Just-in-time transcription program in metabolic pathways

Nature Genetics

Volumn 36, Issue 5, 2004, Pages 486-491

  Zaslaver, Alon ^a   Mayo, Avi E ^a   Rosenberg, Revital ^a   Bashkin, Pnina ^a   Sberro, Hila ^a   Tsalyuk, Miri ^a   Surette, Michael G ^b   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN;

AMINO ACID SYNTHESIS; ARTICLE; CONTROLLED STUDY; ENZYME SYNTHESIS; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC TRANSCRIPTION; MATHEMATICAL ANALYSIS; METABOLIC REGULATION; METABOLISM; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REPORTER GENE;

ALGORITHMS; AMINO ACIDS; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENES, REPORTER; OPERON; PLASMIDS; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); RNA, BACTERIAL; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 2442526837     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1348     Document Type: Article

References (30)

1. Savageau, M.A. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology (Addison-Wesley, Reading, Massachusetts, 1976).
2. Hartwell, L.H., Hopfield, J.J., Leibler, S. & Murray, A.W. From molecular to modular cell biology. Nature 402, C47-C52 (1999).
3. Ronen, M., Rosenberg, R., Shraiman, B.I. & Alon, U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA 99, 10555-10560 (2002).
4. Neidhardt, F.C. (ed.) Escherichia coli and Salmonella Cellular and Molecular Biology (American Society for Microbiology Press, 1996).
5. McAdams, H.H. & Shapiro, L. A bacterial cell-cycle regulatory network operating in time and space. Science 301, 1874-1877 (2003).
6. Heinrich, R. & Klipp, E. Control analysis of unbranched enzymatic chains in states of maximal activity. J. Theor. Biol. 182, 243-252 (1996).
7. Klipp, E., Heinrich, R. & Holzhutter, H.G. Prediction of temporal gene expression. Metabolic optimization by re-distribution of enzyme activities. Eur. J. Biochem. 269, 5406-5413 (2002).
8. Ibarra, R.U., Edwards, J.S. & Palsson, B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-189 (2002).
9. Heinrich, R. & Schuster, S. The Regulation of Cellular Systems (Chapman & Hall, New York, 1996).
10. Gilman, A. & Ross, J. Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model. Biophys. J. 69, 1321-1333 (1995).
11. Segre, D., Vitkup, D. & Church, G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112-15117 (2002).
12. Covert, M.W. & Palsson, B.O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058-28064 (2002).
13. Shen-Orr, S.S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68 (2002).
14. Kalir, S. et al. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292, 2080-2083 (2001).
15. Oh, M.K. & Liao, J.C. Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16, 278-286 (2000).
16. Calvo, J.M. & Matthews, R.G. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol. Rev. 59, 466-490 (1994).
17. Hung, S.P., Baldi, P. & Hatfield, G.W. Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J. Biol. Chem. 277, 40309-40323 (2002).
18. Legrain, C., Halleux, P., Stalon, V. & Glansdorff, N. The dual genetic control of ornithine carbamolytransferase in Escherichia coli. A case of bacterial hybrid enzymes. Eur. J. Biochem. 27, 93-102 (1972).
19. Pettersson, G. Optimal kinetic design of enzymes in a linear metabolic pathway. Biochim. Biophys. Acta 1164, 1-7 (1993).
20. Heinrich, R., Schuster, S. & Holzhutter, H.G. Mathematical analysis of enzymic reaction systems using optimization principles. Eur. J. Biochem 201, 1-21 (1991).
21. Rosenfeld, N., Elowitz, M.B. & Alon, U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323, 785-793 (2002).
22. Rosenfeld, N. & Alon, U. Response delays and the structure of transcription networks. J. Mol. Biol. 329, 645-654 (2003).
23. Charlier, D. et al. Arginine regulon of Escherichia coli K-12, A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression. J. Mol. Biol. 226, 367-386 (1992).
24. Aizawa, S.I. & Kubori, T. Bacterial flagellation and cell division. Genes Cells 3, 625-634 (1998).
25. Savageau, M.A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 252, 546-549 (1974).
26. Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
27. Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C.M. & Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144-2148 (2000).
28. Henkin, T.M. & Yanofsky, C. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24, 700-707 (2002).
29. Cormack, B.P., Valdivia, R.H. & Falkow, S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173, 33-38 (1996).
30. Goh, E.B. et al. Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc. Natl. Acad. Sci. USA 99 (26), 17025-17030 (2002).