Prediction of temporal gene expression: Metabolic optimization by re-distribution of enzyme activities

European Journal of Biochemistry

Volumn 269, Issue 22, 2002, Pages 5406-5413

  Klipp, Edda ^a   Heinrich, Reinhart ^b   Holzhütter, Hermann Georg ^b  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Evolutionary optimization; Gene expression; Mathematical modelling; Metabolic regulation

Indexed keywords

ENZYME;

ARTICLE; CELL METABOLISM; COMPUTER ANALYSIS; CORRELATION ANALYSIS; ENZYME ACTIVITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HOMEOSTASIS; MATHEMATICAL MODEL; METABOLIC REGULATION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; YEAST CELL;

DATABASES; EVOLUTION, MOLECULAR; GENE EXPRESSION; MODELS, THEORETICAL; SOFTWARE; TIME FACTORS; YEASTS;

EID: 0036441029     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.03223.x     Document Type: Article

References (26)

1. DeRisi, J.L., Iyer, V.R. & Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
2. Kuhn, K.M., DeRisi, J.L., Brown, P.O. & Sarnow, P. (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21, 916-927.
3. Ferea, T.L., Botstein, D., Brown, P.O. & Rosenzweig, R.F. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl Acad. Sci. USA 96, 9721-9726.
4. Rep, M., Krantz, M., Thevelein, J.M. & Hohmann, S. (2000) The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J. Biol. Chem. 275, 8290-8300.
5. Cho, R.J., Fromont-Racine, M., Wodicka, L., Feierbach, B., Stearns, T., Legrain, P., Lockhart, D.J. & Davis, R.W. (1998) Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 3752-3757.
6. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J. & Davis, R.W. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2, 65-73.
7. Holter, N.S., Mitra, M., Maritan, A., Cieplak, M., Banavar, J.R. & FedoroR, N.V. (2000) Fundamental patterns underlying gene expression profiles: Simplicity from complexity. Proc. Natl Acad. Sci. USA 97, 8409-8414.
8. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E. Jr, Hieter, P., Vogelstein, B. & Kinzler, K.W. (1997) Characterization of the yeast transcriptome. Cell 88, 243-251.
9. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. & Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 9, 3273-3297.
10. Lashkari, D.A., DeRisi, J.L., McCusker, J.H., Namath, A.F., Gentile, C., Hwang, S.Y., Brown, P.O. & Davis, R.W. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA 94, 13057-13062.
11. Heinrich, R., Schuster, S. & Holzhutter, H.G. (1991) Mathematical analysis of enzymic reaction systems using optimization principles. Eur. J. Biochem. 201, 1-21.
12. Pettersson, G. (1993) Optimal kinetic design of enzymes in a linear metabolic pathway. Biochim. Biophys. Acta. 1164, 1-7.
13. Melendez-Hevia, E., Waddell, T.G., Heinrich, R. & Montero, F. (1997) Theoretical approaches to the evolutionary optimization of glycolysis - Chemical analysis. Eur. J. Biochem. 244, 527-543.
14. Stephani, A. & Heinrich, R. (1998) Kinetic and thermodynamic principles determining the structural design of ATP-producing systems. Bull. Math. Biol. 60, 505-543.
15. Klipp, E. & Heinrich, R. (1999) Competition for enzymes in metabolic pathways: Implications for optimal distributions of enzyme concentrations and for the distribution of flux control. Biosystems 54, 1-14.
16. Brown, G.C. (1991) Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells. J. Theor. Biol. 153, 195-203.
17. Llorens, M., Nuno, J.C., Rodriguez, Y., Melendez-Hevia, E. & Montero, F. (1999) Generalization of the theory of transition times in metabolic pathways: a geometrical approach. Biophys. J. 77, 23-36.
18. Reference with drawn.
19. Heinrich, R. & Schuster, S. (1996) The Regulation of Cellular Systems. Chapman & Hall, New York.
20. Wolf, J. & Heinrich, R. (2000) ERect of cellular interaction on glycolytic oscillations in yeast: A theoretical investigation. Biochem. J. 345, 321-334.
21. Michalewicz, Z. (1992) Genetic Algorithms + Data Structure 1/4 Evolution Programs. Springer Verlag, Berlin.
22. Pontrjagin, L.S., Boltyanski, V.G., Gamkrelidse, R.V. & Mischenko, E.F. (1962) The Mathematical Theory of Optimal Processes. John Wiley, New York.
23. Varner, J. & Ramkrishna, D. (1999) Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 15, 407-425.
24. Varner, J. & Ramkrishna, D. (1998) Application of cybernetic models to metabolic engineering: Investigation of storage pathways. Biotechnol. Bioeng. 58, 282-291.
25. Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C.M. & Shapiro, L. (2000) Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144-2148.
26. Grunenfelder, B., Rummel, G., Vohradsky, J., Roder, D., Langen, H. & Jenal, U. (2001) Proteomic analysis of the bacterial cell cycle. Proc. Natl Acad. Sci. USA 98, 4681-4686.