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. 1982 Oct;44(1):32–46. doi: 10.1128/jvi.44.1.32-46.1982

Nucleotide sequence of bacteriophage f1 DNA.

D F Hill, G B Petersen
PMCID: PMC256238  PMID: 6292494

Abstract

The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.

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Selected References

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

  1. Bailey G. S., Gillett D., Hill D. F., Petersen G. B. Automated sequencing of insoluble peptides using detergent. Bacteriophage fl coat protein. J Biol Chem. 1977 Apr 10;252(7):2218–2225. [PubMed] [Google Scholar]
  2. Beck E., Sommer R., Auerswald E. A., Kurz C., Zink B., Osterburg G., Schaller H., Sugimoto K., Sugisaki H., Okamoto T. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 1978 Dec;5(12):4495–4503. doi: 10.1093/nar/5.12.4495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beck E., Zink B. Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd. Gene. 1981 Dec;16(1-3):35–58. doi: 10.1016/0378-1119(81)90059-7. [DOI] [PubMed] [Google Scholar]
  4. Boyer H. W., Chow L. T., Dugaiczyk A., Hedgpeth J., Goodman H. M. DNA substrate site for the EcoRII restriction endonuclease and modification methylase. Nat New Biol. 1973 Jul 11;244(132):40–43. doi: 10.1038/newbio244040a0. [DOI] [PubMed] [Google Scholar]
  5. Cuypers T., van der Ouderaa F. J., de Jong W. W. The amino acid sequence of gene 5 protein of bacteriophage M 13. Biochem Biophys Res Commun. 1974 Jul 24;59(2):557–563. doi: 10.1016/s0006-291x(74)80016-1. [DOI] [PubMed] [Google Scholar]
  6. Denhardt D. T. The single-stranded DNA phages. CRC Crit Rev Microbiol. 1975 Dec;4(2):161–223. doi: 10.3109/10408417509111575. [DOI] [PubMed] [Google Scholar]
  7. Edens L., Konings R. N., Schoenmakers J. G. Physical mapping of the central terminator for transcription on the bacteriophage M13 genome. Nucleic Acids Res. 1975 Oct;2(10):1811–1820. doi: 10.1093/nar/2.10.1811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hill D. F., Petersen G. B. Nucleotide sequences in bacteriophage f1 DNA: nucleotide sequence of genes V, VII, and VIII. J Virol. 1980 Apr;34(1):40–50. doi: 10.1128/jvi.34.1.40-50.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Konings R. N., Hulsebos T., Van den Hondel C. A. Identification and characterization of the in vitro synthesized gene products of bacteriophage M13. J Virol. 1975 Mar;15(3):570–584. doi: 10.1128/jvi.15.3.570-584.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. LOEB T. Isolation of a bacteriophage specific for the F plus and Hfr mating types of Escherichia coli K-12. Science. 1960 Mar 25;131(3404):932–933. doi: 10.1126/science.131.3404.932. [DOI] [PubMed] [Google Scholar]
  11. Laskey R. A., Mills A. D. Enhanced autoradiographic detection of 32P and 125I using intensifying screens and hypersensitized film. FEBS Lett. 1977 Oct 15;82(2):314–316. doi: 10.1016/0014-5793(77)80609-1. [DOI] [PubMed] [Google Scholar]
  12. Lin T. C., Webster R. E., Konigsberg W. Isolation and characterization of the C and D proteins coded by gene IX and gene VI in the filamentous bacteriophage fl and fd. J Biol Chem. 1980 Nov 10;255(21):10331–10337. [PubMed] [Google Scholar]
  13. Ling V. Fractionation and sequences of the large pyrimidine oligonucleotides from bacteriophage fd DNA. J Mol Biol. 1972 Feb 28;64(1):87–102. doi: 10.1016/0022-2836(72)90322-1. [DOI] [PubMed] [Google Scholar]
  14. Ling V. Pyrimidine sequences from the DNA of bacteriophages fd, fl, and phi X174. Proc Natl Acad Sci U S A. 1972 Mar;69(3):742–746. doi: 10.1073/pnas.69.3.742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Marvin D. A., Hohn B. Filamentous bacterial viruses. Bacteriol Rev. 1969 Jun;33(2):172–209. doi: 10.1128/br.33.2.172-209.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Messing J., Gronenborn B., Müller-Hill B., Hans Hopschneider P. Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3642–3646. doi: 10.1073/pnas.74.9.3642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Model P., Zinder N. D. In vitro synthesis of bacteriophage f1 proteins. J Mol Biol. 1974 Feb 25;83(2):231–251. doi: 10.1016/0022-2836(74)90389-1. [DOI] [PubMed] [Google Scholar]
  19. Moore P., Strauss B. S. Sites of inhibition of in vitro DNA synthesis in carcinogen- and UV-treated phi X174 DNA. Nature. 1979 Apr 12;278(5705):664–666. doi: 10.1038/278664a0. [DOI] [PubMed] [Google Scholar]
  20. Nakashima Y., Konigsberg W. Reinvestigation of a region of the fd bacteriophage coat protein sequence. J Mol Biol. 1974 Sep 25;88(3):598–600. doi: 10.1016/0022-2836(74)90410-0. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Petersen G. B., Reeves J. M. The occurrence of long sequences of consecutive pyrimidine deoxyribonucleotides in the DNA of bacteriophage f1. Biochim Biophys Acta. 1969 Apr 22;179(2):510–512. doi: 10.1016/0005-2787(69)90062-8. [DOI] [PubMed] [Google Scholar]
  23. Pieczenik G., Model P., Robertson H. D. Sequence and symmetry in ribosome binding sites of bacteriophage f1 RNA. J Mol Biol. 1974 Dec 5;90(2):191–124. doi: 10.1016/0022-2836(74)90368-4. [DOI] [PubMed] [Google Scholar]
  24. Pieczenik G. Predicting coding function from nucleotide sequence or survival of "fitness" of tRNA. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3539–3543. doi: 10.1073/pnas.77.6.3539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ravetch J. V., Horiuchi K., Zinder N. D. DNA sequence analysis of the defective interfering particles of bacteriophage f1. J Mol Biol. 1979 Mar 5;128(3):305–318. doi: 10.1016/0022-2836(79)90090-1. [DOI] [PubMed] [Google Scholar]
  26. Ravetch J. V., Horiuchi K., Zinder N. D. Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B. Proc Natl Acad Sci U S A. 1978 May;75(5):2266–2270. doi: 10.1073/pnas.75.5.2266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Ravetch J., Horiuchi K., Model P. Mapping of bacteriophage f1 ribosome binding sites to their cognate genes. Virology. 1977 Sep;81(2):341–351. doi: 10.1016/0042-6822(77)90150-7. [DOI] [PubMed] [Google Scholar]
  28. Roberts R. J. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res. 1980 Jan 11;8(1):r63–r80. doi: 10.1093/nar/8.1.197-d. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. SALIVAR W. O., TZAGOLOFF H., PRATT D. SOME PHYSICAL-CHEMICAL AND BIOLOGICAL PROPERTIES OF THE ROD-SHAPED COLIPHAGE M13. Virology. 1964 Nov;24:359–371. doi: 10.1016/0042-6822(64)90173-4. [DOI] [PubMed] [Google Scholar]
  30. Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
  31. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  32. Sanger F., Donelson J. E., Coulson A. R., Kössel H., Fischer D. Determination of a nucleotide sequence in bacteriophage f1 DNA by primed synthesis with DNA polymerase. J Mol Biol. 1974 Dec 5;90(2):315–333. doi: 10.1016/0022-2836(74)90376-3. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. Simons G. F., Konings R. N., Schoenmakers J. G. Identification of two new capsid proteins in bacteriophage M13. FEBS Lett. 1979 Oct 1;106(1):8–12. doi: 10.1016/0014-5793(79)80683-3. [DOI] [PubMed] [Google Scholar]
  35. Staden R. Sequence data handling by computer. Nucleic Acids Res. 1977 Nov;4(11):4037–4051. doi: 10.1093/nar/4.11.4037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Suggs S. V., Ray D. S. Nucleotide sequence of the origin for bacteriophage M13 DNA replication. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):379–388. doi: 10.1101/sqb.1979.043.01.044. [DOI] [PubMed] [Google Scholar]
  37. Sugimoto K., Sugisaki H., Okamoto T., Takanami M. Studies on bacteriophage fd DNA. IV. The sequence of messenger RNA for the major coat protein gene. J Mol Biol. 1977 Apr 25;111(4):487–507. doi: 10.1016/s0022-2836(77)80065-x. [DOI] [PubMed] [Google Scholar]
  38. Tate W. P., Petersen G. B. A catalogue of the pyrimidine oligodeoxyribonucleotides found in bacteriophage f1 DNA. Virology. 1974 Jan;57(1):64–76. doi: 10.1016/0042-6822(74)90108-1. [DOI] [PubMed] [Google Scholar]
  39. Tate W. P., Petersen G. B. Structure of the filamentous bacteriophages: orientation of the DNA molecule within the phage particle. Virology. 1974 Nov;62(1):17–25. doi: 10.1016/0042-6822(74)90299-2. [DOI] [PubMed] [Google Scholar]
  40. Tate W. P., Petersen G. B. The pyrimidine oligodeoxyribonucleotides from the DNA molecules of bacteriophages f1, fd, and M13. Virology. 1974 Jan;57(1):77–84. doi: 10.1016/0042-6822(74)90109-3. [DOI] [PubMed] [Google Scholar]
  41. Van Den Hondel C. A., Schoenmakers J. G. Cleavage maps of the filamentous bacteriophages M13, fd, fl, and ZJ/2. J Virol. 1976 Jun;18(3):1024–1039. doi: 10.1128/jvi.18.3.1024-1039.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Vovis G. F., Horiuchi K., Zinder N. D. Endonuclease R-EcoRII restriction of bacteriophage f1 DNA in vitro: ordering of genes V and VII, location of an RNA promotor for gene VIII. J Virol. 1975 Sep;16(3):674–684. doi: 10.1128/jvi.16.3.674-684.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]

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