Genomics of bacterial and archaeal virus isolates from extreme aquatic environments

Viruses are ubiquitous, abundant and diverse members of the biosphere. Numerous sequencing projects focusing on isolated viruses and uncultured viral communities (metaviromes) have demonstrated that viruses harbor unprecedented genotypic richness. The genomics of some viruses, for example, tailed bacteriophages infecting several widely known hosts from moderate environments, has been studied relatively well. However, viruses are known to reside in various environments, including the extreme ones, and our knowledge on the genetic make-up of these viral populations is very superficial. In this PhD thesis, the genomics of the archaeal and bacterial viruses isolated from previously sparsely sampled extreme aquatic environments was studied. The genomes of altogether twenty haloarchaeal pleomorphic and tailed viruses from hypersaline environments as well as tailed bacteriophages from the sea ice were sequenced and analyzed. The largest portion of the genomic sequences was shown to encode proteins with no homologues in current databases emphasizing genetic distinctiveness of the studied viruses from the ones described previously. However, all tailed viruses from both hypersaline environment and sea ice were predicted to have a cluster of genes coding for functional analogues of virion assembly and structure components of other tailed phages. Overall arrangement of this gene cluster was conserved. Haloarchaeal pleomorphic viruses were also shown to share a conserved group of genes coding for the structural and hypothetical proteins. Based on the genome organization, haloarchaeal pleomorphic viruses were classified into three subgroups. The members of one of the subgroups were demonstrated to have an unusual genome type, consisting of single-stranded and double-stranded DNA regions. In one of the viruses switches between the regions were found to be associated with a conserved DNA motif. This genome type has not been reported previously for other viruses infecting prokaryotes. To conclude, annotation and analyses of the viral genome contents performed in this PhD thesis offered a glimpse into the diversity of putative functions of the studied viruses. Conducted comparative genomics analyses revealed different levels of relatedness among the viruses within the studied groups and similarities shared with other earlier described viruses. Overall, this work provided new insights into the genomics of understudied viruses residing in hypersaline and cold aquatic environments.Ei saatavill

A Glimpse of the genomic diversity of haloarchaeal tailed viruses

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Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single- or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.Peer reviewe

Related haloarchaeal pleomorphic viruses contain different genome types

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