Regulatory circuit design and evolution using phage λ

Genes and Development

Volumn 18, Issue 17, 2004, Pages 2086-2094

  Atsumi, Shota ^a   Little, John W ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

Circuit design; Evolution of gene regulatory circuitry; Gene regulatory circuit; Lac repressor; Lambda phage; Systems behavior

Indexed keywords

CIS ACTING ELEMENT; DNA BINDING PROTEIN;

ARTICLE; BACTERIOPHAGE LAMBDA; EPIGENETICS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETIC SELECTION; LACTOSE OPERON; LYSOGENIZATION; NONHUMAN; PRIORITY JOURNAL; PROPHAGE; REPRESSOR GENE; ULTRAVIOLET RADIATION; WILD TYPE;

BACTERIA; BACTERIOPHAGE LAMBDA; DNA-BINDING PROTEINS; DOSE-RESPONSE RELATIONSHIP, RADIATION; EVOLUTION; GENE EXPRESSION REGULATION, VIRAL; LYSOGENY; MODELS, BIOLOGICAL; REPRESSOR PROTEINS; SELECTION (GENETICS); ULTRAVIOLET RAYS; VIRAL PROTEINS; VIRUS ACTIVATION;

BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 4444256116     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1226004     Document Type: Article

References (38)

1. Alon, U., Surette, M.G., Barkai, N., and Leibler, S. 1999. Robustness in bacterial chemotaxis. Nature 397: 168-171.
2. Atkinson, M.R., Savageau, M.A., Myers, J.T., and Ninfa, A.J. 2003. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113: 597-607.
3. Betz, J.L., Sasmor, H.M., Buck, F., Insley, M.Y., and Caruthers, M.H. 1986. Base substitution mutants of the lac operator: In vivo and in vitro affinities for lac repressor. Gene 50: 123-132.
4. Calef, E., Avitabile, L.d.G., Marchelli, C., Menna, T., Neubauer, Z., and Soller, A. 1971. The genetics of the anti-immune phenotype of defective λ lysogens. In The bacteriophage lambda (ed. A.D. Hershey), pp. 609-620. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
5. Carroll, S.B. 2000. Endless forms: The evolution of gene regulation and morphological diversity. Cell 101: 577-580.
6. Datsenko, K.A. and Wanner, B.L. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. 97: 6640-6645.
7. Dodd, I.B., Perkins, A.J., Tsemitsidis, D., and Egan, J.B. 2001. Octamerization of λ CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes & Dev. 15: 3013-3022.
8. Dodd, I.B., Shearwin, K.E., Perkins, A.J., Burr, T., Hochschild, A., and Egan, J.B. 2004. Cooperativity in long-range gene regulation by the λ CI repressor. Genes & Dev. 18: 344-354.
9. Eisen, H., Brachet, P., Pereira da Silva, L., and Jacob, F. 1970. Regulation of repressor expression in λ. Proc. Natl. Acad. Sci. 66: 855-862.
10. Elowitz, M.B., and Leibler, S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
11. Gardner, T.S., Cantor, C.R., and Collins, J.J. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
12. Gilbert, W. and Müller-Hill, B. 1966. Isolation of the Lac repressor. Proc. Natl. Acad. Sci. 56: 1891-1898.
13. Guet, C.C., Elowitz, M.B., Hsing, W., and Leibler, S. 2002. Combinatorial synthesis of genetic networks. Science 296: 1466-1470.
14. Hartwell, L.H., Hopfield, J.J., Leibler, S., and Murray, A.W. 1999. From molecular to modular cell biology. Nature 402: C47-C52.
15. Herskowitz, I. and Hagen, D. 1980. The lysis-lysogeny decision of phage λ: Explicit programming and responsiveness. Annu. Rev. Genet. 14: 399-445.
16. Hsieh, W.T., Whitson, P.A., Matthews, K.S., and Wells, R.D. 1987. Influence of sequence and distance between two operators on interaction with the lac repressor. J. Biol. Chem. 262: 14583-14591.
17. Kitano, H. 2002. Systems biology: A brief overview. Science 295: 1662-1664.
18. Kourilsky, P. 1973. Lysogenization by bacteriophage λ. I. Multiple infection and the lysogenic response. Mol. Gen. Genet. 122: 183-195.
19. Little, J.W. and Mount, D.W. 1982. The SOS regulatory system of Escherichia coli. Cell 29: 11-22.
20. Little, J.W., Shepley, D.P., and Wert, D.W. 1999. Robustness of a gene regulatory circuit. EMBO J. 18: 4299-4307.
21. RM promoter: Implications for evolution of gene regulatory circuitry. J. Bacteriol. (in press).
22. Miller, J.H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
23. Muller, J., Oehler, S., and Müller-Hill, B. 1996. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol. 257: 21-29.
24. Powell, B.S., Rivas, M.P., Court, D.L., Nakamura, Y., and Turnbough Jr., C.L., 1994. Rapid confirmation of single copy λ prophage integration by PCR. Nucleic Acids Res. 22: 5765-5766.
25. Ptashne, M. 1992. A genetic switch: Phage λ and higher organisms. Cell Press and Blackwell Scientific Publications, Cambridge, MA.
26. -. 2004. A genetic switch: Phage λ revisited. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Ptashne, M. and Gann, A. 1998. Imposing specificity by localization: Mechanism and evolvability. Curr. Biol. 8: R812-R822.
28. Riggs, A.D., Newby, R.F., and Bourgeois, S. 1970. lac repressor-operator interaction. II. Effect of galactosides and other ligands. J. Mol. Biol. 51: 303-314.
29. Roberts, J.W. 1993. RNA and protein elements of E. coli and λ transcription antitermination complexes. Cell 72: 653-655.
30. Roberts, J.W. and Devoret, R. 1983. Lysogenic induction. In Lambda II (eds. R.W. Hendrix et al.), pp. 123-144. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Schleif, R. 1992. DNA looping. Annu. Rev. Biochem. 61: 199-223.
32. Sergueev, K., Yu, D., Austin, S., and Court, D. 2001. Cell toxicity caused by products of the pL operon of bacteriophage λ. Gene 272: 227-235.
33. Vologodskii, A.V., Levene, S.D., Klenin, K.V., Frank-Kamenetskii, M., and Cozzarelli, N.R. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227: 1224-1243.
34. Wall, M.E., Hlavacek, W.S., and Savageau, M.A. 2004. Design of gene circuits: Lessons from bacteria. Nat. Rev. Genet. 5: 34-42.
35. Whipple, F.W., Kuldell, N.H., Cheatham, L.A., and Hochschild, A. 1994. Specificity determinants for the interaction of λ repressor and P22 repressor dimers. Genes & Dev. 8: 1212-1223.
36. Whitson, P.A., Hsieh, W.T., Wells, R.D., and Matthews, K.S. 1987. Influence of supercoiling and sequence context on operator DNA binding with lac repressor. J. Biol. Chem. 262: 14592-14599.
37. Wolf, D.M. and Arkin, A. P. 2003. Motifs, modules and games in bacteria. Curr. Opin. Microbiol. 6: 125-134.
38. Yokobayashi, Y., Weiss, R., and Arnold, F.H. 2002. Directed evolution of a genetic circuit. Proc. Natl. Acad. Sci. 99: 16587-16591.