The novel gene 'Histone Deacetylase Complex 1' enhances plant growth and abiotic stress tolerance; where, when and with whom?

Lead Research Organisation: University of Glasgow
Department Name: College of Medical, Veterinary &Life Sci

Abstract

Climate change and a growing world population are expected to lead to water scarcity and food shortage in the near future. There is an urgent need to increase yield, water usage efficiency and stress tolerance of food crops. We propose to achieve this through controlled manipulation of plant sensitivity to the 'stress' hormone abscisic acid (ABA). The project builds on our recent discovery of a novel gene from Arabidopsis thaliana, which we called 'Histone de-acetylation complex 1' (HDC1). We found that over-expression of HDC1 led to decreased ABA-sensitivity of germinating seeds and to enhanced growth of mature plants, while deletion of HDC1 had the opposite effects. Thus HDC1 can be used as an adjustable 'hormostat'. This property makes HDC1 an attractive target for crop improvement. For example, in a drought-prone rain-fed field increasing ABA-sensitivity will aid plant recovery after dehydration whereas in an irrigated field decreasing ABA-sensitivity could be a means to sustain biomass production with reduced water input. The question is then; how does HDC1 change ABA-sensitivity? Ancestral precursors of HDC1 in yeast are members of large multi-protein complexes that biochemically modify (de-acetylate) histone proteins that are associated with DNA (chromatin). Histone de-acetylation (HD) determines the overall structure of the DNA which in turn exerts a hyper-level of control over gene activity. Our current hypothesis is that HDC1 'titrates' the stability of a chromatin complex thereby modifying accessibility of the DNA to ABA-dependent regulators and hence ABA-sensitivity. This is an exciting concept because it means that via HDC1 one could gain control over a whole suite of stress responses without the need to tinker with the underlying complex signalling network. However, to exploit the opportunities presented by HDC1 for crop improvement we need to understand exactly how HDC1 operates at the molecular level. For example, the composition of HD complexes and the precise functions of proteins therein are completely unknown in plants.

The aim of this project is to investigate the molecular function of HDC1 in the model plant Arabidopsis. This research will run in parallel to a crop development programme carried out by the Industrial Partner. Reciprocal information flow between the two research programmes will ensure that fundamental discoveries made in the model species can immediately be translated into crop improvement. The work programme has three parts. In the first work package we will use an antibody against HDC1 to identify 'by association' other members of the HDC1-complex in plant protein extracts. We will obtain mutant lines for some of the identified associates and cross them with the HDC1mutant lines. This work will lead to a first understanding of HD complexes in plants, and to the identification of proteins that limit or enhance HDC1 function within the complex. The second work package addresses the question whether HDC1 itself is regulated and how. In particular, we will investigate whether HDC1 is a target for 'hijacking' of the ABA pathways by other hormones ('cross talk') or by pathogens. For this purpose we will measure HDC1 protein levels in plant extracts treated with hormones and pathogen elicitors. In the third work package we will investigate which genes cause the effects of HDC1 on seed germination and growth - the 'targets' of HDC1. In the first instance we will identify all genes that are differentially expressed in wildtype and HDC1 mutant plants using gene chips. To identify the DNA regions that are directly targeted by HDc1 we will pull-down HDC1-associated chromatin with the HDC1-antibody. Finally, we will measure acetylation levels of the chromatin with antibodies that recognize acetylated histone tails. The combined outcomes from this work will greatly enhance our understanding of gene regulation in plants and directly contribute to improving yield and water usage efficiency in crops.

Technical Summary

The proposed project is based on our recent discovery of 'Histone de-acetylation complex 1' (HDC1), a novel gene from Arabidopsis thaliana. We found that over-expression of HDC1 led to hyposensitivity of germinating seeds to the 'stress' hormone ABA and to enhanced growth of mature plants, while HDC1 knockout had the opposite effects. Ancestral precursors of HDC1 in yeast are members of multi-protein histone de-acetylation (HD) complexes. Our working hypothesis is that HDC1 'titrates' the stability of a HD complex thereby modifying accessibility of the DNA to ABA-dependent transcriptional regulators and hence ABA-sensitivity. This is an exciting concept because it means that through HDC1 one could gain control over a whole suite of stress responses while maintaining the integrity of the underlying complex signalling network. However, to exploit the opportunities presented by HDC1 as an adjustable 'hormostat' we need to understand the composition of HD complexes and individual protein functions therein, both of which are completely unknown in plants. The proposed work programme will answer three questions: Does HDC1 form a multi-protein HD complex and what are the partners? Is HDC1 regulated, and how? Does HDC1 regulate other genes, and which ones? In the first work package, using pull-downs, Y2H, BiFC and molecular genetics, we will identify proteins that interact with HDC1 and characterize their functional inter-dependence. In the second work package, employing Western blots and mutants that inhibit or promote specific post-translational modifications, we will explore HDC1-regulation and its role for cross-talk between different hormonal pathways. In the third work package we will identify HDC1 target genes through microarray analysis and ChIP-Sequencing. The outcomes from this project can be expected to cause a gearshift in the way we think about endogenous and biotechnological manipulation of hormone pathways.

Planned Impact

A growing world population combined with unstable climate puts an urgent demand on plant scientists to apply their expertise to avert a pending food crisis. This issue is compounded by the threat of worldwide freshwater scarcity. Many communities worldwide already suffer from inadequate water supply for consumption, hygiene and irrigation. Southern parts of England regularly experience water shortages. UK government and RCUK have recognized the urgency of these problems and have made food and water security priority areas for research. The proposed project directly supports food and water security.
Agriculture accounts for 70 percent of all water withdrawn from "blue water" sources. Any achievements in increasing food production must therefore be measured by the amount of water needed ('crop per drop'). Crop improvement programmes are faced with the dilemma that drought tolerance in plants usually comes at the cost of reduced growth rates due to endogenous hormonal signals that tell the plant to shift from vegetative growth towards protective mechanisms which carry a growth penalty. Recent work in the PI's laboratory has shown that over-expression of a novel gene (HDC1) in the model plant A. thaliana decreases plant sensitivity to the 'stress' hormone ABA and enhances plant growth. These results are of great interest to farmers and agri-food companies as they may provide us with a handle to titrate ABA sensitivity (in the context of intrinsic yield increase or yield preservation) and thus to achieve better growth with less water.
The potential of HDC1 for improving growth and water efficiency in crops has been recognized by Bayer CropScience and their substantial financial support for this grant is evidence of the high potential impact of the proposed project. The Bayer team has already carried out independent phenotypic tests with HDC1-lines from the PI's lab and a common patent application (led by University of Glasgow) is pending. Bayer will embark on a crop focussed research programme which will progress in parallel to the fundamental research programme proposed here. Maximal impact is therefore guaranteed since both research programmes will inform and add value to each other. For instance, the enhancement or inhibition of HDC1-activity by molecular HDC1-interactors, discovered in A. thaliana, can immediately be used to fine-tune the approaches taken in the crop lines generated by Bayer. In turn, new phenotypic or molecular data generated from the crop lines may provide novel information on fundamental mechanisms to be explored in A. thaliana. Considering both the long timelines 'from gene to product' and the difficulties to translate findings from model plants to crops, early engagement of fundamental research with commercial crop research programmes, as proposed here, is crucial if we want to maximize the probability of success and avert a pending food and water crisis.
The proposed project provides ample opportunities for additional gene discovery, especially among newly identified HDC1 target genes, which may encode plant growth regulators and tolerance factors. The project therefore has a strong potential for additional commercialisation opportunities, which will be aided by close interaction with the industrial partner. In case, Bayer does not exercise its option for these opportunities (e.g. outside of its crop or trait focus) then the university will be able to explore these with other agri-food companies.
Research into epigenetic regulation of gene expression has gained enormous momentum over the last decade due to its fundamental importance for understanding development and adaptation to the environment not just in plants but in all organisms. The proposed project will explore the molecular properties of multi-protein complexes involved in epigenetic regulation and the results are expected to make important contributions to academic advancement in the life sciences.
 
Description We have discovered a protein (HDC1) in the model plant Arabidopsis thaliana which controls plant growth and development.

We have shown that over-expression or knock-out of HDC1 alters biochemical modifications of the histone proteins associated with DNA (chromatin). We have shown that over-expression or knock-out of HDC1 alters the expression levels of many genes that function in the regulation of plant growth and development. We have shown that HDC1 increases leaf size and biomass not only in well-watered but also in water-limited conditions. We also found that HDC1 determines the sensitivity of germinating seeds to the water-stress hormone ABA.

We have identified other proteins in the cell nucleus that can physically interact with HDC1; these include histone modifying enzymes such as histone deacetylases and proteins that bind to the histone 3 in the core nucleosome. We discovered that HDC1 can also directly bind to the linker histone 1 (H1). This finding is exciting because it indicates that HDC1 functions at the interface between core nucleosome and linker DNA. We did not find direct HDC1 interaction with repressor proteins or co-repressors.

We truncated the full-length HDC1 protein to a shorter protein that is similar to ancestral Rxt3-like proteins in algae and fungi. We found that the extended N-terminal part of the plant proteins is required for most interactions with other proteins. However, the truncated protein was still able to fully maintain binding to at least one histone 3-binding protein and to histone 1. The truncated protein was also able to restore growth and ABA-sensitivity in the knockout mutants while other developmental phenotypes were not restored. The findings suggest that sequence extension during evolution from algae to plants was necessary to broaden the spectrum of protein interactions and of developmental phenotypes.

Our current working model positions HDC1 at the histone-binding end of histone-deacetylation complexes where it acts as a 'flexible glue' that enhances the stability of the multi-protein complex.

The results listed above have been published in Plant Cell and Plant Physiology, the two top journals of plant science. Additional data obtained from experimental research into the regulation of HDC1 and its down-stream targets are currently being analysed.
Exploitation Route The fundamental knowledge gained from this grant has already been translated into crops by our industrial partner. There is also considerable interest from the academic community. Several other groups have now started to investigate genetic and physical interactions of their 'pet' genes or proteins with HDC1. Our work has therefore triggered enhanced research into the composition and function of multi-protein complexes in the chromatin of plants. Both commercial and academic impact can be expected from this activity.
Sectors Agriculture, Food and Drink

 
Description BBSRC CIRC steering committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Marie Curie Fellowship (IEF)
Amount £176,962 (GBP)
Funding ID 627658 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 08/2014 
End 07/2016
 
Description Industrial Partner 1 
Organisation Bayer
Department Bayer CropScience Ltd
Country United Kingdom 
Sector Private 
PI Contribution Experimental work on BBSRC IPA. Discovery and characterisation of gene function.
Collaborator Contribution Expression in wheat. Glasshouse and field trials.
Impact 1. Patent: WO2014118123-A1 ; CA2899274-A1 ; AU2014211570-A1 ; CN104955947-A ; EP2951298-A1 ; US2015376637-A1 2. License agreement 3. Co-authored publications: Perrella, G et al. (2013) Plant Cell 25: 3491-3505; Perrella, G et al. (2016) Plant Physiol. pp.01760.2015
Start Year 2012
 
Title Increasing tolerance of a plant, plant part, plant organ or plant cell to stress conditions, or accelerating flowering time of a plant, comprises increasing expression and/or activity of histone deacetylase complex 1 (HDC1) protein 
Description Overexpression of the gene HDC1 enhances plant growth. 
IP Reference WO2014118123 
Protection Patent application published
Year Protection Granted 2013
Licensed Yes
Impact Knowledge transfer from academia to industry. Translation of fundamental research in model species (Arabidopsis) to crops (wheat). Field trials with wheat lines are underway.
 
Description "Meet the Expert" at the Glasgow Science Centre 
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 Members of the Amtmann lab set up a display that demonstrated the importance of light for growth of both plants and cyanobacteria. Children built phycobilisomes, the light-harvesting complexes in cyanobacteria, using different coloured pigments. For the enthusiastic ones, we designed a take-home experiment comparing plant growth in the light versus the dark.
Year(s) Of Engagement Activity 2010,2016
URL http://www.glasgowsciencecentre.org/support-us/meet-the-expert.html
 
Description Audio description of HDC1 paper on the GARNet community blog page 'Weeding the Gems'. 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Audio description of HDC1 paper on the GARNet community blog page 'Weeding the Gems'. http://blog.garnetcommunity.org.uk/audio-paper-descriptions/
Year(s) Of Engagement Activity 2016
URL http://blog.garnetcommunity.org.uk/audio-paper-descriptions/
 
Description EMBO practical course on Phenotyping 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Anna Amtmann was a tutor at the EMBO practical course 'Insights into plant biological processes through phenotyping' in Ghent, Belgium. This included a practical computer workshop on using EZ-Rhizo software for the analysis of root architecture.
Year(s) Of Engagement Activity 2015
URL http://events.embo.org/15-plant-phenotyping/
 
Description Editor of Focus Issue 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was invited editor for a focus issue on Chromatin and Epigenetics published by Plant Physiology (August Issue 2015). The focus issues contain a number of review articles alongside original papers and they are an important means to engage and update general and specialised audiences in/on a specific topic of science.
Year(s) Of Engagement Activity 2015
 
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 Schools
Results and Impact Giorgio Perrella and other lab members orgnaised activities for school children in Glasgow Botanic Gardens and Glasgow Science Museum to celebrate the International Fascination of Plants Days. Activities consisted in learning how to isolate DNA and pigments from plants.
Year(s) Of Engagement Activity 2013,2015
URL http://www.plantday12.eu/home.htm
 
Description Frontier Agriculture workshops 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Anna Amtmann was invited tutor at workshops for agronomists organised by Frontier Agriculture Ltd., UK's largest grain marketing business.
Year(s) Of Engagement Activity 2014
 
Description Glasgow Botanic Gardens 200th anniversary 
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 Displays of plant science research carried out at University of Glasgow in the main glasshouse (Kibble Palace) of the Glasgow Botanc Gardens as part of the 200th Anniversary celebratios. Our stalls offered a range of displays and hands-on activities related to our research in plant science as well as instructive games for children.
Year(s) Of Engagement Activity 2017
URL https://www.ugplantsci.org/gallery
 
Description International PhD summer school Utrecht, NL, tutor 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Anna Amtmann was a tutor at the International PhD Summer School on 'Environmental Signaling in Plants' in Utrecht, Netherlands, in 2015.
Year(s) Of Engagement Activity 2015
URL http://web.science.uu.nl/eps/
 
Description Invited presetentation at science conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited speaker at 2nd Workshop on Plant Development & Drought Stress, Pacific Grove, CA, USA. Organised by Carnegie Institute and American Society of Plant Biology (ASPB).
Year(s) Of Engagement Activity 2017
URL https://ww2.eventrebels.com/er/EventHomePage/CustomPage.jsp?ActivityID=21616&ItemID=77745
 
Description Knowledge Exchange and Impact seminars 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Anna Amtmann is a regular speaker at KE/ Impact events organised b y Glasgow University, e.g. KE lunchtime seminar series, MVLS College Open Days, Industry Engagement workshops. She talks about pathways to commercialisation, e.g. achieving a license agreement. These activities are directly linked to the BBSRC IPA.
Year(s) Of Engagement Activity 2013,2014,2015
 
Description Plant Science cartoons 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We produced a booklet featuring research topics in the Glasgow Plant Science Group in the form of cartoons. The booklet was (and is) distributed among visitors of the 200th anniversary celebrations of Glasgow Botanic Gardens and other public events.
Year(s) Of Engagement Activity 2017
URL https://docs.wixstatic.com/ugd/8cabfa_bcc30b9859b347e294d6ffe6c924205b.pdf
 
Description Steering Board Scottish Synthetic BIology Group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Anna Amtmann has joined the steering board of thiis group consisting of representatives from Industry, Scottish Governement and Academia. The aim is to develop measures to increase the use of Synthetic Biology In Industry. Meetings are being held every 3-4 months.
Year(s) Of Engagement Activity 2017