s of virions of
Sulfolobus islandicus filamentous virus, a lipothrixvirus. The length of the bars is 100 nm.
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 24–38nm 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.
Life cycle Rudiviruses, tristromaviruses, and ungulaviruses recognize and bind to extracellular filaments during viral entry into the cell. For rudiviruses and tristromaviruses, these are
type IV pili. After reaching the cell surface, rudiviruses virions disassemble, likely at the same time that viral DNA enters the host cell's
cytoplasm. Once there,
transcription of viral genes begins, starting with proteins that take over the host and defend against host immune systems, such as anti-
CRISPR proteins to protect against CRISPR defense systems. Adnavirians do not encode their own
RNA polymerases, so they rely on host transcription machinery. They do, however, encode proteins that regulate transcription. Most research on adnavirian replication has focused on rudiviruses, but it is known that adnavirians replicate through a variety of mechanisms. Rudiviruses encode a HUH-superfamily
endonuclease, which is thought to initiate
rolling circle replication by
nicking DNA close to the
hairpin at the end of the genome. For SIRV2, a rudivirus, replication occurs through a combination of strand-displacement, rolling-circle, and strand-coupled replication, which creates intermediate molecules resembling brushes that contain many copies of the genome. These intermediates are then processed into individual genomes.
Acidianus filamentous virus 1, an ungulavirus, appears to start replication first by forming a
D-loop, then progressing through a strand-displacement mechanism. Replication then ends with the help of
recombination through the formation of loop-like structures. Classified adnavirians do not encode their own
DNA polymerases, so replication is likely performed by host DNA polymerases. For rudiviruses, DNA polymerase B1 and a
sliding clamp are involved in replication. Ahmunviruses encode homologs of the archaeo-eukaryotic
primase and DNA polymerase sliding clamp, which likely are important during replication. Genes for protein-primed family B DNA polymerases have been identified by
metagenomics in samples of putative adnavirians, suggesting more replication methods are used by them than what is currently known. Virions are assembled and enveloped in the cytoplasm. Characterized adnavirians replicate through the
lytic cycle, leaving the cell through ruptures in the
cell's external membrane (
lysis). Rudivirus and lipothrixvirus virions exit the cell through pyramidal structures commonly called virus-associated pyramids (VAPs). VAPs are made of a small virus-encoded protein and are formed at the same time as virions. At the end of infection, once VAPs reach a certain size, their triangular surfaces come apart like flower petals. This creates openings in the
cell envelope through which the contents of the cytoplasm, including virions, pour out of the cell. Tristromaviruses appear to use a different method of lysis during which cells are sliced open without the formation of surface structures. ==Distribution==