Role of cis-acting sites in stimulation of the phage λ Prm promoter by CI-mediated looping

Journal of Bacteriology

Volumn 195, Issue 15, 2013, Pages 3401-3411

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

^a The University of Arizona   (United States)

^b University of Arizona   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CIS ACTING ELEMENT; DIMER; INTEGRATION HOST FACTOR; RNA POLYMERASE; TETRAMER;

ALLELE; ARTICLE; BACTERIAL MUTATION; BACTERIOPHAGE LAMBDA; CONTROLLED STUDY; GENE ACTIVATION; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION;

BACTERIOPHAGE LAMBDA; BINDING SITES; DNA, VIRAL; DNA-DIRECTED RNA POLYMERASES; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION, VIRAL; INTEGRATION HOST FACTORS; LYSOGENY; OPERATOR REGIONS, GENETIC; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84880729934     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.02148-12     Document Type: Article

References (47)

1. R3: their roles in mediating the effects of repressor and cro. J. Mol. Biol. 139:163-194.
2. RM promoter: implications for evolution of gene regulatory circuitry. J. Bacteriol. 186:7988-7999.
3. Ptashne M, Jeffrey A, Johnson AD, Maurer R, Meyer BJ, Pabo CO, Roberts TM, Sauer RT. 1980. How the λ repressor and cro work. Cell 19:1-11.
4. Ptashne M. 2004. A genetic switch: phage lambda revisited, vol 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
5. Dodd IB, Perkins AJ, Tsemitsidis D, Egan JB. 2001. Octamerization of λ CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. Genes Dev. 15:3013-3022.
6. Dodd IB, Shearwin KE, Perkins AJ, Burr T, Hochschild A, Egan JB. 2004. Cooperativity in long-range gene regulation by the λ CI repressor. Genes Dev. 18:344-354.
7. Anderson LM, Yang H. 2008. A simplified model for lysogenic regulation through DNA looping. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2008:607-610.
8. Anderson LM, Yang H. 2008. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc. Natl. Acad. Sci. U. S. A. 105:5827- 5832.
9. Cui L, Murchland I, Shearwin KE, Dodd IB. 2013. Enhancer-like longrange transcriptional activation by λ CI-mediated DNA looping. Proc. Natl. Acad. Sci. U. S. A. 110:2922-2927.
10. Lewis D, Le P, Zurla C, Finzi L, Adhya S. 2011. Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc. Natl. Acad. Sci. U. S. A. 108:14807-14812.
11. Little JW, Michalowski CB. 2010. Stability and instability in the lysogenic state of phage lambda. J. Bacteriol. 192:6064-6076.
12. Degnan PH, Michalowski CB, Babić AC, Cordes MHJ, Little JW. 2007. Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage λ. Mol. Microbiol. 64:232-244.
13. L promoter. Mol. Microbiol. 30:443-451.
14. L2 tandem promoter of bacteriophage λ. J. Mol. Biol. 260:484-491.
15. Giladi H, Koby S, Gottesman ME, Oppenheim AB. 1992. Supercoiling, integration host factor, and a dual promoter system participate in the control of the bacteriophage λ pL promoter. J. Mol. Biol. 224:937-948.
16. Giladi H, Gottesman M, Oppenheim AB. 1990. Integration host factor stimulates the phage lambda pL promoter. J. Mol. Biol. 213:109-121.
17. Gourse RL, Ross W, Gaal T. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37:687-695.
18. Miller JH. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
19. Little JW, Shepley DP, Wert DW. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
20. Giese KC, Michalowski CB, Little JW. 2008. RecA-dependent cleavage of LexA dimers. J. Mol. Biol. 377:148-161.
21. Atsumi S, Little JW. 2004. Regulatory circuit design and evolution using phage λ. Genes Dev. 18:2086-2094.
22. Michalowski CB, Little JW. 2005. Positive autoregulation of cI is a dispensable feature of the phage λ gene regulatory circuitry. J. Bacteriol. 187:6430-6442.
23. Whipple FW, Kuldell NH, Cheatham LA, Hochschild A. 1994. Specificity determinants for the interaction of λ repressor and P22 repressor dimers. Genes Dev. 8:1212-1223.
24. Simons RW, Houman F, Kleckner N. 1987. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53: 85-96.
25. Sarai A, Takeda Y. 1989. λ repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl. Acad. Sci. U. S. A. 86:6513-6517.
26. Powell BS, Rivas MP, Court DL, Nakamura Y, Turnbough CL, Jr. 1994. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22:5765-5766.
27. Stayrook S, Jaru-Ampornpan P, Ni J, Hochschild A, Lewis M. 2008. Crystal structure of the λ repressor and a model for pairwise cooperative operator binding. Nature 452:1022-1025.
28. Meng WM, Belyaeva T, Savery NJ, Busby SJW, Ross WE, Gaal T, Gourse RL, Thomas MS. 2001. UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase α subunit linker. Nucleic Acids Res. 29:4166-4178.
29. McClure WR. 1980. Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. U. S. A. 77:5634-5638.
30. McClure WR. 1985. Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54:171-204.
31. RM promoter. J. Mol. Biol. 157:493-525.
32. RM promoter. Proc. Natl. Acad.Sci. U. S. A. 80:496-500.
33. R. Biochemistry 31:57-65.
34. R promoter by salt concentration. Biochemistruy 24:4721-4726.
35. Leirmo S, Harrison C, Cayley S, Burgess RR, Record MT, Jr. 1987. Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro. Biochemistry 26:2095-2101.
36. Rao L, Ross W, Appleman JA, Gaal T, Leirmo S, Schlax PJ, Record MT, Jr, Gourse RL. 1994. Factor independent activation of rrnB P1: an "extended" promoter with an upstream element that dramatically increases promoter strength. J. Mol. Biol. 235:1421-1435.
37. RM promoter are sequence nonspecific and activate the promoter to a lesser extent than an introduced UP element of an rRNA promoter. J. Bacteriol. 178:6945-6951.
38. Ross W, Gourse RL. 2005. Sequence-independent upstream DNA-αCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc. Natl. Acad. Sci. U. S. A. 102:291-296.
39. Davis CA, Capp MW, Record MT, Jr, Saecker RM. 2005. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 102:285-290.
40. Jain D, Nickels BE, Hochschild A, Darst SA. 2004. Structure of a ternary transcription activation complex. Mol. Cell 13:45-53.
41. Li M, McClure WR, Susskind MM. 1997. Changing the mechanism of transcriptional activation by phage lambda repressor. Proc. Natl. Acad. Sci. U. S. A. 94:3691-3696.
42. Hwang JJ, Gussin GN. 1988. Interactions between Escherichia coli RNA polymerase and lambda repressor. Mutations in PRM affect repression of PR. J. Mol. Biol. 200:735-739.
43. Rice PA, Yang SW, Mizuuchi K, Nash HA. 1996. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87:1295-1306.
44. Vologodskii AV, Levene SD, Klenin KV, Frank-Kamenetskii M, Cozzarelli NR. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224-1243.
45. Mao C, Carlson NG, Little JW. 1994. Cooperative DNA-protein interactions: effects of changing the spacing between adjacent binding sites. J. Mol. Biol. 235:532-544.
46. Liu Z, Little JW. 1998. The spacing between binding sites controls the mode of cooperative DNA-protein interactions: implications for evolution of regulatory circuitry. J. Mol. Biol. 278:331-338.
47. Senear DF, Brenowitz M, Shea MA, Ackers GK. 1986. Energetics of cooperative protein-DNA interactions: comparison between quantitative deoxyribonuclease footprint titration and filter binding. Biochemistry 25: 7344-7354.