DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally

Journal of Molecular Biology

Volumn 267, Issue 1, 1997, Pages 47-59

  Chen, Ya Fen ^a,b   Helmann, John D ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

^b STANFORD UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

DNA melting; Open complex; Promoter; RNA polymerase; Sigma

Indexed keywords

FLAGELLIN; MAGNESIUM ION; NUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE; THYMINE;

ARTICLE; BACILLUS SUBTILIS; CELL NUCLEUS; DNA DENATURATION; DNA STRAND; DNA TRANSCRIPTION; ENZYME SUBSTRATE COMPLEX; GENETIC CONSERVATION; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROMOTER REGION;

BACILLUS SUBTILIS;

EID: 0031582060     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0853     Document Type: Article

References (76)

1. Achberger E., Whiteley H. R. The role of the δ peptide of the Bacillus subtilis RNA polymerase in promoter selection. J. Biol. Chem. 256:1981;7424-7432.
2. Achberger E., Hilton M. D., Whiteley H. R. The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter. Nucl. Acids Res. 10:1982;2893-2910.
3. Aiyar S. E., Helmann J. D., deHaseth P. L. A mismatch bubble in double-stranded DNA suffices to direct precise transcription initiation by Escherichia coli RNA polymerase. J. Biol. Chem. 269:1994;13170-13184.
4. Arndt K. M., Chamberlin M. J. RNA chain elongation by Escherichia coli RNA polymerase: factors affecting the stability of elongating ternary complexes. J. Mol. Biol. 213:1990;79-108.
5. Beal R. B., Pillai R. P., Chuknyisky P. P., Levy A., Tarien E., Eichorn G. L. Structural studies on the active site of Escherichia coli RNA polymerase. 2. Geometrical relationship of the interacting sites. Biochemistry. 29:1990;5994-6002.
6. Buc H., McClure W. R. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lacUV5 promoter: evidence for a sequential mechanism involving three steps. Biochemistry. 24:1985;2712.
7. Buckle M., Buc H. On the mechanism of promoter recognition by E. coli RNA polymerase. Transcription: Mechanisms and Regulation. 1994;Raven Press, New York.
8. Buckle M., Geiselmann J., Kolb A., Buc H. Protein-DNA cross-linking at the lac promoter. Nucl. Acids Res. 19:1991;833-840.
9. Burns H., Minchin S. Thermal energy requirement for strand separation during transcription initiation: the effect of supercoiling and extended protein DNA contacts. Nucl. Acids Res. 22:1994;3840-3845.
10. Carpousis A. J., Gralla J. D. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at thelac UV5 promoter. Biochemistry. 19:1980;3245-3253.
11. Chamberlin M. J. New models for the mechanism of transcription elongation and its regulation. Harvey Lectures. 88:1995;1-21.
12. Chan C. L., Landick R. New perspectives in RNA chain elongation and termination by E. coli RNA polymerase. Transcription: Mechanisms and Regulation. 1994;Raven Press, New York.
13. Chan P. T., Sullivan J. K., Lebowitz J. Site-directed chemical modification for probing DNA-protein interactions: osmium tetroxide modification of the -10 site of the lac UV5 promoter enhances open complex formation. J. Biol. Chem. 264:1989;21277.
14. A) factor and RNA polymerase with promoters. Biochimie. 74:1992;601-612.
15. D: overproduction, domain analysis, and DNA-binding. J. Mol. Biol. 249:1995;743-753.
16. 32at the groE promoter. J. Mol. Biol. 210:1989;521-530.
17. 2+binding and its structural consequences at the transcription start site. Biochemistry. 34:1995;15624-15632.
18. deHaseth P., Helmann J. D. Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol. Microbiol. 16:1995;817-824.
19. Dobinson K. F., Spiegelman G. B. Effect of the δ subunit of Bacillus subtilis RNA polymerase on initiation of RNA synthesis at two bacteriophage φ29 promoters. Biochemistry. 26:1987;8206-8213.
20. 70exhibit specificity of binding to promoter DNA. Cell. 70:1992;501-512.
21. Drew H. R., Weeks J. R., Travers A. A. Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J. 4:1985;1025-1032.
22. DRNA polymerase requires an upstream promoter element. Proc. Natl Acad. Sci. USA. 92:1995;2582-2586.
23. Gaal T., Ross W., Blatter E. E., Tang H., Jia X., Krishnan V. V., Assa-Munt N., Ebright R. H., Gourse R. L. DNA-binding determinants of the α subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev. 10:1996;16-26.
24. Grimes E., Busby S., Minchin S. Different thermal energy requirement for open complex formation by Escherichia coli RNA polymerase at two related promoters. Nucl. Acids Res. 19:1991;6113-6118.
25. Gross C. A., Lonetto M., Losick R. Bacterial sigma factors. McKnight S. L., Yamamoto K. R. Transcriptional Regulation. 12992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
26. Helmann J. D. Alternative sigma factors and the regulation of flagellar gene expression. Mol. Microbiol. 5:1991;2875-2882.
27. Helmann J. D. Bacterial sigma factors. Conaway R. C., Conaway J. W. Transcription: Mechanisms and Regulation. 1994;Raven Press, New York.
28. Helmann J. D., Chamberlin M. J. Structure and function of bacterial σ factors. Annu. Rev. Biochem. 57:1988;839-872.
29. Hilton M. D., Whiteley H. R. UV cross-linking of the Bacillus subtilis RNA polymerase to DNA in promoter and nonpromoter complexes. J. Biol. Chem. 260:1985;8121-8127.
30. Juang Y.-L., Helmann J. D. The δ subunit of Bacillus subtilis RNA polymerase: an allosteric effector of the initiation and core-recycling phases of transcription. J. Mol. Biol. 239:1994a;1-14.
31. Juang Y.-L., Helmann J. D. A promoter melting region in the primary σ factor of Bacillus subtilis: identification of functionally important aromatic amino acids. J. Mol. Biol. 235:1994b;1470-1488.
32. Juang Y.-L., Helmann J. D. Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations. Biochemistry. 34:1995;8465-8473.
33. Kirkegaard K., Buc H., Spassky A., Wang J. C. Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes. Proc. Natl Acad. Sci. USA. 80:1983;2544-2548.
34. Kovacic R. T. The 0°C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lac UV5. J. Biol. Chem. 262:1987;13654-13661.
35. Krummel B., Chamberlin M. J. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 28:1989;7829-7842.
36. Krummel B., Chamberlin M. J. Structural analysis of ternary complexes of Escherichia coli RNA polymerase: individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J. Mol. Biol. 225:1992;221-237.
37. Kumar S. A. The structure and mechanism of action of bacterial DNA-dependent RNA polymerase. Prog. Biophys. Mol. Biol. 38:1981;165-210.
38. Lampe M., Binnie C., Schmidt R., Losick R. Cloned gene encoding the delta subunit of Bacillus subtilis RNA polymerase. Gene. 67:1988;13-20.
39. 70RNA polymerase with promoter DNA. Eckstein F., Lilley D. M. J. Nucleic Acids and Molecular Biology. 1990;Springer-Verlag, Berlin.
40. López de Saro F., Woody A.-Y. M., Helmann J. D. Structural analysis of the Bacillus subtilisδ factor: a protein polyanion which displaces RNA from RNA polymerase. J. Mol. Biol. 252:1995;189-202.
41. 70subunit fragment from E. coli RNA polymerase. Cell. 87:1996;127-136.
42. Margalit H., Shapiro B. A., Nussinov R., Owens J., Jernigan R. L. Helix stability in prokaryotic promoter regions. Biochemistry. 27:1988;5179-5188.
43. McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54:1985;171-204.
44. Mecsas J., Cowing D. W., Gross C. A. Development of RNA polymerase-promoter contacts during open complex formation. J. Mol. Biol. 220:1991;585-597.
45. Meier T., Schickor P., Wedel A., Cellai L., Heumann H. In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima RNA polymerase-promoter complexes at 75°C using chemical probes. Nucl. Acids Res. 23:1995;988-994.
46. 28form of RNA polymerase. J. Bacteriol. 171:1989;3095-3101.
47. N) holoenzyme closed promoter complexes. J. Biol. Chem. 269:1994;11563-11571.
48. Munson L., Reznikoff W. S. Abortive initiation and long ribonucleic acid synthesis. Biochemistry. 20:1981;2181-2085.
49. Newlands J. T., Ross W., Gosink K. K., Gourse R. L. Factor-independent activation of Escherichia coli rRNA transcription. II. Characterization of complexes ofrrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. J. Mol. Biol. 220:1991;569-583.
50. Nudler E., Avetissova E., Markovtsov V., Goldfarb A. Transcription processivity: protein-DNA interactions holding together the elongation com-plex. Science. 273:1996;211-217.
51. Ozoline O. N., Tsyganov M. A. Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique: compilation analysis. Nucl. Acids Res. 23:1995;4533-4541.
52. Parekh B. S., Hatfield G. W. Transcriptional activation by protein induced DNA bending: evidence for a DNA structural transmission model. Proc. Natl Acad. Sci. USA. 93:1996;1173-1177.
53. Pero J., Nelson J., Fox T. D. Highly asymmetric transcription by RNA polymerase containing phage-SP01-induced polypeptides and a new host protein. Proc. Natl Acad. Sci. USA. 72:1975;1589-1593.
54. Polyakov A., Severinova E., Darst S. A. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell. 83:1995;365-373.
55. Roberts C. W., Roberts J. W. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 86:1996;495-501.
56. A-RNA polymerase that are stabilized by DNA supercoiling. Nucl. Acids Res. 21:1993;935-940.
57. Amutants defective in promoter melting. J. Bacteriol. 176:1994;5218-5224.
58. Ross W., Gosink K. K., Salomon J., Igarishi K., Zou C., Ishihama A., Severinov K., Gourse R. L. A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science. 262:1993;1407-1413.
59. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1990;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
60. Sasse-Dwight S., Gralla J. Footprinting protein-DNA complexes in vivo. Methods Enzymol. 208:1991;146-168.
61. Schickor P., Metzger W., Werel W., Lederer H., Heumann H. Topography of intermediates in transcription initiation of E. coli. EMBO J. 9:1990;2215-2220.
62. Severinov K., Mustaev A., Severinova E., Bass I., Kashlev M., Landick R., Nikiforov V., Goldfarb A., Darst S. A. Assembly of functional Escherichia coli RNA polymerase containing β subunit fragments. Proc. Natl Acad. Sci. USA. 92:1995;4591-4595.
63. 70subunit. J. Mol. Biol. 263:1996;637-647.
64. Siebenlist U. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature. 279:1979;651-652.
65. Spassky A., Kirkegaard K., Buc H. Changes in the DNA structure of the lacUV5 promoter during the formation of an open complex with E. coli RNA polymerase. Biochemistry. 24:1985;2723-2731.
66. Spassky A., Rimsky S., Buc H., Busby S. Correlation between the conformation of Escherichia coli-10 hexamer sequences and promoter strength: use of orthophenanthroline cuprous complex as a structural index. EMBO J. 7:1988;1871-1879.
67. Rpromoter: kinetic evidence for a second open complex requiring Mg(II). Biochemistry. 31:1992;7815-7825.
68. Rtranscription start site. Science. 259:1993;358-361.
69. Travers A. A. Structure and function of E. coli promoter DNA. CRC Crit. Rev. Biochem. 22:1987;181-219.
70. von Hippel P. H., Bear D. G., Morgan W. D., McSwiggen J. A. Protein-nucleic acid interactions in transcription: a molecular analysis. Annu. Rev. Biochem. 53:1984;389-446.
71. Voskuil M. I., Voepel K., Chambliss G. G. The -16 region, a vital sequence for the utilization of a promoter in Bacillus subtilis andEscherichia coli. Mol. Microbiol. 17:1995;271-279.
72. Werel W., Schickor P., Heumann H. Flexibility of the DNA enhances promoter affinity of Escherichia coli RNA polymerase. EMBO J. 10:1991;2589-2594.
73. Whipple F. W., Sonenshein A. L. Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters. J. Mol. Biol. 223:1992;399-414.
74. Wu C. W., Goldthwait D. A. Studies of nucleotide binding to the ribonucleic acid polymerase by a fluorescence technique. Biochemistry. 8:1969a;4450-4458.
75. Wu C. W., Goldthwait D. A. Studies of nucleotide binding to the ribonucleic acid polymerase by equilibrium dialysis. Biochemistry. 8:1969b;4458-4464.
76. Zaychikov E., Martin E., Denissova L., Kozlov M., Markovtsov V., Kashlev M., Heumann H., Nikiforov V., Goldfarb A., Mustaev A. Mapping of catalytic residues in the RNA polymerase active center. Science. 273:1996;107-109.