Abstract
The sequence of a 2.67-kilobase section of the Escherichia coli chromosome that contains the rep gene has been determined. This gene codes for a protein of predicted Mr 72,800, a DNA helicase, which is also a single-stranded DNA-dependent ATPase. The sequenced region contains an open reading frame of the correct length and orientation to encode the Rep protein. A secondary structure for the protein can be formulated from the amino acid sequence. We have compared both the primary and the secondary structures of Rep with other proteins and find the greatest homology between Rep and E. coli helicase II, the product of the uvrD gene.
Full text
PDF










Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Arthur H. M., Bramhill D., Eastlake P. B., Emmerson P. T. Cloning of the uvrD gene of E. coli and identification of the product. Gene. 1982 Oct;19(3):285–295. doi: 10.1016/0378-1119(82)90018-x. [DOI] [PubMed] [Google Scholar]
- Bialkowska-Hobrzanska H., Gilchrist C. A., Denhardt D. T. Escherichia coli rep gene: identification of the promoter and N terminus of the rep protein. J Bacteriol. 1985 Dec;164(3):1004–1010. doi: 10.1128/jb.164.3.1004-1010.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Białkowska-Hobrzanska H., Denhardt D. T. The rep mutation. VII. Cloning and analysis of the functional rep gene of Escherichia coli K-12. Gene. 1984 Apr;28(1):93–102. doi: 10.1016/0378-1119(84)90091-x. [DOI] [PubMed] [Google Scholar]
- Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bridges B. A. Further characterization of repair of 8-methoxypsoralen crosslinks in UV-excision-defective Escherichia coli. Mutat Res. 1984 Nov-Dec;132(5-6):153–160. doi: 10.1016/0167-8817(84)90033-6. [DOI] [PubMed] [Google Scholar]
- Burton Z., Burgess R. R., Lin J., Moore D., Holder S., Gross C. A. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889–2903. doi: 10.1093/nar/9.12.2889. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Christie G. E., Farnham P. J., Platt T. Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4180–4184. doi: 10.1073/pnas.78.7.4180. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cone K. C., Sellitti M. A., Steege D. A. Lac repressor mRNA transcription terminates in vivo in the lac control region. J Biol Chem. 1983 Sep 25;258(18):11296–11304. [PubMed] [Google Scholar]
- Denhardt D. T., Iwaya M., Larison L. L. The rep mutation. II. Its effect on Escherichia coli and on the replication of bacteriophage phi X174. Virology. 1972 Aug;49(2):486–496. doi: 10.1016/0042-6822(72)90500-4. [DOI] [PubMed] [Google Scholar]
- Eisenberg S., Scott J. F., Kornberg A. An enzyme system for replication of duplex circular DNA: the replicative form of phage phi X174. Proc Natl Acad Sci U S A. 1976 May;73(5):1594–1597. doi: 10.1073/pnas.73.5.1594. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fassler J. S., Tessman I., Tessman E. S. Lethality of the double mutations rho rep and rho ssb in Escherichia coli. J Bacteriol. 1985 Feb;161(2):609–614. doi: 10.1128/jb.161.2.609-614.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
- Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982 Nov 25;10(22):7055–7074. doi: 10.1093/nar/10.22.7055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Joyce C. M., Grindley N. D. Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1830–1834. doi: 10.1073/pnas.80.7.1830. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Knight K. L., McEntee K. Affinity labeling of a tyrosine residue in the ATP binding site of the recA protein from Escherichia coli with 5'-p-fluorosulfonylbenzoyladenosine. J Biol Chem. 1985 Aug 25;260(18):10177–10184. [PubMed] [Google Scholar]
- 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]
- Kumura K., Sekiguchi M. Identification of the uvrD gene product of Escherichia coli as DNA helicase II and its induction by DNA-damaging agents. J Biol Chem. 1984 Feb 10;259(3):1560–1565. [PubMed] [Google Scholar]
- Lagrimini L. M., Brentano S. T., Donelson J. E. A DNA sequence analysis package for the IBM personal computer. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):605–614. doi: 10.1093/nar/12.1part2.605. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lane H. E., Denhardt D. T. The rep mutation. IV. Slower movement of replication forks in Escherichia coli rep strains. J Mol Biol. 1975 Sep 5;97(1):99–112. doi: 10.1016/s0022-2836(75)80025-8. [DOI] [PubMed] [Google Scholar]
- Larson R., Messing J. Apple II software for M13 shotgun DNA sequencing. Nucleic Acids Res. 1982 Jan 11;10(1):39–49. doi: 10.1093/nar/10.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maples V. F., Kushner S. R. DNA repair in Escherichia coli: identification of the uvrD gene product. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5616–5620. doi: 10.1073/pnas.79.18.5616. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Matson S. W. Escherichia coli helicase II (urvD gene product) translocates unidirectionally in a 3' to 5' direction. J Biol Chem. 1986 Aug 5;261(22):10169–10175. [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
- 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]
- Mount D. W., Conrad B. Improved programs for DNA and protein sequence analysis on the IBM personal computer and other standard computer systems. Nucleic Acids Res. 1986 Jan 10;14(1):443–454. doi: 10.1093/nar/14.1.443. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
- Pongor S., Guttieri M. J., Cohen L. M., Szalay A. A. Microcomputer programs for prediction and comparative evaluation of protein secondary structure from nucleotide sequence data: application to ribulose-1,5-bisphosphate carboxylase sequences. DNA. 1985 Aug;4(4):319–326. doi: 10.1089/dna.1985.4.319. [DOI] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
- Scott J. F., Kornberg A. Purification of the rep protein of Escherichia coli. An ATPase which separates duplex DNA strands in advance of replication. J Biol Chem. 1978 May 10;253(9):3292–3297. [PubMed] [Google Scholar]
- Takahashi S., Hours C., Chu A., Denhardt D. T. The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can J Biochem. 1979 Jun;57(6):855–866. doi: 10.1139/o79-105. [DOI] [PubMed] [Google Scholar]
- Tessman E. S., Peterson P. K. Bacterial rep- mutations that block development of small DNA bacteriophages late in infection. J Virol. 1976 Nov;20(2):400–412. doi: 10.1128/jvi.20.2.400-412.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tessman E. S., Peterson P. K. Suppression of the ssb-1 and ssb-113 mutations of Escherichia coli by a wild-type rep gene, NaCl, and glucose. J Bacteriol. 1982 Nov;152(2):572–583. doi: 10.1128/jb.152.2.572-583.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Travers A. A. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol. 1980 Feb;141(2):973–976. doi: 10.1128/jb.141.2.973-976.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Yarranton G. T., Gefter M. L. Enzyme-catalyzed DNA unwinding: studies on Escherichia coli rep protein. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1658–1662. doi: 10.1073/pnas.76.4.1658. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zieg J., Maples V. F., Kushner S. R. Recombinant levels of Escherichia coli K-12 mutants deficient in various replication, recombination, or repair genes. J Bacteriol. 1978 Jun;134(3):958–966. doi: 10.1128/jb.134.3.958-966.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]