Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes

ABSTRACT

The International Committee on Taxonomy of Viruses (ICTV) has recently adopted a comprehensive, hierarchical system of virus taxa. The highest ranks in this hierarchy are realms, each of which is considered monophyletic but apparently originated independently of other realms. Here, we announce the creation of a new realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses.

TEXT

In 2018, the International Committee on Taxonomy of Viruses (ICTV) expanded the number of taxonomic ranks available for virus classification from 5 to 15 (1, 2). This development enabled the formal recognition of the evolutionary kinships among distantly related viruses and led to the creation of four realms—virus taxa that are roughly equivalent to the domain rank in cellular taxonomy (3): the realm Riboviria encompasses all RNA viruses and reverse-transcribing viruses that encode homologous RNA-directed RNA polymerases and reverse transcriptases, respectively; the realm Monodnaviria comprises viruses with predominantly single-stranded DNA (ssDNA) genomes and encoding rolling-circle replication initiation endonucleases of the HUH superfamily; the realm Duplodnaviria unifies viruses with double-stranded DNA (dsDNA) genomes that produce virions with icosahedral capsids formed by major capsid proteins (MCPs) with the HK97 fold; and the realm Varidnaviria comprises dsDNA viruses with icosahedral capsids built from MCPs with a double-jelly roll fold (4). However, many virus families remained unassigned to higher taxa due to the lack of demonstrable evolutionary relationships to viruses assigned to the four realms. Here, we announce the creation, and recent official acceptance by the ICTV (https://talk.ictvonline.org/taxonomy/), of a new realm, Adnaviria, which encompasses structurally related archaeal filamentous viruses with dsDNA genomes that adopt the A-form conformation within their virions.

Filamentous viruses infect hosts of all cellular domains, but despite overall similar morphology, virions of eukaryotic, bacterial, and archaeal filamentous viruses are built from capsid proteins with different structural folds (5). Furthermore, the types of the viral genomes that are protected by the corresponding capsid proteins are radically different among viruses infecting hosts from the different domains of life (6–11): all known eukaryotic filamentous viruses have linear ssRNA genomes and are classified in the realm Riboviria (4), all known bacterial filamentous viruses have circular ssDNA genomes and belong to the realm Monodnaviria (4, 12), and all known archaeal filamentous viruses have dsDNA genomes and, until recently, have remained unassigned to taxa ranked higher than order.

Archaeal viruses that form filamentous virions are currently classified into four families: Clavaviridae, Lipothrixviridae, Rudiviridae, and Tristromaviridae (13). Based on the shared gene content, structural similarity of their virions, and homology of the MCPs, the families Lipothrixviridae and Rudiviridae were included in the order Ligamenvirales (14). In virions of both families, the nucleoprotein helix is composed of asymmetric units containing two MCP molecules, a homodimer in the case of rudivirids and a heterodimer of paralogous MCPs in the case of lipothrixvirids (Fig. 1) (11, 15). The MCPs of ligamenviral particles have a unique α-helical fold first found in the MCP of rudivirid Sulfolobus islandicus rod-shaped virus 2 (SIRV2) (16). Lipothrixvirids and rudivirids share a characteristic feature in that the interaction between the MCP dimer and the linear dsDNA genome maintains the DNA in the A form. Consequently, the entire genome adopts the A form in virions (15–18).

FIG 1.

Taxonomic organization of the realm Adnaviria. (A) Taxonomic ranks from family to realm rendered with different colors. (B to D) Cryogenic electron microscopy showing structures of the major capsid protein (MCP) homodimer (characteristic of rudivirids) and heterodimer (characteristic of lipothrixvirids and tristromavirids) (B), MCPs bound to the viral double-stranded DNA (dsDNA) genome in the A-form conformation (C), and side views of the viral nucleocapsid for each constituent family (D). Rudiviridae, Lipothrixviridae, and Tristromaviridae are represented by structures of Sulfolobus islandicus rod-shaped virus 2 (PDB accession no. 3J9X), Acidianus filamentous virus 1 (PDB accession no. 5W7G), and Pyrobaculum filamentous virus 2 (PDB accession no. 6V7B), respectively.

Clavavirids (19, 20) and tristromavirids (21) do not encode proteins with recognizable sequence similarity to proteins of ligamenvirals (22). Hence, the two families were not included in Ligamenvirales. Recently, the structure of particles produced by tristromavirid Pyrobaculum filamentous virus 2 (PFV2) has been characterized by cryogenic electron microscopy (cryo-EM) (23). Unexpectedly, the two nucleocapsid proteins of tristromavirids were found to be structurally related to those of ligamenvirals, and the virion organizations were discovered to be remarkably similar, including the A-form conformation of the genomic dsDNA (23) (Fig. 1). Similar to lipothrixvirids, virions of tristromavirids are enveloped by a lipid membrane (24). Based on the structural similarity between members of the Ligamenvirales and Tristromaviridae, we inferred that they share an origin (23). To formalize this evolutionary relationship, the family Tristromaviridae was assigned to a new order, Primavirales, which, along with Ligamenvirales, was included in a new class, Tokiviricetes.

Members of the Tokiviricetes represent one of the most commonly detected virus groups in terrestrial hot springs and are globally distributed (25–27). Rudivirids have been extensively studied in particular, and many aspects of their life cycles are understood in considerable detail (28). Notably, the mechanisms of genome replication do not appear to be conserved among tokiviricetes. It has been proposed that the rudivirus SIRV2 uses a combination of strand displacement, rolling-circle, and strand-coupled genome replication mechanisms, which generate multimeric, highly branched, “brush-like” intermediates reaching lengths of >1,200 kb (∼34 genome units) (29). The latter are then processed into unit-length, linear genomes with covalently linked hairpin ends. The genome replication of the lipothrixvirid Acidianus filamentous virus 1 has been suggested to start by the formation of a D loop and to progress by the strand displacement replication mechanism, whereas termination relies on recombination events through the formation of terminal loop-like structures, although the genes involved in this unique mechanism of replication remain unknown (30). Similar to rudivirid genomes, tristromavirid genomes have terminal inverted repeats (21), but the replication mechanism of these viruses has not been investigated.

High-resolution structures are now available for virions of six distinct tokiviricetes (11, 15). Like many structurally related viruses in the two other realms of dsDNA viruses (Duplodnaviria and Varidnaviria), there is no detectable sequence similarity among the capsid proteins of viruses from different tokiviricete families, suggesting a vast undescribed diversity of viruses in this part of the virosphere. Indeed, it has been suggested that tokiviricetes were present in the last archaeal common ancestor and possibly even in the last universal cellular ancestor (LUCA) (31). Regardless, the available data unequivocally show that archaeal filamentous viruses do not fall into any of the four established realms. Thus, given the lack of a detectable relationship with other viruses and officially acknowledging the uniqueness of the three families of archaeal filamentous viruses that contain A-form DNA in their virions, a new taxon of the highest rank, the realm Adnaviria, was created for their classification. To bridge the gap between the class and realm taxa, intermediate kingdom and phylum taxa, named Zilligvirae and Taleaviricota, respectively, were established.

In contrast, structural characterization of clavavirid Aeropyrum pernix bacilliform virus 1 (APBV1) particles by cryo-EM confirmed that the fold of its MCP and its overall virion organization are unrelated to those of ligamenviral, tristromavirid, or other characterized virus particles (32). Therefore, notwithstanding their filamentous virions, clavavirids are not included in the realm Adnaviria and likely represent another realm to be established in the future.

ETYMOLOGY OF NEW TAXA

• Adnaviria, from A-form DNA characteristic of viruses in this realm and the suffix -viria for realm taxa.

• Zilligvirae, after Wolfram Zillig (1925 to 2005), a pioneer of research on hyperthermophilic archaeal viruses, and the suffix -virae for kingdom taxa.

• Taleaviricota, from Latin talea, meaning “rod” (referring to the virion morphology), and the suffix -viricota for phylum taxa.

• Tokiviricetes, from Georgian თოკი (toki), meaning “thread,” and the suffix -viricetes for class taxa.

• Primavirales, from Latin prima, meaning “first,” referring to the fact that Thermoproteus tenax virus 1, classified in this order, was the first hyperthermophilic archaeal virus to be isolated in 1983 (33).

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