Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Abstract

SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3700 ARTICLE More generally, none of the viral genes taken separately can adequately represent viral history 52 , especially so in the light of rampant horizontal gene exchange in the viral world 53 . Genetic mosaicism has been previously pointed out as a factor impeding meaningful classification of tailed bacteriophages (order Caudovirales) 54 .…”

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

“…Phage classification will therefore remain a highly demanding and daunting process, unless a genomic taxonomy for viruses is embraced (see [8]). Although a taxonomy that is based on the genome sequence alone might be incorrect due to rampant genomic rearrangements in viruses [23], such an approach may turn out to be the only scalable solution. …”

Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome

“…Viruses similar to the bacterial head-tailed viruses (order Caudovirales) have never been isolated from hyperthermophiles; viruses of this type infect mesophilic Archaea-the extreme halophiles and methanogens (8,9). Not only the morphotypes but also the genomes of hyperthermophilic archaeal viruses are exceptional: more than 90% of their putative genes have no recognizable functions or detectable homologs in other viruses or cellular life forms (6,10,11). Moreover, the ways in which some of these viruses interact with their hosts are also particular, as recently demonstrated by the description of a unique virion release mechanism (12)(13)(14).…”