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. 2007 Jul 16:8:236.
doi: 10.1186/1471-2164-8-236.

Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria

Mart Krupovic  1 , Dennis H Bamford
Affiliations

Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria

Mart Krupovic et al. BMC Genomics. .

Abstract

Background: The origin and evolution of viruses is currently a heavily discussed issue. One element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. The first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". The second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be obtained via lateral gene transfer. Comparing the structures and sequences of the "self" elements, we have proposed that viruses can be grouped into lineages regardless of which domain of life (bacteria, archaea, eukarya) they infect. It has also been suggested that viruses are ancient and possibly predate modern cells.

Results: Here we identified thirteen putative prophages (viral genomes integrated into bacterial chromosome) closely related to the virulent icosahedral tailless lipid-containing bacteriophage PM2. Using the comparative genomics approach, we present evidence to support the viral "self" hypothesis and divide genes of the bacteriophage PM2 and related prophages into "self" and "nonself" categories.

Conclusion: We show here that the previously proposed most conserved viral "self" determinants, the major coat protein and the packaging ATPase, were the only proteins that could be recognized in all detected corticoviral elements. We also argue here that the genes needed for viral genome replication, as well as for host cell lysis, belong to the "nonself" category of genes.Furthermore, we suggest that abundance of PM2-like viruses in the aquatic environment as well as their importance in the ecology of aquatic microorganisms might have been underestimated.

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Figures

Figure 1
Figure 1
Genetic organization of the putative corticoviral prophages, bacteriophage PM2 [19], and the maintenance region of the pAS28 plasmid [26]. Circular PM2 genome map is linearized at a unique EcoRII site [19]. Genes encoding structural and nonstructural proteins (Roman numerals) and ORFs (lower case letters) are visualized as arrows indicating the direction of transcription. The origin of replication (ORI) and the known promoters (kinked arrows) are indicated. All the elements are aligned to the major coat protein-coding gene II of phage PM2, except for the pAS28 maintenance region, which is aligned to the PM2 gene XVI. Genes in the corticoviral elements sharing sequence similarity with those of PM2 are named according to the previously established phage PM2 nomenclature [19] and are coloured blue. Genes in the PM2 genome, as well as in corticoviral elements related to those of the pAS28 plasmid, are coloured red. The viral "self" core, containing genes IX, VII, and II is shaded grey. The late promoter region of phage PM2 and the noncoding region matching its position in all putative prophages is coloured yellow. Recombinase-coding genes and genes encoding replication-associated proteins (other than XII- and ORF1-type) are shown in green and black, respectively. Putative CI repressor- and endolysin-coding genes, as well as the position of the DnaA protein-binding site, are indicated. As a reference point, accession numbers of putative coat proteins of the identified corticoviral prophages are indicated in parenthesis under the corresponding bacterial species name. While exact nucleotide positions of the depicted corticoviral elements can be found in the supplemental material table (see Additional file 1).
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