iSAM: Integrative Systems Analysis of the Shoot Apical Meristem

Lead Research Organisation: Cardiff University
Department Name: School of Biosciences

Abstract

Morphogenesis is the process by which organisms are built up from cells during development. Living organisms and their component organs have defined and recognisable shapes and forms, and this requires the coordinated actions of many cells. However, despite extensive focus on the cellular components, we still do not understand how such complex structures and patterns are produced. The goal of this project is to understand the morphogenetic events leading to growth and organ production in the shoot apical meristem (SAM) of higher plants, in an iterative process of analysis, model building, biological testing and refinement. The SAM is a population of dividing, undifferentiated cells that generates the leaves and other organs of plants in highly ordered patterns at shoot tips throughout the life of the plant. The SAM is a complex self-maintaining and stable structure, housing at its centre a population of stem cells and initiating organs on its periphery. The SAM produces the cells that comprise all aboveground plant tissues, and defines the number, type and position of lateral organs. SAMs are thus the basis of plant architecture and determinants of major agronomic traits. In view of its importance, the SAM has been extensively studied and a wealth of information is available concerning its molecular and cellular components. Nevertheless, we do not understand how these components assemble into the multicellular structures that have specific shapes and growth dynamics. It is this question we wish to address. We will do this through building multi-level computer models of SAM function, based on biological observation of living SAMs and measurements of key parameters, including responses to plant hormones that both define the growth and division of individual cells and coordinate the overall behaviour of the SAM structure. The outcome of the project will be a greatly increased understanding of the cellular basis of morphogenesis in the important SAM system. It will generate many relevant new data that will be organised in a database. This will underpin the first complete spatialised cellular model of SAM growth in the form of a growing virtual tissue, in which cells mechanically interact and respond according to a small network programme determining responses based on quantitative data. This model will be used for predictive experimentation allowing specific questions regarding the maintenance, organogenesis and morphogenesis of the SAM system to be addressed. This proposal links four leading research teams in UK, France and Finland, with a previous track record of several relevant joint collaborations, and bringing synergistic expertise and technologies in imaging, modelling, plant hormones and cell division to address this important systems problem.

Technical Summary

The shoot apical meristem (SAM) of higher plants is a typical example of a complex system, where individual entities, the cells, interact by exchanging signals. It is the overall structure of the interaction network that feeds back on the 'machineries' of individual cells, thereby controlling local growth through the modulation of proliferation rates. Added up, the local cell proliferation rates, patterned by the signalling networks, lead to specific shape changes, which are the emergent properties of the system. To understand the SAM, we will use a complex systems approach. We will focus on the interaction networks, concentrating on two established essential signals, the plant hormones auxin and cytokinin. These integrate stem cell maintenance, organ initiation and meristem organisation through their effects on the component cells. We will provide a detailed spatial description, or map, of these signalling components in the SAM and a quantified link between these signals and cell proliferation rates in different parts of the meristem, based on novel image collection and analysis techniques already developed by the partners that allow data to be captured for the whole SAM structure. These detailed, multidimensional data will be integrated in a specially designed database and then serve as direct input into new predictive mathematical models for morphogenesis and gene regulation that will then be further tested through rounds of experimental perturbation and analysis. The required tools allowing domain-specific inducible gene targeting of hormone and cell regulators have already been developed by the partners, partly in previous collaborations. By iterating an experimental-theoretical loop, we will continuously refine our models toward a three-dimensional (3D) 'virtual shoot apex' with cellular resolution. This virtual shoot apex will integrate our descriptive data with a causal understanding based on our experimentally refined mechanical and regulatory model

Planned Impact

Plants grow and develop by producing new leaves or flowers (organs) at the shoot tip from a small dome of cells called the shoot apical meristem (SAM). The SAM is a complex self-maintaining structure that initiates these new organs on its periphery, and also maintains itself and a population of stem cells within it for the lifetime of the plant. The SAM is thus the source of all above-ground plant tissues. Since it defines the number, type and position of organs, it is the basis of plant architecture and a major determinant of agronomic productivity. The SAM is also responsible for developmental adaptation to the environment. As the ultimate origin of most harvested crops and indeed of all agricultural production, a fuller understanding of SAM function is essential to develop better adapted and higher yielding plant varieties. Although primarily aimed at increasing basic understanding, project outputs will provide key underpinning knowledge for companies interested in crop improvement and breeding, since rate of growth and organ production may limit crop productivity, particularly under stress conditions. Models of SAM function may improve predictability in engineering of plant growth and architecture, and the project could also produce new genetic methods to achieve this. A greater understanding of SAM initiation and development is also key to plant micro-propagation, an industry worth $15Bn globally, whose high costs limit broader application. In addition, global trade in ornamentals is worth $8Bn dollars, and UK hardy plant production about £750M, but macro-propagation of many ornamental perennials is slow. Since many important garden ornamentals are rather recalcitrant to micro-propagation, as are endangered species for which it may provide a route to survival, a greater understanding of hormonal circuits underpinning shoot function could lead to improved techniques and opportunities for this industry, and for species survival. A particular need in UK and Euopean industry and government is for trained personnel whose expertise and practical experience spans disciplinary boundaries, particularly the biological and more technical sciences such as computational analysis and modelling needed in systems approaches. This project will not only build expertise in the applicant's lab, but also provide excellent training in interdisciplinary working, helping to contribute to the highly skilled, flexible and interactive personnel needed for the goal of building the 'Knowledge Based BioEconomy' and its sustaining infrastructure. The applicant has a strong track record of engagement with industry, both in research and commercialisation. He currently has an Industrial CASE award and a fully funded studentship with Bayer CropScience, and in the past ten years has held 12 research grants involving commercial partners, 5 of which were fully industry funded and worth £1.25M. He has also held 5 CASE studentships, 3 with Bayer CropScience. The applicant has also been author of 11 commercially licensed patents, and established a successful spin-out company (Lumora Ltd) based on work arising from BBSRC funding and currently employing 7 R&D staff. He was Academic Director 2004-8 of the Master's in Bioscience Enterprise course jointly with the Judge Business School, Cambridge, involving regular contact with the biotech and funding community. He has personal contacts in most European multinational biotech companies, andnumerous smaller companies. The applicant is thus experienced and well placed to commercialise or publicise as appropriate the outcomes of the research. His lab is also actively involved in wider public engagement activities, including organising an exhibition and workshop exploring plant form and diversity by lab member Dr Walter Dewitte, and presentations to Members of Parliament. Cardiff University also has a strategic partnership with Wales Techniquest to promote science, technology, engineering and maths with young people.

Publications

10 25 50
 
Description Mean cell size at division is generally constant for specific conditions and cell types, but the mechanisms coupling cell growth and cell cycle control with cell size regulation are poorly understood in intact tissues. Here we show that the continuously dividing fields of cells within the shoot apical meristem of Arabidopsis show dynamic regulation of mean cell size dependent on developmental stage, genotype and environmental signals. We show cell size at division and cell cycle length is effectively predicted using a two-stage cell cycle model linking cell growth and two sequential cyclin dependent kinase (CDK) activities, and experimental results concur in showing that progression through both G1/S and G2/M is size dependent. This work shows that cell-autonomous co-ordination of cell growth and cell division previously observed in unicellular organisms also exists in intact plant tissues, and that cell size may be an emergent rather than directly determined property of cells.
Exploitation Route Has led to further funding from BBSRC.
Sectors Agriculture, Food and Drink

 
Description Cardiff School of Biosciences Departmental Post-Doctoral Seed Corn Fund
Amount £800 (GBP)
Organisation Cardiff University 
Sector Academic/University
Country United Kingdom
Start 07/2015 
End 07/2016
 
Description Cardiff Synthetic Biology Initiative Conference Travel Grant
Amount £590 (GBP)
Organisation Cardiff University 
Sector Academic/University
Country United Kingdom
Start 03/2015 
End 04/2015
 
Description Cardiff Synthetic Biology Initiative Project Grant
Amount £46,500 (GBP)
Organisation Cardiff University 
Sector Academic/University
Country United Kingdom
Start 07/2014 
End 07/2015
 
Description Size Matters: A systems approach to understanding cell size control in a developing multicellular tissue
Amount £421,568 (GBP)
Funding ID BB/S003584/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2019 
End 01/2022
 
Title S-G2-M Cell Cycle Reporter 
Description This is a novel reporter that can be used to follow the progression of the cell cycle in live developing tissues. We designed a new genetic construct and transformed this into wild type arabidopsis plants. We also crossed the reporter into mutant Arabidopsis plants. 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact These lines were crucial to the publication of our work and have been distributed to other research groups. 
 
Title Model of Cell Growth and Division 
Description This model simulates plant cell growth and division allowing different links between cell growth and division to be explored. Following publication of the project the model has been made freely available under a creative commons license. 
Type Of Material Computer model/algorithm 
Year Produced 2017 
Provided To Others? Yes  
Impact This model was a central part of a publication. It has also led to the development and submission of a futher interdisciplinary grant application. 
URL https://github.com/Angharad-Jones/CellCycleModel
 
Description ERA-NET Collaboration (ERA-SysBio+) 
Organisation French Institute for Research in Computer Science and Automation
Country France 
Sector Private 
PI Contribution Myself and my team (Angharad Jones, Manuel Forero-Vargas) contributed intellectual input, experimental data, analytical tools and a model of cell growth and division in the shoot apical meristem. Angharad Jones, an experienced post-doc, contributed expertise in live cell imaging and contributed to the establishment of methods that allowed time course data showing the growth and division of individual cells within the shoot apical meristem. Angharad also produced a novel fluorescent cell cycle reporter for use in plants and a model of cell growth and division which complements models produced by collaborators. Manuel Forero-Vargas developed image analysis methods that allowed rapid segmentation and extraction various parameters,that were used to generate important preliminary datasets. All team members contributed expertise and intellectual input to the overall project at regular project meetings, and Angharad and myself authored a review with partners ar ENS Lyon and INRIA. I provided acess to plant growth facilities and a dedicated confocal microscope, both of which were necessary for the generation of the experimental data.
Collaborator Contribution Jan Traas (ENS Lyon) provided expertise in live cell imaging of the shoot apical meristem. He hosted multiple visits by Angharad Jones for training and the joint development of techniques specific to the collection of datasets involving cell division. Jan Traas also provided expertise and intellectual input based on his substantial knowledge and experience in the biology of the shoot apical meristem. Christophe Godin (INRIA) provided access to image analysis software. Hosted visits by Manuel Forero-Vargas, and provided intellectual input regarding the development of modelling aspects of the project.
Impact v
Start Year 2010
 
Description ERA-NET Collaboration (ERA-SysBio+) 
Organisation University of Helsinki
Country Finland 
Sector Academic/University 
PI Contribution Myself and my team (Angharad Jones, Manuel Forero-Vargas) contributed intellectual input, experimental data, analytical tools and a model of cell growth and division in the shoot apical meristem. Angharad Jones, an experienced post-doc, contributed expertise in live cell imaging and contributed to the establishment of methods that allowed time course data showing the growth and division of individual cells within the shoot apical meristem. Angharad also produced a novel fluorescent cell cycle reporter for use in plants and a model of cell growth and division which complements models produced by collaborators. Manuel Forero-Vargas developed image analysis methods that allowed rapid segmentation and extraction various parameters,that were used to generate important preliminary datasets. All team members contributed expertise and intellectual input to the overall project at regular project meetings, and Angharad and myself authored a review with partners ar ENS Lyon and INRIA. I provided acess to plant growth facilities and a dedicated confocal microscope, both of which were necessary for the generation of the experimental data.
Collaborator Contribution Jan Traas (ENS Lyon) provided expertise in live cell imaging of the shoot apical meristem. He hosted multiple visits by Angharad Jones for training and the joint development of techniques specific to the collection of datasets involving cell division. Jan Traas also provided expertise and intellectual input based on his substantial knowledge and experience in the biology of the shoot apical meristem. Christophe Godin (INRIA) provided access to image analysis software. Hosted visits by Manuel Forero-Vargas, and provided intellectual input regarding the development of modelling aspects of the project.
Impact v
Start Year 2010
 
Description ERA-NET Collaboration (ERA-SysBio+) 
Organisation École normale supérieure de Lyon (ENS Lyon)
Country France 
Sector Academic/University 
PI Contribution Myself and my team (Angharad Jones, Manuel Forero-Vargas) contributed intellectual input, experimental data, analytical tools and a model of cell growth and division in the shoot apical meristem. Angharad Jones, an experienced post-doc, contributed expertise in live cell imaging and contributed to the establishment of methods that allowed time course data showing the growth and division of individual cells within the shoot apical meristem. Angharad also produced a novel fluorescent cell cycle reporter for use in plants and a model of cell growth and division which complements models produced by collaborators. Manuel Forero-Vargas developed image analysis methods that allowed rapid segmentation and extraction various parameters,that were used to generate important preliminary datasets. All team members contributed expertise and intellectual input to the overall project at regular project meetings, and Angharad and myself authored a review with partners ar ENS Lyon and INRIA. I provided acess to plant growth facilities and a dedicated confocal microscope, both of which were necessary for the generation of the experimental data.
Collaborator Contribution Jan Traas (ENS Lyon) provided expertise in live cell imaging of the shoot apical meristem. He hosted multiple visits by Angharad Jones for training and the joint development of techniques specific to the collection of datasets involving cell division. Jan Traas also provided expertise and intellectual input based on his substantial knowledge and experience in the biology of the shoot apical meristem. Christophe Godin (INRIA) provided access to image analysis software. Hosted visits by Manuel Forero-Vargas, and provided intellectual input regarding the development of modelling aspects of the project.
Impact v
Start Year 2010
 
Description MorphoGraphX 
Organisation Max Planck Society
Department Max Planck Institute for Plant Breeding Research
Country Germany 
Sector Academic/University 
PI Contribution We produced timecourse datasets of shoot apical meristems that showed cell growth and division.
Collaborator Contribution Dr Richard Smith (Max Planck Institute for Plant Breeding Research) provided access, training and support in the use of MorphoGraphX, a bespoke image analysis tool produced in his lab for the analysis of 3D images of the shoot apical meritem. He also provided intellectual input regarding the development of computational models.
Impact Analysis produced as a result of this collaboration led to a publication.
Start Year 2014
 
Description GARNet Podcast 
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 Other audiences
Results and Impact An interview discussing the published work resulting from the iSAM project was produced in order to publicise the paper and the work. The podcast allowed us to give a general introduction to the work and therefore increase awareness in the work.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=32gBOCE0KCc
 
Description Plants For Life 
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 Designed hands-on activities to introduce members of the public to plant cells and plant genetics. The event has been held in association with various partners including the National Museum of Wales, Y Sennydd (Welsh Assembly) and a local national trust property (Dyffryn Gardens). It is estimated that on average each event has been attended by 50-100 members of the general public spread over all ages from children to pensioners. The hands on activites sparked questions related to the research project and to genetics.
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017