Phycodnaviridae

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Phycodnaviridae
MpV-SP1.png

Image (negative) of Micromonas pusilla virus SP1 ,
bp = base pairs ( genome size )

Systematics
Classification : Viruses
Area : Varidnaviria
Empire : Bamfordvirae
Phylum : Nucleocytoviricota
Class : Megaviricetes
Order : Algavirales
Family : Phycodnaviridae
Taxonomic characteristics
Genome : dsDNA
Baltimore : Group 1
Symmetry : icosahedral
Cover : available
Scientific name
Phycodnaviridae
Left
NCBI  Taxonomy: 10501
ViralZone ( ExPASy , SIB): 145

The Phycodnaviruses , scientifically Phycodnaviridae (from the Greek φῦκος phŷkos "(sea) tang", "(red) algae" and DNA ), form a family of large double-stranded DNA viruses with a genome from 160 to 560  Kb . They infect marine and freshwater algae and belong to a phylum of large viruses that was officially confirmed by the International Committee on Taxonomy of Viruses (ICTV) in March as Nucleocytoviricota (obsolete Nucleocytoplasmaviricota or Nucleocytoplasmic large DNA viruses , NCLDV).

Structure and reproduction

Phycodnaviruses have an icosahedral shape, an internal double lipid layer and they multiply in the cytoplasm of the host cell.

Molecular biological characteristics

Recent studies of the Phycodnavirus genomes have found sophisticated mechanisms of viral DNA replication and transcription processes in these viruses , discovered a new type of potassium channels , found genes that are involved in the apoptosis of the host cell and complex signaling pathways, transcription mechanisms and genes for the Glycosylation of viral proteins discovered. All phycodnaviruses have genes that code for DNA polymerases . However, it is not yet clear whether phycodnaviruses can produce a complete replication complex. They probably need host cell support for replication.

Systematics

External system

In older works there is still the designation Megavirales (of the rank of an order ), in terms of scope either for the entire phylum NCLDV or only for the common class (now Megaviricetes ) with the order Imitervirles of the family Mimiviridae . These designations are obsolete with the ICTV Master Species List # 35 from March 2020.

Internal system

According to ICTV, the following genera officially belong to the phycodnaviruses as of November 2018:

  • Phycodnaviridae
  • Chlorovirus with Paramecium bursaria Chlorella virus 1 (PBCV-1), Acanthocystis turfacea chlorella virus 1 (ATCV-1), ...
  • Coccolithovirus with Emiliania huxleyi virus 86 (EhV-86)
  • Phaeovirus with Ectocarpus siliculosus virus 1 (EsV-1), Feldmannia species virus (FsV), ...
  • Prasinovirus with Micromonas pusilla virus SP1 (MpV-SP1) and Ostreococcus tauri virus OtV5 (OTV5)
  • Prymnesiovirus with Chrysochromulina brevifilum virus PW1 (CbV-PW1)
  • Raphidovirus with Heterosigma akashiwo virus 01 (HaV01, also HaV-01, differentiate between: Heterosigma akashiwo RNA virus - HaRNAV and Heterosigma akashiwo nuclear inclusion virus - HaNIV )

Other species of Phycodnaviridae that have not (yet) been confirmed by ICTV have been suggested:

apparently occasionally misspelled as Yellow Lake Phycodnavirus (YLPV)
  • Yellowstone Lake Phycodnavirus 1 , 2 , 3 (YSLPV1, YSLPV2, YSLPV3)
The names Ylpv-A, Ylpv-B in Kinyanyi et al . (2018) apparently refer to YSLPV1, YSLPV2 as mentioned in Hao et al (2018) Fig. 2b.

Cladogram 2018

The following system follows Schulz et al. (2018) and Hao et al. (2018):

 Phycodnaviridae  


 Chlorovirus type 

Chlorovirus


   

"YSLPV1", "YSLPV2", "YSLPV3"


   

"DSLPV1"


   

Prasinovirus





 Phaeovirus clade 

Phaeovirus


   

" Mollivirus "


   

" Pandoravirus "





   

" Sylvan virus "



   

" Coccolithovirus "



Template: Klade / Maintenance / Style

Kladogram 2019

Koonin et al. (2019) and Rolland et al. (2019) show a somewhat modified family tree in comparison:

 Phycodnaviridae  

 Usurpativirus clade 

" Clandestinivirus ST1 "


   

" Usuepativirus LCD7 "



 Chlorovirus type 

Chlorovirus


   

" Yellowstone lake phycodnacvirus 1 "


   

Prasinovirus





   

Raphidovirus


   

Phaeovirus


 Coccolithovirus clade 

Coccolithovirus


   

" Mollivirus sibericum "


   

" Pandoravirus "





Template: Klade / Maintenance / 3

Template: Klade / Maintenance / Style

The species names given by the authors have been replaced by the associated genera for the sake of simplicity. For the clades informally ( ad hoc ) referred to here, there are subfamily names used earlier by other authors, such as “ Chlorovirinae ” alias Phycodnaviruses s. l. (Koonin) and " Coccolithovirinae ".

Summary

What the proposals have in common is that " Mollivirus " and the Pandora viruses represent a common clade of further developed descendants of the Phycodnaviruses. The only difference is their position relative to the coccolitho- and phaeoviruses. In Koonin et al. (2019) the group of Pandora viruses has a common ancestor with the coccolithoviruses within the family Phycodnaviridae . The coccolithoviruses are genetically only largely related to the common clade of chlorovirus and prasinovirus , which, according to Koonin et al. (2019) also applies to raphidovirus .

The new order Algavirales created by ICTV in March 2020 could possibly become a common home for all these candidates, the main groups would then have the rank of independent families.

Regroupings

The genera Prymnesiovirus and Rapidovirus are not shown: According to recent studies, some candidates previously thought to be Phycodnaviridae are more closely related to the Mimiviridae , i.e. they would fall into the order Imitervirales (extended Mimiviridae ) created by the ICTV within the common class Megaviricetes with the Phycodnaviridae . This applies in particular to the group of Organic Lake Phycodnaviruses (" OLPG ") around the genus Organic Lake Phycodnavirus (OLPV), for which it was proposed to assign them as a subfamily Mesomimivirinae to an extended family Mimiviridae .

Affected by this regrouping are: a.

  • probably within the OLPG:
  • Organic Lake Phycodnavirus 1 and 2 (OLPV1, OLPV2)
  • Phaeocystis globosa virus 12 , 14 , 16 (PgV-12T, PgV-14T, PgV-16T) - PgV-16T definitely belongs to a different virus group than PgV-01T (genus Prymnesiovirus )
  • Phaeocystis pouchetii virus (PpV),
  • Yellowstone Lake Phycodnavirus 4 (YSLPV4) aka Yellowstone lake giant virus (YSLGV) or Yellowstone lake mimivirus
  • Species Prymadium kappa virus RF01 and RF02 (PkV-RF01, PkV-RF02)
  • Chrysochromulina ericina virus 01 (CeV, alias Haptolina ericina virus )
  • presumably outside the OLPG:

It is also possible that the genus Raphidovirus (at least the representative Heterosigma akashiwo virus strain HaV53 ) is not part of the Phycodnaviridae , but in a separate clade, possibly together with Aureococcus anophagefferens virus , for example together with the proposed genus " Choanovirus ".

The rank of a subfamily named Mesomimivirinae within an extended family Mimiviridae was originally proposed for the entire group of candidates concerned . More recent proposals raise this group to the rank of a family Mesomoimiviridae , which would be a sister taxon of the Mimiviridae within the new order Imitervirales (replaces the extended Mimiviridae ).

literature

Web links

References and comments

  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. ^ A b Eugene V. Koonin, Natalya Yutin: Evolution of the Large Nucleocytoplasmatic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism , in: Advances in Virus research, Volume 103, AP January 21, 2019, doi: 10.1016 / bs.aivir .2018.09.002 , pp. 167-202. In Fig. 4 phycodnaviruses is to be understood in the narrower sense ( see s. ) And should belong to the chlorovirus / prasinovirus / 'YLPV' group in Schulz et al. (2018).
  3. ↑ ICTV : Master Species List 2018a v1 , MSL # 33 including all taxa updates since the 2017 release. (Fall 2018)
  4. ↑ 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
  5. ↑ 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: Frontiers in Microbiology . 7, November 30, 2016, p. 1942. doi : 10.3389 / fmicb.2016.01942 . PMID 27965659 . PMC 5127864 (free full text).
  6. ↑ Yuji Tomaru, Yoko Shirai, Keizo Nagasaki: Ecology, physiology and genetics of a phycodnavirus infecting the noxious bloom-forming raphidophyte Heterosigma akashiwo . In: Fisheries Science . 74, No. 4, August 1, 2008, ISSN  1444-2906 , pp. 701-711. doi : 10.1111 / j.1444-2906.2008.01580.x .
  7. ↑ Keizo Nagasaki, Kenji Tarutani, Mineo Yamaguchi: Growth Characteristics of Heterosigma akashiwo Virus and Its Possible Use as a Microbiological Agent for Red Tide Control . In: Applied and Environmental Microbiology . 65, No. 3, March 1, 1999, ISSN  0099-2240 , pp. 898-902. PMID 10049839 . PMC 91120 (free full text).
  8. ↑ a b Christopher R. Schvarcz, Grieg F. Steward: A giant virus infecting green algae encodes key fermentation genes , in: Virology, Volume 518, May 2018, pp. 423-433, doi: 10.1016 / j.virol.2018.03. 010
  9. ↑ a b c d e 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, 7:49 pm (online January 15, 2018), doi: 10.1186 / s12864-018-4432-4 : Yellowstone Lake phycodnavirus (YSLPV, Phycodnaviridae ) versus Yellowstone lake giant virus (YSLGV, Mimiviridae ); next to it DSLPV1 ( Phycodnaviridae )
  10. ↑ a b 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) of November 19, 2018, doi : 10.1038 / s41467-018-07335-2
  11. ↑ a b 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 (Ylpv-A, Ylpv-B)
  12. ↑ 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
  13. ↑ a b c Differentiate phycodnaviruses (possibly Mesomimivirinae ) and their virophages :
    • Yellowstone Lake Phycodnavirus (YSLPV) and Yellowstone Lake giant virus (YSLGV, Mimiviridae ) versus Yellowstone Lake Virophages (YSLVs)
    • Dishui Lake Phycodnavirus (DSLPV) versus Dishui Lake Virophages (DSLVs)
    • Organic Lake Phycodnavirus (OLPV) versus Organic Lake Virophages (OLVs)
    • Qinghai Lake Virophage QLV
    See Hao et al . 2018, as well as NCBI: Dishui Lake virophage (species)
  14. ↑ NCBI: Dishui lake phycodnavirus 1 (species)
  15. ↑ An artificial lake in the model city Nanhui New City in the south of Shanghai ( Pudong ), terminus of line 16 of the Shanghai metro .
  16. ↑ The genera Prymnesiovirus (with species Chrysochromulina brevifilum virus PW1 , CbV-PW1) and Raphidovirus (with species Heterosigma akashiwo virus 01 , HaV01) are not considered in this work, Phaevirus in Schulz et al. (2018) can be read as Phaeovirus . YLPV is obviously to be understood as YSLPV, because the spelling Yellow Lake Phycodnavirus (Ylpv-A, Ylpv-B) is otherwise only found in Kinyanyi et al . (2018). According to Hao et al (2018) Fig. 2b, this must mean YSLPV1 and YSLPV2. For clarification see also Zhang et al . (2015)
  17. ↑ Clara Rolland, Julien Andreani, Amina Cherif Louazani, Sarah Aherfi, Rania Francis, Rodrigo Rodrigues, Ludmila Santos Silva, Dehia Sahmi, Said Mougari, Nisrine Chelkha, Meriem Bekliz, Lorena Silva, Felipe Assis, Fábio Dornas, Jacques Yaacoub Bou Khalil, Isabelle Pagnier, Christelle Desnues, Anthony Levasseur, Philippe Colson, Jônatas Abrahão, Bernard La Scola: Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere , in: Viruses 11 (4), March / April 2019, pii: E312, doi: 10.3390 / v11040312 , PMC 6520786 (free full text), PMID 30935049 , Fig. 2a
  18. ↑ 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
  19. ↑ Natalya Yutin, Eugene V. Koonin: Pandoraviruses are highly derived phycodnaviruses . In: Biology Direct . 8, October 2013, p. 25. doi : 10.1186 / 1745-6150-8-25 . PMID 24148757 .
  20. ↑ Jônatas Abrahão, Lorena Silva, Ludmila Santos Silva, Jacques Yaacoub Bou Khalil, Rodrigo Rodrigues, Thalita Arantes, Felipe Assis, Paulo Boratto, Miguel Andrade, Erna Geessien Kroon, Bergmann Ribeiro, Ivan Bergier, Herve Seligmann, Eric Ghigo, Philippe Colson, Anthony Levasseur, Guido Kroemer, Didier Raoult, Bernard La Scola: Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere . In: Nature Communications . 9, No. 1, February 27, 2018. doi : 10.1038 / s41467-018-03168-1 .
  21. ^ A b 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
  22. ↑ NCBI: Phaeocystis pouchetii virus (species)
  23. ↑ Natalya Yutin, Philippe Colson, Didier Raoult, Eugene V Koonin: Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family , in: Virol J. 2013; 10: 106, April 4, 2013, doi: 10.1186 / 1743-422X-10-106 , PMC 3620924 (free full text), PMID 23557328
  24. ↑ 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
  25. ↑ a b c Sailen Barik: A Family of Novel Cyclophilins, Conserved in the Mimivirus Genus of the Giant DNA Viruses , in: Computational and Structural Biotechnology Journal, Volume 16, July 2018, pp. 231-236, doi: 10.1016 / j. csbj.2018.07.001
  26. ↑ NCBI: Yellowstone lake mimivirus (species)
  27. ↑ Differentiate between the proposed Yellowstone Lake Virophages (YSLVs) and the unrelated, not further classified Yellowstone hot spring archaeal RNA virus (species)
  28. ↑ NCBI: Prymadium kappa virus (species)
  29. ↑ Lucie Gallot-Lavallee, Guillaume Blanc, Jean-Michel Claverie: Comparative genomics of Chrysochromulina Ericina Virus (CeV) and other microalgae-infecting large DNA viruses highlight their intricate evolutionary relationship with the established Mimiviridae family , in: J. Virol., 26 April 2017, doi: 10.1128 / JVI.00230-17
  30. ↑ a b 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
  31. ↑ List of the main “giant” viruses known as of today (PDF) Center National de la Recherche Scientifique, Université Aix Marseille, from April 18, 2018
  32. ↑ Yoshitoshi Ogura, Tetsuya Hayashi, Shoko Ueki: Complete Genome Sequence of a Phycodnavirus, Heterosigma akashiwo Virus Strain 53 , in: Microbiology, September 2016, doi: 10.1128 / genomeA.01279-16 , PubMed 27834719, PDF
  33. ↑ Carolina Reyes, Kenneth Stedman: Are Phaeocystis globosa viruses (OLPG) and Organic Lake phycodnavirus a part of the Phycodnaviridae or Mimiviridae? , Blog on ResearchGate, January 8, 2016