The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages

doi:10.1073/pnas.0501140102

The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages

^*Targanta Therapeutics, 7170 Frederick Banting, Second Floor, Ville Saint Laurent, QC, Canada H4S 2A1; ^‡Institute de Génétique et Microbiologie, Université Paris Sud, Bâtiment 409, 91405 Orsay, France; and ^§Department of Biochemistry and McGill Cancer Center, McGill University, McIntyre Medical Sciences Building, Montreal, QC, Canada H3G 1Y6

Communicated by Louis Siminovitch, Mount Sinai Hospital, Toronto, ON, Canada, February 15, 2005 (received for review January 10, 2005)

Abstract

Bacteriophages are the most abundant life forms in the biosphere. They play important roles in bacterial ecology, evolution, adaptation to new environments, and pathogenesis of human bacterial infections. Here, we report the complete genomic sequences, and predicted proteins of 27 bacteriophages of the Gram-positive bacterium Staphylococcus aureus. Comparative nucleotide and protein sequence analysis indicates that these phages are a remarkable source of untapped genetic diversity, encoding 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated for structure or function, and 522 are proteins with no similarity to other phage or bacterial sequences. Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. aureus phages can be organized into three groups. Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. aureus phage genes. Among the phages in the largest size class (178–214 kbp) that we characterized is phage Twort, the first discovered bacteriophage (responsible for the Twort-D'Herelle effect). These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity.

genomics

Footnotes

↵ ¶ To whom correspondence should be addressed at: McIntyre Medical Sciences Building, Room 810, 3655 Promenade Sir William Osler, McGill University, Montreal, QC, Canada H3G 1Y6. E-mail: jerry.pelletier{at}mcgill.ca.
↵ † While this work was being performed, T.K. and J.L. were employees of Targanta Therapeutics, and M.D., P.G., and J.P. were consultants at Targanta Therapeutics.
Author contributions: M.D., P.G., and J.P. designed research; T.K. and J.L. performed research; T.K. analyzed data; and T.K., P.G., and J.P. wrote the paper.
Abbreviation: NDM, no database match.
Data deposition: The sequences reported in this paper have been deposited in the National Center for Biotechnology (NCBI) database (accession nos. AY954948–AY954970).