Rhodobacter capsulatus nifA1 Promoter: High-GC -10 Regions in High-GC Bacteria and the Basis for Their Transcription

Journal of Bacteriology

Volumn 186, Issue 3, 2004, Pages 740-749

  Richard, Cynthia L ^a   Tandon, Animesh ^a   Kranz, Robert G ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BINDING PROTEIN; PROTEIN NIFA1; PROTEIN NTRC; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; ENZYME ACTIVATION; ESCHERICHIA COLI; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HOUSEKEEPING GENE; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR CLONING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; RHODOBACTER CAPSULATUS; TRANSCRIPTION INITIATION;

BACTERIAL PROTEINS; BASE COMPOSITION; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; PII NITROGEN REGULATORY PROTEINS; PROMOTER REGIONS (GENETICS); RHODOBACTER CAPSULATUS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROTEOBACTERIA; RHODOBACTER; RHODOBACTER CAPSULATUS; RHODOPSEUDOMONAS;

EID: 1642500149     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.3.740-749.2004     Document Type: Article

References (31)

1. Avtges, P., R. G. Kranz, and R. Haselkorn. 1985. Isolation and organization of genes for nitrogen fixation in Rhodopseudomonas capsulata. Mol. Gen. Genet. 201:363-369.
2. 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.
3. Bowman, W. C., S. Du, C. E. Bauer, and R. G. Kranz. 1999. In vitro activation and repression of photosynthesis gene transcription in Rhodobacter capsulatus. Mol. Microbiol. 33:429-437.
4. Bowman, W. C., and R. G. Kranz. 1998. A bacterial ATP-dependent, enhancer binding protein that activates the housekeeping RNA polymerase. Genes Dev. 12:1884-1893.
5. Brock, T. D., and M. T. Madigan. 1991. Biology of microorganisms, 6th ed. Prentice Hall, Inc., Englewood Cliffs, N.J.
6. Casadaban, M. J., A. Martinez-Arias, S. K. Shapira, and J. Chou. 1983. Beta-galactosidase gene fusions for analyzing gene expression in Escherichia coli and yeast. Methods Enzymol. 100:293-308.
7. Cullen, P. J., W. C. Bowman, and R. G. Kranz. 1996. In vitro reconstitution and characterization of the Rhodobacter capsulatus NtrB and NtrC two-component system. J. Biol. Chem. 271:6530-6536.
8. Cullen, P. J., C. K. Kaufman, W. C. Bowman, and R. G. Kranz. 1997. Characterization of the Rhodobacter capsulatus housekeeping RNA polymerase. In vitro transcription of photosynthesis and other genes. J. Biol. Chem. 272:27266-27273.
9. Ditta, G., S. Stanfield, D. Corbin, and D. R. Helinski. 1980. Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl. Acad. Sci. USA 77:7347-7351.
10. Foster-Hartnett, D., and R. G. Kranz. 1992. Analysis of the promoters and upstream sequences of nifA1 and nifA2 in Rhodobacter capsulatus: activation requires ntrC but not rpoN. Mol. Microbiol. 6:1049-1060.
11. Gaal, T., W. Ross, S. T. Estrem, L. H. Nguyen, R. R. Burgess, and R. L. Gourse. 2001. Promoter recognition and discrimination by EsigmaS RNA polymerase. Mol. Microbiol. 42:939-954.
12. Jin, D. J., and C. A. Gross. 1988. Mapping and sequencing of mutations in the Escherichia coli tpoB gene that lead to rifampicin resistance. J. Mol. Biol. 202:45-58.
13. 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.
14. Karls, R. K., D. J. Jin, and T. J. Donohue. 1993. Transcription properties of RNA polymerase holoenzymes isolated from the purple nonsulfur bacterium Rhodobacter sphaeroides. J. Bacteriol. 175:7629-7638.
15. Kranz, R. G., W. C. Bowman, and N. R. Sloan. 1999. Nitrogen fixation: from molecules to crop productivity, p. 79-82. Proceedings of the 12th International Congress on Nitrogen Fixation. Kluwer Academic Press, Dordrecht, The Netherlands.
16. Lee, S. J., and J. D. Gralla. 2001. Sigma38 (rpoS) RNA polymerase promoter engagement via -10 region nucleotides. J. Biol. Chem. 276:30064-30071.
17. Lohrke, S. M., S. Nechaev, H. Yang, K. Severinov, and S. J. Jin. 1999. Transcriptional activation of Agrobacterium tumefaciens virulence gene promoters in Escherichia coli requires the A. tumefaciens rpoA gene, encoding the alpha subunit of RNA polymerase. J. Bacteriol. 181:4533-4539.
18. Manoil, C., and J. Beckwith. 1985. TnphoA: a transposon probe for protein export signals. Proc. Natl. Acad. Sci. USA 82:8129-8133.
19. Marr, M. T., and J. W. Roberts. 1997. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science 276:1258-1260.
20. Mathews, S. A., and R. S. Stephens. 1999. DNA structure and novel amino and carboxyl termini of the Chlamydia sigma 70 analogue modulate promoter recognition. Microbiology 145:1671-1681.
21. 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 E. coli RNA polymerase. Biochemistry 39:12274-12283.
22. Pasternak, C., W. Chen, C. Heck, and G. Klug. 1996. Cloning, nucleotide sequence and characterization of the rpoD gene encoding the primary sigma factor of Rhodobacter capsulatus. Gene 176:177-184.
23. Peck, M. C., T. Gaal, R. F. Fisher, R. L. Gourse, and S. R. Long. 2002. The RNA polymerase alpha subunit from Sinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro. J. Bacteriol. 184:3808-3814.
24. Richard, C. L., A. Tandon, N. R. Sloan, and R. G. Kranz. 2003. RNA polymerase subunit requirements for activation by the enhancer-binding protein Rhodobacter capsulatus NtrC. J. Biol. Chem. 278:31701-31708.
25. Severinov, K., M. Soushko, A. Goldfarb, and V. Nikiforov. 1993. Rifampicin region revisited. New rifampicin-resistant and streptolydigin-resistant mutants in the beta subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 268:14820-14825.
26. 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.
27. Tang, H., K. Severinov, A. Goldfarh, and R. H. Ebright. 1995. Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. USA 92:4902-4906.
28. Wu, J., N. Ohta, A. K. Benson, A. J. Ninfa, and A. Newton. 1997. Purification, characterization, and reconstitution of DNA-dependent RNA polymerases from Caulobacter crescentus. J. Biol. Chem. 272:21558-21564.
29. Yen, H. C., and B. Marrs. 1977. Growth of Rhodopseudomonas capsulata under anaerobic dark conditions with dimethyl sulfoxide. Arch. Biochem. Biophys. 181:411-418.
30. Zalenskaya, K., J. Lee, C. N. Gujuluva, Y. K. Shin, M. Slutsky, and A. Goldfarb. 1990. Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products. Gene 89:7-12.
31. 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.