Viruses of archaea: Structural, functional, environmental and evolutionary genomics

Abstract

Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

“…The virus did not show genomic similarities to known marine MGI viruses or to any genomes in the EVG database. The genome encoded RadA-like ATPase, replication protein A and minichromosome-maintenance helicase genes, which drive the archaeal DNA replication system (Zatopek et al, 2018), presumably to facilitate viral genomic replication in the host (Krupovic et al, 2018). LBVG_51 was mainly detected in the cellular fraction in the hypolimnion (Figs.…”

CASP13 target classification into tertiary structure prediction categories

“…These target EUs displayed a diverse range of sequence similarity (13.5%‐100% HHpred probability) and structure similarity (23.5‐89.4 LGA_S) to known folds. Examples of H‐group assignments with low sequence scores include domains from virus or phage that are known for fast evolution, such as the pectin lyase‐like single‐stranded, right‐handed beta‐helix domain in T0953s2‐D2, the phage tail protein‐like domain in T1021s3‐D1 and T1021s3‐D2, the Phi ETA orf 56‐like protein C‐terminal domain in T0989‐D2, and others, the Phage tail fiber protein trimerization domain in T0953s1, or the RNA bacteriophage capsid protein in T0998. Similarly, fast evolving domains, like RelE‐like toxin domains (T0957s1‐D1, T0968s1, and T0980s1) or colicin D nuclease domain (T0986s1) are involved in bacterial resistance or toxicity.…”

ICTV Virus Taxonomy Profile: Bicaudaviridae

“…The 80 kDa protein appears to be modified in the two-tailed but not in the tail-less virions [1]. High resolution structures of the 32 and 14 kDa proteins have been solved [3,4] and both display unique folds that are not observed in proteins of other classified viruses [5].…”

“…Virions of Acidianus two-tailed virus contain a circular dsDNA of 62 730 bp (41.2 % GC), one of the largest genomes among crenarchaeal viruses [5], predicted to encode 72 proteins and carry four putative transposable elements (Fig. 2).…”