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. 1984 Sep 11;12(17):6727–6739. doi: 10.1093/nar/12.17.6727

Analysis of a cloned colicin Ib gene: complete nucleotide sequence and implications for regulation of expression.

J M Varley, G J Boulnois
PMCID: PMC320112  PMID: 6091036

Abstract

The complete nucleotide sequence of a 2,971 base pair EcoRI fragment carrying the structural gene for colicin Ib has been determined. The length of the gene is 1,881 nucleotides which is predicted to produce a protein of 626 amino acids and of molecular weight 71,364. The structural gene is flanked by likely promoter and terminator signals and in between the promoter and the ribosome binding site is an inverted repeat sequence which resembles other sequences known to bind the LexA protein. Further analysis of the 5' flanking sequences revealed a second region which may act either as a second LexA binding site and/or in the binding of cyclic AMP receptor protein. Comparison of the predicted amino acid sequence of colicin Ib with that of colicins A and E1 reveals localised homology. The implications of these similarities in the proteins and of regulation of the colicin Ib structural gene are discussed.

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Selected References

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  1. Anderson S. Shotgun DNA sequencing using cloned DNase I-generated fragments. Nucleic Acids Res. 1981 Jul 10;9(13):3015–3027. doi: 10.1093/nar/9.13.3015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bolivar F. Construction and characterization of new cloning vehicles. III. Derivatives of plasmid pBR322 carrying unique Eco RI sites for selection of Eco RI generated recombinant DNA molecules. Gene. 1978 Oct;4(2):121–136. doi: 10.1016/0378-1119(78)90025-2. [DOI] [PubMed] [Google Scholar]
  3. Bonner W. M., Laskey R. A. A film detection method for tritium-labelled proteins and nucleic acids in polyacrylamide gels. Eur J Biochem. 1974 Jul 1;46(1):83–88. doi: 10.1111/j.1432-1033.1974.tb03599.x. [DOI] [PubMed] [Google Scholar]
  4. Boulnois G. J. Colicin Ib does not cause plasmid-promoted abortive phage infection of Escherichia coli K-12. Mol Gen Genet. 1981;182(3):508–510. doi: 10.1007/BF00293944. [DOI] [PubMed] [Google Scholar]
  5. Boulnois G. J., Wilkins B. M. A novel priming system for conjugal synthesis of an IncI alpha plasmid in recipients. Mol Gen Genet. 1979 Oct 1;175(3):275–279. doi: 10.1007/BF00397227. [DOI] [PubMed] [Google Scholar]
  6. Dougan G., Sherratt D. The transposon Tn1 as a probe for studying ColE1 structure and function. Mol Gen Genet. 1977 Mar 7;151(2):151–160. doi: 10.1007/BF00338689. [DOI] [PubMed] [Google Scholar]
  7. Easton A. M., Kushner S. R. Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation. Nucleic Acids Res. 1983 Dec 20;11(24):8625–8640. doi: 10.1093/nar/11.24.8625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ebina Y., Kishi F., Nakazawa A. Direct participation of lexA protein in repression of colicin E1 synthesis. J Bacteriol. 1982 Jun;150(3):1479–1481. doi: 10.1128/jb.150.3.1479-1481.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Echarti C., Hirschel B., Boulnois G. J., Varley J. M., Waldvogel F., Timmis K. N. Cloning and analysis of the K1 capsule biosynthesis genes of Escherichia coli: lack of homology with Neisseria meningitidis group B DNA sequences. Infect Immun. 1983 Jul;41(1):54–60. doi: 10.1128/iai.41.1.54-60.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Glazebrook J. A., Forster J. W., Strike P. Regulation of expression of the colicin gene of I1 group plasmid TP110. J Bacteriol. 1983 Jul;155(1):122–128. doi: 10.1128/jb.155.1.122-128.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gottlieb J. H., Duckworth D. H. Location of the abi, col and imm genes on pHU011, a colicin Ib plasmid derivative. Gene. 1983 Dec;26(2-3):301–302. doi: 10.1016/0378-1119(83)90201-9. [DOI] [PubMed] [Google Scholar]
  12. Guyer M. S. The gamma delta sequence of F is an insertion sequence. J Mol Biol. 1978 Dec 15;126(3):347–365. doi: 10.1016/0022-2836(78)90045-1. [DOI] [PubMed] [Google Scholar]
  13. Hardy K. G. Colicinogeny and related phenomena. Bacteriol Rev. 1975 Dec;39(4):464–515. doi: 10.1128/br.39.4.464-515.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  15. Horii T., Ogawa T., Ogawa H. Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):313–317. doi: 10.1073/pnas.77.1.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kenyon C. J., Walker G. C. Expression of the E. coli uvrA gene is inducible. Nature. 1981 Feb 26;289(5800):808–810. doi: 10.1038/289808a0. [DOI] [PubMed] [Google Scholar]
  17. Konisky J. Characterization of colicin Ia and colicin Ib. Chemical studies of protein structure. J Biol Chem. 1972 Jun 25;247(12):3750–3755. [PubMed] [Google Scholar]
  18. 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]
  19. 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]
  20. 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]
  21. Miki T., Ebina Y., Kishi F., Nakazawa A. Organization of the lexA gene of Escherichia coli and nucleotide sequence of the regulatory region. Nucleic Acids Res. 1981 Feb 11;9(3):529–543. doi: 10.1093/nar/9.3.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Mizusawa S., Court D., Gottesman S. Transcription of the sulA gene and repression by LexA. J Mol Biol. 1983 Dec 15;171(3):337–343. doi: 10.1016/0022-2836(83)90097-9. [DOI] [PubMed] [Google Scholar]
  23. Morlon J., Lloubes R., Chartier M., Bonicel J., Lazdunski C. Nucleotide sequence of promoter, operator and amino-terminal region of caa, the structural gene of colicin A. EMBO J. 1983;2(5):787–789. doi: 10.1002/j.1460-2075.1983.tb01501.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Morlon J., Lloubès R., Varenne S., Chartier M., Lazdunski C. Complete nucleotide sequence of the structural gene for colicin A, a gene translated at non-uniform rate. J Mol Biol. 1983 Oct 25;170(2):271–285. doi: 10.1016/s0022-2836(83)80148-x. [DOI] [PubMed] [Google Scholar]
  25. Platt T. Termination of transcription and its regulation in the tryptophan operon of E. coli. Cell. 1981 Apr;24(1):10–23. doi: 10.1016/0092-8674(81)90496-7. [DOI] [PubMed] [Google Scholar]
  26. Pugsley A. P. Transcription regulation of colicin Ib synthesis. Mol Gen Genet. 1981;183(3):522–527. doi: 10.1007/BF00268775. [DOI] [PubMed] [Google Scholar]
  27. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. 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]
  30. Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature. 1975 Mar 6;254(5495):34–38. doi: 10.1038/254034a0. [DOI] [PubMed] [Google Scholar]
  31. Stormo G. D., Schneider T. D., Gold L. M. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2971–2996. doi: 10.1093/nar/10.9.2971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Tokuda H., Konisky J. Mode of action of colicin Ia: effect of colicin on the Escherichia coli proton electrochemical gradient. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2579–2583. doi: 10.1073/pnas.75.6.2579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  34. Wilkins B. M., Boulnois G. J., Lanka E. A plasmid DNA primase active in discontinuous bacterial DNA replication. Nature. 1981 Mar 19;290(5803):217–221. doi: 10.1038/290217a0. [DOI] [PubMed] [Google Scholar]
  35. Yamada M., Ebina Y., Miyata T., Nakazawa T., Nakazawa A. Nucleotide sequence of the structural gene for colicin E1 and predicted structure of the protein. Proc Natl Acad Sci U S A. 1982 May;79(9):2827–2831. doi: 10.1073/pnas.79.9.2827. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]
  37. van den Berg E., Zwetsloot J., Noordermeer I., Pannekoek H., Dekker B., Dijkema R., van Ormondt H. The structure and function of the regulatory elements of the Escherichia coli uvrB gene. Nucleic Acids Res. 1981 Nov 11;9(21):5623–5643. doi: 10.1093/nar/9.21.5623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. van den Elzen P. J., Maat J., Walters H. H., Veltkamp E., Nijkamp H. J. The nucleotide sequence of the bacteriocin promoters of plasmids Clo DF13 and Co1 E1: role of lexA repressor and cAMP in the regulation of promoter activity. Nucleic Acids Res. 1982 Mar 25;10(6):1913–1928. doi: 10.1093/nar/10.6.1913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. van den Elzen P. J., Walters H. H., Veltkamp E., Nijkamp H. J. Molecular structure and function of the bacteriocin gene and bacteriocin protein of plasmid Clo DF13. Nucleic Acids Res. 1983 Apr 25;11(8):2465–2477. doi: 10.1093/nar/11.8.2465. [DOI] [PMC free article] [PubMed] [Google Scholar]

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