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Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions

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Abstract

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 ΦCP39O and ΦCP26F, 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 ΦCP39O was 38,753 base pairs (bp), while the ΦCP26F 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.

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Acknowledgments

The authors thank Mary Ard at the University of Georgia, College of Veterinary Medicine, for preliminary electron microscopy. The investigations were supported by the Agricultural Research Service, USDA CRIS project #6612-32000-046 (BSS, GRS, MS) and a non-funded CRADA #58-6612-7-175 with DEF at JCVI. The proteomics portion of the project was supported by NIH Grant Number P20 RR-016464 from the INBRE Program of the National Center for Research Resources (RW and KS). Sequencing was also supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (AK). The genome sequences were submitted to GenBank with accession numbers EU588980 for the ΦCP39O genome and GQ443085 for the ΦCP26F genome.

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  1. Gregory R. Siragusa

    Present address: Danisco USA, W227 N752 Westmound Dr., Waukesha, WI, 53186, USA

Authors and Affiliations

  1. Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, Athens, GA, 30605, USA

    Bruce S. Seal, Mustafa Simmons, Johnna K. Garrish, Robin L. Kuntz & Gregory R. Siragusa

  2. J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD, 20850, USA

    Derrick E. Fouts

  3. Nevada Proteomics Center, University of Nevada, Reno/MS200, 1664 North Virginia Street, Reno, NV, 89557, USA

    Rebekah Woolsey & Kathleen M. Schegg

  4. Laboratory for Foodborne Diseases, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada

    Andrew M. Kropinski

  5. Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 3W4, Canada

    Andrew M. Kropinski

  6. Felix d’Herelle Reference Center for Bacterial Viruses, Department of Medical Biology, Faculty of Medicine, Laval University, Laval, QC, G1K 7P4, Canada

    Hans-W. Ackermann

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Seal, B.S., Fouts, D.E., Simmons, M. et al. Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions. Arch Virol 156, 25–35 (2011). https://doi.org/10.1007/s00705-010-0812-z

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