A mutation within the β subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters

Journal of Bacteriology

Volumn 192, Issue 21, 2010, Pages 5580-5587

  James, Tamara D ^a   Cashel, Michael ^b   Hinton, Deborah M ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASIA PROTEIN; BACTERIAL PROTEIN; MOTA PROTEIN; RNA POLYMERASE BETA SUBUNIT; UNCLASSIFIED DRUG; BACTERIAL RNA; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; PROTEIN SUBUNIT;

ARTICLE; BACTERIAL GROWTH; BACTERIOPHAGE T4; DNA RNA HYBRIDIZATION; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE MUTATION; GENETIC TRANSCRIPTION; HYDROPHOBICITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; THERMOPHILIC BACTERIUM; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; ENTEROBACTERIA PHAGE T4; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; PHYSIOLOGY; PROTEIN SUBUNIT;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; BACTERIOPHAGE T4; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, VIRAL; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS, GENETIC; PROTEIN SUBUNITS; RNA, BACTERIAL;

EID: 78049396435     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00338-10     Document Type: Article

References (57)

1. 70 subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 272:27435-27443.
2. Barnard, A., A. Wolfe, and S. Busby. 2004. Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Curr. Opin. Microbiol. 7:102-108.
3. 70 region 4 needed for appropriation by the bacteriophage T4 transcription factors AsiA and MotA. J. Mol. Biol. 363:931-944.
4. Beck, L. L., T. G. Smith, and T. R. Hoover. 2007. Look, no hands! Unconventional transcriptional activators in bacteria. Trends Microbiol. 15:530-537.
5. Benson, K. H., and K. N. Kreuzer. 1992. Role of MotA transcription factor in bacteriophage T4 DNA replication. J. Mol. Biol. 228:88-100.
6. 70 to activate middle gene transcription. Mol. Microbiol. 69:331-343.
7. Colland, F., G. Orsini, E. N. Brody, H. Buc, and A. Kolb. 1998. The bacteriophage T4 AsiA protein: a molecular switch for sigma 70-dependent promoters. Mol. Microbiol. 27:819-829.
8. 70 region 4 function. J. Mol. Biol. 343:569-587.
9. Gregory, B. D., B. E. Nickels, S. J. Garrity, E. Severinova, L. Minakhin, R. J. Urbauer, J. L. Urbauer, T. Heyduk, K. Severinov, and A. Hochschild. 2004. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. Proc. Natl. Acad. Sci. U. S. A. 101:4554-4559.
10. Gruber, T. M., and C. A. Gross. 2003. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57:441-466.
11. Guild, N., M. Gayle, R. Sweeney, T. Hollingsworth, T. Modeer, and L. Gold. 1988. Transcriptional activation of bacteriophage T4 middle promoters by the MotA protein. J. Mol. Biol. 199:241-258.
12. Guttman, B., and E. Kutter. 1983. Overview, p. 8-10. In C. K. Mathews, E. M. Kutter, G. Mosig, and P. B. Berget (ed.), Bacteriophage T4. American Society for Microbiology, Washington, DC.
13. Helmann, J. D. 2009. RNA polymerase: a nexus of gene regulation. Methods 47:1-5.
14. Hinton, D. M. 1989. Transcript analyses of the uvsX-40-41 region of bacteriophage T4. Changes in the RNA as infection proceeds. J. Biol. Chem. 264:14432-14439.
15. Hinton, D. M. 1991. Transcription from a bacteriophage T4 middle promoter using T4 MotA protein and phage-modified RNA polymerase. J. Biol. Chem. 266:18034-18044.
16. Hinton, D. M. Transcriptional control in the prereplicative phase of T4 development. Virol. J., in press.
17. Hinton, D. M., R. March-Amegadzie, J. S. Gerber, and M. Sharma. 1996. Bacteriophage T4 middle transcription system: T4-modified RNA polymerase; AsiA, a sigma 70 binding protein; and transcriptional activator MotA. Methods Enzymol. 274:43-57.
18. 70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA. Microbiology 151:1729-1740.
19. Hirata, A., B. J. Klein, and K. S. Murakami. 2008. The X-ray crystal structure of RNA polymerase from Archaea. Nature 451:851-854.
20. Hsu, T., and J. D. Karam. 1990. Transcriptional mapping of a DNA replication gene cluster in bacteriophage T4. Sites for initiation, termination, and mRNA processing. J. Biol. Chem. 265:5303-5316.
21. Kuznedelov, K., L. Minakhin, A. Niedziela-Majka, S. L. Dove, D. Rogulja, B. E. Nickels, A. Hochschild, T. Heyduk, and K. Severinov. 2002. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295:855-857. (Pubitemid 34118366)
22. 70 region 4. EMBO J. 23:2952-2962.
23. March-Amegadzie, R., and D. M. Hinton. 1995. The bacteriophage T4 middle promoter PuvsX: analysis of regions important for binding of the T4 transcriptional activator MotA and for activation of transcription. Mol. Microbiol. 15:649-660.
24. Marshall, P., M. Sharma, and D. M. Hinton. 1999. The bacteriophage T4 transcriptional activator MotA accepts various base-pair changes within its binding sequence. J. Mol. Biol. 285:931-944.
25. Mattson, T., G. Van Houwe, and R. H. Epstein. 1978. Isolation and characterization of conditional lethal mutations in the mot gene of bacteriophage T4. J. Mol. Biol. 126:551-570.
26. Miller, E. S., E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. Ruger. 2003. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67:86-156.
27. 70 subunit of E. coli RNA polymerase and T4 AsiA. J. Mol. Biol. 306:631-642.
28. Murakami, K. S., S. Masuda, and S. A. Darst. 2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296:1280-1284.
29. Murphy, H., and M. Cashel. 2003. Isolation of RNA polymerase suppressors of a (p)ppGpp deficiency. Methods Enzymol. 371:596-601. (Pubitemid 37542760)
30. Nelson, M. A., M. Ericson, L. Gold, and J. F. Pulitzer. 1982. The isolation and characterization of TabR bacteria: hosts that restrict bacteriophage T4 rII mutants. Mol. Gen. Genet. 188:60-68.
31. Orsini, G., M. Ouhammouch, J. P. Le Caer, and E. N. Brody. 1993. The asiA gene of bacteriophage T4 codes for the anti-sigma 70 protein. J. Bacteriol. 175:85-93.
32. Ouhammouch, M., K. Adelman, S. R. Harvey, G. Orsini, and E. N. Brody. 1995. Bacteriophage T4 MotA and AsiA proteins suffice to direct Escherichia coli RNA polymerase to initiate transcription at T4 middle promoters. Proc. Natl. Acad. Sci. U. S. A. 92:1451-1455.
33. Ouhammouch, M., G. Orsini, and E. N. Brody. 1994. The asiA gene product of bacteriophage T4 is required for middle mode RNA synthesis. J. Bacteriol. 176:3956-3965.
34. Paget, M. S., and J. D. Helmann. 2003. The sigma70 family of sigma factors. Genome Biol. 4:203.
35. Pahari, S., and D. Chatterji. 1997. Interaction of bacteriophage T4 AsiA protein with Escherichia coli sigma70 and its variant. FEBS Lett. 411:60-62. (Pubitemid 27298371)
36. 70 subunit of Escherichia coli RNA polymerase. J. Bacteriol. 184:3957-3964.
37. Pene, C., and M. Uzan. 2000. The bacteriophage T4 anti-sigma factor AsiA is not necessary for the inhibition of early promoters in vivo. Mol. Microbiol. 35:1180-1191.
38. 70 proteins in T4-type phages and bacteria that are similar to AsiA, a transcription inhibitor and co-activator of bacteriophage T4. J. Mol. Biol. 344:1183-1197.
39. Pulitzer, J. F., A. Coppo, and M. Caruso. 1979. Host-virus interactions in the control of T4 prereplicative transcription. II. Interaction between tabC (rho) mutants and T4 mot mutants. J. Mol. Biol. 135:979-997.
40. Rabussay, D. 1983. Phage-evoked changes in RNA polymerase, p. 167-173. In C. K. Mathews, E. M. Kutter, G. Mosig, and P. B. Berget (ed.), Bacteriophage T4. American Society for Microbiology, Washington, DC.
41. Schmidt, R. P., and K. N. Kreuzer. 1992. Purified MotA protein binds the -30 region of a bacteriophage T4 middle-mode promoter and activates transcription in vitro. J. Biol. Chem. 267:11399-11407.
42. Schumacher, J., N. Joly, M. Rappas, X. Zhang, and M. Buck. 2006. Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation. J. Struct. Biol. 156:190-199.
43. Severinova, E., K. Severinov, and S. A. Darst. 1998. Inhibition of Escherichia coli RNA polymerase by bacteriophage T4 AsiA. J. Mol. Biol. 279:9-18.
44. Severinova, E., K. Severinov, D. Fenyo, M. Marr, E. N. Brody, J. W. Roberts, B. T. Chait, and S. A. Darst. 1996. Domain organization of the Escherichia coli RNA polymerase sigma 70 subunit. J. Mol. Biol. 263:637-647.
45. Stevens, A. 1973. An inhibitor of host sigma-stimulated core enzyme activity that purifies with DNA-dependent RNA polymerase of E. coli following T4 phage infection. Biochem. Biophys. Res. Commun. 54:488-493.
46. Stevens, A. 1972. New small polypeptides associated with DNA-dependent RNA polymerase of Escherichia coli after infection with bacteriophage T4. Proc. Natl. Acad. Sci. U. S. A. 69:603-607.
47. Stevens, A., and J. C. Rhoton. 1975. Characterization of an inhibitor causing potassium chloride sensitivity of an RNA polymerase from T4 phage-infected Escherichia coli. Biochemistry 14:5074-5079.
48. Stitt, B., and D. M. Hinton. 1994. Regulation of middle-mode transcription, p. 142-160. In J. D. Karam, J. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. Eiserling, L. Black, E. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. American Society for Microbiology, Washington, DC.
49. Stoskiene, G., L. Truncaite, A. Zajanckauskaite, and R. Nivinskas. 2007. Middle promoters constitute the most abundant and diverse class of promoters in bacteriophage T4. Mol. Microbiol. 64:421-434.
50. Studier, F. W., A. H. Rosenberg, J. J. Dunn, and J. W. Dubendorff. 1990. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185:60-89.
51. Truncaite, L., L. Piesiniene, G. Kolesinskiene, A. Zajanckauskaite, A. Driukas, V. Klausa, and R. Nivinskas. 2003. Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised. J. Mol. Biol. 327:335-346.
52. Vassylyev, D. G., S. Sekine, O. Laptenko, J. Lee, M. N. Vassylyeva, S. Borukhov, and S. Yokoyama. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417:712-719. (Pubitemid 34640620)
53. Vassylyev, D. G., M. N. Vassylyeva, A. Perederina, T. H. Tahirov, and I. Artsimovitch. 2007. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448:157-162. (Pubitemid 47067370)
54. Weisberg, R., D. M. Hinton, and S. Adhya. 2008. Transcriptional regulation in bacteriophage, p. 174-186. In B. W. J. Mahy and M. H. V. van Regenmortel (ed.), Encyclopedia of virology, 3rd ed. Elsevier, Oxford, United Kingdom.
55. Werner, F. 2008. Structural evolution of multisubunit RNA polymerases. Trends Microbiol. 16:247-250.
56. Yuan, A. H., and A. Hochschild. 2009. Direct activator/co-activator interaction is essential for bacteriophage T4 middle gene expression. Mol. Microbiol. 74:1018-1030.
57. Yuan, A. H., B. E. Nickels, and A. Hochschild. 2009. The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 106:6597-6602.