Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content
- 1Dairy Products Research Centre
- 2Dairy Production Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork
- 3Department of Microbiology, University College Cork
- 4Department of Biological Sciences, Cork Institute of Technology
- 6Alimentary Pharmabiotic Centre, Cork, Ireland
- 5 University of Tennessee Health Sciences Center, Memphis, Tennessee 38163
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FIG. 1.ORF organization of phage K. ORFs 1 to 118 are indicated by arrows; the numbering corresponds to that in Table 1. Blue arrows, putative lysis module; red arrows, structural module; green arrows, DNA replication and transcription module; grey arrows, proteins with a putative function; black arrows, hypothetical proteins. Arrows with black vertical lines indicate three intron-carried ORFs. Arrows are roughly drawn to scale. Vertical lines mark two putative promoters. L and R, direction of transcription (left or right). Start codons and ribosome binding sites are indicated in boldface, and putative −10 and −35 sites are underlined. Dashed vertical lines represent the positions of four putative tRNAs.
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FIG. 2.Section of the phage proteomic tree illustrating the relationship between phage K and other sequenced Myoviridae. The tree is based on 375 sequenced phage genomes and prophages. Only the section of the tree corresponding to phage K is shown for clarity. The tree joins the remainder of the phages at the dashed line. The PZA-like Podoviridae (Podophage) are highlighted for correlation to reference 36. Phage K is weakly related to both the PZA-like Podoviridae and the Borrelia burgdorferi plasmid prophage, which form unique taxonomic groups.
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FIG. 3.(A) Schematic representation of the phage K polymerase gene interrupted by intron DNA. Dashed lines represent introns pol-I2 and pol-I3, encoding I-KsaII and I-KsaIII, respectively. The in vivo splicing of phage K intron DNA from the polymerase gene is illustrated on a 1% agarose gel. Lane 1, PCR product obtained on phage K DNA with primers PolF and PolR; lane 2, PCR product obtained from cDNA of phage K DNA with primers PolF and PolR; lane 3, 1-kb ladder (New England Biolabs). Sizes of PCR products are indicated on the right in base pairs. The schematic diagram is overlaid with a graph illustrating the percent G+C content in this section of the genome. (B) Schematic representation of the phage K lysin gene interrupted by intron DNA. Dashed lines represent intron lys-I1, encoding I-KsaI. The in vivo splicing of phage K intron DNA from the lysin gene is illustrated on a 1% agarose gel. Lane 1, PCR product obtained on phage K DNA with primers LysF and LysR; lane 2, PCR product obtained from cDNA of phage K with primers LysF and LysR; lane 3, 1-kb ladder (New England Biolabs). Sizes of PCR products are indicated on the right in base pairs. The schematic diagram is overlaid with a graph illustrating the percent G+C content in this section of the genome.
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FIG. 4.One-dimensional SDS-PAGE of phage K proteins stained with Coomassie brilliant blue and schematic diagram of similarities with Listeria phage A511. Bands A, B, C, and D represent the four proteins that were N-terminally sequenced. The N-terminal sequences of each band and the ORF from the genome of phage K to which each band corresponds are shown to the right. Numbering of ORFs for phage A511 corresponds to that in reference 23. Dark grey arrows represent ORFs with a corresponding ORF in each phage, and light grey arrows represent ORFs that have no corresponding ORFs between phages K and A511. Percent identities shared between ORFs of phages K and A511 are indicated in boxes in the schematic diagram.
- American Society for Microbiology
