Singelaviria

''Singelaviria'' is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain a single vertical jelly roll fold. All viruses in ''Singelaviria'' have two major capsid proteins (MCPs) that both have a single jelly roll (SJR) fold. The MCPs form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA), and are vertical, or perpendicular, to the surface of the capsid. Apart from the SJR fold MCP (SJR-MCP), viruses in the realm also share a minor capsid protein (mCP) that also has a vertical SJR, an ATPase that packages viral DNA into the capsid, capsids that are icosahedral in shape, and a lipid membrane inside the capsid that surrounds the viral genome.

Viruses in ''Singelaviria'' infect archaea that inhabit highly saline environments and bacteria that inhabit high-temperature environments. Their genomes consist of double-stranded DNA that is either linear or circular in shape. Some viruses in the realm are capable of replication both by the lytic cycle, which produces virions, and the lysogenic cycle, in which the virus resides in the host cell as an episome. Some viruses in the realm have spikes on the vertices of their capsid that are shaped like horns or propellers.

From 2019 to 2024, viruses in ''Singelaviria'' were classified in the realm ''Varidnaviria'', which contains DNA viruses that encode MCPs that have two vertical jelly roll folds. It was originally believed that such viruses were descended from singelavirians, but further research showed that the two groups of viruses have separate evolutionary origins, so the SJR-MCP lineage was given its own realm, ''Singelaviria'', in 2025. It is believed by virologists that the two MCPs of singelavirians are the result of a gene duplication event of a single MCP encoded by a portoglobovirus-like virus.

Etymology

''Singelaviria'' is a portmanteau of ''sing'', from Latin ''singulus'', which means "single", Latin ''gelata'', which means "jelly", a reference to the jelly roll fold, and -''viria'', the suffix used for virus realms. Members of the realm are called ''singelavirians''. The kingdom ''Helvetiavirae'' is derived from Latin ''helvetia'', which means "Swiss", a reference to Swiss jelly rolls, and -''virae'', the suffix used for virus kingdoms. The phylum ''Dividoviricota'' is from Esperanto ''divido'', which means "division", a reference to the two single jelly roll major capsid proteins, and -''viricota'', the suffix used for virus phyla. The class ''Laserviricetes'' is a portmanteau of Serpentine Lake on Rottnest Island in Australia, where the first sphaerolipovirus, SH1, was discovered, and -''viricetes'', the suffix used for virus classes. Lastly, the order ''Halopanivirales'' is a portmanteau of ''Haloarcula hispanica'', the host of SH1, and -''virales'', the suffix used for virus classes.

Characteristics

All viruses in ''Singelaviria'' contain a capsid that is made primarily of two major capsid proteins that both contain a vertical single jelly roll fold. The major capsid proteins are named so because they are the primary proteins that the capsid is made of. A jelly roll fold is a type of folded structure in a protein in which eight antiparallel beta strands are organized into four antiparallel beta sheets in a layout resembling a jelly roll, also called a Swiss roll. Each beta strand is a specific sequence of amino acids, and these strands bond to their antiparallel strands via hydrogen bonds. The SJR folds are vertical, or perpendicular, to the capsid surface, in contrast to horizontal folds that are parallel to the capsid surface. During the process of assembling the viral capsid, MCPs self-assemble into hexagonal structures, hexons, that contain three copies of both MCPs. Hexons then bond to form the relatively flat triangular sides of the icosahedral capsid.

In addition to the shared MCP, all singelavirians encode a minor capsid protein (mCP) that contains an SJR fold. These mCPs assemble into pentagonal structures, pentons, that form the pentagonal vertices of the icosahedral capsid. Singelavirians also encode a genome packaging ATPase of the FtsK-HerA superfamily. The ATPases in ''Singelaviria'' are enzymes that package the viral DNA into the capsid during the process of assembling virions. FtsK-HerA is a family of proteins that contains a transmembrane domain with four membrane-spanning helices at the start of the protein's amino acid sequence, a central coiled-coil region, and an ATPase with a P-loop fold at the end of the protein's amino acid sequence. FtsK proteins are found in nearly all bacteria and HerA proteins in all archaea and some bacteria.

The capsids of singelavirions are icosahedral in shape. Inside the capsid is a lipid membrane that surrounds the virus's genome. The lipid membrane is obtained from host cell membranes and contains virus-specific proteins embedded in it. Sphaerolipoviruses have two scaffold proteins that guide the position of capsid subunits, called capsomeres, and they have spikes at the vertices of the capsid that attach to the surface of cells. These spikes are made of multiple proteins and are shaped like horns or propellers.

The structure of the genome varies by family: sphaerolipoviruses have linear double-stranded DNA (dsDNA) genomes 28–31 kilobase pairs (kbp) in length, simuloviruses have circular dsDNA genomes 16–19 kbp in length, and matsushitaviruses have circular dsDNA genomes 17–19.6 in length. Sphaerolipoviruses are lytic viruses, i.e. infection leads directly to lysis and death of the host cell. Simuloviruses and matsushitaviruses, on the other hand, are temperate viruses capable of both lytic and lysogenic cycles. During the lysogenic cycle, simuloviruses reside as proviruses in the host cell as extra-chromosomal episomes. Furthermore, they encode a protein that controls the switch from lysogenic to lytic cycles and vice versa. Simuloviruses and sphaerolipoviruses infect archaea that reside in highly saline environments, whereas matshushitaviruses infect bacteria that live in high temperature environments.

Phylogenetics

Singelavirians likely evolved from a portoglobovirus-like virus that encoded a single vertical SJR-MCP. The two SJR-MCPs of singelavirians appear to be the result of a gene duplication event that duplicated the single SJR MCP. The ancestor of the portoglobovirus SJR-MCP is unknown but is hypothesized to be a cellular SJR-containing protein. The minor capsid protein (mCP) is believed to have evolved from cellular pentameric SJR proteins. Singelavirians, like viruses of ''Varidnaviria'', encode an ATPase of the FtsK-HerA superfamily. It is, however, thought that the need for ATP hydrolysis evolved independently in these two groups of viruses and that they incidentally recruited ATPases from the same lineage.

Classification

''Singelaviria'' is monotypic down to the rank of order and contains three families. This taxonomy is shown hereafter.

* Realm: ''Singelaviria''
** Kingdom: ''Helvetiavirae''
*** Phylum: ''Dividoviricota''
**** Class: ''Laserviricetes''
***** Order: ''Halopanivirales''
****** Family: '' Matsushitaviridae'', which infect thermophilic bacteria
****** Family: '' Simuloviridae'', which infect halophilic archaea
****** Family: '' Sphaerolipoviridae'', which infect halophilic archaea

All singelavirians belong to Group I: dsDNA viruses of the Baltimore classification system, which groups viruses together based on how they produce messenger RNA and is commonly used alongside virus taxonomy, which is based on evolutionary history. Realms are the highest level of taxonomy used for viruses and ''Singelaviria'' is one of seven. The others are '' Adnaviria'', ''Duplodnaviria'', ''Monodnaviria'', ''Riboviria'', '' Ribozyviria'', and ''Varidnaviria''.

History

The first singelavirian to be discovered was bacteriophage IN93, a matsuhitavirus discovered in 1995. The first sphaerolipovirus was discovered in 2003: Haloarcula Hispanic virus SH1. That same year, Natrinema virus SNJ1 was the first simulovirus discovered, but it was first mistaken to be a plasmid since it was discovered in its episomal, proviral form, which resembles plasmids. The three families in the realm were initially classified as three genera within the family ''Sphaerolipoviridae'' and named ''Alphaspherolipovirus'', ''Betasphaerolipovirus'', and ''Gammasphaerolipovirus''. In 2020, betasphaerolipoviruses were renamed and moved to the family ''Simuloviridae'', and gammasphaerolipoviruses were renamed and moved to the family ''Matsushitaviridae''. From 2019 to 2024, singelavirians were classified in the realm ''Varidnaviria'', which was created to accommodate all viruses with vertical jelly roll fold MCPs. After it was discovered that single and double vertical jelly roll fold MCP-encoding viruses had different evolutionary origins, the vertical SJR-MCP lineage was given its own realm, ''Singelaviria'', in 2025.

See also

* List of higher virus taxa

References

Further reading

*

{{Baltimore classification

Virus realms