Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data
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Although large-scale gene expression data have been studied from many perspectives, they have not been systematically integrated to infer the regulatory potentials of individual genes in specific pathways. Here we report the analysis of expression patterns of genes in the Calvin cycle from 95 Arabidopsis microarray experiments, which revealed a consistent gene regulation pattern in most experiments. This identified pattern, likely due to gene regulation by light rather than feedback regulations of the metabolite fluxes in the Calvin cycle, is remarkably consistent with the rate-limiting roles of the enzymes encoded by these genes reported from both experimental and modeling approaches. Therefore, the regulatory potential of the genes in a pathway may be inferred from their expression patterns. Furthermore, gene expression analysis in the context of a known pathway helps to categorize various biological perturbations that would not be recognized with the prevailing methods.
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- Buchanan, B.B., Gruissem, W. and Jones, R.L. 2000. Photosynthesis: Biochemistry & Molecular Biology of Plants. American Society of Plant Physiology, Rockville, MD.Google Scholar
- Den-Dor, A. and Yakhini, Z. 1999. Clustering gene expression patterns. In: S. Istrail, P. Pevzner and M.S. Waterman(Eds.) Recomb 99, ACM Press, Washington, DC, p. 188.Google Scholar
- Dudoit, S., Yang, Y.H., Speed, T.P. and Callow, M.J. 2002. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sin. 12: 111.Google Scholar
- Fichtner, K., Quick, W.P., Schulze, E-D, Mooney, H.A., Rodermel, S.R., Bogorad, L. and Stitt, M. 1993. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with 'antisense' rbcS. V. Relationship between photosynthetic rate, storage strategy, biomass allocation and vegetative plant growth at three different nitrogen supplies. Planta 190: 1.CrossRefGoogle Scholar
- Hastie, T., Tibshirani, R., Eisen, M.B., Alizadeh, A., Levy, R., Staudt, L., Chan, W.C., Botstein, D. and Brown, P. 2000. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 1, research0003.1-0003.21.Google Scholar
- Lazzeroni, L. and Owen, A. 2002. Plaid models for gene expression data. Stat. Sin. 12: 61.Google Scholar
- Muschak, M., Hoffmann-Benning, S., Fuss, H., Kossmann, J., Willmitzer, L. and Fisahn, J. 1997. Gas exchange and ultrastructural analysis of transgenic potato plants expressing mRNA antisense construct targeted to the cp-fructose-1,6-bisphosphate phosphatase. Photosynthetica 33: 455.Google Scholar
- Pettersson, G. and Ryde-Pettersson, U. 1988. A mathematical model of the Calvin photosynthesis cycle. Eur. J. Biochem.175: 661.Google Scholar
- Price, G.D., Evans, J.R., Von Caemmerer, S., Yu, J.-W and Badger, M.R. 1995. Specific reduction of chloroplast glyceraldehyde-3-phosphate dehydrogenase activity by antisense RNA reduces CO2 assimilation via a reduction in ribulose bisphosphate regeneration in transgenic tobacco plants. Planta 195: 369.CrossRefPubMedGoogle Scholar
- Quick, W.P., Schurr, U., Scheibe, R., Schulze, E-D, Rodermel, S.R., Bogorad, L. and Stitt, M. 1991. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with 'antisense' rbcS. I. Impact on photosynthesis in ambient growth conditions. Planta 183: 542.CrossRefPubMedGoogle Scholar
- Stitt, M., Quick, W.P., Schurr, U., Schulze, E-D, Rodermel, S.R. and Bogorad, L. 1991. Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with ‘antisense’ rbcS. II. Flux-control coefficients for photosynthesis in varying light, CO2, and air humidity. Planta 183: 555.PubMedGoogle Scholar
- The supplemental materials of this paper are also available at http://plantgenomics.biology.yale.edu/Calvin Cycle.Google Scholar