Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

Abstract

We identified 9371 tailed phage prophages of 20 known types in reported complete genome sequences of 3298 bacteria in the Salmonella genus. These include 4758 P2 type and 744 P22 type prophages. The latter prophage types were found in the genome sequences of 127 and 24 bacterial host genera, increasing the known host ranges of phages in these groups by 114 and 20 genera, respectively. These prophage nucleotide sequences displayed much more diversity than was previously known from the 48 P2 and 24 P22 type authentic phages whose genomes have been sequenced. More detailed analysis of these prophage sequences indicated that major capsid protein (MCP) gene exchange between tailed phage clusters or types is extremely rare and that P22 prophage-encoded tailspikes correspond perfectly with their hosts’ surface polysaccharide structure; thus, MCP and tailspike sequences accurately predict tailed phage type (and thus lifestyle) and host cell surface polysaccharide structure, respectively.

Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates

“…While phages SEN1 and SEN22 showed close sequence relatedness to prototype phages P2 and P22, respectively, phages SEN4/5 and SEN34 were quite different from known phages. Our findings are in accordance with a study by Casjens and Grose [18], where SEN4/5 genomic sequences formed a new, well defined, subcluster within the P2-like cluster. Phage SEN34 was similar to several disparate Lambda-like phages, but did not belong to any of the 17 known lambda clusters described by Grose and Casjens [17].…”

“…To date, almost 200 phage types have been identified in the genus Salmonella [30] and if prophages are included, the number is greater than 9,000 [18]. Prophages appear to be very common in Salmonella , as shown by production of 136 functional phages from 173 S .…”

“…enterica (serovar Typhimurium) isolates [31]. It has been calculated that there are, on average, 2.8 known prophages present per Salmonella genome [18]. While phages and prophages of subsp.…”

“…While phages and prophages of subsp. enterica have been intensively studied (reviewed in [18, 30, 32]), information on phages in other Salmonella subspecies is scarce. In fact, putative prophage sequences were only recently identified in the whole genome sequences of two strains belonging to non- enterica subspecies, i.e.…”

“…Lambda-like, P2-like, and P22-like). In addition, 9371 prophages from 3298 Salmonella genomes were recently identified; out of them, 744 prophages belonged to the P22-like group and 4758 to the P2-like group [18]. …”