Advertisement

PCR and Partial Sequencing of Bacteriophage Genomes

Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 502)

Abstract

PCR is a quick and effective way of identifying the presence and ‘affiliation’ of bacteriophages, or phage-encoded genes from environmental samples, bacterial cells or purified viruses. The limitations are that you have to know what you are looking for in order to find it. Although the bacteriophage world does not have the advantage of a conserved gene, present in all members, there are many phage genes that do show nucleotide conservation even between phages which infect fairly divergent taxa. As more sequence data become available through both metagenomic approaches and the sequencing of complete bacteriophage genomes, PCR primers can be further refined and thus it should be an increasingly useful tool for bacteriophage biology.

Key Words

PCR amplification template dNA sequencing primer 
This is a preview of subscription content, log in to check access.

References

  1. 1.
    Casas, V., et al., Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California. Fems Microbiology Letters, 2006. 261(1): 141–149.CrossRefPubMedGoogle Scholar
  2. 2.
    Millard, A., et al., Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proceedings of the National Academy of Sciences of the United States of America, 2004. 101(30): 11007–11012.CrossRefPubMedGoogle Scholar
  3. 3.
    Fuller, N.J., et al., Occurrence of a sequence in marine cyanophages similar to that of T4 g20 and its application to PCR-based detection and quantification techniques. Applied and Environmental Microbiology, 1998. 64(6): 2051–2060.PubMedGoogle Scholar
  4. 4.
    Marston, M.F. and J.L. Sallee, Genetic diversity and temporal variation in the cyanophage community infecting marine Synechococcus species in Rhode Island’s coastal waters. Appl Environ Microbiol, 2003. 69(8): 4639–47.CrossRefPubMedGoogle Scholar
  5. 5.
    Short, C.M. and C.A. Suttle, Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Applied and Environmental Microbiology, 2005. 71(1): 480–486.CrossRefPubMedGoogle Scholar
  6. 6.
    Filee, J., et al., Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. PNAS, 2005. 102(35): 12471–12476.CrossRefPubMedGoogle Scholar
  7. 7.
    Petrov, V.M., et al., Plasticity of the Gene Functions for DNA Replication in the T4-like Phages. Journal of Molecular Biology, 2006. 361(1): 46.CrossRefPubMedGoogle Scholar
  8. 8.
    Miklic, A. and I. Rogelj, Characterization of lactococcal bacteriophages isolated from Slovenian dairies. International Journal Of Food Science and Technology, 2003. 38: 305–311.CrossRefGoogle Scholar
  9. 9.
    Deveau, H., et al., Biodiversity and Classification of Lactococcal Phages. Appl. Environ. Microbiol., 2006. 72(6): 4338–4346.CrossRefPubMedGoogle Scholar
  10. 10.
    Balding, C., et al., Diversity of phage integrases in Enterobacteriaceae: development of markers for environmental analysis of temperate phages. Environmental Microbiology, 2005. 7(10): 1558–1567.CrossRefPubMedGoogle Scholar
  11. 11.
    Sullivan, M.B., et al., Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts. PLOS, 2006. 4(4): 1344–1357.Google Scholar
  12. 12.
    Baker, A.C., et al., Identification of a Diagnostic Marker To Detect Freshwater Cyanophages of Filamentous Cyanobacteria. Appl. Environ. Microbiol., 2006. 72(9): 5713–5719.CrossRefPubMedGoogle Scholar
  13. 13.
    Kutter, E. and A. Sulakvelidze, Bacteriophages: Biology and Applications. 1 ed. 2005, Boca Raton: CRC Press.510.Google Scholar
  14. 14.
    Sandaa, R.-A. and A. Larsen, Seasonal Variations in Virus-Host Populations in Norwegian Coastal Waters: Focusing on the Cyanophage Community Infecting Marine Synechococcus spp. Appl. Environ. Microbiol., 2006. 72(7): 4610–4618.CrossRefPubMedGoogle Scholar
  15. 15.
    Fuller, N.J., et al., Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Applied and Environmental Microbiology, 2003. 69(5): 2430–2443.CrossRefPubMedGoogle Scholar
  16. 16.
    Wilson, W.H., et al., Analysis of cyanophage diversity and population structure in a south-north transect of the Atlantic ocean. Bulletin de l’Institut oc’eanographique, Monaco, 1999. 19: 209–216.Google Scholar
  17. 17.
    Zhong, Y., et al., Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20. Applied and Environmental Microbiology, 2002. 68(4): 1576–1584.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Lecturer in Microbiology, Department of InfectionImmunity and Inflammation, University of LeicesterUK

Personalised recommendations

Cite protocol

Buy options