Escherichia coli promoters with up elements of different strengths: Modular structure of bacterial promoters

Journal of Bacteriology

Volumn 180, Issue 20, 1998, Pages 5375-5383

  Ross, Wilma ^a   Aiyar, Sarah E ^a   Salomon, Julia ^a   Gourse, Richard L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RNA POLYMERASE;

ALPHA CHAIN; ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA FLANKING REGION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN STRUCTURE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0031691355     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.180.20.5375-5383.1998     Document Type: Article

References (63)

1. Aiyar, S. E., R. L. Gourse, and W. Ross. Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase α subunit. Submitted for publication.
2. Aiyar, S. E., R. L. Gourse, and W. Ross. Unpublished observations.
3. Banner, C. D., C. P. Moran, Jr., and R. Losick. 1983. Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis. J. Mol. Biol. 168:351-365.
4. Belyaeva, T. A., V. A. Rhodius, C. L. Webster, and S. J. W. Busby. 1998. Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase α subunits. J. Mol. Biol. 277:789-804.
5. Blatter, E. E., W. Ross, H. Tang, R. L. Gourse, and R. H. Ebright. 1994. Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78: 889-896.
6. Bracco, L., D. Kotlarz, A. Kolb, S. Diekmann, and H. Buc. 1989. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 8:4289-4296.
7. Bujard, H., M. Brenner, U. Deuschle, W. Kammerer, and R. Knaus. 1987. Structure-function relationship of Escherichia coli promoters, p. 95-103. In W. S. Reznikoff et al. (ed.), RNA polymerase and the regulation of transcription. Elsevier, New York, N.Y.
8. 2+ binding and its structural consequences at the transcription start site. Biochemistry 34:15624-15632.
9. Czarniecki, D., R. J. Noel, Jr., and W. S. Reznikoff. 1997. The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription. J. Bacteriol. 179:423-429.
10. Dickson, R. C., J. Abelson, P. Johnson, W. S. Reznikoff, and W. M. Barnes. 1977. Nucleotide sequence changes produced by mutations in the lac promoter of Escherichia coli. J. Mol. Biol. 111:65-75.
11. 70 exhibit specificity of binding to promoter DNA. Cell 70:501-512.
12. Ellinger, T., D. Behnke, R. Knaus, H. Bujard, and J. U. Gralla. 1994. Context-dependent effects of upstream A-tracts. Stimulation or inhibition of Escherichia coli promoter function. J. Mol. Biol. 239:466-475.
13. Estrem, S. T., T. Gaal, W. Ross, and R. L. Gourse. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA 95:9761-9766.
14. Estrem, S. T., W. Ross, S. Chen, T. Gaal, W. Niu, R. H. Ebright, and R. L. Gourse. Unpublished observations.
15. Finkel, S. E., and R. C. Johnson. 1992. The Fis protein: it's not just for DNA inversion anymore. Mol. Microbiol. 6:3257-3265.
16. Flatow, U., G. V. Rajendrakumar, and S. Garges. 1996. Analysis of the spacer DNA between the cyclic AMP receptor protein binding site and the lac promoter. J. Bacteriol. 178:2436-2439.
17. R promoter. J. Mol. Biol. 240:119-126.
18. D RNA polymerase requires an upstream promoter element. Proc. Natl. Acad. Sci. USA 92:2582-2586.
19. Frisby, D., and P. Zuber. 1991. Analysis of the upstream activating sequence and site of carbon and nitrogen source repression in the promoter of an early-induced sporulation gene of Bacillus subtilis. J. Bacteriol. 173:7557-7564.
20. Gaal, T., L. Rao, S. T. Estrem, J. Yang, R. M. Wartell, and R. L. Gourse. 1994. Localization of the intrinsically bent DNA region upstream of the E. coli rrnB P1 promoter. Nucleic Acids Res. 22:2344-2350.
21. Gaal, T., W. Ross, E. E. Blatter, H. Tang, X. Jia, V. V. Krishnan, N. Assa-Munt, R. H. Ebright, and R. L. Gourse. 1996. DNA-binding determinants of the α subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev. 10:16-26.
22. Gaal, T., M. S. Bartlett, W. Ross, C. L. Turnbough, Jr., and R. L. Gourse. 1997. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science 278:2092-2097.
23. Galas, D. J., M. Eggert, and M. S. Waterman. 1985. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186:117-128.
24. Gartenberg, M. R., and D. M. Crothers. 1991. Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J. Mol. Biol. 219:217-230.
25. L2 tandem promoter of bacteriophage λ. J. Mol. Biol. 260:484-491.
26. 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.
27. Graves, M. C., and J. C. Rabinowitz. 1986. In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for "extended" promoter elements in gram positive organisms. J. Biol. Chem. 261:11409-11415.
28. Harley, C. B., and R. P. Reynolds. 1987. Analysis of E. coli promoter sequences. Nucleic Acids Res. 15:2343-2361.
29. Hawley, D. K., and W. R. McClure. 1983. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:2237-2255.
30. A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23:2351-2360.
31. Hsu, L. M., J. K. Giannini, T.-W. C. Leung, and J. C. Crosthwaite. 1991. Upstream sequence activation of Escherichia coli argT promoter in vivo and in vitro. Biochemistry 30:813-822.
32. Jeon, Y. H., T. Yamazaki, T. Otomo, A. Ishihama, and Y. Kyogoku. 1997. Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain. J. Mol. Biol. 267:953-962.
33. Josaitis, C. A., T. Gaal, W. Ross, and R. L. Gourse. 1990. Sequences upstream of the -35 hexamer of rrnB P1 affect promoter strength and upstream activation. Biochim. Biophys. Acta 1050:307-311.
34. Kolb, A., K. Igarashi, A. Ishihama, M. Lavigne, M. Buckle, and H. Buc. 1993. E. coli RNA polymerase, deleted in the C-terminal part of its α-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucleic Acids Res. 21:319-326.
35. Koo, H.-S., H.-M. Wu, and D. M. Crothers. 1986. DNA bending at adenine thymine tracts. Nature 320:501-506.
36. Landini, P., and M. R. Volkert. 1995. RNA polymerase α subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes. EMBO J. 14:4329-4335.
37. Lavigne, M., M. Herbert, A. Kolb, and H. Buc. 1992. Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J. Mol. Biol. 224:293-306.
38. Lisser, S., and H. Margalit. 1993. Compilation of E. coli mRNA promoter sequences. Nucleic Acids. Res. 21:1507-1516.
39. McAllister, C. F., and E. C. Achberger. 1988. Effect of polyadenine-coutaining curved DNA on promoter utilization in Bacillus subtilis. J. Biol. Chem. 263:11743-11749.
40. McAllister, C. F., and E. C. Achberger. 1989. Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J. Biol. Chem. 264:10451-10456.
41. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
42. Mulligan, M. E., D. K. Hawley, R. Entriken, and W. R. McClure. 1984. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 12:789-800.
43. Murakami, K., J. T. Owens, T. A. Belyaeva, C. F. Meares, S. J. Busby, and A. Ishihama. 1997. Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. Proc. Natl. Acad. Sci. USA 94:11274-11278.
44. Newlands, J., C. Josaitis, W. Ross, and R. L. Gourse. 1992. Both FIS-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res. 20:719-726.
45. Newlands, J. T., W. Ross, K. K. Gosink, and R. L. Gourse. 1991. Factor-independent activation of Escherichia coli rRNA transcription. II. Characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. J. Mol. Biol. 220:560-583.
46. O'Halloran, T. V., B. Frantz, M. K. Shin, D. M. Ralston, and J. G. Wright. 1989. The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell 56:119-129.
47. Ozoline, O. N., and M. A. Tsyganov. 1995. Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique: compilation analysis. Nucleic Acids Res. 23:4533-4541.
48. Ozoline, O. N., A. A. Deev, and M. V. Arkhipova. 1997. Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase. Nucleic Acids Res. 25: 4703-4709.
49. Perez-Martin, J., F. Rojo, and V. de Lorenzo. 1994. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev. 58:268-290.
50. Rao, L., W. Ross, J. A. Appleman, T. Gaal, S. Leirmo, P. Schlax, M. T. Record, and R. L. Gourse. 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.
51. Ross, W. Unpublished observations.
52. Ross, W., J. F. Thompson, J. T. Newlands, and R. L. Gourse. 1990. E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 9:3733-3742.
53. Ross, W., K. K. Gosink, J. Salomon, K. Igarashi, C. Zou, A. Ishihama, K. Severinov, and R. L. Gourse. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407-1413.
54. 1 of Escherichia coli. J. Biol. Chem. 268: 16907-16916.
55. Savery, N. J., V. A. Rhodius, H. J. Wing, and S. J. W. Busby. 1995. Transcription activation at Escherichia coli promoters dependent on the cyclic AMP receptor protein: effects of binding sequences for the RNA polymerase α subunit. Biochem. J. 309:77-83.
56. Schickor, P., W. Metzger, W. Werel, H. Lederer, and H. Heumann. 1990. Topography of intermediates in transcription initiation of E. coli. EMBO J. 9:2215-2220.
57. Suck, D., and C. Oefner. 1986. Structure of DNAse I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA. Nature 321:620-625.
58. R transcription start site. Science 259: 358-361.
59. Tang, H., K. Severinov, A. Goldfarb, D. Fenyo, B. Chait, and R. H. Ebright. 1994. Location, structure, and function of the target of a transcriptional activator protein. Genes Dev. 8:3058-3067.
60. van Putten, A. J., R. de Lang, E. Veltkamp, H. J. J. Nijkamp, P. van Solingen, and J. A. van den Berg. 1986. Methylation-dependent transcription controls plasmid replication of the CloDF13 cop-1(Ts) mutant. J. Bacteriol. 168:728-733.
61. van Ulsen, P., M. Hillebrand, M. Kainz, R. Collard, L. Zulianello, P. van de Putte, R. L. Gourse, and N. Goosen. 1997. Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and integration host factor-mediated activation of the early promoter of bacteriophage Mu. J. Bacteriol. 179:530-537.
62. Youderian, P., S. Bouvier, and M. M. Susskind. 1982. Sequence determinants of promoter activity. Cell 30:843-853.
63. Young, M. A., J. Srinivasan, I. Goljer, S. Kumar, D. L. Beveridge, and P. H. Bolton. 1995. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAA ATGCG). Methods Enzymol. 261:121-144.