Adnaviria is a realm of archaeal viruses that have filamentous virions (i.e., bodies) and linear, double-stranded DNA genomes. Their genomes exist in A-form (A-DNA) and encode a dimeric major capsid protein (MCP) that contains the SIRV2 fold, an alpha-helix bundle with four helices. Adnavirians infect hyperthermophilic (very high temperature), thermoacidophilic (high temperature, highly acidic), and methanotrophic (methane-metabolizing) archaea. They can be found worldwide, though some are concentrated in extreme geothermal environments. The extracellular particles (virions) of adnavirians consist of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some of them, 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 stiff like a rod. In general, enveloped adnavirians are more flexible than non-enveloped ones. At both ends of the virion are protrusions involved in host recognition. Viruses in the realm use a variety of methods to replicate their genomes and rely on host machinery for transcription. Virions are assembled and enveloped in the host cell's cytoplasm. Their A-DNA genome is formed by interactions between pre-genomic B-DNA and the MCP and may be an adaptation to extremely high temperatures. They are lytic viruses, leaving their host through ruptures in the cell's external membrane (lysis). Adnavirians may have infected the last archaeal common ancestor. In general, they have no genetic relation to viruses outside the realm. They were first discovered in the 1980s by Wolfram Zillig and his colleagues. Since its discovery in 1988, the adnavirian Sulfolobus islandicus rod-shaped virus 2 (SIRV2) has become a model for studying virus-host interactions in archaea. The realm Adnaviria was established in 2021 after cryogenic electron microscopy showed that member viruses shared their A-DNA, MCP, and general virion structure.
Classification Adnaviria is monotypic down to the rank of its sole class, Tokiviricetes, which has three orders. This is shown hereafter:
Realm: Adnaviria Kingdom: Zilligvirae Phylum: Taleaviricota Class: Tokiviricetes Order: Ligamenvirales, which contains chiyouviruses, lipothrixviruses, rudiviruses, and ungulaviruses Order: Maximonvirales, which contains ahmunviruses Order: Primavirales, which contains tristromaviruses
Characteristics
Genome Viruses in Adnaviria have linear, double-stranded DNA (dsDNA) genomes that range from about 17.6 to 41.5 kilobase pairs in length. The ends of their genomes contain inverted terminal repeats. Their genomes exist in A-form, also called A-DNA, a dehydrated version of the more typical B-form DNA. A-DNA has a compact right-handed helix with more base pairs per turn than B-DNA, and the base pairs in A-DNA are not perpendicular to the DNA's helix axis. The creation of genomic A-DNA is caused by major capsid protein (MCP) dimers interacting with the phosphodiester bond DNA backbone during virion assembly, covering pre-genomic B-DNA to form a helical nucleoprotein complex that contains genomic A-DNA. The A-form genome may be an adaptation to extremely high temperatures.
Major capsid protein The nucleoprotein helix is composed of asymmetric units of two MCPs. For rudiviruses, this is a homodimer, a molecule formed by the bonding of two identical MCPs. For other adnavirians, it is a heterodimer, a molecule formed by the bonding of two structurally similar MCPs that are paralogous. The MCPs of viruses in Adnaviria have a folded structure that contains an alpha-helix bundle that has four helices, called the SIRV2 fold, named after Sulfolobus islandicus rod-shaped virus 2 (SIRV2). 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 alpha-helical arm that, when a part of MCP dimers, forms a closed claw-like shape that wraps tightly around the dsDNA genome to change it to A-form. Variations in the protein structure exist, but the same base structure is retained in all adnavirians. The MCP genes are the only core genes found in all viruses in the realm.
Structure
The extracellular bodies (virions) of adnavirians are filamentous, i.e., they are long, thin, and cylindrical. Virions are about 400–2,000 nanometers (nm) in length and 24–38 nm in diameter. Lipothrixviruses and ungulaviruses have flexible virions in which the nucleoprotein helix is surrounded by a lipid envelope. Tristromaviruses likewise have flexible, enveloped virions with an additional protein sheath layer between the nucleoprotein complex and the envelope. Envelopes are half as thick as the host cell membrane as they are derived from host diether and tetraether lipids that either are short (archaeol) or can be bent into a U shape. Rudviruses have stiff, non-enveloped, rod-like virions about 600–900 by 23 nm. Non-enveloped adnavirians are more rigid, while enveloped adnavirians are more flexible. 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. These protrusions are usually genus-specific, and they are made of minor structural proteins and involved in host recognition. Ahmunvirus and chiyouvirus virions have not been studied.
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