Icerudivirus SIRV2 explained

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.^[1] Like other viruses in the family, it is common in geothermal environments.^[1] __TOC__

Biology and biochemistry

SIRV2 has a linear double-stranded DNA genome. The viral DNA is replicated by 4 host DNA polymerases: Dpo1 through Dpo4.

The virus has a rod-shaped morphology with a width of 23 nanometers (nm) and a length of 900 nm. Three terminal fibers, 28 nm in length, have been observed on both ends of the virus.^[2] The terminal fibers mediate attachment of the virus to type 4 pili abundantly present on the host cell surface.^{[3] [4]}

SIRV2 is able to survive additions of 6 molar (M) urea, absolute ethanol, octanol-2, and 0.1% Triton X-100 in neutral pH and 25 degrees Celsius. In vitro testing has shown that SIRV2 is still able to infect at 70-80 degrees Celsius and in a pH 3 solution.^[5]

SIRV2gp19 was found to be a single-stranded DNA endonuclease in 2011. This was proven by inducing a mutation in the SIRVgp19 protein Motif II from the amino acid aspartate to alanine which resulted in a loss of nuclease activity. This protein is functional within pH 7-10. Magnesium chloride was found to be a cofactor to this protein in 1971.^[6] Sodium chloride concentrations above 100 mM inhibit SIRV2gp19.

Structure

A three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution has been obtained by cryo–electron microscopy.^[7] 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 suggested a common mechanism with bacterial spores for protecting DNA in the most adverse environments.

Notes and References

1. Martínez-Alvarez. Laura. Deng. Ling. Peng. Xu. 2017-04-19. Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2. Journal of Virology. 91. 13. 10.1128/jvi.00486-17. 28424282. 5469267. 0022-538X.
2. A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the sulfolobus viruses SIRV1 and SIRV2 . Prangishvili . W.. D. . Arnold . H. P. . Götz . D. . Ziese . U. . Holz . I. . Kristjansson . J. K. . Zillig . Genetics . 1999 . 152 . 4 . 1387–96 . 10.1093/genetics/152.4.1387 . 10430569 . 1460677 . 678661646.
3. Quemin . ER . Lucas . S . Daum . B . Quax . TE . Kühlbrandt . W . Forterre . P . Albers . SV . Prangishvili . D . Krupovic . M . First insights into the entry process of hyperthermophilic archaeal viruses. . Journal of Virology . 2013 . 87 . 24 . 13379–85 . 10.1128/JVI.02742-13 . 24089554. 3838266 .
4. Wang . F . Cvirkaite-Krupovic . V . Kreutzberger . MAB . Su . Z . de Oliveira . GAP . Osinski . T . Sherman . N . DiMaio . F . Wall . JS . Prangishvili . D . Krupovic . M . Egelman . EH . An extensively glycosylated archaeal pilus survives extreme conditions. . Nature Microbiology . 2019 . 4 . 8 . 1401–1410 . 10.1038/s41564-019-0458-x . 31110358. 6656605 .
5. Gardner. Andrew F.. Prangishvili. David. Jack. William E.. 2011-06-11. Characterization of Sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease. Extremophiles. 15. 5. 619–624. 10.1007/s00792-011-0385-0. 21667093. 3158340. 1431-0651.
6. Kushner. S. R.. Nagaishi. H.. Templin. A.. Clark. A. J.. 1971-04-01. Genetic Recombination in Escherichia coli: The Role of Exonuclease I. Proceedings of the National Academy of Sciences. 68. 4. 824–827. 10.1073/pnas.68.4.824. 4927675. 0027-8424. 389052. 1971PNAS...68..824K. free.
7. DiMaio . F . Yu . X . Rensen . E . Krupovic . M . Prangishvili . D . Egelman . EH . Virology. A virus that infects a hyperthermophile encapsidates A-form DNA. . Science . 2015 . 348 . 6237 . 914–7 . 10.1126/science.aaa4181 . 25999507. 5512286 .