Biology:Giant virus

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Short description: Very large DNA virus

A giant virus, sometimes referred to as a girus, is a very large virus, some of which are larger than typical bacteria.[1][2] All known giant viruses belong to the phylum Nucleocytoviricota.[3]

Description

While the exact criteria as defined in the scientific literature vary, giant viruses are generally described as viruses having large, pseudo-icosahedral capsids (200 to 400 nanometers in diameter)[4] that may be surrounded by a thick (approximately 100 nm) layer of filamentous protein fibers. The viruses have large, double-stranded DNA genomes (300 to >1000 kilobasepairs) that encode a large contingent of genes (of the order of 1000 genes).[3][5] The best characterized giant viruses are the phylogenetically related mimivirus and megavirus, which belong to the family Mimiviridae (aka Megaviridae), and are distinguished by their large capsid diameters.[3][5] Giant viruses from the deep ocean, terrestrial sources, and human patients contain genes encoding cytochrome P450 (CYP; P450) enzymes. The origin of these P450 genes in giant viruses remains unknown but may have been acquired from an ancient host.[6]

The genomes of many giant viruses encode many unusual genes that are not found in other viruses, including genes involved in glycolysis and the TCA cycle,[7] fermentation,[8] and the cytoskeleton.[9][10][11]

Cryo-EM images of the giant viruses CroV and APMV. (A) Cryo-electron micrograph of four CroV particles. (B) Single CroV particle with concave core depression (white arrow). (C) Single APMV particle. Scale bars in (A–C) represent 2,000 Å.
Phylogeny of Nucleocytoviricota [12]

History

The first giant viruses to be described were chloroviruses of the family Phycodnaviridae. These were discovered in 1981 by Russel H. Meints, James L. Van Etten, Daniel Kuczmarski, Kit Lee, and Barbara Ang. The first chlorovirus was initially called HVCV (Hydra viridis Chlorella virus) since it was first found to infect Chlorella-like algae.[13][14]

Other giant viruses that infected marine flagellates were described later. The first mimivirus (BV-PW1) was described in 1995,[15] but was not recognized as such until its sequenced genome was released as Cafeteria roenbergensis virus (CroV) in 2010.[16] Subsequently, the Giant Virus Acanthamoeba polyphaga Mimivirus was characterized[17] (which had been mistaken as a bacterium in 1993),[18] and then sequenced.[19] The term "girus" was coined to refer to the group in 2006.[20]

Genetics and evolution

The genomes of giant viruses are the largest known for viruses, and contain genes that encode for important elements of translation machinery, a characteristic that had previously been believed to be indicative of cellular organisms. These genes include multiple genes encoding a number of aminoacyl tRNA synthetases, enzymes that catalyze the esterification of specific amino acids or their precursors to their corresponding cognate tRNAs to form an aminoacyl tRNA that is then used during translation.[5] The presence of four aminoacyl tRNA synthetase encoding genes in mimivirus and mamavirus genomes, both species within the Mimiviridae family, as well as the discovery of seven aminoacyl tRNA synthetase genes in the megavirus genome (including those in Mimiviridae) provide evidence that these large DNA viruses may have evolved from a shared cellular genome ancestor by means of genome reduction.[5]

The discovery and subsequent characterization of giant viruses has triggered debate on their evolutionary origins. The two main hypotheses are that they evolved from small viruses by picking up DNA from host organisms; or that they evolved from very complicated organisms via genome reduction, losing various functions including self-reproduction.[21] The possible complicated ancestral organism is also a topic of debate: by one proposal, it might represent a fourth domain of life,[5] but this has been largely discounted.[22][23][24]

Comparison of largest known giant viruses

Largest giant viruses with complete sequenced genomes (As of March 2015)
Giant virus name Genome Length Genes Capsid diameter (nm) Hair cover Genbank #
Bodo saltans virus[25] 1,385,869 1227 proteins (predicted) ~300 yes (~40 nm) MF782455
Megavirus chilensis[26] 1,259,197 1120 proteins (predicted) 440 yes (75 nm) JN258408
Mamavirus[27] 1,191,693 1023 proteins (predicted) 500 yes (120 nm) JF801956
Mimivirus[19][28] 1,181,549 979 proteins 39 non-coding 500 yes (120 nm) NC_014649
M4[29] (Mimivirus "bald" variant) 981,813 756 proteins (predicted) 390 No JN036606
Tupanvirus[30] 1,500,000 1276–1425 proteins ≥450+550[31] KY523104
MF405918[32]
Cafeteria roenbergensis virus[33] 617,453 (730 kb) 544 proteins (predicted) 300 No NC_014637

The whole list is in the Giant Virus Toplist created by the Giant Virus Finder software.[34] As of June 11, 2018, there were 183 listed.[35]

Specific common features among giant viruses
Giant virus name Aminoacyl-tRNA synthetase Octocoral-like 1MutS 2Stargate[36] Known virophage[37] Cytoplasmic virion factory Host
Megavirus chilensis 7 (Tyr, Arg, Met, Cys, Trp, Asn, Ile) yes yes no yes Acanthamoeba (Unikonta, Amoebozoa)
Mamavirus 4 (Tyr, Arg, Met, Cys) yes yes yes yes Acanthamoeba (Unikonta, Amoebozoa)
Mimivirus 4 (Tyr, Arg, Met, Cys) yes yes yes yes Acanthamoeba (Unikonta, Amoebozoa)
M4 (Mimivirus "bald" variant) 3 (Met, Cys, Arg) yes yes Resistant yes Acanthamoeba (Unikonta, Amoebozoa)
Cafeteria roenbergensis virus 1 (Ile) yes no yes yes Phagotrophic protozoan (Heterokonta, Stramenopiles)

1Mutator S (MutS) and its homologs are a family of DNA mismatch repair proteins involved in the mismatch repair system that acts to correct point mutations or small insertion/deletion loops produced during DNA replication, increasing the fidelity of replication. 2A stargate is a five-pronged star structure present on the viral capsid forming the portal through which the internal core of the particle is delivered to the host's cytoplasm.

See also

References

  1. ↑ Reynolds, Kelly A. (2010). "Mysterious Microbe in Water Challenges the Very Definition of a Virus". Water Conditioning & Purification. http://www.wcponline.com/pdf/June_OnTap.pdf. 
  2. ↑ "Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus". Virology Journal 6 (178): 178. October 2009. doi:10.1186/1743-422X-6-178. PMID 19860921. 
  3. ↑ 3.0 3.1 3.2 Van Etten, James L. (July–August 2011). "Giant Viruses". American Scientist 99 (4): 304–311. doi:10.1511/2011.91.304. http://www.americanscientist.org/issues/feature/2011/4/giant-viruses. 
  4. ↑ "Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses". Scientific Reports 7 (5484): 5484. 14 July 2017. doi:10.1038/s41598-017-05824-w. PMID 28710447. Bibcode: 2017NatSR...7.5484X. 
  5. ↑ 5.0 5.1 5.2 5.3 5.4 "Genomics of Megavirus and the elusive fourth domain of Life". Communicative & Integrative Biology 5 (1): 102–6. January 2012. doi:10.4161/cib.18624. PMID 22482024. 
  6. ↑ "On the occurrence of cytochrome P450 in viruses". Proceedings of the National Academy of Sciences of the United States of America 116 (25): 12343–12352. June 2019. doi:10.1073/pnas.1901080116. PMID 31167942. Bibcode: 2019PNAS..11612343L. 
  7. ↑ "Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses". Nature Communications 11 (1710): 1710. 2020. doi:10.1038/s41467-020-15507-2. PMID 32249765. Bibcode: 2020NatCo..11.1710M. 
  8. ↑ "A giant virus infecting green algae encodes key fermentation genes". Virology 518: 423–433. 2018. doi:10.1016/j.virol.2018.03.010. PMID 29649682. 
  9. ↑ "Giant viruses encode novel types of actins possibly related to the origin of eukaryotic actin: the viractins". bioRxiv. 2020. doi:10.1101/2020.06.16.150565. 
  10. ↑ "High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System". mSystems 6 (4): e0029321. 2021. doi:10.1128/mSystems.00293-21. PMID 34254826. 
  11. ↑ "Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton". Frontiers in Microbiology 12: 683294. 7 June 2021. doi:10.3389/fmicb.2021.683294. PMID 34163457. 
  12. ↑ "A phylogenomic framework for charting the diversity and evolution of giant viruses". PLOS Biology 19 (10): e3001430. 2021. doi:10.1371/journal.pbio.3001430. PMID 34705818. 
  13. ↑ Meints, Russel H.; Van Etten, James L.; Kuczmarski, Daniel; Lee, Kit; Ang, Barbara (September 1981). "Viral infection of the symbiotic chlorella-like alga present in Hydra viridis". Virology 113 (2): 698–703. doi:10.1016/0042-6822(81)90198-7. PMID 18635088. 
  14. ↑ Hoshina, Ryo; Shimizu, Mayumi; Makino, Yoichi; Haruyama, Yoshihiro; Ueda, Shin-ichiro; Kato, Yutaka; Kasahara, Masahiro; Ono, Bun-ichiro et al. (13 September 2010). "Isolation and characterization of a virus (CvV-BW1) that infects symbiotic algae of Paramecium bursaria in Lake Biwa, Japan" (in en). Virology Journal 7: 222. doi:10.1186/1743-422X-7-222. ISSN 1743-422X. PMID 20831832. 
  15. ↑ Garza, D. Randy; Suttle, Curtis A. (1995-12-31). "Large double-stranded DNA viruses which cause the lysis of a marine heterotrophic nanoflagellate (Bodo sp) occur in natural marine viral communities". Aquatic Microbial Ecology 9 (3): 133–144. doi:10.3354/ame009203. https://www.int-res.com/articles/ame/9/a009p203.pdf. 
  16. ↑ Fischer, M. G.; Allen, M. J.; Wilson, W. H.; Suttle, C. A. (2010). "Giant virus with a remarkable complement of genes infects marine zooplankton". Proceedings of the National Academy of Sciences 107 (45): 19508–13. doi:10.1073/pnas.1007615107. PMID 20974979. PMC 2984142. Bibcode: 2010PNAS..10719508F. http://pubman.mpdl.mpg.de/pubman/item/escidoc:2272841/component/escidoc:2272838/PNAS_107_2010_19508.pdf. 
  17. ↑ "A giant virus in amoebae". Science 299 (5615): 2033. 2003. doi:10.1126/science.1081867. PMID 12663918. 
  18. ↑ "Giant Viruses" (in en). 2017-02-06. https://www.americanscientist.org/article/giant-viruses. 
  19. ↑ 19.0 19.1 "The 1.2-megabase genome sequence of Mimivirus". Science 306 (5700): 1344–50. November 2004. doi:10.1126/science.1101485. PMID 15486256. Bibcode: 2004Sci...306.1344R. 
  20. ↑ Claverie, Jean-Michel; Ogata, Hiroyuki; Audic, Stéphane; Abergel, Chantal; Suhre, Karsten; Fournier, Pierre-Edouard (April 2006). "Mimivirus and the emerging concept of "giant" virus". Virus Research 117 (1): 133–144. doi:10.1016/j.virusres.2006.01.008. PMID 16469402. https://arxiv.org/ftp/q-bio/papers/0506/0506007.pdf. 
  21. ↑ Bichell, Rae Ellen. "In Giant Virus Genes, Hints About Their Mysterious Origin". All Things Considered. https://www.npr.org/sections/health-shots/2017/04/06/522478901/in-giant-virus-genes-hints-about-their-mysterious-origin. 
  22. ↑ "Giant viruses with an expanded complement of translation system components". Science 356 (6333): 82–85. April 2017. doi:10.1126/science.aal4657. PMID 28386012. Bibcode: 2017Sci...356...82S. https://escholarship.org/content/qt0kf9t6gn/qt0kf9t6gn.pdf?t=oruwia. 
  23. ↑ "Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism". mBio 10 (2): e02497-02418. March 2019. doi:10.1128/mBio.02497-18. PMID 30837339. 
  24. ↑ "Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life". Virology 466–467 (2014): 38–52. 2014. doi:10.1016/j.virol.2014.06.032. PMID 25042053. 
  25. ↑ "The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea". eLife 7: e33014. March 2018. doi:10.7554/eLife.33014. PMID 29582753. 
  26. ↑ "Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae". Proceedings of the National Academy of Sciences of the United States of America 108 (42): 17486–91. October 2011. doi:10.1073/pnas.1110889108. PMID 21987820. Bibcode: 2011PNAS..10817486A. 
  27. ↑ "Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes". Genome Biology and Evolution 3: 737–42. 2011. doi:10.1093/gbe/evr048. PMID 21705471. 
  28. ↑ "Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing". Virology Journal 8 (1): 99. March 2011. doi:10.1186/1743-422X-8-99. PMID 21375749. 
  29. ↑ Boyer, M.; Azza, S.; Barrassi, L.; Klose, T.; Campocasso, A.; Pagnier, I.; Fournous, G.; Borg, A. et al. (2011). "Mimivirus shows dramatic genome reduction after intraamoebal culture". Proceedings of the National Academy of Sciences 108 (25): 10296–301. doi:10.1073/pnas.1101118108. PMID 21646533. Bibcode: 2011PNAS..10810296B. 
  30. ↑ "Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere". Nature Communications 9 (1): 749. February 2018. doi:10.1038/s41467-018-03168-1. PMID 29487281. Bibcode: 2018NatCo...9..749A. 
  31. ↑ head and tail, respectively
  32. ↑ soda lake and deep ocean species of Tupanvirues, respectively
  33. ↑ Fischer, M. G.; Allen, M. J.; Wilson, W. H.; Suttle, C. A. (2010). "Giant virus with a remarkable complement of genes infects marine zooplankton". Proceedings of the National Academy of Sciences 107 (45): 19508–13. doi:10.1073/pnas.1007615107. PMID 20974979. PMC 2984142. Bibcode: 2010PNAS..10719508F. http://pubman.mpdl.mpg.de/pubman/item/escidoc:2272841/component/escidoc:2272838/PNAS_107_2010_19508.pdf. 
  34. ↑ "Giant Virus Toplist". PIT Bioinformatics Group, Department of Computer Science. Eötvös University. 2015-03-26. http://pitgroup.org/giant-virus-toplist/. 
  35. ↑ "Giant Virus Toplist". PIT Bioinformatics Group. 26 March 2015. https://pitgroup.org/giant-virus-toplist/. 
  36. ↑ Sugden, Bill, ed (May 2008). "Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus". PLOS Biology 6 (5): e114. doi:10.1371/journal.pbio.0060114. PMID 18479185. 
  37. ↑ "A virophage at the origin of large DNA transposons". Science 332 (6026): 231–4. April 2011. doi:10.1126/science.1199412. PMID 21385722. Bibcode: 2011Sci...332..231F. 



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