 2016
 
Description Prof. Ralf Bock, Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany 
Organisation Max Planck Society
Department Max Planck Institute of Molecular Plant Physiology
Country Germany 
Sector Charity/Non Profit 
PI Contribution We are providing expertise in the area of chloroplast protein import in order to understand the role of a plastid signalling mutant. We hosted a visiting postdoctoral researcher from Germany in order that skills in this area may be transferred to our collaborators.
Collaborator Contribution Our collaborators provided the initial observations and the mutant genotypes of interest, and are completing the analyses in readiness for publication.
Impact The collaboration is on-going and so has not yet generated any outputs.
Start Year 2015
 
Description Professor Felix Kessler, University of Neuchâtel, Switzerland 
Organisation University of Neuchatel
Country Switzerland 
Sector Academic/University 
PI Contribution A collaboration was established to share knowledge and optimize methods for the native purification of chloroplast translocon complexes using the tandem affinity purification (TAP) technique. As part of this collaboration, a researcher visited the Kessler laboratory for 10 days in 2010 (18th-29th January, 2010). Since then, the collaboration has continued to evolve and take new directions, for example related to the involvement of post-translation modification in the regulation of chloroplast protein import. As a result of the collaboration, Professor was invited visit our department in Oxford on 22 November 2018, and to give a seminar here.
Collaborator Contribution A collaboration was established to share knowledge and optimize methods for the native purification of chloroplast translocon complexes using the tandem affinity purification (TAP) technique. As part of this collaboration, a researcher visited the Kessler laboratory for 10 days in 2010 (18th-29th January, 2010). Since then, the collaboration has continued to evolve and take new directions, for example related to the involvement of post-translation modification in the regulation of chloroplast protein import. As a result of the collaboration, Professor was invited visit our department in Oxford on 22 November 2018, and to give a seminar here.
Impact Jarvis, P. and Kessler, F. (2014) Mechanisms of chloroplast protein import in plants. In: Advances in Plant Biology: Plastid Biology (S.M. Theg and F.-A. Wollman, eds.) Springer, New York, pp. 241-270. Aronsson, H., Combe, J., Patel, R., Agne, B., Martin, M., Kessler, F. and Jarvis, P. (2010) Nucleotide binding and dimerization at the chloroplast pre-protein import receptor, atToc33, are not essential in vivo but do increase import efficiency. Plant J. 63: 297-311.
Start Year 2010
 
Title CONTROL OF PLASTID ASSOCIATED PROTEIN DEGRADATION 
Description The patent application covers the possibility of manipulating CHLORAD to modify diverse aspects of chloroplast function, enabling novel crop improvement strategies; for example, improving the tolerance of crop plants to abiotic stress. 
IP Reference GB1815206.6 
Protection Patent application published
Year Protection Granted 2018
Licensed No
Impact Too early for impact to be assessed.
 
Title CONTROL OF PLASTID ASSOCIATED PROTEIN DEGRADATION I 
Description The patent application covers the possibility of manipulating SP2 and CHLORAD to modify diverse aspects of chloroplast function, enabling novel crop improvement strategies; for example, improving the tolerance of crop plants to abiotic stress. 
IP Reference GB1803833.1 
Protection Patent application published
Year Protection Granted 2018
Licensed No
Impact Too early for impact to be assessed.
 
Title CONTROL OF PLASTID ASSOCIATED PROTEIN DEGRADATION II 
Description The patent application covers the possibility of manipulating PUX10 (CDC48) and CHLORAD to modify diverse aspects of chloroplast function, enabling novel crop improvement strategies; for example, improving the tolerance of crop plants to abiotic stress. 
IP Reference GB1803834.9 
Protection Patent application published
Year Protection Granted 2018
Licensed No
Impact Too early for impact to be assessed.
 
Title Deconvolution software for interpretation of gene sequence data from new CRISPR/Cas9 mutants 
Description We required the deconvolution of Sanger sequencing data to determine if the CRISPR-Cas9 induced mutations of genes of interest were true knockouts (as opposed to non-frameshifting point mutations). To achieve this we wrote a deconvolution program in Python programming language. This software enabled characterization of the heteroallelic CRISPR mutations without the necessity of cloning PCR products of the gene into bacteria (the time-consuming conventional method). It is in the process of being 
Type Of Technology Software 
Year Produced 2019 
Impact Too early to assess. 
 
Description Animation illustrating our new discovery of the CHLORAD pathway, and how it may be manipulated to improve crop performance 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact In conjunction with Oxford Sparks (https://www.oxfordsparks.ox.ac.uk/), we prepared an animation illustrating our new discovery of the CHLORAD pathway, and illustrating in simple terms how it may be manipulated to improve crop performance.
Year(s) Of Engagement Activity 2020
URL https://www.oxfordsparks.ox.ac.uk/content/changing-plant-chloroplasts-improve-crop-performance
 
Description Established a group Twitter account 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A Twitter account (Jarvis Lab, @PaulJarvisLab) for reporting the activities of the group was established in January 2019. We use this to disseminate our research to the general public and a range of different audiences, and to connect with other groups with similar interests in plant biology. During the first two months we had 38 tweets and accumulated 184 followers.
Year(s) Of Engagement Activity 2019
URL https://twitter.com/PaulJarvisLab
 
Description Participation in Fascination of Plant Day (May 2019) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Our group will participate in the Fascination of Plants Day on 11 May 2019. In particular, together with the University of Oxford Botanic Garden, we are preparing an outreach activity explaining the problem of salinity and land degradation. We will have a stand at the "Westgate Oxford" shopping centre on the day.
Year(s) Of Engagement Activity 2019
URL https://epsoweb.org/all-events/fascination-of-plants-day-2019/