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Adnaviria
Adnaviria is a realm of viruses that includes archaeal viruses that have a filamentous virion (i.e. body) and a linear, double-stranded DNA genome.[1] The genome exists in A-form (A-DNA) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some adnaviruses, this helix is surrounded by a lipid membrane called an envelope. Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod. Adnaviria was established in 2020 after cryogenic electron microscopy showed that the viruses in the realm were related due to a shared MCP, A-DNA, and general virion structure. Viruses in Adnaviria infect hyperthermophilic and acidophilic archaea, i.e. archaea that inhabit very high temperature environments and highly acidic environments. Their A-DNA genome may be an adaptation to this extreme environment. Viruses in Adnaviria have potentially existed for a long time, as it is thought that they may have infected the last archaeal common ancestor. In general, they show no genetic relation to any viruses outside the realm. EtymologyAdnaviria takes the first part of its name, Adna-, from A-DNA, which refers to the A-form genomic DNA of all viruses in the realm. The second part, -viria is the suffix used for virus realms. The sole kingdom in the realm, Zilligvirae, is named after Wolfram Zillig (1925–2005) for his research on hyperthermophilic archaea, with the virus kingdom suffix -virae. The name of the sole phylum, Taleaviricota, is derived from Latin talea, which means "rod" and refers to the morphology of viruses in the realm, and the virus phylum suffix -viricota. Lastly, the sole class in the realm, Tokiviricetes, is constructed from Georgian toki (თოკი), which means "thread", and the suffix used for virus classes, -viricetes.[2] CharacteristicsViruses in Adnaviria infect hyperthermophilic and acidophilic archaea and have linear, double-stranded DNA (dsDNA) genomes that range from about 16 to 56 kilobase pairs in length. The ends of their genomes contain inverted terminal repeats.[3][4][5] Their genomes exist in A-form, also called A-DNA,[1] a type of DNA that has a compact right-handed helix with more base pairs per turn than B-form DNA.[6] The creation of genomic A-DNA is caused by an interaction with major capsid protein (MCP) dimers, which, during virion assembly, cover pre-genomic B-DNA to form a helical nucleoprotein complex that contains genomic A-DNA.[2] The A-form genome may be an adaptation to allow DNA survival under extreme conditions.[1] Furthermore, viruses in Adnaviria have high genome redundancy, which also might be an adaptation to survive such extreme environments.[7]  The nucleoprotein helix is composed of asymmetric units of two MCPs. For rudiviruses, this is homodimer, a molecule formed by the bonding of two identical MCPs. For lipothrixviruses and tristromaviruses,[8] it is heterodimer, a molecule formed by the bonding of two different MCPs that are paralogous, i.e. the result of a gene duplication event. The MCPs of viruses in Adnaviria contain a folded structure that consists of a type of alpha-helix bundle that contains four helices,[4] called the SIRV2 fold and named after Sulfolobus islandicus rod-shaped virus 2 (SIRV2).[2] The four-helix bundle is found at the end (C-terminus) of the protein while the beginning (N-terminus) of the protein has an extended α-helical arm that wraps tightly around the dsDNA genome to change it to A-form.[8] Variations in the protein structure exist, but the same base structure is retained in all adnaviruses.[2] Adnaviruses have filamentous virions, i.e. they are long, thin, and cylindrical. Lipothrixviruses and ungulaviruses have flexible virions about 410–2,200 nanometers (nm) in length and 24–38 nm in width in which the nucleoprotein helix is surrounded by a lipid envelope.[3][9][10] Tristromaviruses, about 400 by 32 nm, likewise have flexible virions with an envelope, and they contain an additional protein sheath layer between the nucleoprotein complex and the envelope.[5][9][11] Rudviruses have stiff, non-enveloped, rod-like virions about 600–900 by 23 nm.[4][9] At both ends of the virion, lipothrixviruses and ungulaviruses have mop- or claw-like structures connected to a collar, whereas rudiviruses and tristromaviruses have plugs at each end from which bundles of thin filaments emanate.[3][5][10][12] PhylogeneticsViruses in Adnaviria have potentially existed for a long time, as it is thought that they may have infected the last archaeal common ancestor.[13] In general, they show no genetic relation to viruses outside the realm. The only genes that are shared with other viruses are glycosyltransferases, ribbon-helix-helix transcription factors, and anti-CRISPR proteins. Adnaviruses are morphologically similar to non-archaeal filamentous viruses but their virions are built from different capsid proteins. Viruses of Clavaviridae, a family of filamentous archaeal viruses, likewise possess MCPs and virion organization that show no relation to the MCPs and virion organization of viruses in Adnaviria and for that reason are excluded from the realm.[2][9] ClassificationAdnaviria is monotypic down to the rank of its sole class, Tokiviricetes, which has three orders. This taxonomy is shown hereafter:[2][14]
HistoryViruses of Adnaviria began to be discovered in the 1980s by Wolfram Zillig and his colleagues.[15] To discover these viruses, Zillig developed the methods used to culture their hosts.[16] The first of these to be described were TTV1, TTV2, and TTV3 in 1983.[17] TTV1 was classified as the first lipothrixvirus but is now classified as a tristromavirus.[18] SIRV2, a rudivirus, became a model for studying virus-host interactions[15] after its discovery in 1998.[19] The families Lipothrixviridae and Rudiviridae were then united under the order Ligamenvirales in 2012 based on evidence of their relation.[20][21] Cryogenic electron microscopy would later show in 2020 that the MCPs of tristromaviruses contained a SIRV2-like fold like ligamenviruses, which provided justification for establishing Adnaviria in the same year.[8][22] See alsoReferences
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