Sequence tolerance of the phage λ PRM promoter: Implications for evolution of gene regulatory circuitry

Journal of Bacteriology

Volumn 186, Issue 23, 2004, Pages 7988-7999

  Michalowski, Christine B ^a   Short, Megan D ^a,c   Little, John W ^a,b  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Arizona   (United States)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE LAMBDA; GENE CONTROL; LYSOGENIZATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROPHAGE;

BACTERIOPHAGE LAMBDA; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; GENES, REGULATOR; PROMOTER REGIONS (GENETICS); PROPHAGES;

BACTERIOPHAGE LAMBDA; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 4444360812     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.23.7988-7999.2004     Document Type: Article

References (56)

1. Atsumi, S., and J. W. Little. 2004. Regulatory circuit design and evolution using phage λ. Genes Dev. 18:2086-2094.
2. Buc, H., and W. R. McClure. 1985. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry 24:2712-2723.
3. Churchward, G., D. Belin, and Y. Nagamine. 1984. A pSC101-derived plasmid which shows no sequence homology to other commonly used cloning vectors. Gene 31:165-171.
4. Cohen, S., B. J. Knoll, J. W. Little, and D. W. Mount. 1981. Preferential cleavage of phage lambda repressor monomers by recA protease. Nature 294:182-184.
5. Craig, M. L., O. V. Tsodikov, K. L. McQuade, P. E. Schlax, Jr., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. 1998. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283:741-756.
6. Crowl, R. M., R. P. Boyce, and H. Echols. 1981. Repressor cleavage as a prophage induction mechanism: hypersensitivity of a mutant λ cI protein to RecA-mediated proteolysis. J. Mol. Biol. 152:815-820.
7. RM and efficient switching from lysogeny. Genes Dev. 15:3013-3022.
8. Dodd, I. B., K. E. Shearwin, A. J. Perkins, T. Burr, A. Hochschild, and J. B. Egan. 2004. Cooperativity in long-range gene regulation by the λ CI repressor. Genes Dev. 18:344-354.
9. R promoter. J. Mol. Biol. 240:119-126.
10. Gardner, T. S., C. R. Cantor, and J. J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342.
11. Gimble, F. S., and R. T. Sauer. 1989. Lambda repressor mutants that are better substrates for RecA-mediated cleavage. J. Mol. Biol. 206:29-39.
12. RM promoter of bacteriophage lambda. Gene 54:291-297.
13. RM promoter. J. Mol. Biol. 157:493-525.
14. Herskowitz, I., and D. Hagen. 1980. The lysis-lysogeny decision of phage λ: explicit programming and responsiveness. Annu. Rev. Genet. 14:399-445.
15. Hlavacek, W. S., and M. A. Savageau. 1995. Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. J. Mol. Biol. 248:739-755.
16. Hopkins, N., and M. Ptashne. 1971. Genetics of virulence, p. 571-574. In A. D. Hershey (ed.), The bacteriophage lambda. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
17. Huynh, T. V., R. A. Young, and R. W. Davis. 1985. Constructing and screening cDNA libraries using λgt10 and λgt11, p. 49-80. In D. Glover (ed.), DNA cloning: a practical approach, vol. I. IRL Press, Inc., Boca Raton, Fla.
18. R. J. Mol. Biol. 200:735-739.
19. Jain, D., B. E. Nickels, A. Hochschild, and S. A. Darst. 2004. Structure of a ternary transcription activation complex. Mol. Cell 13:45-53.
20. Juhala, R. J., M. E. Ford, R. L. Duda, A. Youlton, G. F. Hatfull, and R. W. Hendrix. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299:27-51.
21. 70 that result in defects in phage lambda repressor-stimulated transcription. J. Bacteriol. 176:2991-2998.
22. Li, M., H. Moyle, and M. M. Susskind. 1994. Target of the transcriptional activation function of phage lambda cI protein. Science 263:75-77.
23. Little, J. W. 1984. Autodigestion of lexA and phage lambda repressors. Proc. Natl. Acad. Sci. USA 81:1375-1379.
24. Little, J. W. 1993. LexA cleavage and other self-processing reactions. J. Bacteriol. 175:4943-4950.
25. Little, J. W. 1983. The SOS regulatory system: control of its state by the level of RecA protease. J. Mol. Biol. 167:791-808.
26. Little, J. W., and D. W. Mount. 1982. The SOS regulatory system of Escherichia coli. Cell 29:11-22.
27. Little, J. W., D. P. Shepley, and D. W. Wert. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
28. Livny, J., and D. I. Friedman. 2004. Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system. Mol. Microbiol. 51:1691-1704.
29. Mao, C., and J. W. Little. 1998. Mutations affecting cooperative DNA binding of phage HK022 CI repressor. J. Mol. Biol. 279:31-48.
30. R3 and autogenous negative control by repressor. J. Mol. Biol. 139:147-161.
31. R3: their roles in mediating the effects of repressor and cro. J. Mol. Biol. 139:163-194.
32. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
33. Mulligan, M. E., and W. R. McClure. 1986. Analysis of the occurrence of promoter-sites in DNA. Nucleic Acids Res. 14:109-126.
34. Mustard, J. A., and J. W. Little. 2000. Analysis of Escherichia coli RecA interactions with LexA, λ CI, and UmuD by site-directed mutagenesis of recA. J. Bacteriol. 182:1659-1670.
35. 70 region 4 involved in transcription activation by λcI. J. Mol. Biol. 324:17-34.
36. Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
37. Powell, B. S., D. L. Court, Y. Nakamura, M. P. Rivas, and C. L. Turnbough, Jr. 1994. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22:5765-5766.
38. Ptashne, M. 1992. A genetic switch: phage λ and higher organisms. Cell Press and Blackwell Scientific Publications, Cambridge, Mass.
39. Ptashne, M. 2004. A genetic switch: phage lambda revisited. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
40. Revet, B., B. Von Wilcken-Bergmann, H. Bessert, A. Barker, and B. Müller-Hill. 1999. Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Curr. Biol. 9:151-154.
41. Roberts, J. W., and R. Devoret. 1983. Lysogenic induction, p. 123-144. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
42. Rosen, E. D., and G. N. Gussin. 1979. Clustering of Prm mutations of bacteriophage lambda in the region between 33 and 40 nucleotides from the cI transcription start point. Virology 98:393-410.
43. Rosen, E. D., J. L. Hartley, K. Matz, B. P. Nichols, K. M. Young, J. E. Donelson, and G. N. Gussin. 1980. DNA sequence analysis of prm mutations of coliphage lambda. Gene 11:197-205.
44. Ross, W., S. E. Aiyar, J. Salomon, and R. L. Gourse. 1998. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol. 180:5375-5383.
45. Sauer, R. T. 1978. DNA sequence of the bacteriophage λ c1 gene. Nature 276:301-302.
46. Sauer, R. T., and R. Anderegg. 1978. Primary structure of the lambda repressor. Biochemistry 17:1092-1100.
47. Savageau, M. A. 1974. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 252:546-549.
48. Savageau, M. A. 1971. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229:542-544.
49. Shean, C. S., and M. E. Gottesman. 1992. Translation of the prophage lambda cI transcript. Cell 70:513-522.
50. Simons, R. W., F. Houman, and N. Kleckner. 1987. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53:85-96.
51. Whipple, F. W., N. H. Kuldell, L. A. Cheatham, and A. Hochschild. 1994. Specificity determinants for the interaction of λ repressor and P22 repressor dimers. Genes Dev. 8:1212-1223.
52. R region of bacteriophage lambda. J. Bacteriol. 175:5648-5654.
53. R. J. Mol. Biol. 229:37-51.
54. Yen, K. M., and G. N. Gussin. 1973. Genetic characterization of a prm mutant of bacteriophage lambda. Virology 56:300-312.
55. Yokobayashi, Y., R. Weiss, and F. H. Arnold. 2002. Directed evolution of a genetic circuit. Proc. Natl. Acad. Sci. USA 99:16587-16591.
56. Young, R. A., and R. W. Davis. 1983. Efficient isolation of genes by using antibody probes. Proc. Natl. Acad. Sci. USA 80:1194-1198.