Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 Nov 12;12(21):8085–8096. doi: 10.1093/nar/12.21.8085

Identification, physical map location and sequence of the denV gene from bacteriophage T4.

K Valerie, E E Henderson, J K deRiel
PMCID: PMC320281  PMID: 6095188

Abstract

The denV gene from bacteriophage T4, which codes for endonuclease V, a small DNA repair enzyme, has been cloned and identified by an approach combining DNA sequencing and genetics, independent of the phenotypic effect of the cloned gene. Appropriate DenV+ and DenV- deletion mutants were mapped physically to define precisely a region encompassing the denV gene. This region was sequenced in order to identify a protein-coding sequence of the correct size for the denV gene (400-500 bp). Finally, identification was confirmed by sequencing the corresponding fragments cloned from four genetically and phenotypically well-characterized denV mutants. The denV gene is located at 64 kb on the T4 genome, adjacent to the ipII gene, and codes for a basic protein of 138 amino acids with a deduced molecular weight of 16,078.

Full text

PDF
8085

Images in this article

Selected References

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

  1. Behmoaras T., Toulmé J. J., Hélène C. A tryptophan-containing peptide recognizes and cleaves DNA at apurinic sites. Nature. 1981 Aug 27;292(5826):858–859. doi: 10.1038/292858a0. [DOI] [PubMed] [Google Scholar]
  2. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  3. Benz W. C., Berger H. Selective allele loss in mixed infections with T4 bacteriophage. Genetics. 1973 Jan;73(1):1–11. doi: 10.1093/genetics/73.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chace K. V., Hall D. H. Characterization of new regulatory mutants of bacteriophage T4. II. New class of mutants. J Virol. 1975 Apr;15(4):929–945. doi: 10.1128/jvi.15.4.929-945.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Christensen A. C., Young E. T. T4 late transcripts are initiated near a conserved DNA sequence. Nature. 1982 Sep 23;299(5881):369–371. doi: 10.1038/299369a0. [DOI] [PubMed] [Google Scholar]
  6. Coulondre C., Miller J. H., Farabaugh P. J., Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978 Aug 24;274(5673):775–780. doi: 10.1038/274775a0. [DOI] [PubMed] [Google Scholar]
  7. Duker N. J., Hart D. M. Cleavage of DNA at apyrimidinic sites by lysyl-tryptophyl-alpha-lysine. Biochem Biophys Res Commun. 1982 Apr 29;105(4):1433–1439. doi: 10.1016/0006-291x(82)90948-2. [DOI] [PubMed] [Google Scholar]
  8. FREESE E., BAUTZ E., FREESE E. B. The chemical and mutagenic specificity of hydroxylamine. Proc Natl Acad Sci U S A. 1961 Jun 15;47:845–855. doi: 10.1073/pnas.47.6.845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Friedberg E. C., King J. J. Dark repair of ultraviolet-irradiated deoxyribonucleic acid by bacteriophage T4: purification and characterization of a dimer-specific phage-induced endonuclease. J Bacteriol. 1971 May;106(2):500–507. doi: 10.1128/jb.106.2.500-507.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gorini L. Informational suppression. Annu Rev Genet. 1970;4:107–134. doi: 10.1146/annurev.ge.04.120170.000543. [DOI] [PubMed] [Google Scholar]
  11. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 1982 Jun;18(3):199–209. doi: 10.1016/0378-1119(82)90157-3. [DOI] [PubMed] [Google Scholar]
  12. HARM W. Mutants of phage T4 with increased sensitivity to ultraviolet. Virology. 1963 Jan;19:66–71. doi: 10.1016/0042-6822(63)90025-4. [DOI] [PubMed] [Google Scholar]
  13. Isobe T., Black L. W., Tsugita A. Primary structure of bacteriophage T4 internal protein II and characterization of the cleavage upon phage maturation. J Mol Biol. 1976 Apr 5;102(2):349–365. doi: 10.1016/s0022-2836(76)80059-9. [DOI] [PubMed] [Google Scholar]
  14. Kim J. S., Davidson N. Electron microscope heteroduplex study of sequence relations of T2, T4, and T6 bacteriophage DNAs. Virology. 1974 Jan;57(1):93–111. doi: 10.1016/0042-6822(74)90111-1. [DOI] [PubMed] [Google Scholar]
  15. Lloyd R. S., Hanawalt P. C., Dodson M. L. Processive action of T4 endonuclease V on ultraviolet-irradiated DNA. Nucleic Acids Res. 1980 Nov 11;8(21):5113–5127. doi: 10.1093/nar/8.21.5113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lloyd R. S., Hanawalt P. C. Expression of the denV gene of bacteriophage T4 cloned in Escherichia coli. Proc Natl Acad Sci U S A. 1981 May;78(5):2796–2800. doi: 10.1073/pnas.78.5.2796. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mandel M., Higa A. Calcium-dependent bacteriophage DNA infection. J Mol Biol. 1970 Oct 14;53(1):159–162. doi: 10.1016/0022-2836(70)90051-3. [DOI] [PubMed] [Google Scholar]
  18. Marsh R. C., Hepburn M. L. Map of restriction sites on bacteriophage T4 cytosine-containing DNA for endonucleases bamHI, BglII, KpnI, PvuI, SalI, and XbaI. J Virol. 1981 Apr;38(1):104–114. doi: 10.1128/jvi.38.1.104-114.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Nakabeppu Y., Sekiguchi M. Physical association of pyrimidine dimer DNA glycosylase and apurinic/apyrimidinic DNA endonuclease essential for repair of ultraviolet-damaged DNA. Proc Natl Acad Sci U S A. 1981 May;78(5):2742–2746. doi: 10.1073/pnas.78.5.2742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nakabeppu Y., Yamashita K., Sekiguchi M. Purification and characterization of normal and mutant forms of T4 endonuclease V. J Biol Chem. 1982 Mar 10;257(5):2556–2562. [PubMed] [Google Scholar]
  22. Ohmori H., Tomizawa J. I., Maxam A. M. Detection of 5-methylcytosine in DNA sequences. Nucleic Acids Res. 1978 May;5(5):1479–1485. doi: 10.1093/nar/5.5.1479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pawl G., Taylor R., Minton K., Friedberg E. C. Enzymes involved in thymine dimer excision in bacteriophage T4-infected Escherichia coli. J Mol Biol. 1976 Nov;108(1):99–109. doi: 10.1016/s0022-2836(76)80097-6. [DOI] [PubMed] [Google Scholar]
  24. Pierre J., Laval J. Specific nicking of DNA at apurinic sites by peptides containing aromatic residues. J Biol Chem. 1981 Oct 25;256(20):10217–10220. [PubMed] [Google Scholar]
  25. Radany E. H., Friedberg E. C. A pyrimidine dimer-DNA glycosylase activity associated with the v gene product of bacterophage T4. Nature. 1980 Jul 10;286(5769):182–185. doi: 10.1038/286182a0. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Sato K., Sekiguchi M. Studies on temperature-dependent ultraviolet light-sensitive mutants of bacteriophage T4: the structural gene for T4 endonuclease V. J Mol Biol. 1976 Mar 25;102(1):15–26. doi: 10.1016/0022-2836(76)90071-1. [DOI] [PubMed] [Google Scholar]
  28. Schlagman S., Hattman S., May M. S., Berger L. In vivo methylation by Escherichia coli K-12 mec+ deoxyribonucleic acid-cytosine methylase protects against in vitro cleavage by the RII restriction endonuclease (R. Eco RII). J Bacteriol. 1976 May;126(2):990–996. doi: 10.1128/jb.126.2.990-996.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shames R. B., Lorkiewicz Z. K., Kozinski A. W. Injection of ultraviolet-damage-specific enzyme by T4 bacteriophage. J Virol. 1973 Jul;12(1):1–8. doi: 10.1128/jvi.12.1.1-8.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Shimizu K., Sekiguchi M. Introduction of an active enzyme into permeable cells of Escherichia coli: acquisition of ultraviolet light resistance by uvr mutants on introduction of T4 endonuclease V. Mol Gen Genet. 1979 Jan 5;168(1):37–47. doi: 10.1007/BF00267931. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Smith C. A., Hanawalt P. C. Phage T4 endonuclease V stimulates DNA repair replication in isolated nuclei from ultraviolet-irradiated human cells, including xeroderma pigmentosum fibroblasts. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2598–2602. doi: 10.1073/pnas.75.6.2598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Tanaka K., Hayakawa H., Sekiguchi M., Okada Y. Specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells in vivo. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2958–2962. doi: 10.1073/pnas.74.7.2958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tanaka K., Sekiguchi M., Okada Y. Restoration of ultraviolet-induced unscheduled DNA synthesis of xeroderma pigmentosum cells by the concomitant treatment with bacteriophage T4 endonuclease V and HVJ (Sendai virus). Proc Natl Acad Sci U S A. 1975 Oct;72(10):4071–4075. doi: 10.1073/pnas.72.10.4071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Wood W. B., Revel H. R. The genome of bacteriophage T4. Bacteriol Rev. 1976 Dec;40(4):847–868. doi: 10.1128/br.40.4.847-868.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Zachary A., Black L. W. UV irradiation impairs in vivo encapsidation of bacteriophage T4 DNA. J Virol. 1984 May;50(2):293–300. doi: 10.1128/jvi.50.2.293-300.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES