Multiple functions of a feed-forward-loop gene circuit

Journal of Molecular Biology

Volumn 349, Issue 3, 2005, Pages 501-514

  Wall, Michael E ^a   Dunlop, Mary J ^b   Hlavacek, William S ^c  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b California Institute of Technology   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Biological design principles; Controlled mathematical comparison; Escherichia coli; Genetic regulatory circuit; Network motif

Indexed keywords

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; NONHUMAN; POSITIVE FEEDBACK; PREDICTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; THEORETICAL STUDY;

ESCHERICHIA COLI;

EID: 19444376022     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.04.022     Document Type: Article

References (31)

1. W.S. Hlavacek, and M.A. Savageau Rules for coupled expression of regulator and effector genes in inducible circuits J. Mol. Biol. 255 1996 121 139
2. M.E. Wall, W.S. Hlavacek, and M.A. Savageau Design principles for regulator gene expression in a repressible gene circuit J. Mol. Biol. 332 2003 861 876
3. M.E. Wall, W.S. Hlavacek, and M.A. Savageau Design of gene circuits: lessons from bacteria Nature Rev. Genet. 5 2004 34 42
4. S.S. Shen-Orr, R. Milo, S. Mangan, and U. Alon Network motifs in the transcriptional regulation network of Escherichia coli Nature Genet. 31 2002 64 68
5. S. Mangan, and U. Alon Structure and function of the feed-forward loop network motif Proc. Natl Acad. Sci. USA 100 2003 11980 11985
6. R. Schleif Regulation of the L-arabinose operon of Escherichia coli Trends Genet. 16 2000 559 565
7. J.G. Harman Allosteric regulation of the cAMP receptor protein Biochim. Biophys. Acta 1547 2001 1 17
8. H. Salgado, S. Gama-Castro, A. Martinez-Antonio, E. Diaz-Peredo, F. Sanchez-Solano, and M. Peralta-Gil RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 Nucl. Acids Res. 32 2004 D303 D306
9. I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, and I.T. Paulsen EcoCyc: a comprehensive database resource for Escherichia coli Nucl. Acids Res. 33 2005 D334 D337
10. M.J. Weickert, and S. Adhya The galactose regulon of Escherichia coli Mol. Microbiol. 10 1993 245 251
11. J.M. Robert-Baudouy, R.C. Portalier, and F.R. Stoeber Regulation of hexuronate metabolism in Escherichia coli K12. Kinetics of enzyme induction of the hexuronate system Eur. J. Biochem. 43 1974 1 15
12. J. Robert-Baudouy, R. Portalier, and F. Stoeber Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products J. Bacteriol. 145 1981 211 220
13. P. Ritzenthaler, C. Blanco, and M. Mata-Gilsinger Interchangeability of repressors for the control of the uxu and uid operons in E. coli K12 Mol. Gen. Genet. 191 1983 263 270
14. M.J. Weickert, and S. Adhya Control of transcription of gal repressor and isorepressor genes in Escherichia coli J. Bacteriol. 175 1993 251 258
15. P. Ritzenthaler, and M. Mata-Gilsinger Multiple regulation involved in the expression of the uxuR regulatory gene in Escherichia coli K-12 Mol. Gen. Genet. 189 1983 351 354
16. S. Tong, A. Porco, T. Isturiz, and T. Conway Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism J. Bacteriol. 178 1996 3260 3269
17. H. Izu, O. Adachi, and M. Yamada Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli J. Mol. Biol. 267 1997 778 793
18. R. Tsunedomi, H. Izu, T. Kawai, and M. Yamada Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli J. Mol. Microbiol. Biotechnol. 6 2003 41 56
19. R. Tsunedomi, H. Izu, T. Kawai, K. Matsushita, T. Ferenci, and M. Yamada The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli J. Bacteriol. 185 2003 1783 1795
20. N. Peekhaus, and T. Conway Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex J. Bacteriol. 180 1998 1777 1785
21. C. Bausch, N. Peekhaus, C. Utz, T. Blais, E. Murray, T. Lowary, and T. Conway Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for l-idonic acid catabolism in Escherichia coli J. Bacteriol. 180 1998 3704 3710
22. C. Bausch, M. Ramsey, and T. Conway Transcriptional organization and regulation of the l-idonic acid pathway (GntII system) in Escherichia coli J. Bacteriol. 186 2004 1388 1397
23. M. Geanacopoulos, and S. Adhya Functional characterization of roles of GalR and GalS as regulators of the gal regulon J. Bacteriol. 179 1997 228 234
24. M.A. Savageau Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology 1976 Addison-Wesley Reading, MA
25. A. Martinez-Antonio, H. Salgado, S. Gama-Castro, R.M. Gutierrez-Rios, V. Jimenez-Jacinto, and J. Collado-Vides Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach Biotechnol. Bioeng. 84 2003 743 749
26. S. Rigali, M. Schlicht, P. Hoskisson, H. Nothaft, M. Merzbacher, B. Joris, and F. Titgemeyer Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships Nucl. Acids Res. 32 2004 3418 3426
27. M.A. Savageau A theory of alternative designs for biochemical control systems Biomed. Biochim. Acta 44 1985 875 880
28. M.A. Savageau Design principles for elementary gene circuits: elements, methods and examples Chaos 11 2001 142 159
29. Dunlop, M. J., Wall, M. E. (2005). Robustness in gene circuits: clustering of functional responses. In Proceedings of the 24th American Control Conference, Portland, Oregon. In the press.
30. D.S. Hochbaum, and D.B. Shmoys A best possible approximation algorithm for the k-center problem Math. Oper. Res. 10 1985 180 184
31. M.E. Wall, A. Rechtsteiner, and L.M. Rocha Singular value decomposition and principal component analysis D.P. Berrar W. Dubitzky M. Granzow A Practical Approach to Microarray Data Analysis 2003 Kluwer Norwell, MA 91 109