Design and implementation of three incoherent feed-forward motif based biological concentration sensors

Systems and Synthetic Biology

Volumn 1, Issue 3, 2007, Pages 119-128

  Entus, Robert ^a   Aufderheide, Brian ^a   Sauro, Herbert M ^b  

^a KECK GRADUATE INSTITUTE   (United States)

^b University of Washington   (United States)

Author keywords

Feed forward networks; Modules; Simulation; Synthetic biology

Indexed keywords

ESCHERICHIA COLI;

EID: 41349091647     PISSN: 18725325     EISSN: 18725333     Source Type: Journal    
DOI: 10.1007/s11693-007-9008-6     Document Type: Article

References (32)

1. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene-regulation by lambda-phage repressor. Proc Natl Acad Sci USA Biol Sci 79:1129-1133
2. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130-1134
3. 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
4. Belfaiza J, Parsot C, Martel A, Delatour CB, Margarita D, Cohen GN, Saintgirons I (1986) Evolution in biosynthetic pathways - 2 enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region. Proc Natl Acad Sci USA 83:867-871
5. Bray D (1995) Protein molecules as computational elements in living cells. Nature 376:307-312
6. Gottesman S (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58:303-328
7. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52
8. Huang JB, Villemain J, Padilla R, Sousa R (1999) Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription. J Mol Biol 293:457-475
9. Huerta AM, Collado-Vides J (2003) Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol 333:261-278
10. 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
11. Kaern M, Weiss R (2006) Synthetic gene regulatory systems. In: Szallasi Z, Stelling J, Periwal V (eds) System modeling in cellular biology from concepts to nuts and bolts, chap 13. MIT Press, pp 269-298
12. Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005) Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 33:1040-1050
13. Kumar A, Patel SS (1997) Inhibition of T7 RNA polymerase: transcription initiation and transition from initiation to elongation are inhibited by T7 lysozyme via a ternary complex with RNA polymerase and promoter DNA. Biochemistry 36:13954-13962
14. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804
15. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100:11980-11985
16. Mayya V, Loew LM (2005) STAT module can function as a biphasic amplitude filter. Syst Biol 2:43-52
17. 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
18. Moffatt BA, Studier FW (1987) T7 Lysozyme inhibits transcription by T7 RNA-polymerase. Cell 49:221-227
19. Old IG, Phillips SEV, Stockley PG, Saintgirons I (1991) Regulation of methionine biosynthesis in the Enterobacteriaceae. Prog Biophys Mol Biol 56:145-185
20. Phillips SEV, Stockley PG (1996) Structure and function of Escherichia coli met repressor: similarities and contrasts with trp repressor. Phil Trans Roy Soc London B Biol Sci 351:527-535
21. Sauro HM, Kholodenko BN (2004) Quantitative analysis of signaling networks. Prog Biophys Mol Biol 86:5-43
22. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H (2003) Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS 7(4):355-372
23. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18:1262-1268
24. 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
25. 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
26. Stano NM, Patel SS (2004) T7 lysozyme represses T7 RNA polymerase transcription by destabilizing the open complex during initiation. J Biol Chem 279:16136-16143
27. Storz G, Opdyke JA, Zhang AX (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7:140-144
28. Storz G, Altuvia S, Wassarman KM (2005) An abundance of RNA regulators. Annu Rev Biochem 74:199-217
29. Villemain J, Sousa R (1998) Specificity in transcriptional regulation in the absence of specific DNA binding sites: the case of T7 lysozyme. J Mol Biol 281:793-802
30. Weissbach H, Brot N (1991) Microreview regulation of methionine synthesis in Escherichia coli. Mol Microbiol 5(7): 1693-1597
31. Wolf DM, Arkin AP (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6:125-134
32. Zhang X, Studier FW (1997) Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. J Mol Biol 269:10-27