Volvereviria

Genome

Volverevirians, i.e. microviruses,^{[note 1]} have circular, positive-sense, single-stranded DNA genomes.^[3][4] Isolated microvirus genomes range from about 4,200 to 6,100 nucleotides in length, whereas genomes derived from metagenomics expand the range to 3,000 to 8,900 nucleotides in length.^[5] Most of the genome is made of three core genes that encode a major capsid protein (MCP), an endonuclease, and a DNA pilot protein. Varying numbers of smaller genes that encode other proteins are also present.^[6] Genomes have many overlapping reading frames.^[7]

Proteins

Structure

Microvirus extracellular particles (virions) are about 25–30 nanometers in diameter.^[5] The viral genome, on the inside of the virion, is surrounded by an icosahedral capsid made of 60 copies of the MCP.^[4][5][19] DNA-binding proteins associate with the phosphate backbone of the genome and 60 binding sites located near the 3-fold axes of symmetry in viral coat proteins, resulting in the genome being aligned with the capsid's icosahedral symmetry on the interior surface of the capsid.^[19][20] The 60 MCPs organize into 12 pentamers centered on the 12 vertices of the icosahedral capsid. Virions also contain numerous copies of the pilot protein.^[19][21] Characterized microviruses have protrusions on the surface of the capsid, such as spikes, the structure and positioning of these protrusions varying by taxon.^[22] The capsid is not enveloped.^[23][24]

Life cycle

Microviruses attach to the surface of bacteria before entering. The manner by which they enter cells is unclear, but it has been proposed that they bind to an initial receptor before "walking" or "rolling" to attach to a second receptor. The genome is then ejected from the capsid into the bacterium with the aid of pilot proteins and translocated to the site of DNA synthesis in the cytoplasm.^[25] Microviruses do not encode their own replication machinery,^[26] so replication is performed by host DNA polymerases.^[27] The first step during replication is to convert the ssDNA genome to a double-stranded DNA (dsDNA) replicative form (RF) molecule.^[28][29][30] A primosome complex binds to ssDNA and progresses in a 5′ ("five prime") to 3′ ("three prime") direction as it synthesizes RNA primers to prime DNA synthesis by a host DNA polymerase.^[29]

During the next stage, DNA from the RF molecule is copied, which requires the viral Rep protein^[29] and a host superfamily 1 helicase.^[31] Rep binds to the replication origin, nicks the DNA, and forms a covalent bond with the DNA.^[29][30] The helicase unwinds the RF molecule and the host cell ssDNA binding protein (ssb) stabilizes the molecule.^[29] Replication progresses around the genome, using the negative-sense strand as a template to synthesize a positive-sense strand, until one round around the genome is completed. Rep then nicks the newly synthesized origin on the positive-sense strand and connects the ends of the strand together to form a covalently closed circular ssDNA molecule.^[29][30] Synthesis of a complementary negative-sense strand is then done the same way as in the first stage of replication.^[29] Genes can be expressed once the negative-sense strand is synthesized.^[32]

Whether the RF molecule is used to synthesize dsDNA or progeny ssDNA depends on which proteins bind to the RF molecule. If Rep and the host ssb protein bind to the origin, then the RF molecule is used to synthesize dsDNA. If the viral protein C binds in place of ssb, then the RF molecule is used to synthesize progeny ssDNA genomes.^[28] C inhibits dsDNA synthesis,^[29] mediating the switch to ssDNA synthesis.^[33] As genomic ssDNA is synthesized, it is packaged into progeny capsids^[33] after they are assembled.^[29][33] During packaging, DNA-binding proteins enter the procapsid and tether part of the genome to the interior surface of the capsid.^[28]

After progeny have been synthesized, lysis occurs.^[32] phiX174 and its close relatives use single-gene lysis (Sgl),^[34] encoding a single protein that lyses cells for progeny viruses to exit the host cell. This protein is called E for phiX174.^[35][36] In gram-negative bacteria,^[37] E non-competitively inhibits MraY,^[35][38] an enzyme that forms the first lipid-linked intermediate, lipid I, in the peptidoglycan (PG) biosynthesis pathway.^[35] The PG layer is essential to the structure and shape of the bacterial cell envelope, forming multiples layers of the cell wall.^[39] SlyD, a peptidyl-prolyl isomerase, is often required for E-driven lysis,^[35][40] as it likely chaperones the folding of E.^[41] The Sgl proteins of other microviruses have not been studied,^[42] and metagenomic surveys have indicated that E-like proteins are not found in most microviruses.^[43]

Some microviruses are able to become integrated into the genome of their host, becoming a prophage.^[22][44][45] They do this by exploiting host XerCD recombinases that normally resolve dimers created when two copies of replicating bacterial chromosomes undergo homologous recombination. XerC and XerD bind to dif motifs opposite the replication of origin, nick the DNA, and, with other host factors, untangle sister chromosomes and re-connect the ends, which separates the chromosomes. Microvirus sequences that mimic dif motifs may be recognized by XerCD and integrated into the genome. The pilot protein's DNA in the prophage contains a hypervariable region that prevents superinfection of the same cell with other microviruses that have similar hypervariable regions.^[44]

Evolution

Microviruses have a higher mutation rate than dsDNA viruses and other DNA bacteriophages but lower than RNA viruses.^[26][27] They do not, however, necessarily adopt an r-selected reproductive strategy, which produces a large number of progeny, since the number of virions produced per cell in a given amount of time is highly variable.^[46] Horizontal gene transfer (HGT) has been observed in some microviruses, but it does not appear to be important for them.^[26] They do not typically obtain genes from their hosts or other viruses via HGT, with the exception of peptidases and methyltransferases that are widespread in cellular life and virus realms. HGT between microviruses of different genera also appears to be uncommon.^[18]

Etymology

Volvereviria takes the first part of its name from the Latin word "volvere", which means "to roll". This refers to rolling circle replication, which is the method of DNA replication used by viruses in the realm. The second part is -viria,^[76] the suffix used for virus realms.^[77] The only kingdom in the realm, Sangervirae, is named after Frederick Sanger, who used phiX174 to determine the first DNA sequence, with the suffix for virus kingdoms, -virae. The realm's only phylum, Phixviricota, takes its name from phiX174 and the virus phylum suffix -viricota.^[77] Lastly, the realm's sole class, Microviricetes, inherits its name from the former family Microviridae, which was elevated to the rank of class.^[47] Microviricetes is derived from the word "micro", from the Greek word μικρός (mikrós), which refers to the small size of microviruses, and the suffix used for virus classes, -viricetes.^{[citation needed]}