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The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions

Andrew M Kropinski1,2, Dann Turner3, John H E Nash4

  • 1Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada. Phage.Canada@gmail.com.

Viruses
|April 27, 2018
PubMed

Insights

Two bacteriophages, SP-15 and ΦW-14, infecting Bacillus subtilis and Delftia acidovorans, feature hypermodified DNA bases. This extensive modification alters DNA properties and results in unique, genomically singleton viral genomes.

Area of Science:

  • Microbiology and Virology
  • Molecular Biology
  • Genomics

Background:

  • Bacteriophages SP-15 and ΦW-14 belong to the Myoviridae family.
  • Both phages infect Bacillus subtilis and Delftia acidovorans, respectively.
  • A key characteristic is the replacement of approximately 50% of thymine residues with hypermodified bases.

Purpose of the Study:

  • To investigate the genomic characteristics of bacteriophages SP-15 and ΦW-14.
  • To understand the impact of hypermodified DNA bases on viral genome properties.
  • To identify potential genes responsible for base modification and other functions.

Main Methods:

  • Genome sequencing using 454 pyrosequencing technology.
  • Bioinformatic analysis, including BLASTn homology searches.
  • Analysis of genomic content and gene functions, particularly related to metabolism.

Main Results:

  • ΦW-14 has a 157-kb genome (56.3% GC) encoding 236 proteins; SP-15 has a 222-kb genome (38.6% GC) encoding 318 proteins.
  • Hypermodified DNA bases significantly alter DNA physico-chemical properties (Tm, density, restriction endonuclease susceptibility).
  • Both phages are genomic singletons with no significant BLASTn homologs.
  • SP-15 possesses a gene cluster associated with carbohydrate metabolism, while no specific modification genes were identified for ΦW-14.

Conclusions:

  • The extensive DNA base modification in SP-15 and ΦW-14 leads to unique genomic properties and potential functional implications.
  • The genomic novelty of these phages suggests distinct evolutionary paths.
  • Further research is needed to elucidate the precise mechanisms of base modification and their biological significance.
Keywords:
5-hydroxymethyluracil5-hydroxypentyluracilBacillusDNA sequencingDelftiaSP-15alpha-putrescinylthyminebacteriophagehypermodified basesΦW-14

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