Minimal models of the circadian clock in a novel biological system

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences


Photosynthetic organisms are vital to our economy and survival, playing a critical role in the global carbon cycle and affecting the climate of our planet. Recent advances offer us the methods to understand the complex control of growth and activity in photosynthetic organisms. The 24-hour circadian clock is a key regulator in plants, and is also important in cyanobacteria, fungi and animals including humans. The UK teams have shown that rhythmic control of biological activity by the circadian clock increases growth and survival of Arabidopsis thaliana plants, probably because >15% of genes in Arabidopsis are clock-regulated. The Arabidopsis circadian clock is becoming a paradigm for systems biology. The clock mechanism is a small gene network with multiple feedback loops, comprising five pseudo-response regulators, three myb-related proteins, two F-box proteins, and additional plant-specific proteins. Millar's group has modelled a simplified Arabidopsis clock mechanism, with three interlocking feedback loops. Predictions of the models have been validated by new experiments, identifying an additional part of the clock network. This is still a rare achievement in any organism. Including the real complexity of the Arabidopsis clock, however, will greatly enlarge the models, making them more difficult to use and to understand. The dynamics of the clock system are complex. It can generate autonomous, 24-hour biological rhythms of gene expression but in nature the day/night cycle forces the system, resetting the clock. Light signals regulate four different components in the current clock model. In reality, these signals originate from at least eight photoreceptor proteins and probably control additional components. This complexity hampers circadian research in Arabidopsis. A simpler clock system that included only one of each protein type would enormously facilitate the experimental analysis of the clock mechanism. It would provide a natural test for the proposed benefits of complexity in the clock mechanism, giving general insight into other complex clocks for example in humans. If the whole organism were simple, it could reveal much more easily how correct timing of particular clock-regulated biochemical processes led to adaptive benefits. The French team has developed this ideal model. Ostreococcus tauri is the smallest free-living eukaryote, with a circadian system that is closely related to that of Arabidopsis. Crucially, each protein type is represented by only one gene in Ostreococcus. The Bouget lab has developed a unique set of experimental tools for functional genomics in this organism. Their recent results demonstrate that the Ostreococcus clock conserves the same mechanisms and gene interactions as the clock in Arabidopsis, but in a far simpler system. Modelling by the Lefranc group confirms that very simple mathematical models, which were invalidated by data in Arabidopsis, accurately describe the Ostreococcus clock. The world-leading results of the UK and French teams are naturally complementary, but in addition are supported by significant national and institutional investment on both sides. We are poised to make a major impact, gaining significant added value from these resources and opening up a new application area. We will combine the UK team's expertise in complex models, and the wealth of comparative data and models on Arabidopsis, with the French team's experimental system and expertise in nonlinear dynamics. Experimentally, we will generate biological materials to monitor and manipulate all the clock components in Ostreococcus, then use these materials to generate high-quality timeseries data for modelling. We will identify all clock-regulated transcripts and promoter sequences using RNA expression microarrays and promoter arrays. These results will form a case study for Plant Systems Biology, demonstrating the power of a unicellular system to accelerate understanding of core processes.

Technical Summary

Please see text of main proposal for summary, which has a different format in this joint application procedure.


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Description Findings below are for the Edinburgh component of this joint grant. The full programme was run from France, by F-Y Bouget, who reports to the ANR in France. The University of Warwick also contributed to another publication.

a.Detailed and conceptual mathematical models of the Ostreococcus clock gene circuit showed the advantages of complexity in clock gene circuits (which Ostreococus lacks) and in their light inputs (which it has).
Troein et al. Current Biology, 2009.
Troein et al. Plant Journal, 2011; Biomodels ID TroeinOstreoClock_Jan2011.

b. Data on the rhythmic transcriptome in Ostreococcus were used to constrain the most detailed mathematical model of starch metabolism yet published, using a novel modelling method: this showed how this very simple cell can help us to understand more plant science than more complex, higher plant systems.
Sorokina et al. BMC Systems Biology, 2011.

c.Establishing Ostreococcus as an experimental system in Edinburgh: this allowed the paradigm-shifting demonstration of transcription-independent circadian rhythms and their coupling or uncoupling from the transcriptional clock gene circuit.
O'Neill et al. Nature, 2011.
Van Ooijen et al. Current Biology, 2011.
Exploitation Route Design principles for complex robust regulation of complex gene circuits are relevant to synthetic biology, designing other such circuits.

Minimal algal system to study fundamental processes in eukaryotic cells, not only in algal specialty areas e.g. biofuel production.
Sectors Agriculture, Food and Drink,Environment
Description We anticipate that Academic and industrial researchers, working on biological clocks and on algal biology, including biofuels, will use our findings. The academic publications arising from this joint award have been used by other researchers, sufficiently to warrant citation in their own publications: Troein et al. Current Biology 2010: 26 citations Van Ooijen et al. Current Biology 2011: 8 citations Troein et al. Plant Journal 2011: 7 citations Sorokina et al BMC Sys Bio 2011: 3 citations O'Neill et al Nature 2011: 59 citations Measured by Web of Knowledge in September 2012.
Title Mathematical model of the clock gene circuit in the alga Ostreococcus tauri 
Description Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable environmental changes. Detailed understanding of the circadian network of higher plants, such as Arabidopsis thaliana, is hampered by the high number of partially redundant genes. However, the picoeukaryotic alga Ostreococcus tauri, which was recently shown to possess a small number of non-redundant clock genes, presents an attractive alternative target for detailed modelling of circadian clocks in the green lineage. Based on extensive time-series data from in vivo reporter gene assays, we developed a model of the Ostreococcus clock as a feedback loop between the genes TOC1 and CCA1. The model reproduces the dynamics of the transcriptional and translational reporters over a range of photoperiods. Surprisingly, the model is also able to predict the transient behaviour of the clock when the light conditions are altered. Despite the apparent simplicity of the clock circuit, it displays considerable complexity in its response to changing light conditions. Systematic screening of the effects of altered day length revealed a complex relationship between phase and photoperiod, which is also captured by the model. The complex light response is shown to stem from circadian gating of light-dependent mechanisms. This study provides insights into the contributions of light inputs to the Ostreococcus clock. The model suggests that a high number of light-dependent reactions are important for flexible timing in a circadian clock with only one feedback loop. 
Type Of Material Computer model/algorithm 
Year Produced 2011 
Provided To Others? Yes  
Impact Research funding and publications 
Title Model for starch polymerisation and degradation in the alga, Ostreococcus tauri. 
Description BACKGROUND: The storage of photosynthetic carbohydrate products such as starch is subject to complex regulation, effected at both transcriptional and post-translational levels. The relevant genes in plants show pronounced daily regulation. Their temporal RNA expression profiles, however, do not predict the dynamics of metabolite levels, due to the divergence of enzyme activity from the RNA profiles.Unicellular phytoplankton retains the complexity of plant carbohydrate metabolism, and recent transcriptomic profiling suggests a major input of transcriptional regulation. RESULTS: We used a quasi-steady-state, constraint-based modelling approach to infer the dynamics of starch content during the 12 h light/12 h dark cycle in the model alga Ostreococcus tauri. Measured RNA expression datasets from microarray analysis were integrated with a detailed stoichiometric reconstruction of starch metabolism in O. tauri in order to predict the optimal flux distribution and the dynamics of the starch content in the light/dark cycle. The predicted starch profile was validated by experimental data over the 24 h cycle. The main genetic regulatory targets within the pathway were predicted by in silico analysis. CONCLUSIONS: A single-reaction description of starch production is not able to account for the observed variability of diurnal activity profiles of starch-related enzymes. We developed a detailed reaction model of starch metabolism, which, to our knowledge, is the first attempt to describe this polysaccharide polymerization while preserving the mass balance relationships. Our model and method demonstrate the utility of a quasi-steady-state approach for inferring dynamic metabolic information in O. tauri directly from time-series gene expression data. 
Type Of Material Computer model/algorithm 
Year Produced 2011 
Provided To Others? Yes  
Impact Further publications, model development in Arabidopsis.