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Genome Biol Evol. 2014 Jul 10;6(7):1739-47. doi: 10.1093/gbe/evu136.

A phage tail-derived element with wide distribution among both prokaryotic domains: a comparative genomic and phylogenetic study.

Author information

1
Laboratory of Clinical Bacteriology and Molecular Microbiology, Faculty of Medicine, University of Crete, Heraklion, GreecePresent address: The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich, United Kingdom. scoulica@med.uoc.gr sarrispanos@science.agrool.gr.
2
Department of Biology, University of Crete, Heraklion, Greece.
3
Department of Biology, University of Crete, Heraklion, GreeceDepartment of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside.
4
Laboratory of Clinical Bacteriology and Molecular Microbiology, Faculty of Medicine, University of Crete, Heraklion, Greece scoulica@med.uoc.gr sarrispanos@science.agrool.gr.

Abstract

Prophage sequences became an integral part of bacterial genomes as a consequence of coevolution, encoding fitness or virulence factors. Such roles have been attributed to phage-derived elements identified in several Gram-negative species: The type VI secretion system (T6SS), the R- and F-type pyocins, and the newly discovered Serratia entomophila antifeeding prophage (Afp), and the Photorhabdus luminescens virulence cassette (PVC). In this study, we provide evidence that remarkably conserved gene clusters, homologous to Afp/PVC, are not restricted to Gram-negative bacteria but are widespread throughout all prokaryotes including the Archaea. Even though they are phylogenetically closer to pyocins, they share key characteristics in common with the T6SS, such as the use of a chaperon-type AAA+ ATPase and the lack of a host cell lysis mechanism. We thus suggest that Afp/PVC-like elements could be classified as phage-like-protein-translocation structures (PLTSs) rather than as pyocins. The reconstruction of phylogeny and the conserved gene content suggest that the diversification of prophage sequences to PLTS occurred in bacteria early in evolution and only once, but PLTS clusters have been horizontally transferred to some of the bacterial lineages and to the Archaea. The adaptation of this element in such a wide host range is suggestive of its versatile use in prokaryotes.

KEYWORDS:

Afp; PLTS; PVC; T6SS; bacterial protein translocation; phage tail-like element

PMID:
25015235
PMCID:
PMC4122934
DOI:
10.1093/gbe/evu136
[Indexed for MEDLINE]
Free PMC Article

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