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Genetic diversity among five T4-like bacteriophages.
Virol J. 2006 May 23; 3:30.VJ

Abstract

BACKGROUND

Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank.

RESULTS

Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases.

CONCLUSION

Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.

Links

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Authors+Show Affiliations

Nolan JM
Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Dr,, New Orleans, LA 70148, USA. jnolan@uno.edu
Petrov V
No affiliation info available
Bertrand C
No affiliation info available
Krisch HM
No affiliation info available
Karam JD
No affiliation info available

MeSH

Aeromonas hydrophilaAeromonas salmonicidaAnimalsBacteriophage T4BacteriophagesBase SequenceColiphagesComputational BiologyGenetic VariationGenome, ViralHumansMiceMolecular Sequence DataOpen Reading FramesRNA, TransferSequence AlignmentViral Proteins

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

16716236

Citation

Nolan, James M., et al. "Genetic Diversity Among Five T4-like Bacteriophages." Virology Journal, vol. 3, 2006, p. 30.
Nolan JM, Petrov V, Bertrand C, et al. Genetic diversity among five T4-like bacteriophages. Virol J. 2006;3:30.
Nolan, J. M., Petrov, V., Bertrand, C., Krisch, H. M., & Karam, J. D. (2006). Genetic diversity among five T4-like bacteriophages. Virology Journal, 3, 30.
Nolan JM, et al. Genetic Diversity Among Five T4-like Bacteriophages. Virol J. 2006 May 23;3:30. PubMed PMID: 16716236.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic diversity among five T4-like bacteriophages. AU - Nolan,James M, AU - Petrov,Vasiliy, AU - Bertrand,Claire, AU - Krisch,Henry M, AU - Karam,Jim D, Y1 - 2006/05/23/ PY - 2006/03/31/received PY - 2006/05/23/accepted PY - 2006/5/24/pubmed PY - 2006/9/13/medline PY - 2006/5/24/entrez SP - 30 EP - 30 JF - Virology journal JO - Virol J VL - 3 N2 - BACKGROUND: Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. RESULTS: Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. CONCLUSION: Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes. SN - 1743-422X UR - https://www.unboundmedicine.com/medline/citation/16716236/Genetic_diversity_among_five_T4_like_bacteriophages_ DB - PRIME DP - Unbound Medicine ER -