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. 1981 Nov 11;9(21):5623–5643. doi: 10.1093/nar/9.21.5623

The structure and function of the regulatory elements of the Escherichia coli uvrB gene.

E van den Berg, J Zwetsloot, I Noordermeer, H Pannekoek, B Dekker, R Dijkema, H van Ormondt
PMCID: PMC327548  PMID: 6273801

Abstract

The construction and properties of recombinant plasmids carrying the Escherichia coli uvrB gene, including its transcriptional- and translational regulatory elements, is reported. The DNA sequence of the region, which governs the expression of the uvrB gene, has been determined. Within this sequence two non-overlapping DNA segments match the model sequence for Escherichia coli promoters (1). The '-10 regions' and the '-35 regions' of the proposed uvrB promoters are, respectively, 5'TAAAAT (P1), 5'TATAAT (P2) and 5'TTGGCA (P1), 5'GTGATG (P2). The existence and the position of these promoters has been established by elimination of one promoter (P2), using molecular cloning procedures, by length measurements of in vitro synthesized 'run-off' transcripts and by protection of the uvrB regulatory region for S1 nuclease digestion using in vivo made RNA. Potential sites of interaction within the uvrB regulatory region with regulatory proteins, such as the LexA protein (2) and the UvrC protein (3) are discussed.

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Selected References

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

  1. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  2. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  3. Brent R., Ptashne M. The lexA gene product represses its own promoter. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1932–1936. doi: 10.1073/pnas.77.4.1932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burgess R. R. A new method for the large scale purification of Escherichia coli deoxyribonucleic acid-dependent ribonucleic acid polymerase. J Biol Chem. 1969 Nov 25;244(22):6160–6167. [PubMed] [Google Scholar]
  5. Burgess R. R., Jendrisak J. J. A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry. 1975 Oct 21;14(21):4634–4638. doi: 10.1021/bi00692a011. [DOI] [PubMed] [Google Scholar]
  6. Chan P. T., Lebowitz J., Bastia D. Nucleotide sequence determination of a strong promoter of the colicin E 1 plasmid. Analysis of restriction sites protected by RNA polymerase interactions before and after limited transcription. Nucleic Acids Res. 1979 Nov 10;7(5):1247–1262. doi: 10.1093/nar/7.5.1247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976 Sep;9(1):91–99. doi: 10.1016/0092-8674(76)90055-6. [DOI] [PubMed] [Google Scholar]
  9. Fogliano M., Schendel P. F. Evidence for the inducibility of the uvrB operon. Nature. 1981 Jan 15;289(5794):196–198. doi: 10.1038/289196a0. [DOI] [PubMed] [Google Scholar]
  10. Hanawalt P. C., Cooper P. K., Ganesan A. K., Smith C. A. DNA repair in bacteria and mammalian cells. Annu Rev Biochem. 1979;48:783–836. doi: 10.1146/annurev.bi.48.070179.004031. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Howard-Flanders P., Boyce R. P., Theriot L. Three loci in Escherichia coli K-12 that control the excision of pyrimidine dimers and certain other mutagen products from DNA. Genetics. 1966 Jun;53(6):1119–1136. doi: 10.1093/genetics/53.6.1119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kenyon C. J., Walker G. C. DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc Natl Acad Sci U S A. 1980 May;77(5):2819–2823. doi: 10.1073/pnas.77.5.2819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Little J. W., Harper J. E. Identification of the lexA gene product of Escherichia coli K-12. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6147–6151. doi: 10.1073/pnas.76.12.6147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Maniatis T., Jeffrey A., Kleid D. G. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. doi: 10.1073/pnas.72.3.1184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Mount D. W. A mutant of Escherichia coli showing constitutive expression of the lysogenic induction and error-prone DNA repair pathways. Proc Natl Acad Sci U S A. 1977 Jan;74(1):300–304. doi: 10.1073/pnas.74.1.300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Musso R. E., Di Lauro R., Adhya S., de Crombrugghe B. Dual control for transcription of the galactose operon by cyclic AMP and its receptor protein at two interspersed promoters. Cell. 1977 Nov;12(3):847–854. doi: 10.1016/0092-8674(77)90283-5. [DOI] [PubMed] [Google Scholar]
  21. Pannekoek H., Hille J., Noordermeer I. Relief of polarity caused by transposon Tn5: application in mapping a cloned region of the Escherichia coli uvrB locus essential for UV resistance. Gene. 1980 Dec;12(1-2):51–61. doi: 10.1016/0378-1119(80)90015-3. [DOI] [PubMed] [Google Scholar]
  22. Pannekoek H., Maat J., van den Berg E., Noordermeer I. Structure of a promotor on plasmid pMB9 derived from plasmid pSC101. Nucleic Acids Res. 1980 Apr 11;8(7):1535–1550. doi: 10.1093/nar/8.7.1535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pannekoek H., Noordermeer I. A., van Sluis C. A., van de Putte P. Expression of the uvrB gene of Escherichia coli: in vitro construction of a pMB9 uvrB plasmid. J Bacteriol. 1978 Feb;133(2):884–896. doi: 10.1128/jb.133.2.884-896.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Pannekoek H., Noordermeer I., van de Putte P. Expression of the cloned uvrB gene of Escherichia coli: dependency on nonsense suppressors. J Bacteriol. 1979 Jul;139(1):48–53. doi: 10.1128/jb.139.1.48-53.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Pannekoek H., Noordermeer I., van de Putte P. Expression of the cloned uvrB gene of Escherichia coli: mode of transcription and orientation. J Bacteriol. 1979 Jul;139(1):54–63. doi: 10.1128/jb.139.1.54-63.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc Natl Acad Sci U S A. 1975 Mar;72(3):784–788. doi: 10.1073/pnas.72.3.784. [DOI] [PMC free article] [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 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. Saucier J. M., Wang J. C. Angular alteration of the DNA helix by E. coli RNA polymerase. Nat New Biol. 1972 Oct 11;239(93):167–170. doi: 10.1038/newbio239167a0. [DOI] [PubMed] [Google Scholar]
  31. Scherer G. E., Walkinshaw M. D., Arnott S. A computer aided oligonucleotide analysis provides a model sequence for RNA polymerase-promoter recognition in E.coli. Nucleic Acids Res. 1978 Oct;5(10):3759–3773. doi: 10.1093/nar/5.10.3759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Seeberg E. Reconstitution of an Escherichia coli repair endonuclease activity from the separated uvrA+ and uvrB+/uvrC+ gene products. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2569–2573. doi: 10.1073/pnas.75.6.2569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]
  34. Staden R. Further procedures for sequence analysis by computer. Nucleic Acids Res. 1978 Mar;5(3):1013–1016. doi: 10.1093/nar/5.3.1013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sternbach H., Engelhardt R., Lezius A. G. Rapid isolation of highly active RNA polymerase from Escherichia coli and its subunits by matrix-bound heparin. Eur J Biochem. 1975 Dec 1;60(1):51–55. doi: 10.1111/j.1432-1033.1975.tb20974.x. [DOI] [PubMed] [Google Scholar]
  36. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  37. VOGEL H. J., BONNER D. M. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem. 1956 Jan;218(1):97–106. [PubMed] [Google Scholar]
  38. Van Charldorp R., Heus H. A., Van Knippenberg P. H. Adenosine dimethylation of 16S ribosomal RNA: effect of the methylgroups on local conformational stability as deduced from electrophoretic mobility of RNA fragments in denaturing polyacrylamide gels. Nucleic Acids Res. 1981 Jan 24;9(2):267–275. doi: 10.1093/nar/9.2.267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Van Ormondt H., Maat J., De Waard A., Van der Eb A. J. The nucleotide sequence of the transforming HpaI-E fragment of adenovirus type 5 DNA. Gene. 1978 Dec;4(4):309–328. doi: 10.1016/0378-1119(78)90048-3. [DOI] [PubMed] [Google Scholar]
  40. Vogt V. M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. Eur J Biochem. 1973 Feb 15;33(1):192–200. doi: 10.1111/j.1432-1033.1973.tb02669.x. [DOI] [PubMed] [Google Scholar]
  41. 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]
  42. Young R. A., Steitz J. A. Tandem promoters direct E. coli ribosomal RNA synthesis. Cell. 1979 May;17(1):225–234. doi: 10.1016/0092-8674(79)90310-6. [DOI] [PubMed] [Google Scholar]
  43. de Boer H. A., Gilbert S. F., Nomura M. DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):201–209. doi: 10.1016/0092-8674(79)90308-8. [DOI] [PubMed] [Google Scholar]
  44. van Wezenbeek P. M., Hulsebos T. J., Schoenmakers J. G. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd. Gene. 1980 Oct;11(1-2):129–148. doi: 10.1016/0378-1119(80)90093-1. [DOI] [PubMed] [Google Scholar]
  45. van den Elzen P. J., Konings R. N., Veltkamp E., Nijkamp H. J. Transcription of bacteriocinogenic plasmid CloDF13 in vivo and in vitro: structure of the cloacin immunity operon. J Bacteriol. 1980 Nov;144(2):579–591. doi: 10.1128/jb.144.2.579-591.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]

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