Monodnaviria

All prototypical viruses in Monodnaviria encode an endonuclease of the HUH superfamily.[note 1] Endonucleases are enzymes that can cleave phosphodiester bonds within a polynucleotide chain. HUH, or HuH, endonucleases are endonucleases that contain a HUH motif made of two histidine residues separated by a bulky hydrophobic residue and a Y motif that contains one or two tyrosine residues. The HUH endonuclease of ssDNA viruses is often called the replication initiation protein, or simply Rep, because its cleavage initiates replication of the viral genome.[1][2]

Once the viral ssDNA is inside of the host cell, it is replicated by the host cell's DNA polymerase to produce a double-stranded form of the viral genome. Rep then recognizes a short sequence on the 3'-end (usually pronounced "three prime end") at the origin of replication. Upstream from the recognition site, Rep binds to the DNA and nicks the positive-sense strand, creating a nic site. In doing so, Rep binds to the 5'-end (usually pronounced "five prime end") via a tyrosine residue that covalently bonds to the phosphate backbone of DNA, creating a phosphotyrosine molecule that connects Rep to the viral DNA.[2][3][4]

The 3'-end of the nicked strand remains as a free hydroxyl (OH) end that acts a signal for the host DNA polymerase to replicate the genome. Replication commences at the 3'-OH end and is performed by extending the 3'-end of the positive strand using the negative strand as a template for replication. During replication, the original positive strand is gradually displaced by the newly replicated positive strand. After one cycle of replicating the genome, Rep is able to recognize the newly replicated recognition and nic sites on the extended positive strand.[2][3][4]

Rep may nick the positive strand a second time, doing so with a second tyrosine residue, or a new Rep may nick the DNA. Multiple copies of the genome may be produced in a single strand. After the positive strand is completely detached from the negative strand and nicked, the 3'-OH end bonds to the phosphotyrosine of the 5'-end, creating a free circular ssDNA genome that usually is either converted into dsDNA for transcription or further replication or is packaged into newly constructed viral capsids. The replication process can be repeated numerous times on the same circular genome to produce many copies of the original viral genome.[2][3][4]

While the prototypical viruses in Monodnaviria have circular ssDNA genomes and replicate via RCR, some have linear ssDNA genomes with different replication methods, including the families Parvoviridae and Bidnaviridae, assigned to the phylum Cossaviricota of the kingdom Shotokuvirae.[1] Parvoviruses and bidnaviruses use rolling hairpin replication, in which each end of the genome has a hairpin loop, a palindromic structure in which nucleotides are not placed into base pairs. This hairpin loop is nicked from the genome by the endonuclease and replicated to the other strand by the host DNA polymerase, the two strands then being split apart as positive and negative strands with hairpin loops at both ends of both strands.[2][5][6] Bidnaviruses also encode their own protein-primed DNA polymerase that replicates the genome, which is bipartite and packaged into two separate virions, in place of using the host cell's DNA polymerase for replication.[1][3]

Additionally, some viruses in the realm are dsDNA viruses with circular genomes, including Polyomaviridae and Papillomaviridae, also assigned to the phylum Cossaviricota. Instead of replicating via RCR, these viruses use bidirectional DNA replication. Bidirectional DNA replication begins by unwinding the dsDNA at a site called the origin, creating a fork in the DNA molecule where both strands are separated from each other. Each strand is replicated separately at the fork by extending one strand while using the other as a template, replication moving in opposite directions along the genome until the opposite side of the circular genome is reached as replication is completed.[7]

Apart from the aforementioned replication methods, ssDNA viruses in Monodnaviria share a number of other common characteristics. The capsids of ssDNA viruses, which store the viral DNA, are usually icosahedral in shape and composed of either one type of protein or, in the case of parvoviruses, multiple types of proteins. All ssDNA viruses that have had the structure of their capsid proteins analyzed in high resolution have shown to contain a single jelly roll fold in their folded structure.[1][3]

Nearly all families of ssDNA viruses have a positive-sense genome, the sole exception being viruses in the family Anelloviridae, unassigned to a realm, which have a negative-sense genome. In any case, ssDNA viruses have their genomes converted to a dsDNA form prior to transcription, which creates the messenger RNA (mRNA) needed to produce viral proteins from ribosomal translation. CRESS-DNA viruses also have similar genome structures, genome lengths, and gene compositions.[1][3][4][8]

Lastly, ssDNA viruses have a relatively high rate of genetic recombinations and substitution mutations. Genetic recombination, or mixture, of ssDNA genomes can occur between closely related viruses when a gene is replicated and transcribed at the same time, which may cause the host cell's DNA polymerases to switch DNA templates (negative strands) during the process, causing recombination. These recombinations usually occur in the negative strand and either outside of or at the peripheries of genes rather than toward the middle of genes.[3]

The high substitution rate seen in ssDNA viruses is unusual since replication is performed primarily by the host cell's DNA polymerase, which contains proofreading mechanisms to prevent mutations. Substitutions in ssDNA viral genomes may occur because the viral DNA may become oxidatively damaged while the genome is inside the capsid. The prevalence of recombinations and substitutions among ssDNA viruses means that eukaryotic ssDNA viruses can emerge as threatening pathogens.[3]

The eukaryotic CRESS-DNA viruses are associated with a variety of diseases. Plant viruses in the families Geminiviridae and Nanoviridae infect economically important crops, causing significant damage to agricultural productivity. Animal viruses in Circoviridae are associated with many diseases, including respiratory illness, intestinal illness, and reproductive problems. Bacilladnaviruses, which primarily infect diatoms, are thought to have a significant role in controlling algal blooms.[3]

The atypical members of the realm are also associated with many widely known diseases. Parvoviruses are most widely known for causing a lethal infection in canids as well as causing fifth disease in humans.[10] Papillomaviruses and polyomaviruses are known to cause different types of cancers and other diseases. A polyomavirus is responsible for Merkel-cell carcinoma, and papillomaviruses cause various genital and other cancers as well as warts.[11][12]

The Rep protein lacks homologues in cellular organisms, so it can be searched for within an organism's genome to identify if viral DNA has become endogenized as part of the organism's genome. Among eukaryotes, endogenization is most often observed in plants, but it is also observed in animals, fungi, and various protozoans. Endogenization can occur through several means such as the integrase or transpose enzymes or by exploiting the host cell's recombination machinery.[3]

Most endogenized ssDNA viruses are in non-coding regions of the organism's genome, but sometimes the viral genes are expressed, and the Rep protein may be used by the organism. Because viral DNA can become a part of an organism's genome, this represents an example of horizontal gene transfer between unrelated organisms that can be used to study evolutionary history. By comparing related organisms, it is possible to estimate the approximate age of ssDNA viruses. For example, comparison of animal genomes has shown that circoviruses and parvoviruses first integrated into their hosts' genomes at least 40-50 million years ago.[3]