Abstract
The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7–46.8 kb (43.8–44 mol% G+C) encoding 74–81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily “Tunavirinae” with further classification into five genera, namely “Tlslikevirus” (TLS, FSL SP-126), “Kp36likevirus” (KP36, F20), Tunalikevirus (T1, ADB-2 and Shf1), “Rtplikevirus” (RTP, vB_EcoS_ACG-M12) and “Jk06likevirus” (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49). The fact that the viruses related to JK06 have been isolated independently in Israel (JK06) (GenBank Assession #, NC_007291), Canada (vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96) and Mexico (phiKP26, phiJLA23) (between 2005 and 2011) indicates that these similar phages are widely distributed, and that horizontal gene transfer does not always prevent the characterization of bacteriophage evolution. With this new scheme, any new discovered phages with same type can be more properly identified. Genomic- and proteomic- based taxonomic classification of phages would facilitate better understanding phages diversity and genetic traits involved in phage evolution.
Highlights
Tailed bacteriophages with double-strand DNA genomes belonging to the order Caudovirales are the most abundant viruses on earth, accounting for 96% of all the phages observed [1]
This study revealed that phages AHP24, AHS24, AHP42 and AKS96 are closely related members of new proposed genus– ‘‘Jk06likevirus’’
The highest degree of nucleotide identity was shared between AHP24 and AHS24, as they were isolated simultaneously from fecal pats and manure slurry from the same feedlot pen [19]
Summary
Tailed bacteriophages (phages) with double-strand DNA genomes belonging to the order Caudovirales are the most abundant viruses on earth, accounting for 96% of all the phages observed [1]. The Siphoviridae account for .61% of described phages [1] and this family represents the largest group of fully sequenced phages, but no subfamilies, and only nine bacterial-specific phage genera have been described. T1-like phages possess terminally redundant and circularly permuted genomes of ,50 kb, and are currently classified as members of one genus (Tunalikevirus) within Siphoviridae [5]. They have a polyhedral head 60 nm in diameter with an extremely flexible non-contractile tail 151 nm in length and 8 nm in diameter [6]. ICTV only recognizes nine species of phages within this genus with 1, 1, 6 and 1 infecting Cronobacter, Enterobacter, Escherichia coli, and Shigella, respectively
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