Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data

Plant Molecular Biology

Volumn 53, Issue 4, 2003, Pages 467-478

  Sun, Ning ^a   Ma, Ligeng ^b,c   Pan, Deyun ^a   Zhao, Hongyu ^a   Deng, Xing Wang ^b,c  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PEKING UNIVERSITY   (China)

^c YALE UNIVERSITY   (United States)

Author keywords

Calvin cycle; Gene expression; Gene regulation; Microarray; Regulatory potentials

Indexed keywords

COMPUTATIONAL METHODS; DATA REDUCTION; ENZYME KINETICS; GENES; METABOLISM; MOLECULAR BIOLOGY; PERTURBATION TECHNIQUES;

REGULATORY POTENTIAL;

PLANT CELL CULTURE;

CARBOHYDRATE; CARBON DIOXIDE; ENZYME;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; DNA MICROARRAY; DNA RESPONSIVE ELEMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; LIGHT; METABOLISM; NUCLEIC ACID DATABASE; PHENOTYPE; RADIATION EXPOSURE; SIGNAL TRANSDUCTION; STATISTICS;

ARABIDOPSIS; CARBOHYDRATES; CARBON DIOXIDE; DATABASES, NUCLEIC ACID; ENZYMES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, PLANT; LIGHT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; RESPONSE ELEMENTS; SIGNAL TRANSDUCTION;

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA;

EID: 1542475837     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:PLAN.0000019071.12878.9e     Document Type: Article

References (42)

1. Buchanan, B.B., Gruissem, W. and Jones, R.L. 2000. Photosynthesis: Biochemistry & Molecular Biology of Plants. American Society of Plant Physiology, Rockville, MD.
2. 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.
3. Donald, R.G. and Cashmore, A.R. 1990. Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J. 9: 1717-1726.
4. 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.
5. Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. 2001. Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Ass. 96: 1151.
6. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863.
7. 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.
8. Fridlyand, L.E., Backhausen, J.E. and Scheibe, R. 1999. Homeostatic regulation upon changes of enzyme activities in the Calvin cycle as an example for general mechanisms of flux control. What can we expect from transgenic plants? Photosynth. Res. 61: 227.
9. Haake, V., Zrenner, R., Sonnewald, U. and Stitt, M. 1998. A moderate decrease of plastid aldolase activity inhibits photosynthesis, alters the levels of sugars and starch and inhibits growth of potato plants. Plant J. 14: 147.
10. Harrison, E.P., Willingham, N.M., Lloyd, J.C. and Raines, C.A. 1998. Reduced sedoheptulose-1,7-bisphosphatase levels in transgenic tobacco lead to decreased photosynthetic capacity and altered carbohydrate accumulation. Planta 204: 27.
11. 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.
12. Henkes, S., Sonnewald, U., Flachmann, R., Badur, R. and Stitt, M. 2001. A small decrease of plastid transketolase activity in antisense tobacco transformants has dramatic effects on photosynthesis and phenylpropanoid metabolism. Plant Cell 13: 535.
13. Hughes, J.D., Estep, P.W., Tavazoie, S. and Church, G.M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205.
14. Kerr, M.K., Martin, M. and Churchill, G. 2000. Analysis of variance for gene expression microarray data. J. Comp. Biol. 7: 819.
15. Kossmann, J., Sonnewald, U. and Willmitzer, L. 1994. Reduction of the chloroplastic fructose-1,6-bisphosphatase in transgenic potato plants impairs photosynthesis and plant growth. Plant J. 6: 637.
16. Lazzeroni, L. and Owen, A. 2002. Plaid models for gene expression data. Stat. Sin. 12: 61.
17. Li, C. and Wong, W.H. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl. Acad. Sci. USA 98: 31.
18. Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H. and Deng, X.W. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2607.
19. Ma, L., Gao, Y., Qu, L., Chen, Z., Li, J., Zhao, H. and Deng, X.W. 2002. Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14: 2383-2398.
20. Ma, L., Zhao, H. and Deng, X.W. 2003. Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 130: 969-981.
21. Miller, A., Schlagenhaufer, C., Spalding, M. and Rodermel, S.R. 2000. Carbohydrate regulation of leaf development: prolongation of leaf senescence in Rubisco antisense mutants of tobacco. Photosynth. Res. 63: 1.
22. 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.
23. Panda, S., Antoch, M.P., Miller, B.H., Su, A.I., Schook, A.B., Straume, M., Schultz, P.G., Kay, S.A., Takahashi, J.S. and Hogenesch, J.B. 2002. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109: 307-320.
24. 2 assimilation and growth in low irradiance. Plant J. 7: 535.
25. Pettersson, G. and Ryde-Pettersson, U. 1988. A mathematical model of the Calvin photosynthesis cycle. Eur. J. Biochem. 175: 661.
26. Poolman, M., Fell, D. and Thomas, S. 2000. Modeling photosynthesis and its control. J. Exp. Bot. 51: 319.
27. Poolman, M.G., Ölcer, H., Lloyd, J.C., Raines, C.A. and Fell, D.A. 2001. Computer modelling and experimental evidence for two steady states in the photosynthetic Calvin cycle. Eur. J. Biochem. 268: 2810.
28. Puente, P., Wei, N. and Deng, X.W. 1996. Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J. 15: 3732-3743.
29. 2 assimilation via a reduction in ribulose bisphosphate regeneration in transgenic tobacco plants. Planta 195: 369.
30. 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.
31. Roth, F.R., Hughes, J.D., Estep, P.E. and Church, G.M. 1998. Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantitation. Nature Biotech. 16: 939.
32. 2, and air humidity. Planta 183: 555.
33. The supplemental materials of this paper are also available at http://zhao.med.yale.edu/Calvin Cycle.
34. ExPaSy Molecular Biology Server http://us.expasy.org/tools/ pathways/; http://us.expasy.org/enzyme/.
35. Kyoto Encyclopedia of Genes and Genomes (KEGG): http://www. genome.ad.jp/.
36. MIPs Arabidopsis thaliana database (MAtDB): http://mips.gsf. de/proj/thal/.
37. National Center for Biotechnology Information (NCBI): ftp:///ftp. ncbi.nih.gov/.
38. Pathway MicroArray Processor for Arabidopsis (PathMAPA): http://zhao.med.yale.edu/pathmapa.htm.
39. PLACE: http://www.dna.affrc.go.jp/htdocs/PLACE/.
40. The Arabidopsis Information Resource (TAIR): http://www. arabidopsis.org/.
41. Swiss-Prot Protein Knowledgebase: http://us.expasy.org/sprot/.
42. TIGR Arabidopsis thaliana database: http://www.tigr.org/ tdb/e2k1/ath1/.