Saturation mutagenesis of the haloarchaeal bop gene promoter: Identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity

Molecular Microbiology

Volumn 36, Issue 5, 2000, Pages 1175-1183

  Baliga, Nitin S ^a   DasSarma, Shiladitya ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NOVOBIOCIN; OXYGEN; PURINE; PYRIMIDINE; TRANSCRIPTION FACTOR;

DNA SUPERCOILING; ENHANCER REGION; GENE INDUCTION; GENETIC TRANSCRIPTION; HALOBACTERIUM; MUTAGENESIS; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TATA BOX;

ARCHAEAL PROTEINS; BASE SEQUENCE; BINDING SITES; DNA, ARCHAEAL; DNA, SUPERHELICAL; ENHANCER ELEMENTS (GENETICS); GENES, ARCHAEAL; HALOBACTERIUM; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NUCLEAR PROTEINS; PROMOTER REGIONS (GENETICS); TATA BOX; TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION FACTORS;

EID: 0034077513     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2000.01915.x     Document Type: Review

References (30)

1. Baliga, N.S., and DasSarma, S. (1999) Saturation mutagenesis of the TATA box and the upstream activator sequence in the haloarchaeal bop gene promoter. J Bacteriol 181: 2513-2518.
2. Baliga, N.S., Goo, Y., Ng, W.V., Hood, L., Daniels, C.J., and DasSarma, S. (2000) Is gene expression in Halobacerium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 36: 1184-1185.
3. Betlach, M., Friedman, J., Boyer, H.W., and Pfeifer, F. (1984) Characterization of a halobacterial gene affecting bacterioopsin gene expression. Nucleic Acids Res 12: 7949-7959.
4. Buratowski, S. (1997) Multiple TATA-binding factors come back into style. Cell 91: 13-15.
5. Chang, S.H., Majumdar, A., Dunn, R., Makabe, O., RajBhandary, U.L., Khorana, H.G., et al. (1981) Bacteriorhodopsin: partial sequence of mRNA provides amino acid sequence in the precursor region. Proc Natl Acad Sci USA 78: 3398-3402.
6. Cline, S., and Doolittle, W.F. (1987) Efficient transfection of the archaebacterium Halobacterium halobium. J Bacteriol 169: 1341-1344.
7. Danner, S., and Soppa, J. (1996) Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection. Mol Microbiol 19: 1265-1276.
8. DasSarma, S., RajBhandary, U.L., and Khorana, H.G. (1984) Bacterio-opsin mRNA in wild-type and bacterio-opsin deficient Halobacterium halobium strains. Proc Natl Acad Sci USA 81: 125-129.
9. Dixon, R. (1998) The oxygen-responsive NIFL-NIFA complex: a novel two-component regulatory system controlling nitrogenase synthesis in γ-proteobacteria. Arch Microbiol 169: 371-380.
10. Dunn, R., McCoy, J., Simsek, M., Majumdar, A., Chang, S.H., Rajbhandary, U.L., et al. (1981) The bacteriorhodopsin gene. Proc Natl Acad Sci USA 78: 6744-6748.
11. Gropp, F., Gropp, R., and Betlach, M.C. (1995) Effects of upstream deletions on light- and oxygen-regulated bacterio-opsin gene expression in Halobacterium halobium. Mol Microbiol 16: 357-364.
12. Grove, A., Galeone, A., Yu, E., Mayol, L., and Geiduschek, P. (1998) Affinity, stability and polarity of the TATA binding protein governed by flexure at the TATA box. J Mol Biol 282: 731-739.
13. Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D., and Ebright, R.H. (1998) New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev 12: 34-44.
14. Leong, D., Boyer, H., and Betlach, M. (1988) Transcription of genes involved in bacterio-opsin gene expression in mutants of a halophilic archaebacterium. J Bacteriol 170: 4910-4915.
15. Li, X.-Y., and McClure, W.R. (1998) Stimulation of open complex formation by nicks and apurinic sites suggests a role for nucleation of DNA melting in Escherichia coli promoter function. J Biol Chem 273: 23558-23566.
16. Ng, W.-L., Yang, C.-F., Halladay, J.T., Arora, P., and DasSarma, S. (1995) Isolation of genomic and plasmid DNAs from Halobacterium halobium. In Archaea: A Laboratory Manual. Halophiles. DasSarma, S., Robb, F.T., Place, A.R., Sowers, K.R., Schreier, H.J., and Fleischmann, E.M. (eds). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp. 179-184.
17. Ng, W.-L, Ciufo, S.A., Smith, T.M., Bumgardner, R.E., Baskin, D., Faust, J., et al. (1998) Snapshot of a dynamic replicon in a halophilic archaeon: megaplasmid or mini-chromosome? Genome Res 8: 1131-1141.
18. Oesterhelt, D. (1995) Isolation of purple membranes. In Archaea: A Laboratory Manual. Halophiles. DasSarma, S., Robb, F.T., Place, A.R., Sowers, K.R., Schreier, H.J., and Fleischmann, E.M. et al. (eds). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp. 55-57.
19. Pruss, G.J., and Drlica, K. (1989) DNA supercoiling and prokaryotic transcription. Cell 56: 521-523.
20. Qureshi, S.A., and Jackson, S.P. (1998) Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and it's effect on promoter strength. Mol Cell 1: 389-400.
21. Reeve, M.A., and Fuller, C.W. (1995) A novel thermostable polymerase for DNA sequencing. Nature 376: 796-797.
22. Reiter, W.-D., Hüdepohl, U., and Zillig, W. (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.
23. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
24. Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
25. Shand, F.R., and Betlach, M.C. (1991) Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light. J Bacteriol 173: 4692-4699.
26. Soppa, J. (1999) Transcription initiation in Archaea: facts, factors and future aspects. Mol Microbiol 31: 1295-1305.
27. Thomm, M. (1996) Archaeal transcription factors and their role in transcription intiation. FEMS Microbiol Rev 18: 159-171.
28. Thompson, D.K., and Daniels, C.J. (1998) Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements. Mol Microbiol 27: 541-551.
29. Yang, C.-F., and DasSarma, S. (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.
30. Yang, C.-F., Kim, J.-M., Molinari, E., and DasSarma, S. (1996) Genetic and topological analyses of the bop promoter of Halobacterium halobium: stimulation by DNA supercoiling and non-B-DNA structure. J Bacteriol 178: 840-845.