Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

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 predi...

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Vydané v:	BMC systems biology Ročník 5; číslo 1; s. 36
Hlavní autori:	Sorokina, Oksana, Corellou, Florence, Dauvillée, David, Sorokin, Anatoly, Goryanin, Igor, Ball, Steven, Bouget, François-Yves, Millar, Andrew J
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 26.02.2011 BioMed Central Ltd
Predmet:	Algorithms Analysis Biochemistry Biochemistry, Molecular Biology Bioinformatics Biology Biomedical and Life Sciences Carbohydrate metabolism Cellular and Medical Topics Chlorophyta - chemistry Chlorophyta - genetics Chlorophyta - metabolism Chloroplasts Circadian Rhythm - physiology Colleges & universities Computational Biology/Bioinformatics Design DNA microarrays Enzymatic activity Gene Deletion Gene expression Gene Expression Profiling Gene Expression Regulation, Enzymologic - physiology Gene Regulatory Networks - genetics Genetic aspects Genomes Glucose Green algae Influence Life Sciences Metabolism Metabolites Microarray Analysis Models, Biological Physiological Phytoplankton Proteins Research Article Simulation and Modeling Starch Starch - analysis Systems Biology France United Kingdom Glucan Starch Granule Maltose Starch Starch Content
ISSN:	1752-0509, 1752-0509
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Shrnutí:	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.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 PMCID: PMC3056741
ISSN:	1752-0509 1752-0509
DOI:	10.1186/1752-0509-5-36