Revised Genome Sequence of Staphylococcus aureus Bacteriophage K

Abstract

Bacteriophage K is a member of the virulent Twort-like group of myophages infecting Staphylococcus aureus. The revised sequence presented here includes 12,436 bp of additional sequence not present in the previously available phage K genome (GenBank accession no. NC_005880) and updated annotations, and has been reopened at the predicted terminal repeat boundary.

GENOME ANNOUNCEMENT

Staphylococcus aureus is a Gram-positive opportunistic pathogen, many strains of which are antibiotic resistant (1). Among the bacteriophages capable of infecting S. aureus, members of the Twort-like group possess broad host ranges and a virulent lifestyle that makes them attractive as potential therapeutics against this pathogen. Phage K is among the best-studied members of this group, the genome of which was initially published in 2004 (accession no. NC_005880) (2).

Bacteriophage K (ATCC 19685-B1) was obtained from the ATCC and routinely propagated on S. aureus strain Newbould 305. Phage genomic DNA was extracted using previously described methods (3) and sequenced in an Illumina MiSeq 250-bp paired-end run with a 500-bp insert library at the University of Texas Genomic Sequencing and Analysis Facility, Austin, TX. Quality-controlled and trimmed sequences were assembled with Velvet version 1.2.10 (4) to produce a final assembly of 139,831 bp at 30-fold average coverage. Gene prediction was conducted with Glimmer (5) and GeneMark.hmm (6), followed by manual curation. Functional annotations were assigned using a combination of BLASTp (7) and InterProScan version 4.7 (8). Where applicable, the annotation was based on the published phage K annotation, including previously described introns (2).

The phage K unit genome presented here is 139,831 bp in length and contains two large regions of additional sequence not present in the published phage K genome (GenBank accession no. NC_005880) (2). The first, a 2,888-bp region, comprises bases 4191 to 7078, containing genes 11 to 16. A second region of 9,546 bp comprises bases 123190 to 132735 and contains genes 169 to 196. A third 2-bp insertion comprises bases 3087 to 3088 in a noncoding region. The 9,546-bp insertion occurs within K_ORF108 (YP_024536), altering the C terminus of this gene. Other than these differences, the remainder of the phage K genome sequence reported here was found to be identical to the previously reported phage K DNA sequence. The 12,436 bp of new sequence was predicted to contain 35 protein-coding genes. An additional 62 previously unannotated genes were added to the record, bringing the total number of predicted protein-coding genes in phage K to 212 and the coding density to 90.2%. Four tRNA genes were also annotated, encoding predicted Met, Trp, Phe, and Asp tRNAs.

Based on a recent analysis of Twort-like phages, phage K is predicted to possess a terminally redundant nonpermuted genome as demonstrated for other members of the SPO1-like family (9). The phage K genome was reopened at the predicted terminal repeat (TR) boundary based on sequence similarity to the TR boundaries of other Twort-like phages (9) and experimental analysis of a related S. aureus bacteriophage (unpublished data). Phage K is predicted to contain an 8,486-bp terminal redundancy, making the entire packaged genome 148,317 bp in length.

Nucleotide sequence accession number.

This genome sequence was deposited into GenBank under accession no. KF766114.