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.
Article PDF
References
Ackermann H-W (1992) Frequency of morphological phage descriptions. Arch Virol 124: 201–209
Ackermann H-W, DuBow MS (1987) Viruses of prokaryotes, vol I, general properties of bacteriophages. CRC Press, Boca Raton, pp 16, 110, 173–188
Ackermann H-W, DuBow MS (1987) Viruses of prokaryotes, vol II, natural groups of bacteriophages. CRC Press, Boca Raton, pp 55–161, 163–170
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: 69–82
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: 433–440
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: 11669–11673
Bernheimer HP (1979) Lysogenic pneumococci and their bacteriophages. J Bacteriol 138: 618–626
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: 61–67
Braithwaite DK, Ito J (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res 21: 787–802
Butler ET, Chamberlin MJ (1982) Bacteriophage SP6-specific RNA polymerase, I, isolation and characterization of the enzyme. J Biol Chem 257: 5772–5778
Campbell A (1988) Phage evolution and speciation. In: Calendar R (ed) The bacteriophages, vol 1. Plenum Press, New York, pp 1–14
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: 588–598
Casjens S, Hatfull G, Hendrix R (1992) Evolution of dsDNA tailed-bacteriophage genomes. Semin Virol 3: 383–397
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: 1069–1076
Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12: 387–395
Díaz E, López R, García JL (1992) EJ-1, a temperate bacteriophage ofStreptococcus pneumoniae with aMyoviridae morphotype. J Bacteriol 174: 5516–5525
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: 283–286
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: 323–347
Duval-Iflah Y (1972) Recombination in staphylococcal bacteriophages. J Gen Virol 16: 237–243
Eppler K, Wyckoff E, Goates J, Parr R, Casjens S (1991) Nucleotide sequence of the bacteriophage P22 genes required for DNA packaging. Virology 183: 519–538
Fedonkin MA (1990) Precambrian metazoans. In: Briggs DEG, Crowther PR (eds) Paleobiology — a synthesis. Blackwell Scientific Publications, Oxford, pp 17–24
Forsman P, Alatossova T (1991) Genetic variation ofLactobacillus delbrueckii subsp.lactis bacteriophages isolated from cheese processing plants in Finland. Appl Environ Microbiol 57: 1805–1812
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: 61–66
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: 914–918
Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4: 197–202
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: 4232–4240
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: 1462–1477
Haggård-Ljungquist E, Kockum K, Bertani LE (1987) DNA sequences of bacteriophage P2 early genescox andB and their regulatory sites. Mol Gen Genet 208: 52–56
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: 448–455
Harrison SC (1990) Principles of virus structure. In: Fields BN, Knipe DM (eds) Virology, 2nd ed, vol 1. Raven Press, New York, pp 37–61
Hatfull GF, Sarkis GJ (1993) DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol Microbiol 7: 395–405
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 87–103
Ilyina TV, Gorbalenya AE, Koonin EV (1992) Organization and evolution of bacteriophage primasehelicase systems. J Mol Evol 34: 351–357
Inman RB, Schnös M, Simon LD, Six EW, Walker DH (1971) Some morphological properties of P4 bacteriophage and P4 DNA. Virology 44: 67–72
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: 2–9
Jung G, Leavitt MC, Hsieh J-C, Ito J (1987) Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc Natl Acad Sci USA 84: 8287–8291
Kim J, Batt CA (1991) Molecular characterization of aLactococcus lactis bacteriophage F4-1. Food Microbiol 8: 15–26
Klaus S, Krüger DH, Meyer J (1992) Bakterienviren. Gustav Fischer, Jena, pp 35–55, 106–111
Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72: 2197–2206
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: 3111–3115
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: 1745–1755
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: 3206–3211
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: 812–818
McAllister WT, Raskin CA (1993) The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol Microbiol 10: 1–6
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: 3745–3757
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 362–374
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)
Okamoto K, Mudd JA, Mangan J, Huang WM, Subbaiah TV, Marmur J (1968) Properties of the defective phage ofBacillus subtilis. J Mol Biol 34: 413–428
Pemberton JM, Tucker WT (1977) Naturally occurring viral R plasmid with a circular extracellular genome in the extracellular state. Nature 266: 50–51
Platteeuw C, de Vos WM (1992) Location, characterization and expression of lytic enzyme-encoding gene,lytA, ofLactococcus lactis bacteriophage φUS3. Gene 118: 115–120
Rennell D, Poteete A (1985) Phage P22 lysis genes: nucleotide sequence and functional relationships with T4 and λ. Virology 143: 280–289
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: 5065–5070
Rybicki E (1990) The classification of organisms at the edge of life or problems with virus systematics. S Afr J Sci 86: 182–186
Sandmeier H (1994) Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Mol Microbiol 12: 343–350
Schopf JW (1993) Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260: 640–646
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: 24–32
Shearman C, Underwood H, Jury K, Gasson M (1989) Cloning and sequence analysis of aLactococcus bacteriophage lysin gene. Mol Gen Genet 218: 214–221
Sousa R, Chung YJ, Rose JP, Wang B-C (1993) Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature 364: 593–599
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: 4171–4181
Susskind MM, Botstein (1978) Molecular genetics of bacteriophage P22. Microbiol Rev 42: 385–413
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: 353–358
Van Regenmortel MHV (1990) Virus species, a much overlooked but essential concept in virus classification. Intervirology 31: 241–254
Ward CW (1993) Progress towards a higher taxonomy of viruses. Res Virol 144: 419–453
Wilhelm K, Rüger W (1992) Deoxyuridylate-hydroxymethylase of bacteriophage SP01. Virology 189: 640–646
Yarmolinski MB, Sternberg N (1988) Bacteriophage P1. In: Calendar R (ed) The bacteriophages, vol 1. Plenum Press, New York, pp 291–438
Young R (1992) Bacteriophage lysis: mechanism and regulation. Microbiol Rev 56: 430–481
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Ackermann, H.W., Elzanowski, A., Fobo, G. et al. Relationships of tailed phages: a survey of protein sequence identity. Archives of Virology 140, 1871–1884 (1995). https://doi.org/10.1007/BF01384350
Issue Date:
DOI: https://doi.org/10.1007/BF01384350