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. 1991 Mar;173(5):1696–1703. doi: 10.1128/jb.173.5.1696-1703.1991

Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis.

D L Cheo 1, K W Bayles 1, R E Yasbin 1
PMCID: PMC207320  PMID: 1847907

Abstract

DNA damage-inducible (din) genes in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon. To elucidate the mechanisms of SOB regulation, operator/promoter regions from three din loci (dinA, dinB, and dinC) of B. subtilis were cloned. Operon fusions constructed with these cloned din promoter regions rendered reporter genes damage inducible in B. subtilis. Induction of all three din promoters was dependent upon a functional RecA protein. Analysis of these fusions has localized sequences required for damage-inducible expression of the dinA, dinB, and dinC promoters to within 120-, 462-, and 139-bp regions, respectively. Comparison of the nucleotide sequences of these three din promoters with the recA promoter, as well as with the promoters of other loci associated with DNA repair in B. subtilis, has identified the consensus sequence GAAC-N4-GTTC as a putative SOB operator site.

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Selected References

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  1. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  2. Burckhardt S. E., Woodgate R., Scheuermann R. H., Echols H. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1811–1815. doi: 10.1073/pnas.85.6.1811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen N. Y., Zhang J. J., Paulus H. Chromosomal location of the Bacillus subtilis aspartokinase II gene and nucleotide sequence of the adjacent genes homologous to uvrC and trx of Escherichia coli. J Gen Microbiol. 1989 Nov;135(11):2931–2940. doi: 10.1099/00221287-135-11-2931. [DOI] [PubMed] [Google Scholar]
  4. Craig N. L., Roberts J. W. Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor. J Biol Chem. 1981 Aug 10;256(15):8039–8044. [PubMed] [Google Scholar]
  5. Eguchi Y., Ogawa T., Ogawa H. Cleavage of bacteriophage phi 80 CI repressor by RecA protein. J Mol Biol. 1988 Aug 5;202(3):565–573. doi: 10.1016/0022-2836(88)90286-0. [DOI] [PubMed] [Google Scholar]
  6. Fields P. I., Yasbin R. E. DNA repair in B. subtilis: an inducible dimer specific W-reactivation system. Mol Gen Genet. 1983;190(3):475–480. doi: 10.1007/BF00331079. [DOI] [PubMed] [Google Scholar]
  7. Fouet A., Sonenshein A. L. A target for carbon source-dependent negative regulation of the citB promoter of Bacillus subtilis. J Bacteriol. 1990 Feb;172(2):835–844. doi: 10.1128/jb.172.2.835-844.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Friedman B. M., Yasbin R. E. The genetics and specificity of the constitutive excision repair system of Bacillus subtilis. Mol Gen Genet. 1983;190(3):481–486. doi: 10.1007/BF00331080. [DOI] [PubMed] [Google Scholar]
  9. Gillespie K., Yasbin R. E. Chromosomal locations of three Bacillus subtilis din genes. J Bacteriol. 1987 Jul;169(7):3372–3374. doi: 10.1128/jb.169.7.3372-3374.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gralla J. D. Bacterial gene regulation from distant DNA sites. Cell. 1989 Apr 21;57(2):193–195. doi: 10.1016/0092-8674(89)90955-0. [DOI] [PubMed] [Google Scholar]
  11. Gryczan T. J., Contente S., Dubnau D. Characterization of Staphylococcus aureus plasmids introduced by transformation into Bacillus subtilis. J Bacteriol. 1978 Apr;134(1):318–329. doi: 10.1128/jb.134.1.318-329.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Keener S. L., McNamee K. P., McEntee K. Cloning and characterization of recA genes froM Proteus vulgaris, Erwinia carotovora, Shigella flexneri, and Escherichia coli B/r. J Bacteriol. 1984 Oct;160(1):153–160. doi: 10.1128/jb.160.1.153-160.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Laredo J., Wolff V. L., Lovett P. S. Chloramphenicol acetyltransferase specified by cat-86: relationship between the gene and the protein. Gene. 1988 Dec 15;73(1):209–214. doi: 10.1016/0378-1119(88)90327-7. [DOI] [PubMed] [Google Scholar]
  14. Little J. W. Autodigestion of lexA and phage lambda repressors. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1375–1379. doi: 10.1073/pnas.81.5.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Little J. W., Edmiston S. H., Pacelli L. Z., Mount D. W. Cleavage of the Escherichia coli lexA protein by the recA protease. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3225–3229. doi: 10.1073/pnas.77.6.3225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Little J. W., Mount D. W. The SOS regulatory system of Escherichia coli. Cell. 1982 May;29(1):11–22. doi: 10.1016/0092-8674(82)90085-x. [DOI] [PubMed] [Google Scholar]
  17. Little J. W., Mount D. W., Yanisch-Perron C. R. Purified lexA protein is a repressor of the recA and lexA genes. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4199–4203. doi: 10.1073/pnas.78.7.4199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Love P. E., Lyle M. J., Yasbin R. E. DNA-damage-inducible (din) loci are transcriptionally activated in competent Bacillus subtilis. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6201–6205. doi: 10.1073/pnas.82.18.6201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Love P. E., Yasbin R. E. Genetic characterization of the inducible SOS-like system of Bacillus subtilis. J Bacteriol. 1984 Dec;160(3):910–920. doi: 10.1128/jb.160.3.910-920.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Love P. E., Yasbin R. E. Induction of the Bacillus subtilis SOS-like response by Escherichia coli RecA protein. Proc Natl Acad Sci U S A. 1986 Jul;83(14):5204–5208. doi: 10.1073/pnas.83.14.5204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lovett C. M., Jr, Love P. E., Yasbin R. E. Competence-specific induction of the Bacillus subtilis RecA protein analog: evidence for dual regulation of a recombination protein. J Bacteriol. 1989 May;171(5):2318–2322. doi: 10.1128/jb.171.5.2318-2322.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lovett C. M., Jr, Love P. E., Yasbin R. E., Roberts J. W. SOS-like induction in Bacillus subtilis: induction of the RecA protein analog and a damage-inducible operon by DNA damage in Rec+ and DNA repair-deficient strains. J Bacteriol. 1988 Apr;170(4):1467–1474. doi: 10.1128/jb.170.4.1467-1474.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lovett C. M., Jr, Roberts J. W. Purification of a RecA protein analogue from Bacillus subtilis. J Biol Chem. 1985 Mar 25;260(6):3305–3313. [PubMed] [Google Scholar]
  24. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Radding C. M. Homologous pairing and strand exchange in genetic recombination. Annu Rev Genet. 1982;16:405–437. doi: 10.1146/annurev.ge.16.120182.002201. [DOI] [PubMed] [Google Scholar]
  27. Radman M. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci. 1975;5A:355–367. doi: 10.1007/978-1-4684-2895-7_48. [DOI] [PubMed] [Google Scholar]
  28. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sauer R. T., Ross M. J., Ptashne M. Cleavage of the lambda and P22 repressors by recA protein. J Biol Chem. 1982 Apr 25;257(8):4458–4462. [PubMed] [Google Scholar]
  30. Sauer R. T., Yocum R. R., Doolittle R. F., Lewis M., Pabo C. O. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature. 1982 Jul 29;298(5873):447–451. doi: 10.1038/298447a0. [DOI] [PubMed] [Google Scholar]
  31. Sedgwick S. G., Goodwin P. A. Differences in mutagenic and recombinational DNA repair in enterobacteria. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4172–4176. doi: 10.1073/pnas.82.12.4172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Sedgwick S. G., Goodwin P. A. Interspecies regulation of the SOS response by the E. coli lexA+ gene. Mutat Res. 1985 May;145(3):103–106. doi: 10.1016/0167-8817(85)90015-x. [DOI] [PubMed] [Google Scholar]
  33. Shaw W. V. Chloramphenicol acetyltransferase from chloramphenicol-resistant bacteria. Methods Enzymol. 1975;43:737–755. doi: 10.1016/0076-6879(75)43141-x. [DOI] [PubMed] [Google Scholar]
  34. Shinagawa H., Iwasaki H., Kato T., Nakata A. RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1806–1810. doi: 10.1073/pnas.85.6.1806. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Stranathan M. C., Bayles K. W., Yasbin R. E. The nucleotide sequence of the recE+ gene of Bacillus subtilis. Nucleic Acids Res. 1990 Jul 25;18(14):4249–4249. doi: 10.1093/nar/18.14.4249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Walker G. C. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev. 1984 Mar;48(1):60–93. doi: 10.1128/mr.48.1.60-93.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. West S. C., Countryman J. K., Howard-Flanders P. Purification and properties of the recA protein of Proteus mirabilis. Comparison with Escherichia coli recA protein; specificity of interaction with single strand binding protein. J Biol Chem. 1983 Apr 10;258(7):4648–4654. [PubMed] [Google Scholar]
  39. West S. C., Little J. W. P. mirabilis RecA protein catalyses cleavage of E. coli LexA protein and the lambda repressor in vitro. Mol Gen Genet. 1984;194(1-2):111–113. doi: 10.1007/BF00383505. [DOI] [PubMed] [Google Scholar]
  40. Witkin E. M. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol Rev. 1976 Dec;40(4):869–907. doi: 10.1128/br.40.4.869-907.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  42. Yasbin R. E. DNA repair in Bacillus subtilis. II. Activation of the inducible system in competent bacteria. Mol Gen Genet. 1977 Jun 8;153(2):219–225. [PubMed] [Google Scholar]
  43. Yasbin R. E., Fields P. I., Andersen B. J. Properties of Bacillus subtilis 168 derivatives freed of their natural prophages. Gene. 1980 Dec;12(1-2):155–159. doi: 10.1016/0378-1119(80)90026-8. [DOI] [PubMed] [Google Scholar]
  44. Yasbin R. E., Wilson G. A., Young F. E. Transformation and transfection in lysogenic strains of Bacillus subtilis: evidence for selective induction of prophage in competent cells. J Bacteriol. 1975 Jan;121(1):296–304. doi: 10.1128/jb.121.1.296-304.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Youngman P. J., Perkins J. B., Losick R. Genetic transposition and insertional mutagenesis in Bacillus subtilis with Streptococcus faecalis transposon Tn917. Proc Natl Acad Sci U S A. 1983 Apr;80(8):2305–2309. doi: 10.1073/pnas.80.8.2305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Youngman P., Perkins J. B., Losick R. A novel method for the rapid cloning in Escherichia coli of Bacillus subtilis chromosomal DNA adjacent to Tn917 insertions. Mol Gen Genet. 1984;195(3):424–433. doi: 10.1007/BF00341443. [DOI] [PubMed] [Google Scholar]
  47. Youngman P., Zuber P., Perkins J. B., Sandman K., Igo M., Losick R. New ways to study developmental genes in spore-forming bacteria. Science. 1985 Apr 19;228(4697):285–291. doi: 10.1126/science.228.4697.285. [DOI] [PubMed] [Google Scholar]
  48. de Vos W. M., de Vries S. C., Venema G. Cloning and expression of the Escherichia coli recA gene in Bacillus subtilis. Gene. 1983 Nov;25(2-3):301–308. doi: 10.1016/0378-1119(83)90234-2. [DOI] [PubMed] [Google Scholar]

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