Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses.
AP-MS, affinity-purification mass spectrometry
Alternative ORFs
DEP, differentially expressed proteins
FDR, false discovery rate
FPKM, fragments per kilobase of exon model per million reads mapped
Flavivirus
HCIP, highly confident interacting proteins
HCMV, human cytomegalovirus
LFQ, label free quantification
MS, mass spectrometry
ORF, open reading frame
PSM, peptide spectrum match
Protein network
Proteogenomics
Proteome profiling
ZIKV, Zika virus
Zika
altProt, alternative protein
ncRNA, non-coding RNA
sORF, small open reading frame
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2020
2020
Historique:
received:
29
04
2020
revised:
07
10
2020
accepted:
08
10
2020
entrez:
2
11
2020
pubmed:
3
11
2020
medline:
3
11
2020
Statut:
epublish
Résumé
The Zika virus is a flavivirus that can cause fulminant outbreaks and lead to Guillain-Barré syndrome, microcephaly and fetal demise. Like other flaviviruses, the Zika virus is transmitted by mosquitoes and provokes neurological disorders. Despite its risk to public health, no antiviral nor vaccine are currently available. In the recent years, several studies have set to identify human host proteins interacting with Zika viral proteins to better understand its pathogenicity. Yet these studies used standard human protein sequence databases. Such databases rely on genome annotations, which enforce a minimal open reading frame (ORF) length criterion. An ever-increasing number of studies have demonstrated the shortcomings of such annotation, which overlooks thousands of functional ORFs. Here we show that the use of a customized database including currently non-annotated proteins led to the identification of 4 alternative proteins as interactors of the viral capsid and NS4A proteins. Furthermore, 12 alternative proteins were identified in the proteome profiling of Zika infected monocytes, one of which was significantly up-regulated. This study presents a computational framework for the re-analysis of proteomics datasets to better investigate the viral-host protein interplays upon infection with the Zika virus.
Identifiants
pubmed: 33133425
doi: 10.1016/j.csbj.2020.10.010
pii: S2001-0370(20)30432-3
pmc: PMC7585943
doi:
Types de publication
Journal Article
Langues
eng
Pagination
2836-2850Informations de copyright
© 2020 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Front Neurosci. 2018 Oct 26;12:778
pubmed: 30416425
Viruses. 2019 Sep 19;11(9):
pubmed: 31546825
Biochem Biophys Res Commun. 2017 Nov 18;493(2):992-997
pubmed: 28943432
Mol Cell Proteomics. 2018 Nov;17(11):2242-2255
pubmed: 30037810
Theranostics. 2020 Jan 1;10(4):1479-1499
pubmed: 32042317
PLoS Comput Biol. 2014 Jul 31;10(7):e1003754
pubmed: 25080083
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nat Commun. 2019 Sep 27;10(1):4430
pubmed: 31562326
J Dev Biol. 2016 Mar 25;4(2):
pubmed: 29615582
Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15933-8
pubmed: 17043244
Cell. 2018 Dec 13;175(7):1931-1945.e18
pubmed: 30550790
Nat Biotechnol. 2015 Jan;33(1):22-4
pubmed: 25574629
Nat Rev Genet. 2020 Mar;21(3):191-201
pubmed: 31848477
Nat Protoc. 2014 Nov;9(11):2539-54
pubmed: 25275790
Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268
pubmed: 31777944
N Engl J Med. 2009 Jun 11;360(24):2536-43
pubmed: 19516034
Biochim Biophys Acta Gen Subj. 2019 Oct;1863(10):1458-1470
pubmed: 31128158
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Nature. 2011 Dec 21;481(7381):365-70
pubmed: 22190034
J Proteome Res. 2020 Jan 3;19(1):537-542
pubmed: 31755270
Bioinformatics. 2020 Jan 15;36(2):422-429
pubmed: 31350877
Cell. 2009 Jul 23;138(2):389-403
pubmed: 19615732
J Vis Exp. 2019 Apr 11;(146):
pubmed: 31033953
Dev Genes Evol. 2014 Dec;224(4-6):261-8
pubmed: 25079045
Trends Microbiol. 2004 Oct;12(10):458-65
pubmed: 15381195
HFSP J. 2009 Oct;3(5):290-306
pubmed: 20357887
Nat Methods. 2014 Nov;11(11):1114-25
pubmed: 25357241
MMWR Morb Mortal Wkly Rep. 2016 Jan 29;65(3):59-62
pubmed: 26820244
Front Genet. 2018 Dec 04;9:595
pubmed: 30564270
Nucleic Acids Res. 2019 Jan 8;47(D1):D403-D410
pubmed: 30299502
Cell. 2015 Jul 16;162(2):425-440
pubmed: 26186194
mBio. 2017 Jan 10;8(1):
pubmed: 28074025
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Nat Rev Genet. 2014 Mar;15(3):193-204
pubmed: 24514441
Lancet. 2016 Apr 9;387(10027):1531-1539
pubmed: 26948433
Cell. 2016 Mar 24;165(1):22-33
pubmed: 27015305
Bioinformatics. 2017 Jan 1;33(1):135-136
pubmed: 27605098
Trends Biochem Sci. 2016 Aug;41(8):665-678
pubmed: 27261332
Cell Biosci. 2016 Jun 10;6:42
pubmed: 27293547
Elife. 2017 Oct 30;6:
pubmed: 29083303
Nature. 2018 Sep;561(7722):253-257
pubmed: 30177828
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
Nucleic Acids Res. 2020 Jan 8;48(D1):D682-D688
pubmed: 31691826
Methods Mol Biol. 2013;1064:43-70
pubmed: 23996249
Cell Stem Cell. 2016 May 5;18(5):587-90
pubmed: 26952870
J Virol. 2006 May;80(9):4623-32
pubmed: 16611922
Science. 2020 Mar 6;367(6482):1140-1146
pubmed: 32139545
Nat Commun. 2020 Mar 11;11(1):1306
pubmed: 32161257
Virol J. 2017 Nov 7;14(1):217
pubmed: 29116029
Sci Rep. 2018 Jul 18;8(1):10872
pubmed: 30022098
Cell Rep. 2014 Sep 11;8(5):1365-79
pubmed: 25159147
Science. 2016 Aug 12;353(6300):aaf8160
pubmed: 27417495
Curr Protoc Bioinformatics. 2019 Mar;65(1):e68
pubmed: 30485709
Mol Cell Proteomics. 2013 Sep;12(9):2383-93
pubmed: 23720762
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Brief Bioinform. 2018 Jul 20;19(4):636-643
pubmed: 28137767
Development. 2017 Oct 1;144(19):3547-3561
pubmed: 28827394
mBio. 2019 Jul 9;10(4):
pubmed: 31289184
Proteomics. 2009 Sep;9(18):4421-4
pubmed: 19725076
Cell Host Microbe. 2016 Sep 14;20(3):342-356
pubmed: 27545046
PLoS One. 2011;6(6):e20873
pubmed: 21695130
Science. 2012 Nov 23;338(6110):1088-93
pubmed: 23180859
Curr Protoc Bioinformatics. 2015 Mar 09;49:8.19.1-8.19.16
pubmed: 25754993
Mol Cell Proteomics. 2014 Sep;13(9):2513-26
pubmed: 24942700
Biochem Biophys Res Commun. 2017 Oct 28;492(4):587-596
pubmed: 28576494
Neuron. 2014 Feb 5;81(3):471-83
pubmed: 24507186
Genes (Basel). 2017 Aug 21;8(8):
pubmed: 28825667
Nature. 2011 May 19;473(7347):337-42
pubmed: 21593866
Front Microbiol. 2017 Aug 17;8:1557
pubmed: 28861068
Proteomics. 2011 Mar;11(5):996-9
pubmed: 21337703
Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152
pubmed: 31686107
Nucleic Acids Res. 2020 Feb 20;48(3):1029-1042
pubmed: 31504789
Nature. 2017 May 25;545(7655):505-509
pubmed: 28514442
J Proteomics. 2010 Oct 10;73(11):2092-123
pubmed: 20816881
Exp Cell Res. 2020 Jul 1;392(1):111997
pubmed: 32302626
Genome Res. 2018 May;28(5):609-624
pubmed: 29626081
J Virol. 2018 Mar 14;92(7):
pubmed: 29321322
Nucleic Acids Res. 2018 Jan 4;46(D1):D497-D502
pubmed: 29140531
Adv Exp Med Biol. 2016;926:49-64
pubmed: 27686805
BMC Bioinformatics. 2012;13 Suppl 16:S2
pubmed: 23176207
Proteomics. 2018 May;18(10):e1700058
pubmed: 28627015
Semin Diagn Pathol. 2019 May;36(3):170-176
pubmed: 31006554