Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Oct 25;17(20):8033–8045. doi: 10.1093/nar/17.20.8033

Molecular organization of sbcC, a gene that affects genetic recombination and the viability of DNA palindromes in Escherichia coli K-12.

I S Naom 1, S J Morton 1, D R Leach 1, R G Lloyd 1
PMCID: PMC334945  PMID: 2530497

Abstract

The sbcC gene product of Escherichia coli interferes with the growth of a lambda red gam phage carrying a long palindrome in its DNA. This phenotype was used to identify recombinant plasmids harbouring the wild-type gene and to isolate sbcC mutant derivatives carrying Tn1000 insertions. Analysis of these plasmids located sbcC between proC and phoR at a slightly different position from that reported before (Lloyd, R.G. and Buckman, C. 1985, J. Bacteriol. 164, 836-844). Nucleotide sequencing revealed that the gene spans a DNA segment of 3.3 kb that encodes a poorly expressed protein of 118 kDa and which lies downstream of a gene of unknown function that encodes a polypeptide of 45 kDa. The amino acid sequence of SbcC contains a nucleotide binding fold similar to that in RecB and other recombination proteins.

Full text

PDF
8033

Images in this article

Selected References

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

  1. Benson F. E., Illing G. T., Sharples G. J., Lloyd R. G. Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes. Nucleic Acids Res. 1988 Feb 25;16(4):1541–1549. doi: 10.1093/nar/16.4.1541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boidol W., Simonis M., Töpert M., Siewert G. Recombinant plasmids with genes for the biosynthesis of alkaline phosphatase of Escherichia coli. Mol Gen Genet. 1982;185(3):510–512. doi: 10.1007/BF00334150. [DOI] [PubMed] [Google Scholar]
  3. Bradley M. K., Smith T. F., Lathrop R. H., Livingston D. M., Webster T. A. Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens. Proc Natl Acad Sci U S A. 1987 Jun;84(12):4026–4030. doi: 10.1073/pnas.84.12.4026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chalker A. F., Leach D. R., Lloyd R. G. Escherichia coli sbcC mutants permit stable propagation of DNA replicons containing a long palindrome. Gene. 1988 Nov 15;71(1):201–205. doi: 10.1016/0378-1119(88)90092-3. [DOI] [PubMed] [Google Scholar]
  5. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  6. Cohen A., Clark A. J. Synthesis of linear plasmid multimers in Escherichia coli K-12. J Bacteriol. 1986 Jul;167(1):327–335. doi: 10.1128/jb.167.1.327-335.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Finch P. W., Emmerson P. T. The nucleotide sequence of the uvrD gene of E. coli. Nucleic Acids Res. 1984 Jul 25;12(14):5789–5799. doi: 10.1093/nar/12.14.5789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Finch P. W., Storey A., Brown K., Hickson I. D., Emmerson P. T. Complete nucleotide sequence of recD, the structural gene for the alpha subunit of Exonuclease V of Escherichia coli. Nucleic Acids Res. 1986 Nov 11;14(21):8583–8594. doi: 10.1093/nar/14.21.8583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Finch P. W., Storey A., Chapman K. E., Brown K., Hickson I. D., Emmerson P. T. Complete nucleotide sequence of the Escherichia coli recB gene. Nucleic Acids Res. 1986 Nov 11;14(21):8573–8582. doi: 10.1093/nar/14.21.8573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Finch P. W., Wilson R. E., Brown K., Hickson I. D., Tomkinson A. E., Emmerson P. T. Complete nucleotide sequence of the Escherichia coli recC gene and of the thyA-recC intergenic region. Nucleic Acids Res. 1986 Jun 11;14(11):4437–4451. doi: 10.1093/nar/14.11.4437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gram H., Rüger W. Genes 55, alpha gt, 47 and 46 of bacteriophage T4: the genomic organization as deduced by sequence analysis. EMBO J. 1985 Jan;4(1):257–264. doi: 10.1002/j.1460-2075.1985.tb02344.x. [DOI] [PMC free article] [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. Hashimoto-Gotoh T., Franklin F. C., Nordheim A., Timmis K. N. Specific-purpose plasmid cloning vectors. I. Low copy number, temperature-sensitive, mobilization-defective pSC101-derived containment vectors. Gene. 1981 Dec;16(1-3):227–235. doi: 10.1016/0378-1119(81)90079-2. [DOI] [PubMed] [Google Scholar]
  14. Hickson I. D., Robson C. N., Atkinson K. E., Hutton L., Emmerson P. T. Reconstitution of RecBC DNase activity from purified Escherichia coli RecB and RecC proteins. J Biol Chem. 1985 Jan 25;260(2):1224–1229. [PubMed] [Google Scholar]
  15. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Konigsberg W., Godson G. N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Feb;80(3):687–691. doi: 10.1073/pnas.80.3.687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kosiba B. E., Schleif R. Arabinose-inducible promoter from Escherichia coli. Its cloning from chromosomal DNA, identification as the araFG promoter and sequence. J Mol Biol. 1982 Mar 25;156(1):53–66. doi: 10.1016/0022-2836(82)90458-2. [DOI] [PubMed] [Google Scholar]
  18. Leach D. R., Stahl F. W. Viability of lambda phages carrying a perfect palindrome in the absence of recombination nucleases. 1983 Sep 29-Oct 5Nature. 305(5933):448–451. doi: 10.1038/305448a0. [DOI] [PubMed] [Google Scholar]
  19. Lindsey J. C., Leach D. R. Slow replication of palindrome-containing DNA. J Mol Biol. 1989 Apr 20;206(4):779–782. doi: 10.1016/0022-2836(89)90584-6. [DOI] [PubMed] [Google Scholar]
  20. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  21. Lloyd R. G., Buckman C. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12. J Bacteriol. 1985 Nov;164(2):836–844. doi: 10.1128/jb.164.2.836-844.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Makino K., Shinagawa H., Amemura M., Nakata A. Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12. J Mol Biol. 1986 Jul 5;190(1):37–44. doi: 10.1016/0022-2836(86)90073-2. [DOI] [PubMed] [Google Scholar]
  24. Malone R. E., Chattoraj D. K., Faulds D. H., Stahl M. M., Stahl F. W. Hotspots for generalized recombination in the Escherichia coli chromosome. J Mol Biol. 1978 Jun 5;121(4):473–491. doi: 10.1016/0022-2836(78)90395-9. [DOI] [PubMed] [Google Scholar]
  25. O'Neill M. C. Escherichia coli promoters. I. Consensus as it relates to spacing class, specificity, repeat substructure, and three-dimensional organization. J Biol Chem. 1989 Apr 5;264(10):5522–5530. [PubMed] [Google Scholar]
  26. Riley M., Anilionis A. Evolution of the bacterial genome. Annu Rev Microbiol. 1978;32:519–560. doi: 10.1146/annurev.mi.32.100178.002511. [DOI] [PubMed] [Google Scholar]
  27. Rostas K., Morton S. J., Picksley S. M., Lloyd R. G. Nucleotide sequence and LexA regulation of the Escherichia coli recN gene. Nucleic Acids Res. 1987 Jul 10;15(13):5041–5049. doi: 10.1093/nar/15.13.5041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sancar A., Hack A. M., Rupp W. D. Simple method for identification of plasmid-coded proteins. J Bacteriol. 1979 Jan;137(1):692–693. doi: 10.1128/jb.137.1.692-693.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sancar A., Stachelek C., Konigsberg W., Rupp W. D. Sequences of the recA gene and protein. Proc Natl Acad Sci U S A. 1980 May;77(5):2611–2615. doi: 10.1073/pnas.77.5.2611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. 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]
  31. Sharp P. M., Li W. H. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. doi: 10.1093/nar/15.3.1281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Shurvinton C. E., Stahl M. M., Stahl F. W. Large palindromes in the lambda phage genome are preserved in a rec+ host by inhibiting lambda DNA replication. Proc Natl Acad Sci U S A. 1987 Mar;84(6):1624–1628. doi: 10.1073/pnas.84.6.1624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Smith G. R. Homologous recombination in procaryotes. Microbiol Rev. 1988 Mar;52(1):1–28. doi: 10.1128/mr.52.1.1-28.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Smith G. R., Kunes S. M., Schultz D. W., Taylor A., Triman K. L. Structure of chi hotspots of generalized recombination. Cell. 1981 May;24(2):429–436. doi: 10.1016/0092-8674(81)90333-0. [DOI] [PubMed] [Google Scholar]
  36. Tommassen J., Heimstra P., Overduin P., Lugtenberg B. Cloning of phoM, a gene involved in regulation of the synthesis of phosphate limitation inducible proteins in Escherichia coli K12. Mol Gen Genet. 1984;195(1-2):190–194. doi: 10.1007/BF00332745. [DOI] [PubMed] [Google Scholar]
  37. West S. C., Emmerson P. T. Induction of protein synthesis in Escherichia coli following UV- or gamma-irradiation, mitomycin C treatment or tif Expression. Mol Gen Genet. 1977 Feb 28;151(1):57–67. doi: 10.1007/BF00446913. [DOI] [PubMed] [Google Scholar]
  38. 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]

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

RESOURCES