Ligand-receptor-like kinase signalling in Arabidopsis root development

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

Abstract

Food security represents a major global issue, and it was put forward by the crop scientist Jonathan Lynch that a 'second green revolution' should be a priority. This should focus on root architecture, since root branching critically influences nutrient and water uptake efficiency. However, root architecture has not been a trait selected for by plant breeders in major cereal crops. In addition, in multicellular organisms, cell-cell communication plays a crucial role in patterning, growth and interaction with the environment. For example, a tight control of formative cell divisions - which are mainly asymmetric (stem) cell divisions - to produce tissues and organs and to prevent over-proliferation is crucial for the postembryonic growth and development of plants. This control of formative cell divisions is not only critical in plants, but also in animals to prevent irregular divisions or cancers. We recently identified a protein, the membrane-associated receptor-like kinase ACR4, which is crucial in the control of root architecture and which is a key regulator of formative cell divisions in the root of the model plant Arabidopsis thaliana. ACR4 has originally been described in maize for its role in other processes, and provides an obvious starting point for the detailed analysis of the role of receptor-like kinase signaling pathways in root architecture and in registering and conveying positional information. This research proposal aims to further characterize this ligand/receptor signaling mechanism that can integrate mobile signaling molecules to control formative cell divisions during organogenesis and, as such, provides an excellent tool to study short range, cell-cell communication during growth and development. First, we will identify those transcriptional changes that affect cell identity in the main and lateral root downstream of a ligand-driven cue from neighbouring cells. These data will provide us with a large number of transcriptional markers for other experiments. Second, unequivocal identification of the ligand is crucial to fully understand receptor-like kinase-mediated signaling pathways. One important aspect is how ligand-dependent directional cues from surrounding cells modulate receptor-like kinase signaling. We will identify and localize ligands for the ACR4 receptor-like kinase. Third, the three dimensional structure of eukaryotic membrane proteins has only been determined very limitedly. We will determine the folding and structure of purified receptor domain protein and use that for detailed analyses. Fourth, temporary and reversible phosphorylation of proteins is one of the most important post-translational modifications with a regulatory function, such as the control of transcriptional changes. Therefore, we will identify the substrates of ACR4 during main and lateral root development. Sixth, with the knowledge that we will gain on ligand-receptor-like kinase signaling and what is known about hormone signaling and transcriptional networks in the same processes, we will build a comprehensive model.

Technical Summary

The past decade researchers have mainly focused on the analyses of phytohormone gradients and mobile transcription factors to explain patterning. Especially in the root, model processes, such as the root meristem and lateral root initiation are fairly well understood on the level of transcriptional changes and hormonal control, but very little attention has been given to an alternative way of cell-cell communication using ligand-receptor-like kinase systems. Lately more of these receptor-like kinases and potential ligands have been described in root meristem maintenance and patterning, making it a perfect moment to start investigating how these receptor-like kinases and their respective ligands control the same and different developmental processes and what their common and independent targets are. In brief, in this project, I will use different and interdisciplinary strategies, based on state of the art transcriptomics, chemical genomics, proteomics, interactomics, associomics and more in depth analysis on the single gene/protein/ligand level to put forward a model describing ligand/receptor-mediated cell-cell communication during formative cell divisions, and, more specifically, to identify key components in the ACR4-dependent signalling cascade. The aspects this project plans to address have been rarely covered focusing on one receptor-like kinase, and will allow elucidating the mechanisms and structural aspects behind one crucial signalling pathway, such as: 1. Identification of downstream transcriptional changes, to clarify if signalling pathways across developmental processes are conserved. 2. Identification of substrates involved in development on a genome-wide scale, which - to our knowledge - has only been done for BRI1. 3. Identification and physical interaction of ligands with their receptor, for which only a small number have been demonstrated.

Planned Impact

With this project we will elucidate the modes of action of ligand-receptor-like kinase signalling in roots. Next to other control mechanisms, these signalling pathways are important for understanding root architecture. This ambitious project demands skills in Arabidopsis molecular genetics, plant molecular cell biology, proteomics, and I have gained invaluable experience of a systems approach whilst working at the Department of Plant Systems Biology (Gent, Belgium). The multidisciplinary expertise, resources and tools that have been assembled for this project uniquely position us to create, test and validate the role of ligand-receptor-like kinase signalling in root development. The knowledge gained from this study in the model system Arabidopsis thaliana will help scientists understand this basic signalling mechanism and how best to manipulate root growth and enhance crop yield. These outputs provide practical solutions for improving crop performance and deliver food security, a strategic priority area supported by the BBSRC. The project will also generate a number of new and innovative experimental tools and data resources. Furthermore, the results will be integrated in the available models for root development. All these aspects of the research project would be of interest to a wide spectrum of researchers from other disciplines. In this respect, I will also attempt to create new links by participating in workshops to provide training or information dissemination, and by attending international meetings. Currently, an ongoing collaboration with Dr. Remco Sprangers (Max Planck for Developmental Biology, Tübingen, Germany) will lead to the purification and 3D analysis of the receptor domain. But also within the Centre for Plant Integrative Biology (CPIB), a BBSRC/EPSRC Centre for Integrative Systems Biology, and the University of Nottingham, this interdisciplinary project can benefit from the available tools and technology. For example, the proteomics faciity headed by Dr. Susan Lidell (University of Nottingham) will be assisting in the phosphoproteomics part of the project. I will disseminate results at scientific conferences, and through published journal articles. The institute routinely prepares press releases for high profile papers and I also regularly publish articles in review journals. Finally, I will regularly make public presentations about topical issues such as GMO's to increase public awareness, but also provide the public with a balanced view on the pros and cons of GMO's.

Publications

10 25 50
 
Description Using various approaches we uncovered the involvement and role of key factors in mediating root architecture. For some of these, we identified the mode-of-action.
Exploitation Route Some leads discovered in Arabidopsis can be tested in crops. In some cases, such as for CLE26, we did test the impact on e.g. wheat and tomato.
Sectors Agriculture, Food and Drink

 
Description Collaboration with A. G. Rao 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution - joint publication
Collaborator Contribution - in vitro biochemistry data for joint publication
Impact Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1447-52. doi: 10.1073/pnas.1525122113. PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I.
Start Year 2012
 
Description 3 minute thesis - Stephanie Smith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact '3 minute thesis' competition - Stephanie Smith won 3rd prize for the Nottingham Heat - was uploaded to YouTube as well
Year(s) Of Engagement Activity 2013
 
Description EOS interview - Ive De Smet 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact I was interviewed for a popular scientific magazine (EOS)
Year(s) Of Engagement Activity 2012
 
Description European Researcher's night - Priya Ramakrishna 
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 European Researcher's night at the Wollaton Park organised by Nottingham City Council; (Science fair) Science demonstration to students of secondary school level and above to encourage them to take up careers in STEM
Year(s) Of Engagement Activity 2014
 
Description PubhD - Stephanie Smith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A 10 minute talk to non-specialist audiences on the topic of the PhD of Stephanie Smith
Year(s) Of Engagement Activity 2014
 
Description Research Showcase 2014 - Priya Ramakrishna 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Open community event for people to come hear about the research taking place at the university and question them about what it means for society. Research communicated via posters presentation.
Year(s) Of Engagement Activity 2014
 
Description SET for Britain - Priya Ramakrishna 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Portcullis House, House of Commons, London, UK; A poster competition that involves presenting your research to a range of politicians and a panel of expert judges
Year(s) Of Engagement Activity 2015
 
Description Science @ Sutton Bonington - Stephanie Smith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Plant Science talk: 'Science @ Sutton Bonington' - General event for the public
Year(s) Of Engagement Activity 2014
 
Description Science @ Sutton Bonington - Stephanie Smith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 'Scary Plants' talk: 'Science @ Sutton Bonington' - General event for the public,
Year(s) Of Engagement Activity 2012
 
Description Science visit - Ive De Smet 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I participated in a guided visit of Brownies to University Science labs
Year(s) Of Engagement Activity 2012
 
Description Set For Britain - Ive De Smet 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact I presented my work at the House of Commons
Year(s) Of Engagement Activity 2012
 
Description What is it like to research plant science? - Stephanie Smith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact talk at 3rd Summer School in Plants & Crops Sutton Bonington - Summer school for 16-18 year olds
Year(s) Of Engagement Activity 2014