Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 Dec 11;18(23):6771–6777. doi: 10.1093/nar/18.23.6771

Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis.

J C Alonso 1, K Shirahige 1, N Ogasawara 1
PMCID: PMC332730  PMID: 2124672

Abstract

In Bacillus subtilis the recM gene, whose product is associated with DNA repair and recombination, has been located between the dnaX and rrnA genes. The recM gene has been cloned and analyzed. Analysis of the nucleotide sequence (3.741-kilobase) around recM revealed five open reading frames (orf). We have assigned recM and dnaX to two of this orf, given the gene order dnaX-orf107-recM-orf74-orf87. The organization of genes of the dnaX-orf107-recM region resembles the organization of genes in the dnaX-orf12-recR region of the Escherichia coli chromosome. Proteins of 24.2 and 17.0 kDa would result from translation of the wild type and in vitro truncated recM genes, and radioactive bands of proteins of molecular weights of 24.5 and 17.0 kDa were detected by the use of the T7promoter-expression system. The RecM protein contains a potential zinc finger domain for nucleic acid binding and a putative nucleotide binding sequence that is present in many proteins that bind and hydrolyze ATP. Strains, in which the recM gene has been insertionally inactivated, were generated and show a phenotype essentially the same as previously described recM mutants.

Full text

PDF
6771

Images in this article

6775Image
on p.6775

Selected References

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

  1. Alonso J. C., Stiege C. A., Tailor R. H., Viret J. F. Functional analysis of the dna (Ts) mutants of Bacillus subtilis: plasmid pUB110 replication as a model system. Mol Gen Genet. 1988 Nov;214(3):482–489. doi: 10.1007/BF00330484. [DOI] [PubMed] [Google Scholar]
  2. Alonso J. C., Tailor R. H., Lüder G. Characterization of recombination-deficient mutants of Bacillus subtilis. J Bacteriol. 1988 Jul;170(7):3001–3007. doi: 10.1128/jb.170.7.3001-3007.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alonso J. C., Trautner T. A. A gene controlling segregation of the Bacillus subtilis plasmid pC194. Mol Gen Genet. 1985;198(3):427–431. doi: 10.1007/BF00332934. [DOI] [PubMed] [Google Scholar]
  4. Armengod M. E., García-Sogo M., Lambíes E. Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12. J Biol Chem. 1988 Aug 25;263(24):12109–12114. [PubMed] [Google Scholar]
  5. Berg J. M. Zinc fingers and other metal-binding domains. Elements for interactions between macromolecules. J Biol Chem. 1990 Apr 25;265(12):6513–6516. [PubMed] [Google Scholar]
  6. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Biswal N., Kleinschmidt A. K., Spatz H. C., Trautner T. A. Physical properties of the DNA of bacteriophage SP50. Mol Gen Genet. 1967;100(1):39–55. doi: 10.1007/BF00425774. [DOI] [PubMed] [Google Scholar]
  8. Blinkowa A. L., Walker J. R. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res. 1990 Apr 11;18(7):1725–1729. doi: 10.1093/nar/18.7.1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Brendel V., Trifonov E. N. A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Res. 1984 May 25;12(10):4411–4427. doi: 10.1093/nar/12.10.4411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Brune M., Schumann R., Wittinghofer F. Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli. Nucleic Acids Res. 1985 Oct 11;13(19):7139–7151. doi: 10.1093/nar/13.19.7139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ceglowski P., Lüder G., Alonso J. C. Genetic analysis of rec E activities in Bacillus subtilis. Mol Gen Genet. 1990 Jul;222(2-3):441–445. doi: 10.1007/BF00633853. [DOI] [PubMed] [Google Scholar]
  12. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Doolittle R. F., Johnson M. S., Husain I., Van Houten B., Thomas D. C., Sancar A. Domainal evolution of a prokaryotic DNA repair protein and its relationship to active-transport proteins. Nature. 1986 Oct 2;323(6087):451–453. doi: 10.1038/323451a0. [DOI] [PubMed] [Google Scholar]
  14. Flower A. M., McHenry C. S. The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame. Nucleic Acids Res. 1986 Oct 24;14(20):8091–8101. doi: 10.1093/nar/14.20.8091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Flower A. M., McHenry C. S. The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting. Proc Natl Acad Sci U S A. 1990 May;87(10):3713–3717. doi: 10.1073/pnas.87.10.3713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fukuoka T., Moriya S., Yoshikawa H., Ogasawara N. Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J Biochem. 1990 May;107(5):732–739. doi: 10.1093/oxfordjournals.jbchem.a123117. [DOI] [PubMed] [Google Scholar]
  17. Gassel M., Alonso J. C. Expression of the recE gene during induction of the SOS response in Bacillus subtilis recombination-deficient strains. Mol Microbiol. 1989 Sep;3(9):1269–1276. doi: 10.1111/j.1365-2958.1989.tb00277.x. [DOI] [PubMed] [Google Scholar]
  18. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  19. Jones J. S., Weber S., Prakash L. The Saccharomyces cerevisiae RAD18 gene encodes a protein that contains potential zinc finger domains for nucleic acid binding and a putative nucleotide binding sequence. Nucleic Acids Res. 1988 Jul 25;16(14B):7119–7131. doi: 10.1093/nar/16.14.7119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  21. Lampe M. F., Bott K. F. Genetic and physical organization of the cloned gyrA and gyrB genes of Bacillus subtilis. J Bacteriol. 1985 Apr;162(1):78–84. doi: 10.1128/jb.162.1.78-84.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lee S. H., Kanda P., Kennedy R. C., Walker J. R. Relation of the Escherichia coli dnaX gene to its two products--the tau and gamma subunits of DNA polymerase III holoenzyme. Nucleic Acids Res. 1987 Oct 12;15(19):7663–7675. doi: 10.1093/nar/15.19.7663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Leonhardt H. Identification of a low-copy-number mutation within the pUB110 replicon and its effect on plasmid stability in Bacillus subtilis. Gene. 1990 Sep 28;94(1):121–124. doi: 10.1016/0378-1119(90)90477-9. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Mahdi A. A., Lloyd R. G. Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair. Mol Gen Genet. 1989 Apr;216(2-3):503–510. doi: 10.1007/BF00334397. [DOI] [PubMed] [Google Scholar]
  26. Mahdi A. A., Lloyd R. G. The recR locus of Escherichia coli K-12: molecular cloning, DNA sequencing and identification of the gene product. Nucleic Acids Res. 1989 Sep 12;17(17):6781–6794. doi: 10.1093/nar/17.17.6781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Menzel R., Gellert M. Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J Bacteriol. 1987 Mar;169(3):1272–1278. doi: 10.1128/jb.169.3.1272-1278.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Moffatt B. A., Studier F. W. T7 lysozyme inhibits transcription by T7 RNA polymerase. Cell. 1987 Apr 24;49(2):221–227. doi: 10.1016/0092-8674(87)90563-0. [DOI] [PubMed] [Google Scholar]
  30. Ogasawara N., Moriya S., Mazza G., Yoshikawa H. A Bacillus subtilis dnaG mutant harbours a mutation in a gene homologous to the dnaN gene of Escherichia coli. Gene. 1986;45(2):227–231. doi: 10.1016/0378-1119(86)90259-3. [DOI] [PubMed] [Google Scholar]
  31. Ogasawara N., Moriya S., Yoshikawa H. Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames. Nucleic Acids Res. 1985 Apr 11;13(7):2267–2279. doi: 10.1093/nar/13.7.2267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ogasawara N., Moriya S., Yoshikawa H. Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome. Nucleic Acids Res. 1983 Sep 24;11(18):6301–6318. doi: 10.1093/nar/11.18.6301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ogasawara N., Moriya S., von Meyenburg K., Hansen F. G., Yoshikawa H. Conservation of genes and their organization in the chromosomal replication origin region of Bacillus subtilis and Escherichia coli. EMBO J. 1985 Dec 1;4(12):3345–3350. doi: 10.1002/j.1460-2075.1985.tb04087.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Quiñones A., Kaasch J., Kaasch M., Messer W. Induction of dnaN and dnaQ gene expression in Escherichia coli by alkylation damage to DNA. EMBO J. 1989 Feb;8(2):587–593. doi: 10.1002/j.1460-2075.1989.tb03413.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Robertson J. B., Gocht M., Marahiel M. A., Zuber P. AbrB, a regulator of gene expression in Bacillus, interacts with the transcription initiation regions of a sporulation gene and an antibiotic biosynthesis gene. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8457–8461. doi: 10.1073/pnas.86.21.8457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rottländer E., Trautner T. A. Genetic and transfection studies with B, subtilis phage SP 50. I. Phage mutants with restricted growth on B. subtilis strain 168. Mol Gen Genet. 1970;108(1):47–60. doi: 10.1007/BF00343184. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Schaefer C., Messer W. Directionality of DnaA protein/DNA interaction. Active orientation of the DnaA protein/dnaA box complex in transcription termination. EMBO J. 1989 May;8(5):1609–1613. doi: 10.1002/j.1460-2075.1989.tb03545.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Serrano R. Structure and function of proton translocating ATPase in plasma membranes of plants and fungi. Biochim Biophys Acta. 1988 Feb 24;947(1):1–28. doi: 10.1016/0304-4157(88)90017-2. [DOI] [PubMed] [Google Scholar]
  40. Struck J. C., Vogel D. W., Ulbrich N., Erdmann V. A. A dnaZX-like open reading frame downstream from the Bacillus subtilis scRNA gene. Nucleic Acids Res. 1988 Mar 25;16(6):2720–2720. doi: 10.1093/nar/16.6.2720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986 May 5;189(1):113–130. doi: 10.1016/0022-2836(86)90385-2. [DOI] [PubMed] [Google Scholar]
  42. Tsuchihashi Z., Kornberg A. ATP interactions of the tau and gamma subunits of DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem. 1989 Oct 25;264(30):17790–17795. [PubMed] [Google Scholar]
  43. Tsuchihashi Z., Kornberg A. Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2516–2520. doi: 10.1073/pnas.87.7.2516. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. 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]
  45. 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]
  46. Yin K. C., Blinkowa A., Walker J. R. Nucleotide sequence of the Escherichia coli replication gene dnaZX. Nucleic Acids Res. 1986 Aug 26;14(16):6541–6549. doi: 10.1093/nar/14.16.6541. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES