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. 1986 Nov 11;14(21):8637–8654. doi: 10.1093/nar/14.21.8637

Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4.

K Valerie, J Stevens, M Lynch, E E Henderson, J K de Riel
PMCID: PMC311883  PMID: 3024113

Abstract

The complete 7.2-kb nucleotide sequence from the 58.3 to 65.5-kb early region of bacteriophage T4 has been determined by Maxam and Gilbert sequencing. Computer analysis revealed at least 20 open reading frames (ORFs) within this sequence. All major ORFs are transcribed from the left strand, suggesting that they are expressed early during infection. Among the ORFs, we have identified the ipIII, ipII, denV and tk genes. The ORFs are very tightly spaced, even overlapping in some instances, and when ORF interspacing occurs, promoter-like sequences can be implicated. Several of the sequences preceding the ORFs, in particular those at ipIII, ipII, denV, and orf61.9, can potentially form stable stem-loop structures.

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Selected References

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

  1. Black L. W. Ahmad-Zadeh C,+AHMADAAZADEH C: Internal proteins of bacteriophage T4D: their characterization and relation to head structure and assembly. J Mol Biol. 1971 Apr 14;57(1):71–92. doi: 10.1016/0022-2836(71)90120-3. [DOI] [PubMed] [Google Scholar]
  2. Black L. W. Bacteriophage T4 internal protein mutants: isolation and properties. Virology. 1974 Jul;60(1):166–179. doi: 10.1016/0042-6822(74)90374-2. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  5. Broida J., Abelson J. Sequence organization and control of transcription in the bacteriophage T4 tRNA region. J Mol Biol. 1985 Oct 5;185(3):545–563. doi: 10.1016/0022-2836(85)90071-3. [DOI] [PubMed] [Google Scholar]
  6. Capaldi R. A., Vanderkooi G. The low polarity of many membrane proteins. Proc Natl Acad Sci U S A. 1972 Apr;69(4):930–932. doi: 10.1073/pnas.69.4.930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Chace K. V., Hall D. H. Isolation of mutants of bacteriophage T4 unable to induce thymidine kinase activity. J Virol. 1973 Aug;12(2):343–348. doi: 10.1128/jvi.12.2.343-348.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chu F. K., Maley G. F., Maley F., Belfort M. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc Natl Acad Sci U S A. 1984 May;81(10):3049–3053. doi: 10.1073/pnas.81.10.3049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clewell D. B., Helinski D. R. Effect of growth conditions on the formation of the relaxation complex of supercoiled ColE1 deoxyribonucleic acid and protein in Escherichia coli. J Bacteriol. 1972 Jun;110(3):1135–1146. doi: 10.1128/jb.110.3.1135-1146.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fukada K., Gossens L., Abelson J. The cloning of a T4 transfer RNA gene cluster. J Mol Biol. 1980 Feb 25;137(2):213–234. doi: 10.1016/0022-2836(80)90326-5. [DOI] [PubMed] [Google Scholar]
  12. Godson G. N., Vapnek D. A simple method of preparing large amounts of phiX174 RF 1 supercoiled DNA. Biochim Biophys Acta. 1973 Apr 11;299(4):516–520. doi: 10.1016/0005-2787(73)90223-2. [DOI] [PubMed] [Google Scholar]
  13. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  14. Gram H., Liebig H. D., Hack A., Niggemann E., Rüger W. A physical map of bacteriophage T4 including the positions of strong promoters and terminators recognized in vitro. Mol Gen Genet. 1984;194(1-2):232–240. doi: 10.1007/BF00383522. [DOI] [PubMed] [Google Scholar]
  15. Gram H., Rüger W. Genes 55, alpha gt, 47 and 46 of bacteriophage T4: the genomic organization as deduced by sequence analysis. EMBO J. 1985 Jan;4(1):257–264. doi: 10.1002/j.1460-2075.1985.tb02344.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Hanahan D., Meselson M. Plasmid screening at high colony density. Gene. 1980 Jun;10(1):63–67. doi: 10.1016/0378-1119(80)90144-4. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. King G. J., Huang W. M. Identification of the origins of T4 DNA replication. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7248–7252. doi: 10.1073/pnas.79.23.7248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Marchin G. L. Mutations in a nonessential viral gene permit bacteriophage T4 to form plaques on Escherichia coli valS ts relA. Science. 1980 Jul 11;209(4453):294–295. doi: 10.1126/science.6992274. [DOI] [PubMed] [Google Scholar]
  21. Marinus M. G., Morris N. R. Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J Bacteriol. 1973 Jun;114(3):1143–1150. doi: 10.1128/jb.114.3.1143-1150.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. McPheeters D. S., Christensen A., Young E. T., Stormo G., Gold L. Translational regulation of expression of the bacteriophage T4 lysozyme gene. Nucleic Acids Res. 1986 Jul 25;14(14):5813–5826. doi: 10.1093/nar/14.14.5813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Meselson M., Yuan R. DNA restriction enzyme from E. coli. Nature. 1968 Mar 23;217(5134):1110–1114. doi: 10.1038/2171110a0. [DOI] [PubMed] [Google Scholar]
  25. Mileham A. J., Murray N. E., Revel H. R. Gamma-T4 hybrid bacteriophage carrying the thymidine kinase gene of bacteriophage T4. J Virol. 1984 May;50(2):619–622. doi: 10.1128/jvi.50.2.619-622.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Nilsson B., Uhlén M., Josephson S., Gatenbeck S., Philipson L. An improved positive selection plasmid vector constructed by oligonucleotide mediated mutagenesis. Nucleic Acids Res. 1983 Nov 25;11(22):8019–8030. doi: 10.1093/nar/11.22.8019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. O'Farrell P. H., Kutter E., Nakanishi M. A restriction map of the bacteriophage T4 genome. Mol Gen Genet. 1980;179(2):421–435. doi: 10.1007/BF00425473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Owen J. E., Schultz D. W., Taylor A., Smith G. R. Nucleotide sequence of the lysozyme gene of bacteriophage T4. Analysis of mutations involving repeated sequences. J Mol Biol. 1983 Apr 5;165(2):229–248. doi: 10.1016/s0022-2836(83)80255-1. [DOI] [PubMed] [Google Scholar]
  30. Peacock A. C., Dingman C. W. Molecular weight estimation and separation of ribonucleic acid by electrophoresis in agarose-acrylamide composite gels. Biochemistry. 1968 Feb;7(2):668–674. doi: 10.1021/bi00842a023. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. 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]
  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. Snyder L., Gold L., Kutter E. A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A. 1976 Sep;73(9):3098–3102. doi: 10.1073/pnas.73.9.3098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Staden R., McLachlan A. D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 1982 Jan 11;10(1):141–156. doi: 10.1093/nar/10.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Stueber D., Bujard H. Transcription from efficient promoters can interfere with plasmid replication and diminish expression of plasmid specified genes. EMBO J. 1982;1(11):1399–1404. doi: 10.1002/j.1460-2075.1982.tb01329.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Valerie K., Henderson E. E., de Riel J. K. Expression of a cloned denV gene of bacteriophage T4 in Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4763–4767. doi: 10.1073/pnas.82.14.4763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Valerie K., Henderson E. E., deRiel J. K. Identification, physical map location and sequence of the denV gene from bacteriophage T4. Nucleic Acids Res. 1984 Nov 12;12(21):8085–8096. doi: 10.1093/nar/12.21.8085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Yamamoto K. R., Alberts B. M., Benzinger R., Lawhorne L., Treiber G. Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Virology. 1970 Mar;40(3):734–744. doi: 10.1016/0042-6822(70)90218-7. [DOI] [PubMed] [Google Scholar]
  42. Yee J. K., Marsh R. C. Locations of bacteriophage T4 origins of replication. J Virol. 1985 May;54(2):271–277. doi: 10.1128/jvi.54.2.271-277.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]

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