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. 1990 Jan;64(1):24–36. doi: 10.1128/jvi.64.1.24-36.1990

Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions.

D Ghisotti 1, S Finkel 1, C Halling 1, G Dehò 1, G Sironi 1, R Calendar 1
PMCID: PMC249035  PMID: 2403440

Abstract

We sequenced the leftmost 2,640 base pairs of bacteriophage P4 DNA, thus completing the sequence of the 11,627-base-pair P4 genome. The newly sequenced region encodes three nonessential genes, which are called gop, beta, and cII (in order, from left to right). The gop gene product kills Escherichia coli when the beta protein is absent; the gop and beta genes are transcribed rightward from the same promoter. The cII gene is transcribed leftward to a rho-independent terminator. Mutation of this terminator creates a temperature-sensitive phenotype, presumably owing to a defect in expression of the beta gene.

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Selected References

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

  1. Alano P., Dehò G., Sironi G., Zangrossi S. Regulation of the plasmid state of the genetic element P4. Mol Gen Genet. 1986 Jun;203(3):445–450. doi: 10.1007/BF00422069. [DOI] [PubMed] [Google Scholar]
  2. Aota S., Gojobori T., Ishibashi F., Maruyama T., Ikemura T. Codon usage tabulated from the GenBank Genetic Sequence Data. Nucleic Acids Res. 1988;16 (Suppl):r315–r402. doi: 10.1093/nar/16.suppl.r315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. BERTANI L. E. LYSOGENIC CONVERSION BY BACTERIOPHAGE P2 RESULTING IN AN INCREASED SENSITIVITY OF ESCHERICHIA COLI TO 5-FLUORODEOXYURIDINE. Biochim Biophys Acta. 1964 Aug 12;87:631–640. doi: 10.1016/0926-6550(64)90281-6. [DOI] [PubMed] [Google Scholar]
  4. Barrett K. J., Marsh M. L., Calendar R. Interactions between a satellite bacteriophage and its helper. J Mol Biol. 1976 Sep 25;106(3):683–707. doi: 10.1016/0022-2836(76)90259-x. [DOI] [PubMed] [Google Scholar]
  5. Berk A. J., Sharp P. A. Spliced early mRNAs of simian virus 40. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1274–1278. doi: 10.1073/pnas.75.3.1274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. 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]
  8. Brennan R. G., Matthews B. W. The helix-turn-helix DNA binding motif. J Biol Chem. 1989 Feb 5;264(4):1903–1906. [PubMed] [Google Scholar]
  9. Calendar R., Ljungquist E., Deho G., Usher D. C., Goldstein R., Youderian P., Sironi G., Six E. W. Lysogenization by satellite phage P4. Virology. 1981 Aug;113(1):20–38. doi: 10.1016/0042-6822(81)90133-1. [DOI] [PubMed] [Google Scholar]
  10. Dale E. C., Christie G. E., Calendar R. Organization and expression of the satellite bacteriophage P4 late gene cluster. J Mol Biol. 1986 Dec 20;192(4):793–803. doi: 10.1016/0022-2836(86)90029-x. [DOI] [PubMed] [Google Scholar]
  11. Dehò G. Circular genetic map of satellite bacteriophage P4. Virology. 1983 Apr 15;126(1):267–278. doi: 10.1016/0042-6822(83)90478-6. [DOI] [PubMed] [Google Scholar]
  12. Dehò G., Ghisotti D., Alano P., Zangrossi S., Borrello M. G., Sironi G. Plasmid mode of propagation of the genetic element P4. J Mol Biol. 1984 Sep 15;178(2):191–207. doi: 10.1016/0022-2836(84)90139-6. [DOI] [PubMed] [Google Scholar]
  13. Dehó G., Zangrossi S., Ghisotti D., Sironi G. Alternative promoters in the development of bacteriophage plasmid P4. J Virol. 1988 May;62(5):1697–1704. doi: 10.1128/jvi.62.5.1697-1704.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dodd I. B., Egan J. B. Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J Mol Biol. 1987 Apr 5;194(3):557–564. doi: 10.1016/0022-2836(87)90681-4. [DOI] [PubMed] [Google Scholar]
  15. Evans R. M., Hollenberg S. M. Zinc fingers: gilt by association. Cell. 1988 Jan 15;52(1):1–3. doi: 10.1016/0092-8674(88)90522-3. [DOI] [PubMed] [Google Scholar]
  16. Flensburg J., Calendar R. Bacteriophage P4 DNA replication. Nucleotide sequence of the P4 replication gene and the cis replication region. J Mol Biol. 1987 May 20;195(2):439–445. doi: 10.1016/0022-2836(87)90664-4. [DOI] [PubMed] [Google Scholar]
  17. Garcia G. M., Mar P. K., Mullin D. A., Walker J. R., Prather N. E. The E. coli dnaY gene encodes an arginine transfer RNA. Cell. 1986 May 9;45(3):453–459. doi: 10.1016/0092-8674(86)90331-4. [DOI] [PubMed] [Google Scholar]
  18. Garen A. Sense and nonsense in the genetic code. Three exceptional triplets can serve as both chain-terminating signals and amino acid codons. Science. 1968 Apr 12;160(3824):149–159. doi: 10.1126/science.160.3824.149. [DOI] [PubMed] [Google Scholar]
  19. Ghisotti D., Zangrossi S., Sironi G. An Escherichia coli gene required for bacteriophage P2-lambda interference. J Virol. 1983 Dec;48(3):616–626. doi: 10.1128/jvi.48.3.616-626.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gibbs W., Goldstein R. N., Wiener R., Lindqvist B., Calendar R. Satellite bacteriophage P4: characterization of mutants in two essential genes. Virology. 1973 May;53(1):24–39. doi: 10.1016/0042-6822(73)90462-5. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  23. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 1981 Sep 25;151(3):389–409. doi: 10.1016/0022-2836(81)90003-6. [DOI] [PubMed] [Google Scholar]
  24. Kahn M., Ow D., Sauer B., Rabinowitz A., Calendar R. Genetic analysis of bacteriophage P4 using P4-plasmid ColE1 hybrids. Mol Gen Genet. 1980 Feb;177(3):399–412. doi: 10.1007/BF00271478. [DOI] [PubMed] [Google Scholar]
  25. Kraft R., Tardiff J., Krauter K. S., Leinwand L. A. Using mini-prep plasmid DNA for sequencing double stranded templates with Sequenase. Biotechniques. 1988 Jun;6(6):544-6, 549. [PubMed] [Google Scholar]
  26. Krevolin M. D., Calendar R. The replication of bacteriophage P4 DNA in vitro. Partial purification of the P4 alpha gene product. J Mol Biol. 1985 Apr 20;182(4):509–517. doi: 10.1016/0022-2836(85)90237-2. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. Landschulz W. H., Johnson P. F., McKnight S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
  29. Lin C. S. Nucleotide sequence of the essential region of bacteriophage P4. Nucleic Acids Res. 1984 Nov 26;12(22):8667–8684. doi: 10.1093/nar/12.22.8667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lindahl G., Sironi G., Bialy H., Calendar R. Bacteriophage lambda; abortive infection of bacteria lysogenic for phage P2. Proc Natl Acad Sci U S A. 1970 Jul;66(3):587–594. doi: 10.1073/pnas.66.3.587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lindqvist B. H. Recombination between satellite phage P4 and its helper P2. I. In vivo and in vitro construction of P4: :P2 hybrid satellite phage. Gene. 1981 Sep;14(4):231–241. doi: 10.1016/0378-1119(81)90156-6. [DOI] [PubMed] [Google Scholar]
  32. Lindqvist B. H., Six E. W. Replication of bacteriophage P4 DNA in a nonlysogenic host. Virology. 1971 Jan;43(1):1–7. doi: 10.1016/0042-6822(71)90218-2. [DOI] [PubMed] [Google Scholar]
  33. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  34. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Mullin D. A., Garcia G. M., Walker J. R. An E. coli DNA fragment 118 base pairs in length provides dnaY+ complementing activity. Cell. 1984 Jun;37(2):669–674. doi: 10.1016/0092-8674(84)90399-4. [DOI] [PubMed] [Google Scholar]
  36. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Pierson L. S., 3rd, Kahn M. L. Integration of satellite bacteriophage P4 in Escherichia coli. DNA sequences of the phage and host regions involved in site-specific recombination. J Mol Biol. 1987 Aug 5;196(3):487–496. doi: 10.1016/0022-2836(87)90026-x. [DOI] [PubMed] [Google Scholar]
  39. Raftery L. A., Yarus M. Site-specific mutagenesis of Escherichia coli gltT yields a weak, glutamic acid-inserting ochre suppressor. J Mol Biol. 1985 Jul 20;184(2):343–345. doi: 10.1016/0022-2836(85)90385-7. [DOI] [PubMed] [Google Scholar]
  40. Raftery L. A., Yarus M. Systematic alterations in the anticodon arm make tRNA(Glu)-Suoc a more efficient suppressor. EMBO J. 1987 May;6(5):1499–1506. doi: 10.1002/j.1460-2075.1987.tb02392.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Raimondi A., Donghi R., Montaguti A., Pessina A., Dehò G. Analysis of spontaneous deletion mutants of satellite bacteriophage P4. J Virol. 1985 Apr;54(1):233–235. doi: 10.1128/jvi.54.1.233-235.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Reeve J. N. Bacteriophage infection of minicells: a general method for identification of "in vivo" bacteriophage directed polypeptide biosynthesis. Mol Gen Genet. 1977 Dec 14;158(1):73–79. doi: 10.1007/BF00455121. [DOI] [PubMed] [Google Scholar]
  43. Reeve J. Use of minicells for bacteriophage-directed polypeptide synthesis. Methods Enzymol. 1979;68:493–503. doi: 10.1016/0076-6879(79)68038-2. [DOI] [PubMed] [Google Scholar]
  44. Rusche J. R., Howard-Flanders P. Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase. Nucleic Acids Res. 1985 Mar 25;13(6):1997–2008. doi: 10.1093/nar/13.6.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. 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]
  46. Sasaki I., Bertani G. Growth abnormalities in Hfr derivatives of Escherichia coli strain C. J Gen Microbiol. 1965 Sep;40(3):365–376. doi: 10.1099/00221287-40-3-365. [DOI] [PubMed] [Google Scholar]
  47. Sauer B., Ow D., Ling L., Calendar R. Mutants of satellite bacteriophage P4 that are defective in the suppression of transcriptional polarity. J Mol Biol. 1981 Jan 5;145(1):29–46. doi: 10.1016/0022-2836(81)90333-8. [DOI] [PubMed] [Google Scholar]
  48. Shore D., Dehò G., Tsipis J., Goldstein R. Determination of capsid size by satellite bacteriophage P4. Proc Natl Acad Sci U S A. 1978 Jan;75(1):400–404. doi: 10.1073/pnas.75.1.400. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Six E. W., Klug C. A. Bacteriophage P4: a satellite virus depending on a helper such as prophage P2. Virology. 1973 Feb;51(2):327–344. doi: 10.1016/0042-6822(73)90432-7. [DOI] [PubMed] [Google Scholar]
  50. Six E. W. The helper dependence of satellite bacteriophage P4: which gene functions of bacteriophage P2 are needed by P4? Virology. 1975 Sep;67(1):249–263. doi: 10.1016/0042-6822(75)90422-5. [DOI] [PubMed] [Google Scholar]
  51. Souza L., Geisselsoder J., Hopkins A., Calender R. Physical mapping of the satellite phage P4 genome. Virology. 1978 Apr;85(2):335–342. doi: 10.1016/0042-6822(78)90442-7. [DOI] [PubMed] [Google Scholar]
  52. Tabor S., Richardson C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767–4771. doi: 10.1073/pnas.84.14.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. 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]
  54. Wiman M., Bertani G., Kelly B., Sasaki I. Genetic map of Escherichia coli strain C. Mol Gen Genet. 1970;107(1):1–31. doi: 10.1007/BF00433220. [DOI] [PubMed] [Google Scholar]
  55. 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]
  56. Younghusband H. B., Egan J. B., Inman R. B. Characterization of the DNA from bacteriophage P2-186 hybrids and physical mapping of the 186 chromosome. Mol Gen Genet. 1975 Sep 29;140(2):101–110. doi: 10.1007/BF00329778. [DOI] [PubMed] [Google Scholar]

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