Coccolithovirus

Coccolithovirus
Systematics
Classification : Viruses Area : Varidnaviria Empire : Bamfordvirae Phylum : Nucleocytoviricota Class : Megaviricetes Order : Algavirales Family : Phycodnaviridae Genre : Coccolithovirus Type : Emiliania huxleyi virus 86
Taxonomic characteristics
Genome : dsDNA linear Baltimore : Group 1 Symmetry : icosahedral Cover : available
Scientific name
Coccolithovirus
Short name
EhV-86
Left
NCBI  Taxonomy: 346673 ViralZone ( ExPASy , SIB): 589

Coccolithovirus is a kind of double-stranded DNA - Giant viruses in the family phycodnaviridae . Algae , especially Emiliania huxleyi , a species of the Isochrysidales (together with the Coccolithales, sometimes referred to as Coccolithophorida or English as Coccolithophores )serve as natural hosts.

As of March 2019, there is only one species in this genus that has been confirmed by the International Committee on Taxonomy of Viruses (ICTV), the Emiliania huxleyi virus 86 (EhV-86). As a genus of DNA giant viruses, Coccolithovirus is assigned to the Phylum Nucleocytoviricota (outdated Nucleocytoplasmic large DNA viruses , NCLDV).

construction

Coccolithoviruses are enveloped, icosahedral and have a diameter in the range of 100–220 nm . Their genome is linear with a size of 410-415 kilobases . That means your DNA should code for around 472 proteins .

Propagation cycle

The giant viruses of NCLDV either replicate exclusively in the cytoplasm of the host cell or begin their life cycle in the host nucleus , but complete it in the cytoplasm. In the case of EhV-86, the infection strategy is not fully understood, but Mackinder et al. proposed the following model in 2009:

The virus enters the host cell by endocytosis , followed by the fusion of the lipid membrane of the virus with the vacuole membrane of the host and the release of the virus nucleoprotein core into the cytoplasm. Alternatively, the virus membrane could fuse directly with the host plasma membrane. The viral genome is then released from the capsid into the nucleus, where it is replicated by the viral DNA polymerase . The replicated genome is packed into assembled capsids in the cytoplasm, and the newly formed (about 400–1000) virions (virus particles) are transported to the plasma membrane and released by a controlled budding mechanism (en .: budding , see also Rabiesvirus §Replication ), which leads to the Host cell disintegration leads.

As is known, E. huxleyi can cause seasonal algal blooms that can reach 250,000 km², with the cell density in the upper 200 m increasing from 10 ³ to 10 ⁵ cells per ml of seawater. This algal bloom usually collapses after 5–8 days. Several studies have shown that algal bloom breakdown is intrinsically related to coccolithovirus infection.

The virus is transmitted between the algae hosts by passive diffusion. In addition, EhV-DNA was also found in copepods , which suggests that virus-carrying zooplankton contributes to an increased spread of the viruses.

Genome

Between 1999 and 2008 alone, 14 EhV strains were isolated mainly from the English Channel , but also from the Norwegian and Scottish coasts.

Although partial sequences of all of these 14 strains are available due to the highly repetitive nature of the genome, EhV-86 is the only strain that has been fully sequenced and officially recognized as a species by the ICTV (as of March 2019).

The sequencing of EhV-86 revealed a circular genome with a length of 407,339 bp with a GC content of 40.2% and a predicted 472 coding sequences (CDS, corresponds approximately to: genes). Remarkably, 80% of these putative genes do not have any database - homologues . Functions that could be assigned a function based on sequence similarity or matches with the protein domain include DNA and RNA polymerase subunits, eight proteases, and at least four genes that code for proteins involved in sphingolipid biosynthesis. It has been shown that these were obtained from the host by horizontal gene transfer .

Systematics

Internal system

In addition to the species Emiliania huxleyi virus 86 confirmed by the International Committee on Taxonomy of Viruses (ICTV), a number of other species, such as Emiliania huxleyi virus 145 , have been proposed. In total, the NCBI names more than 17 proposed members of the genre:

• Species Emiliania huxleyi virus 86 (EhV-86, ICTV-confirmed)
• Species Emiliania huxleyi virus 18 (EhV-18)
• Species Emiliania huxleyi virus 84 (EhV-84)
• Species Emiliania huxleyi virus 88 (EhV-88)
• Species Emiliania huxleyi virus 99B1 (EhV-99B1)
• Species Emiliania huxleyi virus 145 (EhV-145)
• Species Emiliania huxleyi virus 156 (EhV-156)
• Species Emiliania huxleyi virus 163 (EhV-163)
• Species Emiliania huxleyi virus 164 (EhV-164)
• Species Emiliania huxleyi virus 201 (EhV-201)
• Species Emiliania huxleyi virus 202 (EhV-202)
• Species Emiliania huxleyi virus 203 (EhV-203)
• Species Emiliania huxleyi virus 204 (EhV-204)
• Species Emiliania huxleyi virus 205 (EhV-205)
• Species Emiliania huxleyi virus 206 (EhV-2061)
• Species Emiliania huxleyi virus 207 (EhV-207)
• Species Emiliania huxleyi virus 208 (EhV-208)
• Species Emiliania huxleyi virus 209 (EhV-209)
• Species Emiliania huxleyi virus V2 (EhV-V2)

Phylogenetic relationships according to Guglielmini et al. (2019), Fig. 2:

Coccolithovirus	Emiliania huxleyi virus 202     Emiliania huxleyi virus 99B1     Emiliania huxleyi virus 86     Emiliania huxleyi virus 88

External system

The following system follows Schulz et al. , (2018) expanded (and slightly corrected) after Hao et al. (2018), agrees with Guglielmini et al. (2019):

Phycodnaviridae	Chlorovirus type  Chlorovirus    Yellowstone Lake Phycodnavirus 1 , 2 , 3    Dishui Lake Phycodnavirus     Prasinovirus    Phaeovirus     Mollivirus     Pandora virus     " Sylvan virus "  Coccolithovirinae  Coccolithovirus

Koonin and Yutin (2018) give a different account. The Phycodnaviridae are no longer monophyletic here, in particular Raphidovirus with HaV occupies an intermediate position between the two branches of the remaining Phycodnaviridae and the extended Mimiviridae , without themselves - unlike the "OLPG" members, AaV and TetV-1 - belonging to these:

Phycodnaviridae - Mimiviridae clade

Chlorovirus type  Chlorovirus        Yellowstone Lake Phycodnavirus 1 , 2     Yellowstone Lake Phycodnavirus 3     Dishui Lake Phycodnavirus     Prasinovirus  Coccolitho- Phaeovirus type  Phaeovirus     Mollivirus     Pandora virus  Coccolithovirinae  Coccolithovirus  Raphidovirus  Heterosigma akashiwo virus 01  extended Mimiviridae  s. l.  (conventional)  Mimiviridae  s. s. ( Megamimivirinae , toilet viruses , cafeteria viruses )  Mesomimivirinae  " OLPG "     Aureococcus anophagefferens virus     Tetraselmis virus 1

The second scenario would allow the Mollivirus clade as proposed as the Molliviridae family , and the Pandoraviruses as proposed as “ Pandoraviridae ” as well. The Chlorovirus clade would be Phycodnaviridae s. s. . Using the names introduced by ICTV in March 2020 with the Master Species List # 35, 'extended Mimiviridae ' can be replaced by the order Imitervirales and the ' Phycodnaviridae - Mimiviridae clade' by the class Megaviricetes in the above cladogram . This fits in with a suggestion by Filée (2018) that the Mimiviridae extension - classified here as the subfamily Mesomimivirinae - should instead be elevated to the rank of a family as Mesomomoviridae . This would then be the sister taxon of the Mimiviridae .

Another alternative view can be found in Johannessen et al. (2015), Fig. S2.

Research history

Willie H. Wilson et al. at the University of East Anglia's Marine Biological Association (MBA) and the Plymouth Marine Laboratory (PML) first observed the virus in 1999. In the summer of 2005, researchers at the Plymouth Marine Laboratory (again Willie Wilson et al. ) and the Sanger Institute examined (MTG Holden et al. ) Sequenced the genome for the EhV-86 strain and found 472 protein genes. According to the genome, EhV-86 is therefore a giant virus and the largest marine virus known to date.

When the coccolithovirus genome was first examined, a gene sequence was discovered that is responsible for the production of ceramide . Ceramide is a controlling factor for cell death (apoptosis). Coccolithovirus is believed to prolong the life of Emiliania huxleyi while it uses the host cell to replicate. This is a unique ability not previously seen in any other viral genome.

See also

• Mimivirus - the most prominent giant virus
• Mycoplasma genitalium , Pelagibacter ubique - some of the smallest bacteria known
• Nanoarchaeum - the smallest of the known archaea
• Parvovirus - the smallest known virus

Individual evidence

1. ↑ ^{a b c d e} ICTV: ICTV Master Species List 2019.v1 , New MSL including all taxa updates since the 2018b release, March 2020 (MSL # 35)
2. ^ Jean-Michel Claverie: Giant viruses in the oceans: the 4th Algal Virus Workshop In: Virology Journal. 2005.
3. ↑ Sanger institute home for Emiliania huxleyi virus 86 ( Memento of the original from June 14, 2006 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. 
4. ↑ Giantviruses.org top viruses by genome size
5. ↑ ^{a b} Plymouth Marine Laboratory press release
6. ↑ Niyaz Yoosuf, Natalya Yutin, Philippe Colson, Svetlana A. Shabalina, Isabelle Pagnier, Catherine Robert, Said Azza, Thomas Klose, Jimson Wong, Michael G. Rossmann, Bernard La Scola, Didier Raoult, Eugene V. Koonin: Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage , in: Genome Biol Evol. 4 (12), December 4, 2012, pp. 1324-1330, doi: 10.1093 / gbe / evs109 , PMC 3542560 (free full text), PMID 23221609
7. ↑ ^{a b} Viral Zone. ExPASy, accessed December 19, 2015 . 
8. ^ ICTV: Virus Taxonomy. Retrieved December 19, 2018 . 
9. ↑ ^{a b} ICTV Master Species List 2018b.v2
10. ↑ LCM Mackinder, CA Worthy, G. Biggi, M. Hall, KP Ryan, A. Varsani, GM Harper, WH Wilson, C. Brownlee, DC Schroeder: A unicellular algal virus, Emilienia huxleyi virus 86, exploits an animal-like infection strategy. In: Journal of general Virology. 90, 2009, pp. 2306-2316.
11. ↑ DC Schroeder, J. Oke, M. Hall, G. Malin, WH Wilson: Viral succession observed during an Emilinaia huxleyi bloom. In: Applied and Environmental Microbiology. 69, 2003, pp. 2484-2490, PMC 154549 (free full text).
12. ↑ WH Wilson, GA Tarran, D. Schroeder, M. Cox, J. Oke, G. Malin: isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel. In: Journal of the Marine Biological Association of the United Kingdom. 82, 2002, pp. 369-377.
13. ↑ MJ Frada, D. Schatz, V. Farstey, JE Ossolinski, H. Sabanay, S. Ben-Dor, I. Koren, A. Vardi: Zooplankton May Serve as Transmission Vectors for Viruses Infecting Algal Blooms in the Ocean. In: Current Biology. 24, 2014, pp. 2592-2597.
14. Jump up ↑ JI Nissimov, JA Napier, SA Kimmance, MJ Allen: Permanent draft genomes of four new coccolithoviruses: EhV-18, EhV-145, EhV-156 and EhV-164. In: Marine Genomics. 15, 2014, pp. 7-8.
15. ↑ JI Nissimov, CA Worthy, P. Rooks, JA Napier, SA Kimmance, MR Henn, H. Ogata, MJ Allen: Draft genome sequence of the Coccolithovirus EhV-84. In: Standards in Genomic Science. 5, 2011, pp. 1-11.
16. ↑ JI Nissimov, CA Worthy, P. Rooks, JA Napier, SA Kimmance, MR Henn, H. Ogata, MJ Allen: Draft Genome Sequence of Four Coccolithop Viruses: Emiliania huxleyi Virus EhV-88, EhV-201, EhV-207 and EhV -208. In: Journal of Virology , 86 (5), 2012, pp. 2896-2897, PMC 3302265 (free full text).
17. ↑ JI Nissimov, CA Worthy, P. Rooks, JA Napier, SA Kimmance, MR Henn, H. Ogata, MJ Allen: Draft Genome Sequence of the Coccolithopvirus Emiliania huxleyi Virus 202. In: Journal of Virology. 86 (4), 2012, pp. 380-2381.
18. ↑ JI Nissimov, CA Worthy, P. Rooks, JA Napier, SA Kimmance, MR Henn, H. Ogata, MJ Allen: Draft Genomic Sequence of the Coccolithovirus Emiliania huxleyi Virus 203. In: Journal of Virology , 85 (24), 2011 , Pp. 13468-13469, PMC 3233127 (free full text).
19. ^ WH Wilson, DC Schroeder, MJ Allen, MTG Holden, J. Parkhill, BG Barrell, C. Churcher, N. Hamlin, K. Mungall, H. Norbertczak, MA Quail, C. Price, E. Rabbinowitsch, D. Walker , M. Craigon, D. Roy, P. Ghazal: Complete Genome Sequence and Lytic Phase Transcription Profile of a Coccolithovirus. In: Science. Volume 309, Issue 5737, 2005, pp. 1090-1092. doi: 10.1126 / science.1113109
20. ↑ David M. Needham, Alexandra Z. Worden et al .: A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators , in: PNAS, 23 September 2019, doi: 10.1073 / pnas.1907517116 , ISSN  0027-8424 , here: Supplement 1 (xlsx)
21. ↑ A. Monier, A. Pagarete, C. De Vargas, MJ Allen, B. Read, J. Claverie, H. Ogata, C. De Vargas: Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus . In: Genome Research. 19, 2009, pp. 1441-1449.
22. ↑ Jean-Michel Claverie, Chantal Abergel: Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes . In: Viruses . 2018 Sep; 10 (9), September 18, 2018, p. 506, doi: 10.3390 / v10090506 , PMC 6163669 (free full text), PMID 30231528 , Tab. 2
23. ↑ Julien Andreani, Jacques YB Khalil, Emeline Baptiste, Issam Hasni, Caroline Michelle, Didier Raoult, Anthony Levasseur, Bernard La Scola: Orpheovirus IHUMI-LCC2: A New Virus among the Giant Viruses , in: Front. Microbiol., January 22, 2018, doi: 10.3389 / fmicb.2017.02643
24. ↑ NCBI: unclassified coccolithovirus (genus)
25. ↑ NCBI: Coccolithovirus (genus)
26. ↑ Graziel Oliveira, Bernard La Scola, Jônatas Abrahão: Giant virus vs amoeba: fight for supremacy , in: Virol J 16, 126, November 4, 2019, doi: 10.1186 / s12985-019-1244-3 , PDF
27. ↑ ^{a b} Julien Guglielmini, Anthony C. Woo, Mart Krupovic, Patrick Forterre, Morgan Gaia: Diversification of giant and large eukaryotic dsDNnA viruses predated the origin of modern eukaryotes , in: PNAS 116 (39), 10./24. September 2019, pp. 19585-19592, doi: 10.1073 / pnas.1912006116 , PMID 31506349 , Fig. 2
28. ↑ Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M. Ryan, Feiqiao B. Yu, Rex R. Malmstrom, Jeffrey Blanchard, Tanja Woyke: Hidden diversity of soil giant viruses , in: Nature Communicationsvolume 9, Article number: 4881 (2018 ) from November 19, 2018, doi: 10.1007 / s00705-016-2853-4
29. ↑ Hao Chen, Weijia Zhang, Xiefei Li, Yingjie Pan, Shuling Yan, Yongjie Wang: The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses , in: BMC Genomics, December 2018, doi: 10.1186 / s12864-018- 4432-4
30. ↑ NCBI: Phycodnaviridae (family)
31. ↑ ^{a b c d} Fumito Maruyama, Shoko Ueki: Evolution and Phylogeny of Large DNA Viruses, Mimiviridae and Phycodnaviridae Including Newly Characterized Heterosigma akashiwo Virus. In: Front. Microbiol. November 30, 2016, doi: 10.3389 / fmicb.2016.01942 , PMC 5127864 (free full text), PMID 27965659 .
32. ^ ^{A b c} Eugene V. Koonin, Natalya Yutin: Multiple evolutionary origins of giant viruses , in: F1000 Research. November 22, 2018, doi: 10.12688 / f1000research.16248.1 , version 1.
33. ^ ^{A b} Michael J. Allen, Declan C. Schroeder, Matthew TG Holden, William H. Wilson: Evolutionary History of the Coccolithoviridae. In: Molecular Biology and Evolution. Volume 23, Issue 1, January 1, 2006, pp. 86-92, doi: 10.1093 / molbev / msj010
34. ↑ New giant virus discovered - virus detected off Hawaii is the largest cell parasite of plant organisms to date, on: scinexx from May 4, 2018
35. ↑ List of the main “giant” viruses known as of today (PDF) Center National de la Recherche Scientifique, Université Aix Marseille, from April 18, 2018.
36. ↑ Chantal Abergel: Giant viruses physiology. March 24, 2017, Laboratoire Information Génomique et Structurale (IGS), Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
37. ↑ Claire Bertelli, Linda Mueller, Vincent Thomas, Trestan Pillonel, Nicolas Jacquier, Gilbert Greub: Cedratvirus lausannensis - digging into Pithoviridae diversity. In: Environmental Microbiology. 19 (10), 2017, pp. 4022-4034, doi: 10.1111 / 1462-2920.13813
38. ↑ Bruno Guigliarelli, Bénédicte Burlat: PhD proposal: Structure and functional role of a new iron-sulfur protein family in giant viruses. (PDF) Ecole Doctorale des Sciences Chimiques ED250, 2017.
39. ↑ Natalya Yutin, Yuri I. Wolf, Eugene V. Koonin: Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. In: Virology , Oct. 0, 2014, pp. 38–52, PMID 25042053 , doi: 10.1016 / j.virol.2014.06.032 , PMC 4325995 (free full text), see Supplement 04
40. ↑ Jonathan Filée: Giant viruses and their mobile genetic elements: the molecular symbiosis hypothesis , in: Current Opinion in Virology, Volume 33, December 2018, pp. 81-88; bioRxiv : 2018/04/11/299784 ( preprint full text)
41. ↑ Torill Vik Johannessen, Gunnar Bratbak, Aud Larsenb, Hiroyuki Ogatac, Elianne S. Egged, Bente Edvardsen, Wenche Eikremd, Ruth-Anne Sandaaa: Characterization of three novel giant viruses reveals huge diversity among viruses infecting Prymnesiales (Haptophyta) , in: Virology , Volume 476, February 2015, pp. 180-188, doi: 10.1016 / j.virol.2014.12.014 , PMID 25546253 , Fig. S2

literature

• MJ Allen, DC Schroeder, MT Holden, WH Wilson: Evolutionary History of the Coccolithoviridae. In: Mol Biol Evol. 23, 2006, pp. 86-92.
• E. Paasche: A review of the coccolithophorid Emiliania huxleyi (Prymnesiophyceae), with particular reference to growth, coccolith formation, and calcification-photosynthesis interactions. In: Phycologia. 40 (6), 2001, pp. 503-552. doi: 10.2216 / i0031-8884-40-6-503.1
• MJ Allen, DC Schroeder, WH Wilson: Preliminary characterization of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi. In: Archives of Virology. 151, 2006, pp. 525-535. doi: 10.1007 / s00705-005-0647-1
• MJ Allen, T. Forster, DC Schroeder, M. Hall, D. Roy, P. Ghazal, WH Wilson: Locus specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. In: Journal of Virology , 80, 2006, pp. 7699-7705, PMC 1563701 (free full text).
• MJ Allen, JA Howard, KS Lilley, WH Wilson: Proteomic analysis of the EhV-86 virion. In: Proteome Science. 6 (11), 2008. doi: 10.1186 / 1477-5956-6-11
• Fumito Maruyama, Shoko Ueki: Evolution and Phylogeny of Large DNA Viruses, Mimiviridae and Phycodnaviridae Including Newly Characterized Heterosigma akashiwo Virus. In: Front. Microbiol. November 30, 2016. doi: 10.3389 / fmicb.2016.01942
• Dickson Kinyanyi, George Obiero, Peris W Amwayi, Stephen Mwaniki, Mark Wamalwa: In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein , in: PeerJ 6 (4): e4396 (2018 ), doi: 10.7717 / peerj.4396 , p. 13, especially Fig. 7
• Weijia Zhang, Jinglie Zhou, Taigang Liu, Yongxin Yu, Yingjie Pan, Shuling Yan, Yongjie Wang: Four novel algal virus genomes discovered from Yellowstone Lake metagenomes , in: Scientific Reports volume 5, Article No. 15131, 2015, doi: 10.1038 / srep15131 , abstract

Web links

• Viral zone : coccolithovirus
• ICTV