Structure and function of negative feedback loops at the interface of genetic and metabolic networks

Nucleic Acids Research

Volumn 34, Issue 8, 2006, Pages 2455-2462

  Krishna, Sandeep ^a   Andersson, Anna M C ^a   Semsey, Szabolcs ^a   Sneppen, Kim ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; TRANSCRIPTION FACTOR; REPRESSOR PROTEIN;

ARTICLE; BACTERIAL GENETICS; BACTERIAL METABOLISM; CONTROLLED STUDY; DISSOCIATION; ESCHERICHIA COLI; MATHEMATICAL MODEL; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; STEADY STATE; BIOLOGICAL MODEL; DOWN REGULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; SIGNAL TRANSDUCTION;

ESCHERICHIA COLI;

DOWN-REGULATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, GENETIC; PROMOTER REGIONS (GENETICS); REPRESSOR PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 33646711199     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl140     Document Type: Article

References (25)

1. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C.C. and Collado-Vides,J. (2001) Regulondb (version 3.2): Transcriptional regulation and operon organization in Escherichia coli k-12. Nucleic Acids Res., 29, 72-74.
2. Keseler,I., Collado-Vides,J., Gama-Castro,S., Ingraham,J., Paley,S., Paulsen,I., Peralta-Gil,M. and Karp,P. (2005) Ecocyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337.
3. Edwards,J.S. and Palsson,B.O. (2000) The Escherichia coli mg1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA, 97, 5528-5533.
4. Gardner,T.S., Cantor,C.R. and Collins,J.J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339-342.
5. Kobayashi,H., Kaern,M., Araki,M., Chung,K., Gardner,T.S., Cantor,C.R. and Collins,J.J. (2004) Programmable cells: Interfacing natural and engineered gene networks. Proc. Natl Acad. Sci. USA, 101, 8414-8419.
6. Guido,N.J., Wang,X., Adalsteinsson,D., McMillen,D., Hasty,J., Cantor,C.R., Elston,T.C. and Collins,J.J. (2006) A bottom-up approach to gene regulation. Nature, 439, 856-860.
7. Shen-Orr,S.S., Milo,R., Mangan,S. and Alon,U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet., 31, 64-68.
8. Mangan,S. and Alon,U. (2003) Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA, 100, 11980-11985.
9. Hartwell,L.H., Hopfield,J.J., Leibler,S. and Murray,A.W. (1999) From molecular to modular cell biology. Nature, 402, C47-C52.
10. Jacob,F. and Monod,J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3, 318-356.
11. Lamark,T., Rokenes,T.P., McDougall,J. and Storm,A.R. (1996) The complex bet promoters of Escherichia coli: Regulation by oxygen (arca), choline (beti), and osmotic stress. J. Bacteriol., 178, 1655-1662.
12. Rokenes,T.P., Lamark,T. and Storm,A.R. (1996) Dna-binding properties of the beti repressor protein of Escherichia coli: The inducer choline stimulates beti-dna complex formation. J. Bacteriol., 178, 1663-1670.
13. Ansari,A.Z., Bradner,J.E. and O'Halloran,T.V. (1995) Dna-bend modulation in a repressor-to-activator switching mechanism. Nature, 374, 371-375.
14. Meng,L.M., Kilstrup,M. and Nygaard,P. (1990) Autoregulation of purr repressor synthesis and involvement of purr in the regulation of purb, purc, purl, purmn and guaba expression in Escherichia coli. Eur. J. Biochem., 187, 373-379.
15. Meng,L.M. and Nygaard,P. (1990) Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli. Mol. Microbiol., 4, 2187-2192.
16. Oehler,S., Eismann,E.R., Kramer,H. and Muller-Hill,B. (1990) The three operators of the lac operon cooperate in repression. EMBO J., 9, 973-979.
17. Barkley,M.D., Riggs,A.D., Jobe,A. and Burgeois,S. (1975) Interaction of effecting ligands with lac repressor and repressor-operator complex. Biochemistry, 14, 1700-1712.
18. Dekel,E. and Alon,U. (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature, 436, 588-592.
19. Bintu,L., Buchler,N.E., Garcia,H.G., Gerland,U., Hwa,T., Kondev,J. and Phillips,R. (2005) Transcriptional regulation by the numbers: Models. Curr. Opin. Genet. Dev., 15, 116-124.
20. Bintu,L., Buchler,N.E., Garcia,H.G., Gerland,U., Hwa,T., Kondev,J., Kuhlman,T. and Phillips,R. (2005) Transcriptional regulation by the numbers: Applications. Curr. Opin. Genet. Dev., 15, 125-135.
21. Rosenfeld,N., Elowitz,M.B. and Alon,U. (2002) Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol., 323, 785-793.
22. Gottesman,S. (2002) Stealth regulation: Biological circuits with small rna switches. Genes Dev., 16, 2829-2842.
23. Axelsen,J.B. and Sneppen,K. (2004) Quantifying the benefits of translation regulation in the unfolded protein response. Phys. Biol., 1, 159-165.
24. Gragarov,A., Zeng,L., Zhao,X., Burkholder,M. and Gottesman,M.E. (1994) Specificity of dnak-peptide binding. J. Mol. Biol., 235, 848.
25. Arnvig,K.B., Pedersen,S. and Sneppen,K. (2000) Thermodynamics of heat shock response. Phys. Rev. Lett., 84, 3005-3008.