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Inducible Clostridium perfringens bacteriophages ?S9 and ?S63: Different genome structures and a fully functional sigK intervening element.

ABSTRACT: Two inducible temperate bacteriophages ?S9 and ?S63 from Clostridium perfringens were sequenced and analyzed. Isometric heads and long non-contractile tails classify ?S9 and ?S63 in the Siphoviridae family, and their genomes consist of 39,457 bp (?S9) and 33,609 bp (?S63) linear dsDNA, respectively. ?S63 has 3'-overlapping cohesive genome ends, whereas ?S9 is the first Clostridium phage featuring an experimentally proven terminally redundant and circularly permuted genome. A total of 50 and 43 coding sequences were predicted for ?S9 and ?S63, respectively, organized into 6 distinct lifestyle-associated modules typical for temperate Siphoviruses. Putative functions could be assigned to 26 gene products of ?S9, and to 25 of ?S63. The ?S9 attB attachment and insertion site is located in a non-coding region upstream of a putative phosphorylase gene. Interestingly, ?S63 integrates into the 3' part of sigK in C. perfringens, and represents the first functional skin-element-like phage described for this genus. With respect to possible effects of lysogeny, we did not obtain evidence that ?S9 may influence sporulation of a lysogenized host. In contrast, interruption of sigK, a sporulation associated gene in various bacteria, by the ?S63 prophage insertion is more likely to affect sporulation of its carrier.

SUBMITTER: Kim KP

PROVIDER: S-EPMC3442830 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63: Different genome structures and a fully functional sigK intervening element.

Kim Kwang-Pyo KP Born Yannick Y Lurz Rudi R Eichenseher Fritz F Zimmer Markus M Loessner Martin J MJ Klumpp Jochen J

Bacteriophage 20120401 2

Two inducible temperate bacteriophages ΦS9 and ΦS63 from Clostridium perfringens were sequenced and analyzed. Isometric heads and long non-contractile tails classify ΦS9 and ΦS63 in the Siphoviridae family, and their genomes consist of 39,457 bp (ΦS9) and 33,609 bp (ΦS63) linear dsDNA, respectively. ΦS63 has 3'-overlapping cohesive genome ends, whereas ΦS9 is the first Clostridium phage featuring an experimentally proven terminally redundant and circularly permuted genome. A total of 50 and 43 c ...[more]

PMID: 23050219

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Project description:Poultry intestinal material, sewage and poultry processing drainage water were screened for virulent Clostridium perfringens bacteriophages. Viruses isolated from broiler chicken offal washes (O) and poultry feces (F), designated ?CP39O and ?CP26F, respectively, produced clear plaques on host strains. Both bacteriophages had isometric heads of 57 nm in diameter with 100-nm non-contractile tails characteristic of members of the family Siphoviridae in the order Caudovirales. The double-strand DNA genome of bacteriophage ?CP39O was 38,753 base pairs (bp), while the ?CP26F genome was 39,188 bp, with an average GC content of 30.3%. Both viral genomes contained 62 potential open reading frames (ORFs) predicted to be encoded on one strand. Among the ORFs, 29 predicted proteins had no known similarity while others encoded putative bacteriophage capsid components such as a pre-neck/appendage, tail, tape measure and portal proteins. Other genes encoded a predicted DNA primase, single-strand DNA-binding protein, terminase, thymidylate synthase and a transcription factor. Potential lytic enzymes such as a fibronectin-binding autolysin, an amidase/hydrolase and a holin were encoded in the viral genomes. Several ORFs encoded proteins that gave BLASTP matches with proteins from Clostridium spp. and other Gram-positive bacterial and bacteriophage genomes as well as unknown putative Collinsella aerofaciens proteins. Proteomics analysis of the purified viruses resulted in the identification of the putative pre-neck/appendage protein and a minor structural protein encoded by large open reading frames. Variants of the portal protein were identified, and several mycobacteriophage gp6-like protein variants were detected in large amounts relative to other virion proteins. The predicted amino acid sequences of the pre-neck/appendage proteins had major differences in the central portion of the protein between the two phage gene products. Based on phylogenetic analysis of the large terminase protein, these phages are predicted to be pac-type, using a head-full DNA packaging strategy.

Dataset Information

Inducible Clostridium perfringens bacteriophages ?S9 and ?S63: Different genome structures and a fully functional sigK intervening element.

Publications

Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63: Different genome structures and a fully functional sigK intervening element.

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