Even though global earth surface temperatures are predicted to rise over the coming century we know very little of how plants cope with temperature change. The BBSRC/EPSRC-funded ROBuST project seeks to understand the molecular circuitry that enables plants to react to or withstand sometimes extreme daily and seasonal temperature changes. To do this we are combining experimentation, computational modelling and mathematical approaches to establish how temperature modifies signalling through a central regulatory network (Figure 1). Our cross-disciplinary work programme has identified novel thermal signalling mechanisms, defined new hypotheses in silico that are tested in the lab, and determined general principles that underlie temperature signalling.
Figure 1. A simplified schematic of the ROBuST study network that comprises the interconnected pathways of light, cold acclimation and the clock. These pathways coordinate the temporal regulation of major metabolic, and regulatory pathways as well as whole plant level responses.
Determine the principles that underlie network robustness + sensitivity across ambient temperatures
The ROBuST Team 2012 (top left to right)
Peter Gould, Julia Foreman, Tomasz Zielinski, Gavin Steel, Joe Hemsted, Maria Costa, Andrew Millar, Mirela Domijian, Valeire Clark, David Rand, Rob Smith, Antony Hall, Jayne Griffiths, Ben Wareham, Mat Williams, Yin-Hoon Chew, Hiroshi Momiji, Kelly Stewart, Dana Macgregor, Karen Halliday and Kate Sidaway-Lee.
Management team: Dr Karen Halliday (lead), Prof. Andrew Millar, Prof. Mathew Williams, Dr Stephen Gilmore (University of Edinburgh), Dr Steve Penfield (University of Exeter), Dr Anthony Hall (University of Liverpool), Prof. David Rand and Dr Barbel Finkenstädt (University of Warwick), Prof. Mike White (University of Manchester), Prof. Ian Graham (University of York).
Project Coordinator: Julia Foreman
Admin Assistant: Valerie Clark
Other ROBuST members. First project coordinator: Colin Moran; PDRAs: Aurora Piňas Fernàndez, Arnab Ganguli, Anne Moore, Gabriela Toledo-Ortiz; Techs: Sue Bird, Jack Young.
Tools and resources
Biological Data Repository (Biodare)
BioDare (www.biodare.ed.ac.uk) is an online facility to share, store, analyse and disseminate timeseries data, focussing on circadian clock data, with browser and web service interfaces. Toolbox features include an improved, speedier FFT-NLLs routine and ROBuST’s Spectrum Resampling tool that will analyse rhythmic time series data (Zielinski et al., PLoS One 2014). BioDare currently stores >20M datapoints from >1200 experiments generated on both on-project and externally.
If you would like to use BioDare please contact Tomasz.Zielinski@ed.ac.uk
Data Analysis Software
ROBuST produced a broad range of data analysis and theoretical tools. See: http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/
1. Sensitivity Analysis Software for Systems (SASSy): The SASSy software suite for model analysis has been extended with the addition of tools such as phase IRCs. It can be used as an engineering tool for complex systems, such as the temperature regulated models (Gould et al. Molecular Systems Biology 2013).
2. Spectrum Resampling. The Spectrum Resampling algorithm provides a robust period analysis with statistically well-defined confidence intervals on period estimates (Costa et al. Biostatistics 2013). A refactored version is now available online via BioDare.
3. Reconstructing Transcription Open Software (ReTrOS): ReTrOS software back-calculates transcriptional dynamics from observed reporter gene timeseries. The latest form of the ReTrOS application for timeseries has been documented by Warwick and the SynthSys team, and refactoring into Java is underway.
4. CoAST (Comparative Analysis of Sets of TimeSeries). This more recent package addresses the challenge of analyzing large numbers of LUC timeseries to identify consistent features across multiple replicate timeseries. Data that have been back-calculated using RetrOS are detrended using a powerful wavelet filter with a GUI, prior to the cross-comparison.
The ROBuST p:LUC Line Collection
The ROBuST LUC collection comprises the most comprehensive assembly of p:LUC reporter lines (total = 176) in a single (Col) accession.
It comprises: Col WT expressing p::LUC constructs for ~40 clock, light and temperature genes; 40 genotypes harbouring the pCor15a::LUC, pCCR2::LUC, pCAB2::LUC bioluminescence markers. The whole collection currently being deposited at NASC (http://arabidopsis.info/).
Johansson* H, Jones*, HJ, Foreman J, Hemsted JR, Stewart K, Grima R. Halliday KJ. Arabidopsis cell expansion is controlled by a photothermal switch. Nature Commun. 2014 5:4848.
Chew YH, Wenden B, Flis A, Mengin V, Taylor J, Davey CL, Tindal C, Thomas H, Ougham HJ, de Reffye P, Stitt M, Williams M, Muetzelfeldt R, Halliday KJ, Millar AJ. A Multi-Scale Digital Arabidopsis Predicts Individual Organ and Whole-Organism Growth. Proc. Natl. Acad. Sci. U S A. 2014 Sep 30;111(39):E4127-36.
Toledo-Ortiz G, Johansson H, Lee KP, Bou-Torrent J, Stewart K, Steel G, Rodríguez-Concepción M, Halliday KJ. The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription. PLoS Genet. 2014 10(6):e1004416.
Sidaway-Lee K, Costa MJ, Rand DA, Finkenstadt B, Penfield S. Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response. Genome Biol. 2014 Mar 3;15(3):R45; 25.
Moore A, Zielinski T, Millar AJ. Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure. Methods Mol Biol. 2014;1158:13-44.
Zielinski T, Moore AM, Troup E, Halliday KJ, Millar AJ. Strengths and limitations of period estimation methods for circadian data. PLoS One. 2014 9(5):e96462.
McWatters HG, Toledo-Ortiz G, and Karen J. Halliday KJ. Temperature and light signal integration, Book: Temperature and Plant Development. Eds: Franklin and Wigge, Feb. 2014, ISBN: 978-1-118-30820-2
Franklin KA, Toledo-Ortiz G, Pyott DE, Halliday KJ. Interaction of light and temperature signalling. J. Exp. Bot. 2014 65(11):2859-71. doi: 10.1093/jxb/eru059. Review.
Chew YH, Smith RW, Jones HJ, Seaton DD, Grima R, Halliday KJ. Mathematical models light up plant signaling. Plant Cell. 2014 26(1):5-20
Macgregor DR, Gould P, Foreman J, Griffiths J, Bird S, Page R, Stewart K, Steel G, Young J, Paszkiewicz K, Millar AJ, Halliday KJ, Hall AJ, Penfield S. High Expression of OSMOTICALLY RESPONSIVE GENES 1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis. Plant Cell. 2013, Nov 19.
Seaton DD, Ebenhöh O, Millar AJ, Pokhilko A. Regulatory principles and experimental approaches to the circadian control of starch turnover. J R Soc Interface. 2013 11(91):20130979. doi: 10.1098/rsif.2013.0979.
Keily J, MacGregor DR, Smith RW, Millar AJ, Halliday KJ, Penfield S. Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock. Plant J. 2013, 76(2):247-57.
Costa MJ, Finkenstädt B, Roche V, Lévi F, Gould PD, Foreman J, Halliday K, Hall A, Rand DA. Inference on periodicity of circadian time series. Biostatistics. 2013, 14(4):792-806.
Kusakina J, Gould PD, Hall A. A fast circadian clock at high temperatures is a conserved feature across Arabidopsis accessions and likely to be important for vegetative yield. Plant Cell Environ. 2014 37(2):327-40.
Gould PD, Ugarte N, Domijan M, Costa M, Foreman J, Macgregor D, Rose K, Griffiths J, Millar AJ, Finkenstädt B, Penfield S, Rand DA, Halliday KJ, Hall AJ. Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Mol Syst Biol. 2013;9:650.
Vaistij FE, Gan Y, Penfield S, Gilday AD, Dave A, He Z, Josse EM, Choi G, Halliday KJ, Graham IA. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proc Natl Acad Sci U S A. 2013, 110(26):10866-71.
Sorokin A, Selkov G, Goryanin I. A user-defined data type for the storage of time series data allowing efficient similarity screening. European Journal of Pharmaceutical Sciences 2012, 46 272–274.
Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ. The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 2012, 8:574.
Song YH, Smith RW, To BJ, Millar AJ, Imaizumi T. FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science. 2012, 336(6084):1045-9.
Chew YH, Wilczek AM, Williams M, Welch SM, Schmitt J, Halliday KJ. An augmented Arabidopsis phenology model reveals seasonal temperature control of flowering time. New Phytol. 2012, 194(3):654-65.
Guerriero ML, Pokhilko A, Piňas Fernàndez A, Halliday KJ, Millar AJ, Hillston J. Stochastic properties of the plant circadian clock. Journal of the Royal Society:Interface 2011; August 31.
Komorowski M, Costa M, Rand DA, Stumpf ML. Sensitivity, robustness and identifiability in stochastic chemical kinetics models. Proceedings of the National Academy of Sciences 2011; 108 (21) p8645-8650.
Griffiths J, Halliday K. Plant development: light exposure directs meristem fate. Curr Biol. 2011 Oct 11;21(19):R817-9.
Foreman J, Johansson AH, Hornitschek P, Josse EM, Fankhauser C, Halliday KJ. Light receptor action is critical for maintaining plant biomass at warm ambient temperatures. Plant Journal 2010; 65(3) p441-452.
Moran CN and Halliday KJ. Fruit developments; new directions for an old pathway. Current Biology 2010; 21; 20(24) R1081-3.
Chew YH and Halliday KJ. A stress-free walk from Arabidopsis to crops. Current Opinions in Biotechnology 2011; 22(2) p281-286.
Domijan D, Rand DA. Balance equations can buffer noisy and sustained environmental perturbations of circadian clocks. Journal of the Royal Society:Interface Focus 1(2010) p177-186
Calder M, Gilmore S, Hillston J, Vyshemirsky V. Formal Methods for Biochemical Signalling Pathways. Chapter 6 of Formal Methods: State of the Art and New Directions. Springer London, 2010.
Sidaway-Lee K, Josse E-M, Brown A, Graham IA, Halliday KJ, and Penfield S. A molecular link between daytime temperature and plant growth rate. Current Biology. 2010 20(16):1493-97
Spiller DG, Wood CD, Rand DA, White MR. Measurement of single-cell dynamics. Nature 2010 465(7299):736-45.
Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ. Prediction of photoperiodic regulators from quantitative gene circuit models. Cell. 2009 139(6):1170-9.
Penfield S, Hall A. A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis. Plant Cell. 2009 21(6):1722-32.
Gould PD, Diaz P, Hogben C, Kusakina J, Salem R, Hartwell J, Hall A. Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. Plant J. 2009 58(5):893-901.
Penfield S, King J. Towards a systems biology approach to understanding seed dormancy and germination. Proc Biol Sci. 2009 276(1673):3561-9.
Robust Associated Papers
Feillet C, Krusche P, Tamanini F, Janssens RC, Downey MJ, Martin P, Teboul M, Saito S, Lévi FA, Bretschneider T, van der Horst GT, Delaunay F, Rand DA. Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. Proc Natl Acad Sci U S A. 2014 111(27):9828-33.
Vaistij FE, Gan Y, Penfield S, Gilday AD, Dave A, He Z, Josse EM, Choi G, Halliday KJ, Graham IA. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proc Natl Acad Sci U S A. 2013 110(26):10866-71.
Rowland L, Hill TC, Stahl C, Siebicke L, Burban B, Zaragoza-Castells J, Ponton S, Bonal D, Meir P, Williams M. Evidence for strong seasonality in the carbon storage and carbon use efficiency of an Amazonian forest. Glob Chang Biol. 2013 Aug 29.
Jenkins DJ, Finkenstädt B, Rand DA. A temporal switch model for estimating transcriptional activity in gene expression. Bioinformatics. 2013, 29(9):1158-65.
Sus O, Heuer MW, Meyers TP, Williams M. (2013) A data assimilation framework for constraining upscaled cropland carbon flux seasonality and biometry with MODIS.Biogeosciences: 10, 2451-2466. doi:10.5194/bg-10-2451-2013.
Street LE, Subke JA, Sommerkorn M, Sloan V, Ducrotoy H, Phoenix GK, Williams M. The role of mosses in carbon uptake and partitioning in arctic vegetation. New Phytol. 2013, 199(1):163-75.
Penfield S, Springthorpe V. Understanding chilling responses in Arabidopsis seeds and their contribution to life history. Philos Trans R Soc Lond B Biol Sci. 2012, 367(1586):291-7.
Josse EM, Gan Y, Bou-Torrent J, Stewart KL, Gilday AD, Jeffree CE, Vaistij FE, Martínez-García JF, Nagy F, Graham IA, Halliday KJ. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell. 2011 Apr;23(4):1337-51.
Kendall SL, Hellwege A, Marriot P, Whalley C, Graham IA, Penfield S. Induction of dormancy in Arabidopsis summer annuals requires parallel regulation of DOG1 and hormone metabolism by low temperature and CBF transcription factors. Plant Cell. 2011 23(7):2568-80.
O'Neill JS, van Ooijen G, Le Bihan T, Millar AJ. Circadian clock parameter measurement: characterization of clock transcription factors using surface plasmon resonance. J Biol Rhythms. 2011, 26(2):91-8.
Edwards KD, Akman OE, Knox K, Lumsden PJ, Thomson AW, Brown PE, Pokhilko A, Kozma-Bognar L, Nagy F, Rand DA, Millar AJ. Quantitative analysis of regulatory flexibility under changing environmental conditions. Mol Syst Biol. 2010 6:424.
Spiller DG, Wood CD, Rand DA, White MR. Measurement of single-cell dynamics. Nature 2010, 465(7299):736-45.
Penfield S, Josse EM, Halliday KJ. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy. Plant Mol Biol. 2010, 73(1-2):89-95.