Identification of target promoters for the Bacillus subtilis extracytoplasmic function σ factor, σ(W)

Molecular Microbiology

Volumn 31, Issue 1, 1999, Pages 361-371

  Huang, Xuejun ^a   Gaballa, Ahmed ^a   Cao, Min ^a   Helmann, John D ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; HYDROLASE; PENICILLIN BINDING PROTEIN; PEPTIDASE; RACEMASE; SIGMA FACTOR; SIGNAL PEPTIDE;

ARTICLE; BACILLUS SUBTILIS; CYTOPLASM; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; REPORTER GENE; SEQUENCE HOMOLOGY;

BACILLUS SUBTILIS; CHROMOSOME MAPPING; CYTOPLASM; GENE EXPRESSION REGULATION, BACTERIAL; MUTAGENESIS; PHENOTYPE; PROMOTER REGIONS (GENETICS); REGULON; SIGMA FACTOR;

BACILLUS SUBTILIS; POSIBACTERIA;

EID: 0032952070     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1999.01180.x     Document Type: Article

References (52)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Asano, Y., Ito, H., Dairi, T., and Kato, Y. (1996) An alkaline D-stereospecific endopeptidase with beta-lactamase activity from Bacillus cereus. J Biol Chem 271: 30256-30262.
3. Bickel, P.E., Scherer, P.E., Schnitzer, J.E., Oh, P., Lisanti, M.P., and Lodish, H.F. (1997) Flotillin and epidermal surface antigen define a new family of caveolae-associated integral membrane protein. J Biol Chem 272: 13793-13802.
4. Brissette, J.L., Weiner, L., Ripmaster, T.L., and Model, P. (1991) Characterization and sequence of the Escherichia coli stress-induced psp operon. J Mol Biol 220: 35-48.
5. Brutsche, S., and Braun, V. (1997) SigX of Bacillus subtilis replaces the ECF sigma factor Fecl of Escherichia coli and is inhibited by RsiX. Mol Gen Genet 256: 416-425.
6. Bugg, T.D.H., and Walsh, C.T. (1993) Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance. Nature Prod Rep 9: 199-215.
7. Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
8. Confalonieri, F., and Duguet, M. (1995) A 200-amino acid ATPase module in search of a basic function. BioEssays 17: 639-650.
9. Correia, F.F., Lamont, R., Bayer, M., Rosan, B., and DiRienzo, J.M. (1997) Cloning and sequencing of a mutated locus that affects fimbrial tuft organization and corncob formation in Streptococcus crista CC5A. Int J Oral Biol 22: 241-248.
10. Deuerling, E., Mogk, A., Richter, C., Purucker, M., and Schumann, W. (1997) The ftsH gene of Bacillus subtilis is involved in major cellular processes such as sporulation, stress adaptation and secretion. Mol Microbiol 23: 921-933.
11. Duez, C., Piron-Fraipont, C., Joris, B., Dusart, J., Urdea, M.S., Martial, J.A., et al. (1987) Primary structure of the Streptomyces R61 extracellular DD-peptidase. 1. Cloning into Streptomyces lividans and nucleotide sequence of the gene. Eur J Biochem 162: 509-518.
12. Finney, N.S. (1998) Enantioselective epoxide hydrolysis: catalysis involving microbes, mammals and metals. Chem Biol 5: R73-R79.
13. Galbiati, F., Volonte, D., Goltz, J.S., Steele, Z., Sen, J., Jurcsak, J., et al. (1998) Identification, sequence, and developmental expression of invertebrate flotillins from Drosophila melanogaster. Gene 210: 229-237.
14. Ge, Z.M., and Taylor, D.E. (1996) Sequencing, expression and genetic characterization of the Helicobacter pylori ftsH gene encoding a protein homologous to members of a novel putative ATPase family. J Bacteriol 178: 6151-6157.
15. Harwood, C.R., and Cutting, S.M. (1990) Molecular Biological Methods for Bacillus. Chichester, UK: John Wiley & Sons Ltd.
16. Hecht, H.J., Sobek, H., Haag, T., Pfeifer, O., and van Pée, K.H. (1994) The metal-ion-free oxidoreductase from Streptomyces aureofaciens has an alpha-beta hydrolase fold. Nature Struct Biol 1: 532-537.
17. A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 23: 2351-2360.
18. Hertz, G.Z., and Stormo, G.D. (1996) Escherichia coli promoter sequences: analysis and prediction. In Methods in Enzymology. Adhya, S. (ed.). San Diego, CA: Academic Press, pp. 30-42.
19. Hofmann, K., and Stoffel, W. (1993) TMbase - A database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 347: 166.
20. Honjo, M., Nakayama, A., Fukazawa, K., Kawamura, K., Ando, K., Hori, M., et al. (1990) A novel Bacillus subtilis gene involved in negative control of sporulation and degradative-enzyme production. J Bacteriol 172: 1783-1790.
21. X factor using a consensus-directed search. J Mol Biol 279: 165-173.
22. X protein is an extracytoplasmic function sigma factor contributing to the survival of high temperature stress. J Bacteriol 179: 2915-2921.
23. X regulon. J Bacteriol 180: 3765-3770.
24. Ichihara, S., Suzuki, T., Suzuki, M., and Mizushima, S. (1986) Molecular cloning and sequencing of the sppA gene and characterization of the encoded protease IV, a signal peptide peptidase, of Escherichia coli. J Biol Chem 261: 9405-9411.
25. Jack, R.W., Tagg, J.R., and Ray, B. (1995) Bacteriocins of Gram-positive bacteria. Microbiol Rev 59: 171-200.
26. Kelly, J.A., Dideberg, O., Charlier, P., Wery, J.P., Libert, M., Moews, P.C., et al. (1986) On the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target. Science 231: 1429-1431.
27. Knehr, M., Thomas, H., Arand, M., Gebel, T., Zeller, H.D., and Oesch, F. (1993) Isolation and characterization of a cDNA encoding rat liver cytosolic epoxide hydrolase and its functional expression in Escherichia coli. J Biol Chem 268: 17623-17627.
28. Kovach, M.E., Hughes, K.J., Everiss, K.D., and Peterson, K.M. (1994) Identification of a ToxR-activated gene, tagE, that lies within the accessory colonization factor gene cluster of Vibrio cholerae. Gene 148: 91-95.
29. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, A., et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
30. Lonetto, M.A., Brown, K.L., Rudd, K.E., and Buttner, M.J. (1994) Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial σ factors involved in the regulation of extracytoplasmic functions. Proc Natl Acad Sci USA 91: 7573-7577.
31. Miller, J.H. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 352-255.
32. Missiakas, D., and Raina, S. (1998) The extracytoplasmic function sigma factors: role and regulation. Mol Microbiol 28: 1059-1066.
33. Moszer, I., Glaser, P., and Danchin, A. (1995) SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141: 261-268.
34. Nakai, K., and Kanehisa, M. (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins: Struct Function Genet 11: 95-110.
35. Novak, P., and Dev, I.K. (1988) Degradation of signal peptide by protease IV and oligopeptidase A. J Bacteriol 170: 5067-5075.
36. O'Gara, J.P., Gomelsky, M., and Kaplan, S. (1997) Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4.1. Appl Environ Microbiol 63: 4713-4720.
37. van Pée, K.H. (1996) Biosynthesis of halogenated metabolites by bacteria. Annu Rev Microbiol 50: 375-399.
38. Pelletier, l., Pfeifer, O., Altenbuchner, J., and van Pée, K.H. (1994) Cloning of a second non-haem bromoperoxidase gene from Streptomyces aureofaciens ATCC 10762: sequence analysis, expression in Streptomyces lividans and enzyme purification. Microbiology 140: 509-516.
39. Popham, D.L., and Setlow, P. (1993) Cloning, nucleotide sequence, and regulation of the Bacillus subtilis pbpE operon, which codes for penicillin-binding protein 4* and an apparent amino acid racemase. J Bacteriol 175: 2917-2925.
40. Rink, R., Fennema, M., Smids, M., Dehmel, U., and Janssen, D.B. (1997) Primary structure and catalytic mechanism of the epoxide hydrolase from Agrobacterium radiobacter AD1. J Biol Chem 272: 14650-14657.
41. Ross, W., Gosink, K.K., Salomon, J., Igarishi, K., Zou, C., Ishihama, A., et al. (1993) A third recognition element in bacterial promoters: DNA binding by the a subunit of RNA polymerase. Science 262: 1407-1413.
42. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1990) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
43. Slack, F.J., Mueller, J.P., and Sonenshein, A.L. (1993) Mutations that relieve nutritional repression of the Bacillus subtilis dipeptide permease operon. J Bacteriol 175: 4605-4614.
44. Sowell, M.O., and Buchanan, C.E. (1983) Changes in penicillin-binding proteins during sporulation of Bacillus subtilis. J Bacteriol 153: 1331-1337.
45. Strauch, M.A. (1995) Delineation of AbrB-binding sites on the Bacillus subtilis spoOH, kinB, ftsAZ, and pbpE promoters and use of a derived homology to identify a previously unsuspected binding site in the bsuB1 methylase promoter. J Bacteriol 177: 6999-7002.
46. Strauch, M.A., and Hoch, J.A. (1993) Transition-state regulators: sentinels of Bacillus subtilis post-exponential gene expression. Mol Microbiol 7: 337-342.
47. Suzuki, T., Itoh, A., Ichihara, S., and Mizushima, S. (1987) Characterization of three sppA gene coding for protease IV, a signal peptide peptidase of Escherichia coli. J Bacteriol 169: 2523-2528.
48. Tomita, H., Fujimoto, S., Tanimoto, K., and Ike, Y. (1997) Cloning and genetic and sequence analyses of the bacteriocin 21 determinant encoded on the Enterococcus faecalis pheromone-responsive conjugative plasmid pPD1. J Bacteriol 179: 7843-7855.
49. Uptain, S.M., Kane, C.M., and Chamberlin, M.J. (1997) Basic mechanisms of transcript elongation and its regulation. Annu Rev Biochem 66: 117-172.
50. Yohda, M., Endo, I., Abe, Y., Ohta, T., Iida, T., Maruyama, T., et al. (1996) Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY. J Biol Chem 271: 22017-22021.
51. Zuber, P., and Losick, R. (1987) Role of AbrB and SpoOA- and SpoOB-dependent utilization of a sporulation promoter in Bacillus subtilis. J Bacteriol 169: 2223-2230.
52. Zuber, P., Nakano, M.M., and Marehiel, M.A. (1993) Peptide antibiotics. In Bacillus subtilis and other Gram-positive bacteria. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology Press, pp. 897-916.