AGODB: a comprehensive domain annotation database of argonaute proteins.
Journal
Database : the journal of biological databases and curation
ISSN: 1758-0463
Titre abrégé: Database (Oxford)
Pays: England
ID NLM: 101517697
Informations de publication
Date de publication:
07 09 2022
07 09 2022
Historique:
received:
03
01
2022
revised:
18
07
2022
accepted:
30
08
2022
entrez:
7
9
2022
pubmed:
8
9
2022
medline:
9
9
2022
Statut:
ppublish
Résumé
Argonaute (Ago) proteins are widely expressed in almost all organisms. Eukaryotic Ago (eAgo) proteins bind small RNA guides forming RNA-induced silencing complex that silence gene expression, and prokaryotic Ago (pAgo) proteins defend against invading nucleic acids via binding small RNAs or DNAs. pAgo proteins have shown great potential as a candidate 'scissors' for gene editing. Protein domains are fundamental units of protein structure, function and evolution; however, the domains of Ago proteins are not well annotated/curated currently. Therefore, full functional domain annotation of Ago proteins is urgently needed for researchers to understand the function and mechanism of Ago proteins. Herein, we constructed the first comprehensive domain annotation database of Ago proteins (AGODB). The database curates detailed information of 1902 Ago proteins, including 1095 eAgos and 807 pAgos. Especially for long pAgo proteins, all six domains are annotated and curated. Gene Ontology (GO) enrichment analysis revealed that Ago genes in different species were enriched in the following GO terms: biological processes (BPs), molecular function and cellular compartment. GO enrichment analysis results were integrated into AGODB, which provided insights into the BP that Ago genes may participate in. AGODB also allows users to search the database with a variety of options and download the search results. We believe that the AGODB will be a useful resource for understanding the function and domain components of Ago proteins. This database is expected to cater to the needs of scientific community dedicated to the research of Ago proteins. http://i.uestc.edu.cn/agodb/.
Identifiants
pubmed: 36068786
pii: 6693399
doi: 10.1093/database/baac078
pmc: PMC9448894
pii:
doi:
Substances chimiques
Argonaute Proteins
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
Références
Mol Cell. 2013 Sep 12;51(5):594-605
pubmed: 24034694
Mol Cell. 2004 Jul 23;15(2):185-97
pubmed: 15260970
Science. 2004 Sep 3;305(5689):1434-7
pubmed: 15284453
Interdiscip Sci. 2020 Mar;12(1):109-116
pubmed: 31741225
J Cancer. 2015 Jul 16;6(9):877-82
pubmed: 26284139
Nucleic Acids Res. 2015 May 26;43(10):5120-9
pubmed: 25925567
J Adv Res. 2020 Apr 29;24:317-324
pubmed: 32455006
PLoS One. 2017 May 17;12(5):e0177097
pubmed: 28520746
Bioinformatics. 2010 Mar 1;26(5):680-2
pubmed: 20053844
Comput Struct Biotechnol J. 2021 Feb 02;19:1145-1153
pubmed: 33680357
Mol Biol Rep. 2021 May;48(5):4837-4849
pubmed: 34117606
Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325
pubmed: 34086934
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
FEBS Lett. 2002 Feb 20;513(1):129-34
pubmed: 11911892
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Nucleic Acids Res. 2019 Jun 20;47(11):5809-5821
pubmed: 31069393
Nature. 2020 Nov;587(7835):632-637
pubmed: 32731256
Cell. 2020 Sep 17;182(6):1545-1559.e18
pubmed: 32846159
Nucleic Acids Res. 2017 Sep 6;45(15):9149-9163
pubmed: 28911094
EMBO J. 1998 Jan 2;17(1):170-80
pubmed: 9427751
Nat Rev Microbiol. 2018 Jan;16(1):5-11
pubmed: 28736447
mBio. 2018 Dec 18;9(6):
pubmed: 30563906
BMC Bioinformatics. 2011 Mar 31;12:90
pubmed: 21453511
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
Nucleic Acids Res. 2017 Jan 4;45(D1):D200-D203
pubmed: 27899674
Genome Biol. 2008;9(2):210
pubmed: 18304383
Science. 2004 Sep 3;305(5689):1437-41
pubmed: 15284456
Biol Chem. 2018 May 24;399(6):525-547
pubmed: 29447113
Biol Direct. 2013 Jun 08;8:13
pubmed: 23758928
Nat Struct Mol Biol. 2014 Sep;21(9):743-53
pubmed: 25192263
Nature. 2014 Mar 13;507(7491):258-261
pubmed: 24531762
Proc Natl Acad Sci U S A. 1998 May 26;95(11):5857-64
pubmed: 9600884
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500