Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Feb 25;16(4):1541–1549. doi: 10.1093/nar/16.4.1541

Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes.

F E Benson 1, G T Illing 1, G J Sharples 1, R G Lloyd 1
PMCID: PMC336333  PMID: 3279394

Abstract

The nucleotide sequence of a 2505 bp region of the Escherichia coli chromosome containing the LexA regulated ruv gene has been determined. A sequence of 1631 bp encoding two non-overlapping open reading frames that constitute a single operon and which specify polypeptides with predicted molecular weights of 22172 daltons and 37177 daltons respectively, was identified as the most probable sequence for ruv. Each of the two open reading frames, designated ruvA and ruvB, is preceded by a reasonable Shine-Dalgarno sequence. Two 16 bp sequences (SOS boxes) that match the consensus sequence for binding LexA protein are located 5' to ruvA in a region that provides a possible single promoter for expression of both ruvA and ruvB, with the second SOS box overlapping the putative -35 region. A possible transcriptional terminator is located 137 bp downstream of ruvB. The amino acid sequence predicted for RuvB contains a region that matches a highly conserved sequence found in several DNA repair and recombination proteins that bind ATP.

Full text

PDF
1541

Selected References

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

  1. Arikan E., Kulkarni M. S., Thomas D. C., Sancar A. Sequences of the E. coli uvrB gene and protein. Nucleic Acids Res. 1986 Mar 25;14(6):2637–2650. doi: 10.1093/nar/14.6.2637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Attfield P. V., Benson F. E., Lloyd R. G. Analysis of the ruv locus of Escherichia coli K-12 and identification of the gene product. J Bacteriol. 1985 Oct;164(1):276–281. doi: 10.1128/jb.164.1.276-281.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Backendorf C., Spaink H., Barbeiro A. P., van de Putte P. Structure of the uvrB gene of Escherichia coli. Homology with other DNA repair enzymes and characterization of the uvrB5 mutation. Nucleic Acids Res. 1986 Apr 11;14(7):2877–2890. doi: 10.1093/nar/14.7.2877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brendel V., Hamm G. H., Trifonov E. N. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J Biomol Struct Dyn. 1986 Feb;3(4):705–723. doi: 10.1080/07391102.1986.10508457. [DOI] [PubMed] [Google Scholar]
  5. Brent R., Ptashne M. Mechanism of action of the lexA gene product. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4204–4208. doi: 10.1073/pnas.78.7.4204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brosius J. Plasmid vectors for the selection of promoters. Gene. 1984 Feb;27(2):151–160. doi: 10.1016/0378-1119(84)90136-7. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Cole S. T. Characterisation of the promoter for the LexA regulated sulA gene of Escherichia coli. Mol Gen Genet. 1983;189(3):400–404. doi: 10.1007/BF00325901. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Finch P., Emmerson P. T. Nucleotide sequence of the regulatory region of the uvrD gene of Escherichia coli. Gene. 1983 Nov;25(2-3):317–323. doi: 10.1016/0378-1119(83)90236-6. [DOI] [PubMed] [Google Scholar]
  13. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fry D. C., Kuby S. A., Mildvan A. S. ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc Natl Acad Sci U S A. 1986 Feb;83(4):907–911. doi: 10.1073/pnas.83.4.907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gren E. J. Recognition of messenger RNA during translational initiation in Escherichia coli. Biochimie. 1984 Jan;66(1):1–29. doi: 10.1016/0300-9084(84)90188-3. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Horii T., Ogawa T., Ogawa H. Nucleotide sequence of the lexA gene of E. coli. Cell. 1981 Mar;23(3):689–697. doi: 10.1016/0092-8674(81)90432-3. [DOI] [PubMed] [Google Scholar]
  18. Husain I., Van Houten B., Thomas D. C., Sancar A. Sequences of Escherichia coli uvrA gene and protein reveal two potential ATP binding sites. J Biol Chem. 1986 Apr 15;261(11):4895–4901. [PubMed] [Google Scholar]
  19. Irino N., Nakayama K., Nakayama H. The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation. Mol Gen Genet. 1986 Nov;205(2):298–304. doi: 10.1007/BF00430442. [DOI] [PubMed] [Google Scholar]
  20. Irino N., Nakayama K., Nakayama H. The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation. Mol Gen Genet. 1986 Nov;205(2):298–304. doi: 10.1007/BF00430442. [DOI] [PubMed] [Google Scholar]
  21. Kitagawa Y., Akaboshi E., Shinagawa H., Horii T., Ogawa H., Kato T. Structural analysis of the umu operon required for inducible mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4336–4340. doi: 10.1073/pnas.82.13.4336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Lloyd R. G., Benson F. E., Shurvinton C. E. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol Gen Genet. 1984;194(1-2):303–309. doi: 10.1007/BF00383532. [DOI] [PubMed] [Google Scholar]
  25. Lloyd R. G., Buckman C., Benson F. E. Genetic analysis of conjugational recombination in Escherichia coli K12 strains deficient in RecBCD enzyme. J Gen Microbiol. 1987 Sep;133(9):2531–2538. doi: 10.1099/00221287-133-9-2531. [DOI] [PubMed] [Google Scholar]
  26. Lloyd R. G., Picksley S. M., Prescott C. Inducible expression of a gene specific to the RecF pathway for recombination in Escherichia coli K12. Mol Gen Genet. 1983;190(1):162–167. doi: 10.1007/BF00330340. [DOI] [PubMed] [Google Scholar]
  27. Looman A. C., Bodlaender J., Comstock L. J., Eaton D., Jhurani P., de Boer H. A., van Knippenberg P. H. Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli. EMBO J. 1987 Aug;6(8):2489–2492. doi: 10.1002/j.1460-2075.1987.tb02530.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lupski J. R., Ruiz A. A., Godson G. N. Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12. Mol Gen Genet. 1984;195(3):391–401. doi: 10.1007/BF00341439. [DOI] [PubMed] [Google Scholar]
  29. Mills D. R., Kramer F. R. Structure-independent nucleotide sequence analysis. Proc Natl Acad Sci U S A. 1979 May;76(5):2232–2235. doi: 10.1073/pnas.76.5.2232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nakayama N., Arai N., Bond M. W., Kaziro Y., Arai K. Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli. J Biol Chem. 1984 Jan 10;259(1):97–101. [PubMed] [Google Scholar]
  31. Otsuji N., Iyehara H., Hideshima Y. Isolation and characterization of an Escherichia coli ruv mutant which forms nonseptate filaments after low doses of ultraviolet light irradiation. J Bacteriol. 1974 Feb;117(2):337–344. doi: 10.1128/jb.117.2.337-344.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Perry K. L., Elledge S. J., Mitchell B. B., Marsh L., Walker G. C. umuDC and mucAB operons whose products are required for UV light- and chemical-induced mutagenesis: UmuD, MucA, and LexA proteins share homology. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4331–4335. doi: 10.1073/pnas.82.13.4331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Picksley S. M., Lloyd R. G., Buckman C. Genetic analysis and regulation of inducible recombination in Escherichia coli K-12. Cold Spring Harb Symp Quant Biol. 1984;49:469–474. doi: 10.1101/sqb.1984.049.01.053. [DOI] [PubMed] [Google Scholar]
  34. Pinkham J. L., Platt T. The nucleotide sequence of the rho gene of E. coli K-12. Nucleic Acids Res. 1983 Jun 11;11(11):3531–3545. doi: 10.1093/nar/11.11.3531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Reddy P., Peterkofsky A., McKenney K. Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression. Proc Natl Acad Sci U S A. 1985 Sep;82(17):5656–5660. doi: 10.1073/pnas.82.17.5656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. 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]
  37. 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]
  38. Sancar A., Sancar G. B., Rupp W. D., Little J. W., Mount D. W. LexA protein inhibits transcription of the E. coli uvrA gene in vitro. Nature. 1982 Jul 1;298(5869):96–98. doi: 10.1038/298096a0. [DOI] [PubMed] [Google Scholar]
  39. 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]
  40. Sancar G. B., Sancar A., Little J. W., Rupp W. D. The uvrB gene of Escherichia coli has both lexA-repressed and lexA-independent promoters. Cell. 1982 Mar;28(3):523–530. doi: 10.1016/0092-8674(82)90207-0. [DOI] [PubMed] [Google Scholar]
  41. 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]
  42. 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]
  43. Shurvinton C. E., Lloyd R. G., Benson F. E., Attfield P. V. Genetic analysis and molecular cloning of the Escherichia coli ruv gene. Mol Gen Genet. 1984;194(1-2):322–329. doi: 10.1007/BF00383535. [DOI] [PubMed] [Google Scholar]
  44. Shurvinton C. E., Lloyd R. G. Damage to DNA induces expression of the ruv gene of Escherichia coli. Mol Gen Genet. 1982;185(2):352–355. doi: 10.1007/BF00330811. [DOI] [PubMed] [Google Scholar]
  45. Strike P., Lodwick D. Plasmid genes affecting DNA repair and mutation. J Cell Sci Suppl. 1987;6:303–321. doi: 10.1242/jcs.1984.supplement_6.20. [DOI] [PubMed] [Google Scholar]
  46. Walker G. C. Inducible DNA repair systems. Annu Rev Biochem. 1985;54:425–457. doi: 10.1146/annurev.bi.54.070185.002233. [DOI] [PubMed] [Google Scholar]
  47. 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]
  48. Wertman K. F., Mount D. W. Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12. J Bacteriol. 1985 Jul;163(1):376–384. doi: 10.1128/jb.163.1.376-384.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. 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