Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2011
Publication Date: June 1, 2011
Citation: Oakley, B., Morales, C., Seal, B.S., Hiett, K.L., Talundzic, E., Volozhantsev, N.V. 2011. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable rates of evolution within a core genome. Biomed Central (BMC) Genomics. 12:212. Interpretive Summary: Bacteriophages (phages) are viruses that infect bacteria. Because each type of phage only infects a certain type of bacterium, phages and their gene products are an important potential alternative to broad-spectrum antibiotics to control undesirable pathogenic bacteria. Proper biotechnological use of bacteriophage gene products requires a thorough understanding of phage biology and genetics. Our lab personnel sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Two genes in particular were of interest: the phage holin which creates holes in bacterial membranes and the endolysin, a protein that enzymatically digests the bacterial membrane. Comparisons of these four genomes to 26 others previously published produced three important results. 1) Phage proteins that lyse pathogenic bacteria are conserved across large evolutionary distances and thus must represent a successful evolutionary strategy for bacterial control. 2) Of the genes shared by the four genomes, the phage endolysins are among the most variable, suggesting highly specific targeting of bacterial strains is possible . 3) The portion of the endolysin protein responsible for recognition of the bacterial cell wall is much less variable than the enzymatically-active portion of the protein. A ‘mix-and-match’ bioengineering approach with the two portions of the protein may allow tailoring of host-specificity. The ongoing search for alternatives to currently used antibiotics in animal feeds and for therapeutic veterinary or medical use will require continued analyses of phages and their genetics. This research has helped determine the structure, function and potential applications of these phages and their gene products as alternatives to conventional antibiotics for specific bacterial pathogens.
Technical Abstract: Background: Biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context. We sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results: Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase) and a holin (PF04531). Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1) strongly significant host-specific sequence variation within the endolysin, and 2) a protein domain architecture unique to our phage genomes in which the endolysin gene is located upstream of its associated holin gene. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The core genome was comprised of four other variable pfam families, and a conserved core genome in which genes belonging to 12 pfam families, including the holin genes, were nearly identical. Conclusions: Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and have significant variability and host-specificity even among closely related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for the structure, function and potential applications of these phages and their gene products as alternatives to conventional antibiotics.