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

Abstract

BackgroundBacteriophages of the Leviviridae 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. Leviviridae 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.ResultsPhage M has the smallest known Leviviridae 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 Leviviridae 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.ConclusionsThe 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.

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

“…9 top). Like Enterobacteria phage M, it may also encode a +1 frameshift lysis protein inside of the RdRp gene (53). The predicted lysis protein contains a gram-negative signal peptide and a transmembrane domain and may form pores in the plasma membrane, dissipating proton motive force and inducing cell autolysis (54).…”

A viral protein antibiotic inhibits lipid II flippase activity

“…Previously, the A 2 protein of levivirus Qβ and the E protein of the microvirus φ X174 were shown to be ‘protein antibiotics’ that inhibit the MurA and MraY steps of the PG synthesis pathway 2–4 . Here, we investigated the mechanism of action of an unrelated lysis protein, Lys M , of the Escherichia coli levivirus M 5 . We show that Lys M inhibits the translocation of the final lipid-linked PG precursor called lipid II across the cytoplasmic membrane by interfering with the activity of MurJ.…”

“…1a) and found that lysis genes appear to have evolved at different sites after speciation of the phage to infect cells with new pili receptors 5 . In particular, levivirus M has its lys M gene embedded in the +1 reading frame of rep .…”

“…However, in Qβ, the maturation protein A 2 has evolved an additional ability to inhibit MurA 4 . Like these factors, lys M occupies no dedicated genetic space 5 , highlighting the ability of small phages to maximize their coding capacity. Recent analysis of publicly available metagenomes and transcriptomes has revealed that the ssRNA leviviruses are more ubiquitous and diverse than previously appreciated 17,18 , at least in part because of extensive use of RNase during virome sampling.…”

The True Story and Advantages of RNA Phage Capsids as Nanotools

“…Out of such efforts, 19 new genomes of icosahedral RNA phages [286], genomes from the phages M [287], C-1 and HgalI [288], DL52 and DL54 [289], from a so-called JS-like group [290] and of the phages EC and MB [291], have been described.…”