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. 1998 Aug 1;26(15):3584–3590. doi: 10.1093/nar/26.15.3584

The -16 region of Bacillus subtilis and other gram-positive bacterial promoters.

M I Voskuil 1, G H Chambliss 1
PMCID: PMC147726  PMID: 9671823

Abstract

The Bacillus subtilis alpha-amylase promoter amy P contains an essential TGTG motif (-16 region) upstream of the -10 region. Mutations of this region significantly reduced in vitro promoter strength. A -15 G-->C transversion eliminated transcription from amy P by both B.subtilis and Escherichia coli RNA polymerase (RNAP). A second alpha-amylase promoter ( amy P2) also required the -16 region for function. To determine conserved sequences in promoters containing -16 region elements, sequences of 64 B.subtilis promoters with the second TG motif of the -16 region were aligned and analyzed. Unlike the E.coli class of 'extended -10 promoters', with a similar TG motif but lacking a -35 region, the -16 region promoters contain highly conserved -35 regions. They also contain conserved A n and T n tracts upstream of the -35 region. In addition, we analyzed all available gram-positive bacterial promoter compilations to determine the generality of the -16 region. From this analysis, the -16 region TRTG motif (R = purine) appears to be a basic element found in a large portion of gram-positive bacterial promoters and is, in the case of at least the alpha-amylase promoters, necessary for transcription by the major form of B.subtilis and E.coli RNAP.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Albano M., Hahn J., Dubnau D. Expression of competence genes in Bacillus subtilis. J Bacteriol. 1987 Jul;169(7):3110–3117. doi: 10.1128/jb.169.7.3110-3117.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Belyaeva T., Griffiths L., Minchin S., Cole J., Busby S. The Escherichia coli cysG promoter belongs to the 'extended -10' class of bacterial promoters. Biochem J. 1993 Dec 15;296(Pt 3):851–857. doi: 10.1042/bj2960851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burns H. D., Belyaeva T. A., Busby S. J., Minchin S. D. Temperature-dependence of open-complex formation at two Escherichia coli promoters with extended -10 sequences. Biochem J. 1996 Jul 1;317(Pt 1):305–311. doi: 10.1042/bj3170305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burns H., Minchin S. Thermal energy requirement for strand separation during transcription initiation: the effect of supercoiling and extended protein DNA contacts. Nucleic Acids Res. 1994 Sep 25;22(19):3840–3845. doi: 10.1093/nar/22.19.3840. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carter M. J., Milton I. D. An inexpensive and simple method for DNA purifications on silica particles. Nucleic Acids Res. 1993 Feb 25;21(4):1044–1044. doi: 10.1093/nar/21.4.1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chan B., Busby S. Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. Gene. 1989 Dec 14;84(2):227–236. doi: 10.1016/0378-1119(89)90496-4. [DOI] [PubMed] [Google Scholar]
  7. Chan B., Spassky A., Busby S. The organization of open complexes between Escherichia coli RNA polymerase and DNA fragments carrying promoters either with or without consensus -35 region sequences. Biochem J. 1990 Aug 15;270(1):141–148. doi: 10.1042/bj2700141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chang B. Y., Doi R. H. Overproduction, purification, and characterization of Bacillus subtilis RNA polymerase sigma A factor. J Bacteriol. 1990 Jun;172(6):3257–3263. doi: 10.1128/jb.172.6.3257-3263.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chang B. Y., Shyu Y. T., Doi R. H. The interaction between Bacillus subtilis sigma-A (sigma A) factor and RNA polymerase with promoters. Biochimie. 1992 Jul-Aug;74(7-8):601–612. doi: 10.1016/0300-9084(92)90131-w. [DOI] [PubMed] [Google Scholar]
  10. Glasel J. A. Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios. Biotechniques. 1995 Jan;18(1):62–63. [PubMed] [Google Scholar]
  11. Hager D. A., Jin D. J., Burgess R. R. Use of Mono Q high-resolution ion-exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase. Biochemistry. 1990 Aug 28;29(34):7890–7894. doi: 10.1021/bi00486a016. [DOI] [PubMed] [Google Scholar]
  12. Harley C. B., Reynolds R. P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Helmann J. D. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 1995 Jul 11;23(13):2351–2360. doi: 10.1093/nar/23.13.2351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Henkin T. M., Sonenshein A. L. Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis. Mol Gen Genet. 1987 Oct;209(3):467–474. doi: 10.1007/BF00331151. [DOI] [PubMed] [Google Scholar]
  15. Juang Y. L., Helmann J. D. The delta subunit of Bacillus subtilis RNA polymerase. An allosteric effector of the initiation and core-recycling phases of transcription. J Mol Biol. 1994 May 27;239(1):1–14. doi: 10.1006/jmbi.1994.1346. [DOI] [PubMed] [Google Scholar]
  16. Keilty S., Rosenberg M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J Biol Chem. 1987 May 5;262(13):6389–6395. [PubMed] [Google Scholar]
  17. Kumar A., Malloch R. A., Fujita N., Smillie D. A., Ishihama A., Hayward R. S. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter. J Mol Biol. 1993 Jul 20;232(2):406–418. doi: 10.1006/jmbi.1993.1400. [DOI] [PubMed] [Google Scholar]
  18. Matern H. T., Klein J. R., Henrich B., Plapp R. Determination and comparison of Lactobacillus delbrueckii ssp. lactis DSM7290 promoter sequences. FEMS Microbiol Lett. 1994 Sep 15;122(1-2):121–128. doi: 10.1111/j.1574-6968.1994.tb07154.x. [DOI] [PubMed] [Google Scholar]
  19. Moran C. P., Jr, Lang N., LeGrice S. F., Lee G., Stephens M., Sonenshein A. L., Pero J., Losick R. Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol Gen Genet. 1982;186(3):339–346. doi: 10.1007/BF00729452. [DOI] [PubMed] [Google Scholar]
  20. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nakayama T., Munoz L., Doi R. H. A procedure to remove protease activities from Bacillus subtilis sporulating cells and their crude extracts. Anal Biochem. 1977 Mar;78(1):165–170. doi: 10.1016/0003-2697(77)90020-3. [DOI] [PubMed] [Google Scholar]
  22. Pouwels P. H., Leer R. J. Genetics of lactobacilli: plasmids and gene expression. Antonie Van Leeuwenhoek. 1993;64(2):85–107. doi: 10.1007/BF00873020. [DOI] [PubMed] [Google Scholar]
  23. Pátek M., Eikmanns B. J., Pátek J., Sahm H. Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif. Microbiology. 1996 May;142(Pt 5):1297–1309. doi: 10.1099/13500872-142-5-1297. [DOI] [PubMed] [Google Scholar]
  24. Rao L., Ross W., Appleman J. A., Gaal T., Leirmo S., Schlax P. J., Record M. T., Jr, Gourse R. L. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol. 1994 Feb 4;235(5):1421–1435. doi: 10.1006/jmbi.1994.1098. [DOI] [PubMed] [Google Scholar]
  25. Ross W., Gosink K. K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R. L. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 1993 Nov 26;262(5138):1407–1413. doi: 10.1126/science.8248780. [DOI] [PubMed] [Google Scholar]
  26. Sabelnikov A. G., Greenberg B., Lacks S. A. An extended -10 promoter alone directs transcription of the DpnII operon of Streptococcus pneumoniae. J Mol Biol. 1995 Jul 7;250(2):144–155. doi: 10.1006/jmbi.1995.0366. [DOI] [PubMed] [Google Scholar]
  27. Solnick J. V., Hansen L. M., Syvanen M. The major sigma factor (RpoD) from Helicobacter pylori and other gram-negative bacteria shows an enhanced rate of divergence. J Bacteriol. 1997 Oct;179(19):6196–6200. doi: 10.1128/jb.179.19.6196-6200.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Strohl W. R. Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res. 1992 Mar 11;20(5):961–974. doi: 10.1093/nar/20.5.961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Vandamme P., Falsen E., Rossau R., Hoste B., Segers P., Tytgat R., De Ley J. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol. 1991 Jan;41(1):88–103. doi: 10.1099/00207713-41-1-88. [DOI] [PubMed] [Google Scholar]
  30. Voskuil M. I., Voepel K., Chambliss G. H. The -16 region, a vital sequence for the utilization of a promoter in Bacillus subtilis and Escherichia coli. Mol Microbiol. 1995 Jul;17(2):271–279. doi: 10.1111/j.1365-2958.1995.mmi_17020271.x. [DOI] [PubMed] [Google Scholar]
  31. Wösten M. M., Boeve M., Koot M. G., van Nuenen A. C., van der Zeijst B. A. Identification of Campylobacter jejuni promoter sequences. J Bacteriol. 1998 Feb;180(3):594–599. doi: 10.1128/jb.180.3.594-599.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yamada M., Kubo M., Miyake T., Sakaguchi R., Higo Y., Imanaka T. Promoter sequence analysis in Bacillus and Escherichia: construction of strong promoters in E. coli. Gene. 1991 Mar 1;99(1):109–114. doi: 10.1016/0378-1119(91)90041-9. [DOI] [PubMed] [Google Scholar]
  33. Yamaguchi K., Nagata Y., Maruo B. Isolation of mutants defective in alpha-amylase from Bacillus subtilis: genetic analyses. J Bacteriol. 1974 Aug;119(2):416–424. doi: 10.1128/jb.119.2.416-424.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. deHaseth P. L., Helmann J. D. Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol Microbiol. 1995 Jun;16(5):817–824. doi: 10.1111/j.1365-2958.1995.tb02309.x. [DOI] [PubMed] [Google Scholar]

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