Advertisement

Archives of Virology

, Volume 140, Issue 10, pp 1871–1884 | Cite as

Relationships of tailed phages: a survey of protein sequence identity

  • H. -W. Ackermann
  • A. Elzanowski
  • G. Fobo
  • G. Stewart
Virology Division News

Summary

Using a multiple alignment program, we surveyed about 150 proteins from 35 tailed phages and calculated identity percentages. Sequence similarities are generally weak, indicating an extensive diversification of tailed phages. Related proteins occur in phages of different morphology and host range. DNA and RNA polymerases, integrases, muramidases, and several other tailed phage proteins appear to be acquired from bacteria. Tailed phages seem to be a monophyletic group and to constitute a polythetic order. Proteins common to all tailed phages may be detected by comparing the three-dimensional structure of major head and tail proteins. Amino acid alignments have presently no impact on the definition of high-level taxa of tailed phages.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Ackermann H-W (1992) Frequency of morphological phage descriptions. Arch Virol 124: 201–209PubMedGoogle Scholar
  2. 2.
    Ackermann H-W, DuBow MS (1987) Viruses of prokaryotes, vol I, general properties of bacteriophages. CRC Press, Boca Raton, pp 16, 110, 173–188Google Scholar
  3. 3.
    Ackermann H-W, DuBow MS (1987) Viruses of prokaryotes, vol II, natural groups of bacteriophages. CRC Press, Boca Raton, pp 55–161, 163–170Google Scholar
  4. 4.
    Ackermann H-W, DuBow MS, Jarvis AW, Jones LA, Krylov VN, Maniloff J, Rocourt J, Safferman RS, Schneider J, Seldin L, Sozzi T, Stewart PR, Werquin M, Wunsche L (1992) The species concept and its application to tailed phages. Arch Virol 124: 69–82PubMedGoogle Scholar
  5. 5.
    Argos P, Landy A, Abremski K, Egan JB, Haggard-Ljungquist E, Hoess RH, Kahn ML, Kalionis B, Narayana SVL, Pierson LS, Sternberg N, Leong JM (1986) The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J5: 433–440PubMedGoogle Scholar
  6. 6.
    Bechhofer DH, Hue KK, Shub DA (1994). An intron in the thymidylate synthase gene ofBacillus bacteriophage β22: Evidence for independent evolution of a gene, its group I intron, and the intron reading frame. Proc Natl Acad Sci USA 91: 11669–11673PubMedGoogle Scholar
  7. 7.
    Bernheimer HP (1979) Lysogenic pneumococci and their bacteriophages. J Bacteriol 138: 618–626PubMedGoogle Scholar
  8. 8.
    Boizet B, Lahbib-Mansais Y, Dupont L, Ritzenthaler P, Mata M (1990) Cloning, expression and sequence analysis of an endolysin-encoded gene ofLactobacillus bulgancus bacteriophage mvl. Gene 94: 61–67PubMedGoogle Scholar
  9. 9.
    Braithwaite DK, Ito J (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res 21: 787–802PubMedGoogle Scholar
  10. 10.
    Butler ET, Chamberlin MJ (1982) Bacteriophage SP6-specific RNA polymerase, I, isolation and characterization of the enzyme. J Biol Chem 257: 5772–5778PubMedGoogle Scholar
  11. 11.
    Campbell A (1988) Phage evolution and speciation. In: Calendar R (ed) The bacteriophages, vol 1. Plenum Press, New York, pp 1–14Google Scholar
  12. 12.
    Casjens S, Eppler K, Parr R, Poteete AR (1989) Nucleotide sequence of the bacteriophage P22 and gene19 to3 region: identification of a new gene required for lysis. Virology 171: 588–598PubMedGoogle Scholar
  13. 13.
    Casjens S, Hatfull G, Hendrix R (1992) Evolution of dsDNA tailed-bacteriophage genomes. Semin Virol 3: 383–397Google Scholar
  14. 14.
    Christiansen B, Johnsen MG, Stenby E, Vogensen FK, Hammer K (1994) Characterization of the lactococcal temperate phage TP901-1 and its site-specific integration. J Bacteriol 176: 1069–1076PubMedGoogle Scholar
  15. 15.
    Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12: 387–395Google Scholar
  16. 16.
    Díaz E, López R, García JL (1992) EJ-1, a temperate bacteriophage ofStreptococcus pneumoniae with aMyoviridae morphotype. J Bacteriol 174: 5516–5525PubMedGoogle Scholar
  17. 17.
    Dietz A, Weisser H-J, Kössel H, Hausmann R (1990) The gene forKlebsiella bacteriophage K11 RNA polymerase: sequence and comparison with the homologous genes of phages T7, T3, and SP6. Mol Gen Genet 221: 283–286PubMedGoogle Scholar
  18. 18.
    Doskočil J, Štorchová H, Štokrová J, Forstová J, Meyer J (1988) Correlation of physical maps and some genetic functions in the genomes of the κ-ϑ phage family ofBacillus licheniformis. Mol Gen Genet 214: 323–347Google Scholar
  19. 19.
    Duval-Iflah Y (1972) Recombination in staphylococcal bacteriophages. J Gen Virol 16: 237–243PubMedGoogle Scholar
  20. 20.
    Eppler K, Wyckoff E, Goates J, Parr R, Casjens S (1991) Nucleotide sequence of the bacteriophage P22 genes required for DNA packaging. Virology 183: 519–538PubMedGoogle Scholar
  21. 21.
    Fedonkin MA (1990) Precambrian metazoans. In: Briggs DEG, Crowther PR (eds) Paleobiology — a synthesis. Blackwell Scientific Publications, Oxford, pp 17–24Google Scholar
  22. 22.
    Forsman P, Alatossova T (1991) Genetic variation ofLactobacillus delbrueckii subsp.lactis bacteriophages isolated from cheese processing plants in Finland. Appl Environ Microbiol 57: 1805–1812Google Scholar
  23. 23.
    Fremaux C, de Antoni GL, Raya PR, Klaenhammer TR (1993) Genetic organization and sequence of the region encoding integrative functions fromLactobacillus gasseri temperate bacteriophage φadh. Gene 126: 61–66PubMedGoogle Scholar
  24. 24.
    García E, García JL, García P, Arrarás A, Sánchez-Puelles JM, López R (1988) Molecular evolution of lytic enzmes ofStreptococcus pneumoniae and its bacteriophages. Proc Natl Acad Sci USA 85: 914–918PubMedGoogle Scholar
  25. 25.
    Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4: 197–202PubMedGoogle Scholar
  26. 26.
    Goodman SD, Scocca JJ (1989) Nucleotide sequence and expression of the gene for the site-specific integration protein from bacteriophage HP1 ofHaemophilus influenzea. J Bacteriol 171: 4232–4240PubMedGoogle Scholar
  27. 27.
    Haggård-Ljungquist E, Halling C, Calendar R (1992) DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal gene transfer of tail fiber genes among unrelated bacteriophages. J Bacteriol 174: 1462–1477PubMedGoogle Scholar
  28. 28.
    Haggård-Ljungquist E, Kockum K, Bertani LE (1987) DNA sequences of bacteriophage P2 early genescox andB and their regulatory sites. Mol Gen Genet 208: 52–56PubMedGoogle Scholar
  29. 29.
    Hardy LW, Finer-Moore JS, Montfort WR, Jones MO, Santi DV, Stroud RM (1987) Atomic structure of thymidylate synthase: target for rational drug design. Science 235: 448–455PubMedGoogle Scholar
  30. 30.
    Harrison SC (1990) Principles of virus structure. In: Fields BN, Knipe DM (eds) Virology, 2nd ed, vol 1. Raven Press, New York, pp 37–61Google Scholar
  31. 31.
    Hatfull GF, Sarkis GJ (1993) DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol Microbiol 7: 395–405PubMedGoogle Scholar
  32. 32.
    Heringa J, Argos P (1994) Evolution of viruses as recorded by their polymerase sequences. In: Morse SS (ed) The evolutionary biology of viruses. Raven Press, New York, pp 87–103Google Scholar
  33. 33.
    Ilyina TV, Gorbalenya AE, Koonin EV (1992) Organization and evolution of bacteriophage primasehelicase systems. J Mol Evol 34: 351–357PubMedGoogle Scholar
  34. 34.
    Inman RB, Schnös M, Simon LD, Six EW, Walker DH (1971) Some morphological properties of P4 bacteriophage and P4 DNA. Virology 44: 67–72PubMedGoogle Scholar
  35. 35.
    Jarvis AW, Fitzgerald GF, Mata M, Mercenier A, Neve H, Powell IB, Ronda C, Saxelin M, Teuber M (1991) Species and type phages of lactococcal bacteriophages. Intervirology 32: 2–9PubMedGoogle Scholar
  36. 36.
    Jung G, Leavitt MC, Hsieh J-C, Ito J (1987) Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc Natl Acad Sci USA 84: 8287–8291PubMedGoogle Scholar
  37. 37.
    Kim J, Batt CA (1991) Molecular characterization of aLactococcus lactis bacteriophage F4-1. Food Microbiol 8: 15–26Google Scholar
  38. 38.
    Klaus S, Krüger DH, Meyer J (1992) Bakterienviren. Gustav Fischer, Jena, pp 35–55, 106–111Google Scholar
  39. 39.
    Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72: 2197–2206PubMedGoogle Scholar
  40. 40.
    Lee MH, Pascopella L, Jacobs WR, Hatfull GF (1991) Site-specific integration of mycobacteriophage L5: integration-proficient vectors forMycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guérin. Proc Natl Acad Sci USA 88: 3111–3115PubMedGoogle Scholar
  41. 41.
    Lillehaug D, Birkeland N-K (1993) Characterization of genetic elements required for site-specific integration of the temperate lactococcal bacteriophage φLC3 and construction of integration-negative φLC3 mutants. J Bacteriol 175: 1745–1755PubMedGoogle Scholar
  42. 42.
    Lillehaug D, Lindqvist BH, Birkeland NK (1991) Characterization of φLC3, aLactococcus lactis subsp.cremoris temperate bacteriophage with cohesive single-stranded DNA ends. Appl Environ Microbiol 57: 3206–3211PubMedGoogle Scholar
  43. 43.
    Mata M, Trautwetter A, Luthaud G, Ritzenthaler P (1986) Thirteen virulent and temperate bacteriophages ofLactobacillus bulgaricus andLactobacillus lactis belong to a single DNA homology group. Appl Environ Microbiol 52: 812–818Google Scholar
  44. 44.
    McAllister WT, Raskin CA (1993) The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol Microbiol 10: 1–6PubMedGoogle Scholar
  45. 45.
    Mercier J, Lachapelle J, Couture F, Lafond M, Vézina G, Boissinot M, Lévesque RC (1990) Structural and functional characterization oftnpI, a recombinase locus in TN21 and related β-lactamase transposons. J Bacteriol 172: 3745–3757PubMedGoogle Scholar
  46. 46.
    Mosig G (1983) T4 genes and gene products. In: Mathews CK, Kutter EM, Mosig G, Berget PB (eds) Bacteriophage T4. American Society for Microbiology, Washington, pp 362–374Google Scholar
  47. 47.
    Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD (eds) Virus Taxonomy. Classification and Nomenclature of Viruses, Sixth Report of the International Committee on Taxonomy of Viruses. Springer, Wien New York (Arch Virol [Suppl] 10)Google Scholar
  48. 48.
    Okamoto K, Mudd JA, Mangan J, Huang WM, Subbaiah TV, Marmur J (1968) Properties of the defective phage ofBacillus subtilis. J Mol Biol 34: 413–428PubMedGoogle Scholar
  49. 49.
    Pemberton JM, Tucker WT (1977) Naturally occurring viral R plasmid with a circular extracellular genome in the extracellular state. Nature 266: 50–51PubMedGoogle Scholar
  50. 50.
    Platteeuw C, de Vos WM (1992) Location, characterization and expression of lytic enzyme-encoding gene,lytA, ofLactococcus lactis bacteriophage φUS3. Gene 118: 115–120PubMedGoogle Scholar
  51. 51.
    Rennell D, Poteete A (1985) Phage P22 lysis genes: nucleotide sequence and functional relationships with T4 and λ. Virology 143: 280–289PubMedGoogle Scholar
  52. 52.
    Romero A, Lopez R, Garcia P (1990) Sequence of theStreptococcus pneumoniae bacteriophage HB-3 amidase reveals high homology with the major host autolysin. J Bacteriol 172: 5065–5070Google Scholar
  53. 53.
    Rybicki E (1990) The classification of organisms at the edge of life or problems with virus systematics. S Afr J Sci 86: 182–186Google Scholar
  54. 54.
    Sandmeier H (1994) Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Mol Microbiol 12: 343–350PubMedGoogle Scholar
  55. 55.
    Schopf JW (1993) Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260: 640–646PubMedGoogle Scholar
  56. 56.
    Sharibjanova TO, Akhverdian VZ, Krylov VN (1992) A comparative study of DNA homology and morphology ofPseudomonas aeruginosa bacteriophages to reveal phylogenetic relationships and for an express-classification. Genetika 28: 24–32Google Scholar
  57. 57.
    Shearman C, Underwood H, Jury K, Gasson M (1989) Cloning and sequence analysis of aLactococcus bacteriophage lysin gene. Mol Gen Genet 218: 214–221PubMedGoogle Scholar
  58. 58.
    Sousa R, Chung YJ, Rose JP, Wang B-C (1993) Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature 364: 593–599PubMedGoogle Scholar
  59. 59.
    Sun J, Inouye M, Inouye S (1991) Association of a retroelement with a P4-like cryptic prophage (retronphage øR73) integrated into the selenocystyl tRNA gene ofEscherichia coli. J Bacteriol 173: 4171–4181PubMedGoogle Scholar
  60. 60.
    Susskind MM, Botstein (1978) Molecular genetics of bacteriophage P22. Microbiol Rev 42: 385–413PubMedGoogle Scholar
  61. 61.
    Temple L, Forsburg SL, Calendar R, Christie GE (1991) Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. Virology 181: 353–358PubMedGoogle Scholar
  62. 62.
    Van Regenmortel MHV (1990) Virus species, a much overlooked but essential concept in virus classification. Intervirology 31: 241–254PubMedGoogle Scholar
  63. 63.
    Ward CW (1993) Progress towards a higher taxonomy of viruses. Res Virol 144: 419–453PubMedGoogle Scholar
  64. 64.
    Wilhelm K, Rüger W (1992) Deoxyuridylate-hydroxymethylase of bacteriophage SP01. Virology 189: 640–646PubMedGoogle Scholar
  65. 65.
    Yarmolinski MB, Sternberg N (1988) Bacteriophage P1. In: Calendar R (ed) The bacteriophages, vol 1. Plenum Press, New York, pp 291–438Google Scholar
  66. 66.
    Young R (1992) Bacteriophage lysis: mechanism and regulation. Microbiol Rev 56: 430–481PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1995

Authors and Affiliations

  • H. -W. Ackermann
    • 1
  • A. Elzanowski
    • 2
  • G. Fobo
    • 3
  • G. Stewart
    • 4
  1. 1.Felix d'Hérelle Reference Center for Bacterial Viruses, Department of Microbiology, Faculty of MedicineLaval UniversitySainte-FoyCanada
  2. 2.National Center for Biotechnology InformationNational Library of Medicine/NIHBethesdaUSA
  3. 3.Max-Planck-Institut für BiochemieMartinsried b. MünchenGermany
  4. 4.STELA Research Center, Faculty of AgricultureLaval UniversitySainte-FoyCanada

Personalised recommendations