The incoherent feed-forward loop can generate non-monotonic input functions for genes

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Kaplan, Shai ^a   Bren, Anat ^a   Dekel, Erez ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

E. coli; Feed forward loop; Galactose system; Input function

Indexed keywords

CYCLIC AMP; GALACTOSE; REPRESSOR PROTEIN;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE ACTIVATION; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN MOTIF; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE DELETION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PROMOTER REGION;

ESCHERICHIA COLI;

COMPUTER SIMULATION; CYCLIC AMP; ESCHERICHIA COLI; GALACTOSE; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; REPRESSOR PROTEINS;

EID: 47349095809     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.43     Document Type: Article

References (37)

1. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton: Chapman and Hall/CRC
2. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461
3. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006 0008
4. Baker CH, Tomlinson SR, Garcia AE, Harman JG (2001) Amino acid substitution at position 99 affects the rate of CRP subunit exchange. Biochemistry 40: 12329-12338
5. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434: 1130-1134
6. Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R (2004) Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci USA 101: 6355-6360
7. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R (2005) Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev 15: 125-135
8. Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173: 33-38
9. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640-6645
10. Eichenberger P, Fujita M, Jensen ST, Conlon EM, Rudner DZ, Wang ST, Ferguson C, Haga K, Sato T, Liu JS, Losick R (2004) The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol 2: e328
11. Entus R, Aufderheide B, Herbert M, Sauro MH (2007) Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Syst Synthetic Biol. Published online
12. Geanacopoulos M, Adhya S (1997) Functional characterization of roles of GalR and GalS as regulators of the gal regulon. J Bacteriol 179: 228-234
13. Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ (2006) A bottom-up approach to gene regulation. Nature 439: 856-860
14. Holland MM, Leib TK, Gerlt JA (1988) Isolation and characterization of a small catalytic domain released from the adenylate cyclase from Escherichia coli by digestion with trypsin. J Biol Chem 263: 14661-14668
15. Ishihara S, Fujimoto K, Shibata T (2005) Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes Cells 10: 1025-1038
16. Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U (2008) Diverse two-dimensional input-functions control bacterial sugar genes. Mol Cell 29: 786-792
17. Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Bonavides-Martinez C, Ingraham J (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35: 7577-7590
18. Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33: D334-D337
19. Kuhlman T, Zhang Z, Saier Jr MH, Hwa T (2007) Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc Natl Acad Sci USA 104: 6043-6048
20. Lahav R, Gammie A, Tavazoie S, Rose MD (2007) Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol 27: 818-829
21. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804
22. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100: 11980-11985
23. Mangan S, Itzkovitz S, Zaslaver A, Alon U (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081
24. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827
25. Murphy KF, Balazsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 104: 12726-12731
26. Neidhart FCE (1996) Escherichia coli and Salmonella Cellular and Molecular Biology. Washington, USA: American Society of Microbiology Press
27. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381
28. Ronen M, Rosenberg R, Shraiman BI, Alon U (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 99: 10555-10560
29. Semsey S, Krishna S, Sneppen K, Adhya S (2007) Signal integration in the galactose network of Escherichia coli. Mol Microbiol 65: 465-476
30. Semsey S, Virnik K, Adhya S (2006) Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA. J Mol Biol 358: 355-363
31. Setty Y, Mayo AE, Surette MG, Alon U (2003) Detailed map of a cis-regulatory input function. Proc Natl Acad Sci USA 100: 7702-7707
32. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68
33. Temme K, Salis H, Tullman-Ercek D, Levskaya A, Hong S-H, Voigt CA (2008) Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island 1. J Mol Biol 377: 47-61
34. Weickert MJ, Adhya S (1993) The galactose regulon of Escherichia coli. Mol Microbiol 10: 245-251
35. Yakoby N, Lembong J, Schüpbach T, Shvartsman SY (2008) Drosophila eggshell is patterned by sequential action of feedforward and feedback loops. Development 135: 343-351
36. Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-628
37. Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U (2004) Just-in-time transcription program in metabolic pathways. Nat Genet 36: 486-491