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''Icerudivirus'' is a genus of
viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...
in the family ''
Rudiviridae ''Rudiviridae'' is a family of viruses with linear double stranded DNA genomes that infect archaea. The viruses of this family are highly thermostable and can act as a template for site-selective and spatially controlled chemical modification. Fu ...
''. These viruses are non-enveloped, stiff-rod-shaped viruses with linear dsDNA genomes, that infect hyperthermophilic
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
of the species ''
Sulfolobus islandicus ''Sulfolobus'' is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain. ''Sulfolobus'' species grow in volcanic springs with optimal growth occurring at pH 2-3 and temperatures of 75-80 °C, making them ...
''. There are three species in the genus.


Taxonomy

The following species are assigned to the genus: * ''Icerudivirus SIRV1'', common name
Sulfolobus islandicus rod-shaped virus 1 Sulfolobus islandicus rod-shaped virus 1 (SIRV1) is a virus in the order ''Ligamenvirales''. Its only known host is the Archaean ''Sulfolobus islandicus''. The species was first documented from a hot spring sample in Yellowstone National Park ...
(SIRV1) * ''Icerudivirus SIRV2'', common name
Sulfolobus islandicus rod-shaped virus 2 Sulfolobus islandicus rod-shaped virus 2, also referred to as SIRV2, is an archaeal virus whose only known host is the archaeon ''Sulfolobus islandicus''. This virus belongs to the family ''Rudiviridae.'' Like other viruses in the family, it is c ...
(SIRV2) * ''Icerudivirus SIRV3'' ''Icerudivirus'' was previously named ''Rudivirus'' but was renamed in 2020.


Discovery

SIRV1 and SIRV2 were produced by colony-cloned ''
Sulfolobus islandicus ''Sulfolobus'' is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain. ''Sulfolobus'' species grow in volcanic springs with optimal growth occurring at pH 2-3 and temperatures of 75-80 °C, making them ...
'' strains. The two strains were isolated from samples taken in 1994 from different
solfataric A fumarole (or fumerole) is a vent in the surface of the Earth or other rocky planet from which hot volcanic gases and vapors are emitted, without any accompanying liquids or solids. Fumaroles are characteristic of the late stages of volcani ...
fields in
Iceland Iceland ( is, Ísland; ) is a Nordic island country in the North Atlantic Ocean and in the Arctic Ocean. Iceland is the most sparsely populated country in Europe. Iceland's capital and largest city is Reykjavík, which (along with its s ...
, the
Kverkfjöll Kverkfjöll (; 1,764 m) is a mountain range situated on the north-eastern border of the glacier Vatnajökull in Iceland. With the glacier Kverkjökull, it is between the Vatnajökull glacier and the Dyngjufjöll mountains. The mountains are act ...
and
Hveragerði Hveragerði (, "hot-spring yard") is a town and municipality in the south of Iceland, 45 km east of Reykjavík on Iceland's main ringroad, Route 1 (Iceland), Route 1. The river Varmá runs through the town. Overview The surrounding area ...
, which are separated by a distance of 250 km. These Icelandic solfataric acidic hot springs reach a temperature of 88 °C and pH 2.5.


Structure

Virions are non-enveloped, consisting of a tube-like
superhelix A superhelix is a molecular structure in which a helix is itself coiled into a helix. This is significant to both proteins and genetic material, such as overwound circular DNA. The earliest significant reference in molecular biology is from 1971 ...
formed by dsDNA and the major structural protein, with plugs at each end to which three tail fibers are anchored. These tail fibers appear to be involved in
adsorption Adsorption is the adhesion of atoms, ions or molecules from a gas, liquid or dissolved solid to a surface. This process creates a film of the ''adsorbate'' on the surface of the ''adsorbent''. This process differs from absorption, in which a f ...
onto the host cell surface and are formed by one of the minor structural proteins. SIRV1 and SIRV2 are stiff rods of about 23 nm in width, but differing in length—SIRV1 is about 830 nm and SIRV2 is about 900 nm long. They present a central channel of approx. 6 nm that encapsidates the DNA genome. At each terminus of the rod there is a plug of approx. 48 nm in length and 6 nm in diameter that fills the terminal portion of the cavity, together with three tail fibres of approx. 28 nm in length. A three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution has been obtained by cryo–electron microscopy. The structure revealed a previously unknown form of virion organization, in which the alpha-helical major capsid protein of SIRV2 wraps around the DNA, making it inaccessible to solvent. The viral DNA was found to be entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments.


Genome

The genome is composed of linear dsDNA and ranges from 24 kb (ARV1) to 35 kb (SIRV2). The two strands of the linear genomes are covalently linked and, at both ends of the genome, there are inverted terminal repeats. The ''
Sulfolobus ''Sulfolobus'' is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain. ''Sulfolobus'' species grow in volcanic springs with optimal growth occurring at pH 2-3 and temperatures of 75-80 °C, making them ...
'' rudiviruses size up to 32.3 kbp for SIRV1 and 35.8 kbp for SIRV2, with inverted terminal repeats of 2029 bp at the ends of the linear genome. The
G+C content G, or g, is the seventh letter in the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is ''gee'' (pronounced ), plural ''gees''. History The ...
of both genomes is extremely low, of only 25%, whereas the genome of ''
Sulfolobus solfataricus ''Saccharolobus solfataricus'' is a species of thermophilic archaeon. It was transferred from the genus ''Sulfolobus'' to the new genus ''Saccharolobus'' with the description of Saccharolobus caldissimus in 2018. It was first isolated and disco ...
'' (the sequenced genome closest to the virus host) hits 37%. Although the sequences of the inverted terminal repeats of the rudiviruses are different, they all carry the motif AATTTAGGAATTTAGGAATTT near the genome ends, which may constitute a signal for the
Holliday junction A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the ju ...
resolvase and
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
.


Transcriptional patterns and transcription regulation

The
transcriptional Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules calle ...
patterns of SIRV1 and SIRV2 are relatively simple, with few temporal expression differences. In contrast, at least 10% of its genes were predicted to have of different DNA binding motifs in the proteins they code and were assigned to be putative
transcriptional regulators Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...
. A high proportion of viral genes coding for
DNA binding protein DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, becaus ...
s with the ribbon-helix-helix (RHH) DNA binding motifs has been suggested. The abundance of genes coding for proteins belonging to the RHH superfamily present in the genomes of crenarchaea and their viruses could underline the important role of these proteins in host and viral gene
transcription regulation In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from alt ...
under harsh conditions. Protein SvtR was the first crenarchaeal RHH regulator characterized in details and also the first viral coded
transcriptional regulators Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...
within the
Archaeal Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...
domain. It strongly represses the transcription of the minor structural protein and, to a lesser extent, of its own gene. The structure is very similar to that of bacterial RHH proteins despite the low sequence similarity, such as CopG, a bacterial plasmid copy number control regulator. A ''Sulfolobus islandicus'' coded transcription activator, Sta1, has also been shown to activate transcription of several viral genes.


Viral life cycle

SIRV2 recognizes its host by binding to type 4 pili abundantly present on the cell surface. The virus initially binds to the tip of the pilus and subsequently advances along the pilus to the cell surface, where the virion disassembles and the SIRV2 genome is internalized by an unknown mechanism. SIRV2 is a
lytic The lytic cycle ( ) is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteri ...
virus that kills the host cell as a consequence of elaborated mechanisms orchestrated by the virus. Massive degradation of the host
chromosomes A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
occurs because of virus infection and virion assembly occurs in the
cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...
. Virions are released from the host cell through a mechanism that involves the formation of specific cellular structures.


Potential applications in nanotechnology

SIRV2 can act as a template for site-selective and spatially controlled chemical modification. Both the ends and the body of the virus, or the ends only, can be chemically addressed, thus SIRV2 can be regarded as a structurally unique nanobuilding block.Steinmetz, N.F., Bize, A., Findlay, K.C., Lomonossoff, G.P., Manchester, M., Evans, D.J. and Prangishvili, D. (2008) Site-specific and spatially controlled addressability of a new viral nanobuilding block: S''ulfolobus islandicus'' rod-shaped virus 2. Adv. Funct. Mater. 18, 3478–3486


References


External links

{{Taxonbar, from=Q1807886 Virus genera