Genetic and topological analyses of the bop promoter of Halobacterium halobium: Stimulation by DNA supercoiling and non-B-DNA structure

Journal of Bacteriology

Volumn 178, Issue 3, 1996, Pages 840-845

  Yang, Chin Fen ^a   Kim, Jong Myoung ^a   Molinari, Elizabeth ^a   Dassarma, Shiladitya ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA B; DNA Z;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; DNA CONFORMATION; DNA SUPERCOILING; GENETIC TRANSCRIPTION; HALOBACTERIUM SALINARUM; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PURPLE MEMBRANE; TRANSCRIPTION INITIATION;

BACTERIA (MICROORGANISMS); HALOBACTERIUM SALINARUM;

EID: 0030043986     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.3.840-845.1996     Document Type: Article

References (44)

1. Betlach, M., J. Friedman, H. W. Boyer, and F. Pfeifer. 1984. Characterization of a halobacterial gene affecting bacterio-opsin gene expression. Nucleic Acids Res 12:7949-7958.
2. s promoter mediate its transcriptional response to DNA supercoiling. J. Mol. Biol 195:89-97.
3. Carty, M., and R. Menzel. 1989. The unexpected antitermination of gyrA-directed transcripts is enhanced by DNA relaxation. Proc Natl Acad Sci. USA 86:8882-3886.
4. Cimmino, C., G. L. Scoarughi, and P. Donini. 1993. Stringency and relaxation among the halobacteria. J. Bacteriol. 175:6659-6662.
5. Cline, S. W., and W. F. Doolittle. 1987 Efficient transfection of the archaebacterium Halobacterium halobium. J. Bacteriol 169:1341-1344.
6. DasSarma, S., U. L. RajBhandary, and H. G. Khorana. 1984. Bacterio-opsin mRNA in wild-type and bacterio-opsin-deficient Halobacterium halobium strains. Proc. Natl. Acad. Sci USA 81:125-129.
7. Dixon, R. A., N. C. Henderson, and S. Austin. 1988. DNA supercoiling and aerobic regulation of transcription from the Klebstella pneumoniae nifLA promoter. Nucleic Acids Res 16:9933-9946.
8. Drlica, K. 1992 Control of bacterial DNA supercoiling Mol. Microbiol. 6:425-433.
9. Drummond, M. H., and J. C. Wootton. 1987. Sequence of nifL from Klebstella pneumoruae: mode of action and relationship to two families of regulatory proteins. Mol. Microbiol. 1:37-44.
10. Dunaway, M., and E. A. Ostrander. 1993. Local domains of supercoiling activate a eukaryotic promoter in vivo. Nature (London) 361:746-748
11. Dunn, R., J. McCoy, M. Simsek, A. Majumdar, S. H. Chang, U. L. RaJBhandary, and H. G. Khorana. 1981. The bacteriorhodopsin gene Proc. Natl. Acad. Sci. USA 78:6744-6748.
12. Franco, R. J., and K. Drlica. 1989. Gyrase inhibitors can increase gyrA expression and DNA supercoiling. J. Bacteriol. 171:6573-6579.
13. Garges, S., and S. Adhya. 1985. Sites of allosteric shift in the structure of the cyclic AMP receptor protein Cell 41:745-751.
14. Gropp, F., and M. C. Betlach. 1994. The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor Proc. Natl Acad. Sci. USA 91:5475-5479.
15. Gropp, F., R. Gropp, and M. C. Betlach. 1995. Effects of upstream deletions on light- and oxygen-regulated bacterio-opsin gene expression in Halobacterium halobium Mol. Microbiol. 16:357-364.
16. Hackett, N. R., M. P. Krebs, S. DasSarma, W. Goebel, U. L. RajBhandary, and H. G. Khorana. 1990 Nucleotide sequence of a high copy number plasmid from Halobacterium strain GRB. Nucleic Acids Res. 18:3408.
17. Hain, J., W.-D. Reiter, U. Hudepohl, and W. Zillig. 1992 Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 20: 5423-5428.
18. Higgins, C. F., J. C. D. Hinton, S. J. Hulton, T. Owen-Hughes, G. D. Pavitt, and A. Seirafi. 1990 Protein H1, a role for chromatin structure in the regulation of bacterial gene expression and virulence? Mol. Microbiol. 4:2007-2012
19. n does not differ from that of Z-DNA. Proc. Natl. Acad Sci. USA 91:9549-9553.
20. Holmes, M. L., and M. L. Dyall-Smith. 1990 A plasmid vector with a selectable marker for halophilic archaebacteria J Bacteriol 172:756-761.
21. Johnson, B. H. 1992. Generation and detection of Z-DNA. Methods Enzymol. 211:127-159
22. Lam, W. L., and W. F. Doolittle. 1989 Shuttle vectors for the archaebacterium Halobacterium volcanii Proc Natl. Acad Sci. USA 86:5478-5482.
23. Lee, H.-S., F. Narberhaus, and S. Kustu. 1993. In vitro activity of NifL, a signal transduction protein for biological nitrogen fixation J. Bacteriol 175: 7683-7688
24. Leong, D., H. Boyer, and M. Betlach. 1988. Transcription of genes involved in bacterio-opsin gene expression in mutants of a halophilic archaebacterium. J. Bacteriol. 170:4910-4915.
25. Leong, D., F. Pfeifer, H. Boyer, and M. Betlach. 1988. Characterization of a second gene involved in bacterio-opsin gene expression in a halophilic archaebacterium. J Bacteriol. 170:4903-1909
26. Menzel, R., and M. Gellert. 1987. Modulation of transcription by DNA supercoiling a deletion analysis of the Escherichia coli gyrA and gyrB promoters. Proc. Natl. Acad. Sci. USA 84:4185-4189.
27. Mojica, F. J. M., F. Charbonnier, G. Juez, F. Rodríguez-Valera, and P. Forterre. 1994 Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol. 176:4966-4973.
28. Ng, W.-L., and S. DasSarma. 1993. Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100. J. Bacteriol. 175:4584-4596.
29. Ng, W.-L., C.-F. Yang, J. T. Halladay, P. Arora, and S. DasSarma. 1995. Isolation of genomic and plasmid DNAs from Halobacterium halobium. p. 179-184. In S. DasSarma et al. (ed), Archaea: a laboratory manual - halophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
30. Owen-Hughes, T. A., G. D. Pavitt, D. S. Santos, J. M. Sidebotham, C. S. J. Hulton, J. C. D. Hinton, and C. F. Higgins. 1992. The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression. Cell 71:255-265.
31. Reiter, W.-D., U. Hüdepohl, and W. Zillig. 1990. Mutational analysis of an archaebacterial promoter, essential role of a TATA-box for transcription efficiency and start-site selection in vitro. Proc. Natl. Acad Sci. USA 87: 9509-9513
32. Saiki, R. K., D. H. Geifand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
33. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989 Molecular cloning a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory. Cold Spring Harbor, N Y.
34. Sanger, F., S. Nicklen, and A. R. Coulson. 1977 DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci USA 74:5463-5467.
35. Sapienza, C., and W. F. Doolittle. 1982. Unusual physical organization of the Halobacterium genome. Nature (London) 295:384-389.
36. Shand, R. F., and M. C. Betlach. 1991 Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light. J Bacteriol 173:4692-4699.
37. Sioud, M., G. Baldacci, A. M. de Recondo, and P. Forterre. 1988 Novobiocin induces positive supercoiling of small plasmids from halophilic archaebacteria in vivo. Nucleic Acids Res 16:1379-1391.
38. Spudich, E. N., R. A. Bogomolni, and J. L. Spudich. 1986. Genetic and biochemical resolution of the chromophoric polypeptide of halorhodopsin. Biochem Biophys. Res Commun. 112:332-338.
39. Spudich, J. L. Personal communication.
40. Stoeckenius, W., R. H. Rozier, and R. A. Bogomolni. 1979. Bacteriorhodopsin and purple membrane of halobacteria. Biochim. Biophys. Acta 505:215-278
41. Wang, J.-Y., and M. Syvanen. 1992. DNA twist as a transcriptional sensor for environmental changes. Mol Microbiol. 6:1861-1866.
42. Wedel, A., D. S. Weiss, D. Popham, P. Dröge, and S. Kustu. 1990. A bacterial enhancer functions to tether a transcriptional activator near a promoter. Science 248:486-490.
43. Yang, C.-F. 1994. Ph.D. thesis University of Massachusetts, Amherst.
44. Yang, C.-F., and S. DasSarma. 1990. Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor. J. Bacteriol. 172:4118-4121.