Escherichia coli RNA polymerase recognition of a σ70- dependent promoter requiring a -35 DNA element and an extended -10 TGn motif

Journal of Bacteriology

Volumn 188, Issue 24, 2006, Pages 8352-8359

  Hook Barnard, India ^a   Johnson, Xanthia B ^a,b   Hinton, Deborah M ^a  

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

^b Domestic Violence Program   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; DNA; PERMANGANATE POTASSIUM; RNA POLYMERASE; SIGMA FACTOR;

ARTICLE; DNA BINDING; DNA TEMPLATE; ENZYME ASSAY; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF;

BASE SEQUENCE; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS (GENETICS); SIGMA FACTOR;

ESCHERICHIA COLI;

EID: 33845452240     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00853-06     Document Type: Article

References (54)

1. Barne, K. A., J. A. Bown, S. J. Busby, and S. D. Minchin. 1997. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the "extended-10" motif at promoters. EMBO J. 16:4034-4040.
2. Browning, D. F., and S. J. Busby. 2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2:57-65.
3. Callaci, S., E. Heyduk, and T. Heyduk. 1999. Core RNA polymerase from Escherichia coli induces a major change in the domain arrangement of the sigma 70 subunit. Mol. Cell 3:229-238.
4. Campbell, E. A., O. Muzzin, M. Chlenov, J. L. Sun, C. A. Olson, O. Weinman, M. L. Trester-Zedlitz, and S. A. Darst. 2002. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell 9:527-539.
5. Chan, B., A. Spassky, and S. Busby. 1990. The organization of open complexes between Escherichia coli RNA polymerase and DNA fragments carrying promoters either with or without consensus -35 region sequences. Biochem. J. 270:141-148.
6. Cheng, Y., S. M. Dylla, and C. L. Turnbough, Jr. 2001. A long T.A tract in the upp initially transcribed region is required for regulation of upp expression by UTP-dependent reiterative transcription in Escherichia coli. J. Bacteriol. 183:221-228.
7. 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 down-stream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283:741-756.
8. Daniels, D., P. Zuber, and R. Losick. 1990. Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter. Proc. Natl. Acad. Sci. USA 87:8075-8079.
9. Dombroski, A. J. 1997. Recognition of the -10 promoter sequence by a partial polypeptide of sigma70 in vitro. J. Biol. Chem. 272:3487-3494.
10. Dombroski, A. J., B. D. Johnson, M. Lonetto, and C. A. Gross. 1996. The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing. Proc. Natl. Acad. Sci. USA 93:8858-8862.
11. Fenton, M. S., and J. D. Gralla. 2001. Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization. Proc. Natl. Acad. Sci. USA 98:9020-9025.
12. Fenton, M. S., S. J. Lee, and J. D. Gralla. 2000. Escherichia coli promoter opening and -10 recognition: mutational analysis of sigma70. EMBO J. 19:1130-1137.
13. Grana, D., T. Gardella, and M. M. Susskind. 1988. The effects of mutations in the ant promoter of phage P22 depend on context. Genetics 120:319-327.
14. 70 function in vivo. Mol. Microbiol. 56:1208-1219.
15. Gruber, T. M., and C. A. Gross. 2003. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57:441-466.
16. Hawley, D. K., and W. R. McClure. 1983. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:2237-2255.
17. 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.
18. 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.
19. Hinton, D. M., S. Pande, N. Wais, X. B. Johnson, M. Vuthoori, A. Makela, and I. Hook-Barnard. 2005. Transcriptional takeover by sigma appropriation: remodeling of the sigma70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and coactivator AsiA. Microbiology 151:1729-1740.
20. Hinton, D. M., S. Vuthoori, and R. Mulamba. 2006. The bacteriophage T4 inhibitor and coactivator AsiA inhibits Escherichia coli RNA Polymerase more rapidly in the absence of sigma70 region 1.1: evidence that region 1.1 stabilizes the interaction between sigma70 and core. J. Bacteriol. 188:1279-1285.
21. Juang, Y. L., and J. D. Helmann. 1994. A promoter melting region in the primary sigma factor of Bacillus subtilis: identification of functionally important aromatic amino acids. J. Mol. Biol. 235:1470-1488.
22. Keener, J., and M. Nomura. 1993. Dominant lethal phenotype of a mutation in the -35 recognition region of Escherichia coli sigma 70. Proc. Natl. Acad. Sci. USA 90:1751-1755.
23. Kumar, A., R. A. Malloch, N. Fujita, D. A. Smillie, A. Ishihama, and R. S. Hayward. 1993. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter. J. Mol. Biol. 232:406-418.
24. Lewis, D. E., and S. Adhya. 2004. Axiom of determining transcription start points by RNA polymerase in Escherichia coli. Mol. Microbiol. 54:692-701.
25. Lim, H. M., H. J. Lee, S. Roy, and S. Adhya. 2001. A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding. Proc. Natl. Acad. Sci. USA 98:14849-14852.
26. Lisser, S., and H. Margalit. 1993. Compilation of Escherichia coli mRNA promoter sequences. Nucleic Acids Res. 21:1507-1516.
27. Lisser, S., and H. Margalit. 1994. Determination of common structural features in Escherichia coli promoters by computer analysis. Eur. J. Biochem. 223:823-830.
28. Liu, J., and C. L. Turnbough, Jr. 1994. Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli. J. Bacteriol. 176:2938-2945.
29. 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.
30. Matlock, D. L., and T. Heyduk. 2000. Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by Escherichia coli RNA polymerase. Biochemistry 39:12274-12283.
31. Maxam, A. M., and W. Gilbert. 1980. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:499-560.
32. McClure, W. R., D. K. Hawley, P. Youderian, and M. M. Susskind. 1983. DNA determinants of promoter selectivity in Escherichia coli. Cold Spring Harbor Symp. Quant. Biol. 47(Pt. 1):477-481.
33. Miroslavova, N. S., and S. J. Busby. 2006. Investigations of the modular structure of bacterial promoters. Biochem. Soc. Symp. 73:1-10.
34. Mitchell, J. E., D. Zheng, S. J. Busby, and S. D. Minchin. 2003. Identification and analysis of "extended-10" promoters in Escherichia coli. Nucleic Acids Res. 31:4689-4695.
35. Mulligan, M. E., J. Brosius, and W. R. McClure. 1985. Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J. Biol. Chem. 260:3529-3538.
36. Murakami, K. S., and S. A. Darst. 2003. Bacterial RNA polymerases: the whole story. Curr. Opin. Struct. Biol. 13:31-39.
37. Murakami, K. S., S. Masuda, E. A. Campbell, O. Muzzin, and S. A. Darst. 2002. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296:1285-1290.
38. 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.
39. Paget, M. S., and J. D. Helmann. 2003. The sigma70 family of sigma factors. Genome Biol. 4:203.
40. Panaghie, G., S. E. Aiyar, K. L. Bobb, R. S. Hayward, and P. L. de Haseth. 2000. Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex. J. Mol. Biol. 299:1217-1230.
41. Pande, S., A. Makela, S. L. Dove, B. E. Nickels, A. Hochschild, and D. M. Hinton. 2002. The bacteriophage T4 transcription activator MotA interacts with the far-C-terminal region of the sigma70 subunit of Escherichia coli RNA polymerase. J. Bacteriol. 184:3957-3964.
42. Qi, F., C. Liu, L. S. Heath, and C. L. Turnbough, Jr. 1996. In vitro assay for reiterative transcription during transcriptional initiation by Escherichia coli RNA polymerase. Methods Enzymol. 273:71-85.
43. Sanderson, A., J. E. Mitchell, S. D. Minchin, and S. J. Busby. 2003. Substitutions in the Escherichia coli RNA polymerase sigma70 factor that affect recognition of extended -10 elements at promoters. FEBS Lett. 544:199-205.
44. Sasse-Dwight, S., and J. D. Gralla. 1989. KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264:8074-8081.
45. Siegele, D. A., J. C. Hu, W. A. Walter, and C. A. Gross. 1989. Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206:591-603.
46. Studier, F. W. 1991. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219:37-44.
47. Thouvenot, B., B. Charpentier, and C. Branlant. 2004. The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants. Biochem. J. 383:371-382.
48. Tomsic, M., L. Tsujikawa, G. Panaghie, Y. Wang, J. Azok, and P. L. deHaseth. 2001. Different roles for basic and aromatic amino acids in conserved region 2 of Escherichia coli sigma(70) in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase-promoter complexes. J. Biol. Chem. 276:31891-31896.
49. Tsujikawa, L., O. V. Tsodikov, and P. L. deHaseth. 2002. Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex. Proc. Natl. Acad. Sci. USA 99:3493-3498.
50. Vuthoori, S., C. W. Bowers, A. McCracken, A. J. Dombroski, and D. M. Hinton. 2001. Domain 1.1 of the sigma(70) subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes. J. Mol. Biol. 309:561-572.
51. Waldburger, C., and M. M. Susskind. 1994. Probing the informational content of Escherichia coli sigma 70 region 2.3 by combinatorial cassette mutagenesis. J. Mol. Biol. 235:1489-1500.
52. Whipple, F. W. 1998. Genetic analysis of prokaryotic and eukaryotic DNA-binding proteins in Escherichia coli. Nucleic Acids Res. 26:3700-3706.
53. Wilson, C., and A. J. Dombroski. 1997. Region 1 of sigma70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase. J. Mol. Biol. 267:60-74.
54. Zuber, P., J. Healy, H. L. Carter III, S. Cutting, C. P. Moran, Jr., and R. Losick. 1989. Mutation changing the specificity of an RNA polymerase sigma factor. J. Mol. Biol. 206:605-614.