Diversity of pili-specific bacteriophages: genome sequence of IncM plasmid-dependent RNA phage M

• Main Authors: Rumnieks Janis, Tars Kaspars
• Format: Article
• Language: English
• Published: BMC 2012-11-01
• Series: BMC Microbiology
• Subjects: <it>Leviviridae</it>; RNA phage; Pili-specific phage; IncM; Conjugative plasmid; Lysis
• Online Access: http://www.biomedcentral.com/1471-2180/12/277

<p>Abstract</p> <p>Background</p> <p>Bacteriophages of the <it>Leviviridae</it> family are small RNA viruses with linear, positive-sense, single-stranded RNA genomes that encode only four proteins. All phages of this family require bacterial pili to attach to and infect cells. <it>Leviviridae</it> phages utilizing F-pili for this purpose have been extensively studied. RNA phages specific for conjugative plasmid-encoded pili other than that of plasmid F have been isolated, but are much less understood and their relation to the F-pili-specific phages in many cases is not known.</p> <p>Results</p> <p>Phage M has the smallest known <it>Leviviridae</it> genome to date and has the typical genome organization with maturation, coat and replicase genes in the 5′ to 3′ direction. The lysis gene is located in a different position than in other known <it>Leviviridae</it> phages and completely overlaps with the replicase gene in a different reading frame. It encodes a 37 residue long polypeptide that contains a transmembrane helix like the other known lysis proteins of leviviruses. Sequence identities of M proteins to those of other phages do not exceed 25% for maturation protein, 51% for coat protein and 41% for replicase. Similarities in protein sequences and RNA secondary structures at the 3′ untranslated region place phage M together with phages specific for IncP, IncC and IncH, but not IncF plasmid-encoded pili. Phylogenetic analysis using the complete genome sequences and replicase proteins suggests that phage M represents a lineage that branched off early in the course of RNA phage specialization on different conjugative plasmids.</p> <p>Conclusions</p> <p>The genome sequence of phage M shows that it is clearly related to other conjugative pili-specific leviviruses but has an atypical location of the lysis gene. It provides a better view on the remarkable diversification of the plasmid-specific RNA phages.</p>