T4-Like Genome Organization of the Escherichia coli O157:H7 Lytic Phage AR1

Abstract

We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. It carries a total of 281 potential open reading frames (ORFs) and 10 putative tRNA genes. Of these, 126 predicted proteins could be classified into six viral orthologous group categories, with at least 18 proteins of the structural protein category having been detected by tandem mass spectrometry. Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. The major diverse features between these phages include the modules of distal tail fibers and the types and numbers of internal proteins, tRNA genes, and mobile elements. Codon usage analysis suggested that the presence of AR1-encoded tRNAs may be relevant to the codon usage of structural proteins. Furthermore, protein sequence analysis of AR1 gp37, a potential receptor binding protein, indicated that eight residues in the C terminus are unique to O157:H7 T4-like phages AR1 and PP01. These residues are known to be located in the T4 receptor recognition domain, and they may contribute to specificity for adsorption to the O157:H7 strain.

Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7

“…Therefore, to increase the phage infection range and inhibition efficiency, phage cocktails containing different phages have been developed and used for inhibition of pathogens such as Salmonella and E. coli O157:H7 (52,67,69). Although a few broad-host-range phages have been reported (6,31,34), the bacteriophage AR1 is the only phage reported to date that can inhibit both Salmonella and E. coli O157:H7 (24,42). AR1 is reported to infect many serotypes of E. coli and S. enterica serovar Enteritidis and serovar Choleraesuis, but not serovar Typhimurium.…”

A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome

“…In either a freshwater or saltwater environment, cyanophages are ubiquitous and play an important role in water ecosystems (46,52,61,66). Generally, the complete genome sequences of cyanophages can provide significant clues for better understanding of the biological properties, ecological effects, and coevolutionary relationships between cyanophages and their hosts (10,17,18,21,27,29). Some cyanophage genomes have been sequenced (32,35,44,49,51,60,64), which has revealed the presence of cyanobacterial genes involved in central energy metabolism and their host's survival.…”

Isolation, characterization and complete genome sequence of PhaxI: a phage of Escherichia coli O157 : H7

“…Previous studies resulted in isolating several lytic O157 : H7 coliphages such as PP01, e11/2, e4/1c, CEV1, KH1, KH4, KH5, SH1, AKFV33, rv5, wV8, AR1, SFP10 and CBA120 (Kudva et al, 1999;Kutter et al, 2011;Liao et al, 2011;Morita et al, 2002;Niu et al, 2012;O'Flynn et al, 2004;Park et al, 2012;Raya et al, 2006;Sheng et al, 2006;Villegas et al, 2009). Some of them lyse both E. coli O157 : H7 and other pathogens of the family Enterobacteriaceae.…”

“…Some of them lyse both E. coli O157 : H7 and other pathogens of the family Enterobacteriaceae. For example, AR1 is active on Shigella dysenteriae and Salmonella enterica and SFP10 lyses Salmonella typhimurium (Liao et al, 2011;Park et al, 2012). From the O157 phages, AKFV33, Rv5, wV8, AR1, SFP10 and CBA120 are completely sequenced (GenBank accession numbers NC_017969.1, NC_011041.1, NC_ 012749.1, AP011113.1, HQ259103.1 and JN593240.1, respectively).…”