Regulation of Biological Signalling by Temperature (ROBUST)

Lead Research Organisation: University of Warwick
Department Name: Warwick Systems Biology Centre


Agriculture underpins European industry with an annual turnover of more than ¤1 trillion and is essential for our survival. As resources dwindle and world populations grow, our demands on agriculture will also increase. As climate changes in the coming decades, current trends suggest that global temperatures will rise. Not only is mean temperature set to change but weather systems are also becoming less predictable: an unprecedented frost this year resulted in a failure of the Californian citrus crop, costing the industry $450 million. The combination of increased demand on agriculture and the changes in global climate and weather extremes represent a major challenge for science in the 21st century. To meet this challenge, we need to know how plants both respond to and protect against temperature changes. The same issues apply to other environmental factors across all biological systems, therefore, understanding this is a major goal for experimental and theoretical scientists. In recent years reductionist science, where biological pathways are studied in isolation, has not identified plant temperature sensors. It also cannot address how temperature effects that cross the many, interacting pathways, which we now know are involved. We take a multi-disciplinary approach and focus our studies on one of the best characterised signalling networks in plants. We will combine expertise from biologists that specialise in molecular and cell biology, plant physiology and climate change; and theoreticians that specialise in statistical, mathematical and computer science approaches to analyse and model biological systems. To provide vital independent expertise and avenues for collaboration we have invited a panel of experts from industry and academia, to meet with us on a yearly basis. We will analyse how temperature influences the interlinked pathways of light, 24-hour clock and cold signalling. We conduct our studies in the model plant Arabidopsis as it offers severaladvantages: 1. we have already developed the most advanced mathematical model in plant signalling, for a section of our network; 2. our network pathways are already well defined, with many useful tools and resources in Arabidopsis; and 3. the pathways in plants of economic and ecological importance appear to be closely related, so our results can readily be translated to other species. To capture a meaningful view of how temperature-regulated molecular events translate to important physiological traits we will conduct our analysis at molecular, cellular and whole plant levels. Our first task will be to expand our model with the pre-existing knowledge for the rest of our network. We will measure the response of all our network components over a range of temperatures and integrate these data into our preliminary model. This, approach will locate the temperature-sensitive and -tolerant parts of the network in an unbiased fashion: the important point is that the temperature responses that matter will not be caused by single components, but by many acting together. We cannot understand this complexity without computer models. Our models will help inform our experiments, to home in on the molecular mechanisms that control the network's properties. Finally, we will test the role of important network components in controlling agriculturally and ecologically relevant traits in whole plants. In summary, this project will develop the most advanced signalling network model in plants, define network features that permit responsiveness and tolerance, and identify plant temperature sensors. Our work will address fundamental questions in biology and create the knowledge base required to meet the challenge to develop crops better able to withstand a range of climatic conditions. Our multidisciplinary collaboration will also provide training and extension of 'Systems Biology' approaches to universities with no current expertise and to our industrial collaborators.

Technical Summary

Understanding robustness and sensitivity of networks is a key goal of systems biology. We will investigate for the first time how a complex signalling network responds to temperature. Our system comprises the Arabidopsis light, circadian clock and cold tolerance pathways, parts of which are buffered against temperature while other responses are exquisitely sensitive. The system is well characterised under standard conditions, and the applicants are leaders in identifying and modelling the effects of temperature on this network. We will, therefore, abstract a model capturing this knowledge, incorporating and expanding on our published model of the circadian clock. A comprehensive assessment of how each component responds to temperature will be key to understanding the buffering capacity of the system. Using specific expertise and facilities at the collaborating institutions, we will investigate: - promoter activity, RNA expression, RNA/protein abundance and degradation, and protein/protein interaction at the molecular level - localisation and co-localisation at the sub-organelle, sub-cellular and cellular level - how mutating genes within the network alters the buffer capacity - how altering the temperature sensitivity of this system affects whole-plant performance The experimental data will be compiled in order to estimate new parameter values: here, recently-developed statistical methods can make best use of our high-quality, timeseries data from intact plants. A new mathematical approach to model simplification will allow us to focus our studies on reduced models of the key components identified from the data, in a rigorous and principled way. As demonstrated by the enthusiastic support from industry, the knowledge base and modelling tools will contribute to developing higher-yielding crops resistant to environmental stresses, such as increasing global temperatures. Our programme will also provide extensive training of personnel in systems biology.


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Description This grant was joint with Edinburgh and other universities. The project PI is Dr Karen Halliday (Edinburgh) and the Findings Report has been uploaded with his report on this grant.
Exploitation Route See above.
Sectors Agriculture, Food and Drink
Description This grant was joint with Edinburgh and other universities. The project PI is Dr Karen Halliday (Edinburgh) and the Narrative Impact has been uploaded with his report on this grant.
Sector Agriculture, Food and Drink
Description BBSRC Grouped
Amount £246,768 (GBP)
Funding ID BB/I004521/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 07/2010 
End 06/2013
Title PeTTSy (Perturbation Theory Toolbox for Systems) 
Description This is a GUI based Matlab toolbox which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation based models. 
Type Of Technology Webtool/Application 
Year Produced 2015 
Impact Has enabled analysis of complex dynamics of big systems that was not possible before. 
Title ReTrOS: Reconstructing Transcription Open Software 
Description Matlab based software to reconstruct transcription profiles e.g. from time-course (LUC-, GFP- etc) imaging data. Written in Matlab 2009b, and distributed with test data. 
Type Of Technology Webtool/Application 
Year Produced 2010 
Impact Mainly used by biological community. 
Title Spectrum Resampler 
Description A period fitting algorithm with a graphical front end for Matlab, which imports periodic time series data from Microsoft Excel xls files. This work was produced in collaboration with the Universities of Liverpool and Edinburgh, as part of the ROBuST project, funded by BBSRC and EPSRC under the SABR initiative. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact Enables calculation of period with rigorous error estimates. Used within biological and biomedical communities studying circadian oscillations.