Yaravirus: A novel 80-nm virus infecting
NCLDV
ORFan
Yaravirus
capsid
metagenomics
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
14 07 2020
14 07 2020
Historique:
pubmed:
1
7
2020
medline:
22
9
2020
entrez:
1
7
2020
Statut:
ppublish
Résumé
Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs of
Identifiants
pubmed: 32601223
pii: 2001637117
doi: 10.1073/pnas.2001637117
pmc: PMC7368276
doi:
Substances chimiques
Viral Proteins
0
Banques de données
GENBANK
['MT293574']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
16579-16586Déclaration de conflit d'intérêts
The authors declare no competing interest.
Références
Intervirology. 2010;53(5):310-20
pubmed: 20551683
Proc Natl Acad Sci U S A. 2016 May 31;113(22):6206-11
pubmed: 27185929
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Structure. 2003 Jan;11(1):7-9
pubmed: 12517334
Front Microbiol. 2019 Aug 23;10:1951
pubmed: 31507563
Viruses. 2016 Nov 03;8(11):
pubmed: 27827884
F1000Res. 2018 Nov 22;7:
pubmed: 30542614
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7
pubmed: 21558174
Comput Appl Biosci. 1992 Jun;8(3):275-82
pubmed: 1633570
Nat Commun. 2018 Feb 27;9(1):749
pubmed: 29487281
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
Adv Virus Res. 2019;103:167-202
pubmed: 30635076
Nat Commun. 2018 Jun 11;9(1):2285
pubmed: 29891839
Comp Funct Genomics. 2003;4(4):432-41
pubmed: 18629076
Front Microbiol. 2019 Aug 21;10:1801
pubmed: 31496997
Viruses. 2016 Oct 28;8(11):
pubmed: 27801826
Nat Protoc. 2015 Jun;10(6):845-58
pubmed: 25950237
Front Microbiol. 2018 Nov 27;9:2668
pubmed: 30538677
Sci Rep. 2017 Sep 5;7(1):10480
pubmed: 28874689
Virus Res. 2006 Apr;117(1):156-84
pubmed: 16494962
Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2401-E2410
pubmed: 28265094
Nucleic Acids Res. 2001 Jun 15;29(12):2607-18
pubmed: 11410670
J Virol. 2019 Dec 12;94(1):
pubmed: 31597770
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
pubmed: 15980461
J Virol. 2019 Feb 19;93(5):
pubmed: 30541841
Nature. 2020 Feb;578(7795):432-436
pubmed: 31968354
Mol Biol Evol. 2016 Jun;33(6):1635-8
pubmed: 26921390
Science. 2004 Nov 19;306(5700):1344-50
pubmed: 15486256
Genome Biol Evol. 2014 Jun 13;6(7):1603-10
pubmed: 24929085
Front Microbiol. 2015 Nov 10;6:1256
pubmed: 26635738
Electrophoresis. 2009 Jun;30 Suppl 1:S162-73
pubmed: 19517507
J Virol. 2017 Jun 26;91(14):
pubmed: 28446673
Front Microbiol. 2018 Sep 06;9:2098
pubmed: 30237791
Viruses. 2017 Jan 20;9(1):
pubmed: 28117683
Bioinformatics. 2016 Jul 1;32(13):1933-42
pubmed: 27153688
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19585-19592
pubmed: 31506349
Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21848-53
pubmed: 20007369
Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5327-35
pubmed: 26351664
J Virol. 2015 Jul;89(13):6585-94
pubmed: 25878099
Clin Microbiol Infect. 2019 Feb;25(2):147-154
pubmed: 30267933
Mol Biol Evol. 2018 Feb 1;35(2):518-522
pubmed: 29077904
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Nucleic Acids Res. 2017 Jan 4;45(D1):D313-D319
pubmed: 27899672
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303
pubmed: 29788355
Genome Biol Evol. 2016 Dec 14;8(11):3351-3363
pubmed: 27811174
Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677
pubmed: 30289528
J Virol. 2018 Jun 13;92(13):
pubmed: 29695424
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
J Virol. 2006 Dec;80(23):11678-85
pubmed: 16971431
Microbiol Mol Biol Rev. 2020 Mar 4;84(2):
pubmed: 32132243
mBio. 2020 Jan 14;11(1):
pubmed: 31937645
Viruses. 2017 Mar 17;9(3):
pubmed: 28304329
Virol J. 2018 Jan 24;15(1):22
pubmed: 29368617
BMC Genomics. 2008 Jan 19;9:24
pubmed: 18205946
Bioinformatics. 2011 Feb 1;27(3):343-50
pubmed: 21134891
Curr Opin Virol. 2011 Aug;1(2):118-24
pubmed: 22440622
Virol J. 2009 Dec 17;6:223
pubmed: 20017929
J Struct Biol. 1996 Jan-Feb;116(1):71-6
pubmed: 8742726
J Cell Biol. 1963 Apr;17:208-12
pubmed: 13986422
Sci Rep. 2018 Mar 5;8(1):4000
pubmed: 29507337
Science. 2013 Jul 19;341(6143):281-6
pubmed: 23869018