Stability and instability in the lysogenic state of phage lambda

Journal of Bacteriology

Volumn 192, Issue 22, 2010, Pages 6064-6076

  Little, John W ^a,b   Michalowski, Christine B ^a  

^a University of Arizona   (United States)

^b University of Arizona   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN CI; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BACTERIOPHAGE LAMBDA; CULTURE MEDIUM; DNA SEQUENCE; GENE CONTROL; GENE MUTATION; LYSOGENIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; WILD TYPE;

BACTERIOLYSIS; BACTERIOPHAGE LAMBDA; CULTURE MEDIA; GENE EXPRESSION REGULATION, VIRAL; LYSOGENY; MUTATION; PROMOTER REGIONS, GENETIC; REPRESSOR PROTEINS; VIRAL REGULATORY AND ACCESSORY PROTEINS;

ENTEROBACTERIA PHAGE LAMBDA;

EID: 78049435111     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00726-10     Document Type: Article

References (63)

1. Anderson, L. M., and H. Yang. 2008. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc. Natl. Acad. Sci. U. S. A. 105:5827-5832.
2. Anderson, L. M., and H. Yang. 2008. A simplified model for lysogenic regulation through DNA looping. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2008:607-610.
3. Atsumi, S., and J. W. Little. 2006. Role of the lytic repressor in prophage induction of phage λ as analyzed by a module-replacement approach. Proc. Natl. Acad. Sci. U. S. A. 103:4558-4563.
4. Atsumi, S., and J. W. Little. 2004. Regulatory circuit design and evolution using phage λ. Genes Dev. 18:2086-2094.
5. Aurell, E., S. Brown, J. Johanson, and K. Sneppen. 2002. Stability puzzles in phage λ. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:051914.
6. Babić, A. C., and J. W. Little. 2007. Cooperative DNA binding by CI repressor is dispensable in a phage λ variant. Proc. Natl. Acad. Sci. U. S. A. 104:17741-17746.
7. Baek, K., S. Svenningsen, H. Eisen, K. Sneppen, and S. Brown. 2003. Single-cell analysis of λ immunity regulation. J. Mol. Biol. 334:363-372.
8. Bailone, A., A. Levine, and R. Devoret. 1979. Inactivation of prophage λ repressor in vivo. J. Mol. Biol. 131:553-572.
9. Becskei, A., and L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature 405:590-593.
10. Brooks, K., and A. J. Clark. 1967. Behavior of λ bacteriophage in a recombination deficient strain of E. coli. Virology 1:283-293.
11. Capaldo-Kimball, F., and S. D. Barbour. 1971. Involvement of recombination genes in growth and viability of Escherichia coli K-12. J. Bacteriol. 106:204-212.
12. 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.
13. Cohen, S., B. J. Knoll, J. W. Little, and D. W. Mount. 1981. Preferential cleavage of phage λ repressor monomers by recA protease. Nature 294:182-184.
14. Cox, M. M., M. F. Goodman, K. N. Kreuzer, D. J. Sherratt, S. J. Sandler, and K. J. Marians. 2000. The importance of repairing stalled replication forks. Nature 404:37-41.
15. Degnan, P. H., C. B. Michalowski, A. C. Babić, M. H. J. Cordes, and J. W. Little. 2007. Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage λ. Mol. Microbiol. 64:232-244.
16. Delbrück, M. 1945. The burst size distribution in the growth of bacterial viruses (bacteriophages). J. Bacteriol. 50:131-135.
17. RM and efficient switching from lysogeny. Genes Dev. 15:3013-3022.
18. 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.
19. Ferrell, J. E., Jr. 2002. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 14:140-148.
20. Folkmanis, A., W. Maltzman, P. Mellon, A. Skalka, and H. Echols. 1977. The essential role of the cro gene in lytic development by bacteriophage λ. Virology 81:352-362.
21. Frankel, A. D., and P. S. Kim. 1991. Modular structure of transcription factors: implications for gene regulation. Cell 65:717-719.
22. Giese, K. C., C. B. Michalowski, and J. W. Little. 2008. RecA-dependent cleavage of LexA dimers. J. Mol. Biol. 377:148-161.
23. Gimble, F. S., and R. T. Sauer. 1985. Mutations in bacteriophage λ repressor that prevent RecA-mediated cleavage. J. Bacteriol. 162:147-154.
24. - proteins in the autodigestion and RecA-mediated cleavage reactions. J. Mol. Biol. 192:39-47.
25. Gimble, F. S., and R. T. Sauer. 1989. λ repressor mutants that are better substrates for RecA-mediated cleavage. J. Mol. Biol. 206:29-39.
26. Golding, I., J. Paulsson, S. M. Zawilski, and E. C. Cox. 2005. Real-time kinetics of gene activity in individual bacteria. Cell 123:1025-1036.
27. Hartl, D. L., and D. E. Dykhuizen. 1984. The population genetics of Escherichia coli. Annu. Rev. Genet. 18:31-68.
28. He, G., R. A. Shankar, M. Chzhan, A. Samouilov, P. Kuppusamy, and J. L. Zweier. 1999. Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging. Proc. Natl. Acad. Sci. U. S. A. 96:4586-4591.
29. Hendrix, R. W., and R. L. Duda. 1992. Bacteriophage λPaPa: not the mother of all λ phages. Science 258:1145-1148.
30. Hershey, A. D., and R. Rotman. 1949. Genetic recombination between host-range and plaque-type mutants of bacteriophage in single bacterial cells. Genetics 34:44-71.
31. Jain, D., B. E. Nickels, A. Hochschild, and S. A. Darst. 2004. Structure of a ternary transcription activation complex. Mol. Cell 13:45-53.
32. 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.
33. Kaiser, A. D. 1955. A genetic study of the temperate coliphage λ. Virology 1:424-443.
34. Little, J. W. 1993. LexA cleavage and other self-processing reactions. J. Bacteriol. 175:4943-4950.
35. Little, J. W. 1983. The SOS regulatory system: control of its state by the level of RecA protease. J. Mol. Biol. 167:791-808.
36. Little, J. W., and D. W. Mount. 1982. The SOS regulatory system of Escherichia coli. Cell 29:11-22.
37. Little, J. W., D. P. Shepley, and D. W. Wert. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
38. Livny, J., and D. I. Friedman. 2004. Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system. Mol. Microbiol. 51:1691-1704.
39. McAdams, H. H., and A. Arkin. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. U. S. A. 94:814-819.
40. McCool, J. D., E. Long, J. F. Petrosino, H. A. Sandler, S. M. Rosenberg, and S. J. Sandler. 2004. Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy. Mol. Microbiol. 53:1343-1357.
41. Michalowski, C. B., and J. W. Little. 2005. Positive autoregulation of cI is a dispensable feature of the phage λ gene regulatory circuitry. J. Bacteriol. 187:6430-6442.
42. RM promoter: implications for evolution of gene regulatory circuitry. J. Bacteriol. 186:7988-7999.
43. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
44. Mount, D. W. 1976. A method for the isolation of phage mutants altered in their response to lysogenic induction. Mol. Gen. Genet. 145:165-167.
45. Nielsen, H. J., B. Youngren, F. G. Hansen, and S. Austin. 2007. Dynamics of Escherichia coli chromosome segregation during multifork replication. J. Bacteriol. 189:8660-8666.
46. Pakula, A. A., V. B. Young, and R. T. Sauer. 1986. Bacteriophage lambda cro mutations: effects on activity and intracellular degradation. Proc. Natl. Acad. Sci. U. S. A. 83:8829-8833.
47. Pennington, J. M., and S. M. Rosenberg. 2007. Spontaneous DNA breakage in single living Escherichia coli cells. Nat. Genet. 39:797-802.
48. Powell, B. S., M. P. Rivas, D. L. Court, Y. Nakamura, and C. L. Turnbough, Jr. 1994. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22:5765-5766.
49. Reichardt, L., and A. D. Kaiser. 1971. Control of λ repressor synthesis. Proc. Natl. Acad. Sci. U. S. A. 68:2185-2189.
50. Rosenfeld, N., J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. 2005. Gene regulation at the single-cell level. Science 307:1962-1965.
51. Rozanov, D. V., R. D'Ari, and S. P. Sineoky. 1998. RecA-independent pathways of lambdoid prophage induction in Escherichia coli. J. Bacteriol. 180:6306-6315.
52. Sarai, A., and Y. Takeda. 1989. λ repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl. Acad. Sci. U. S. A. 86:6513-6517.
53. Savageau, M. A. 1983. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122:732-744.
54. Schubert, R. A., I. B. Dodd, J. B. Egan, and K. E. Shearwin. 2007. Cro's role in the CI-Cro bistable switch is critical for λ's transition from lysogeny to lytic development. Genes Dev. 21:2461-2472.
55. RM promoter. Proc. Natl. Acad. Sci. U. S. A. 80:496-500.
56. 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.
57. Skarstad, K., E. Boye, and H. B. Steen. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J. 5:1711-1717.
58. Slilaty, S. N., and J. W. Little. 1987. Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism. Proc. Natl. Acad. Sci. U. S. A. 84:3987-3991.
59. Stayrook, S., P. Jaru-Ampornpan, J. Ni, A. Hochschild, and M. Lewis. 2008. Crystal structure of the λ repressor and a model for pairwise cooperative operator binding. Nature 452:1022-1025.
60. Takeda, Y., A. Sarai, and V. M. Rivera. 1989. Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc. Natl. Acad. Sci. U. S. A. 86:439-443.
61. Thirion, J. P., and M. Hofnung. 1972. On some genetic aspects of phage λ resistance in E. coli K12. Genetics 71:207-216.
62. Vieira, J., and J. Messing. 1987. Production of single-stranded plasmid DNA. Methods Enzymol. 153:3-11.
63. 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.