Next-generation large-scale binary protein interaction network for Drosophila melanogaster.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
15 04 2023
15 04 2023
Historique:
received:
17
08
2022
accepted:
04
04
2023
medline:
18
4
2023
entrez:
15
4
2023
pubmed:
16
4
2023
Statut:
epublish
Résumé
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
Identifiants
pubmed: 37061542
doi: 10.1038/s41467-023-37876-0
pii: 10.1038/s41467-023-37876-0
pmc: PMC10105736
doi:
Substances chimiques
Drosophila Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
2162Subventions
Organisme : NIAMS NIH HHS
ID : R01 AR057352
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG007118
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Informations de copyright
© 2023. The Author(s).
Références
Cell. 2014 Nov 20;159(5):1212-1226
pubmed: 25416956
Curr Biol. 2010 Oct 26;20(20):1799-808
pubmed: 20888228
J Genomics. 2015 Jul 01;3:75-81
pubmed: 26157507
Annu Rev Biochem. 2010;79:37-64
pubmed: 20367032
Nucleic Acids Res. 2012 Aug;40(15):e115
pubmed: 22730293
Genes Dev. 1999 Aug 15;13(16):2098-107
pubmed: 10465787
PLoS Genet. 2010 Jan 15;6(1):e1000814
pubmed: 20084099
Nat Commun. 2019 Aug 29;10(1):3907
pubmed: 31467278
Science. 2013 Nov 8;342(6159):737-40
pubmed: 24114784
Nucleic Acids Res. 1991 Jul 25;19(14):4008
pubmed: 1861999
Science. 2022 Mar 4;375(6584):eabk2432
pubmed: 35239393
PLoS One. 2014 Jun 20;9(6):e100385
pubmed: 24949626
Nat Rev Genet. 2002 Mar;3(3):176-88
pubmed: 11972155
Nucleic Acids Res. 2019 Jan 8;47(D1):D759-D765
pubmed: 30364959
Dis Model Mech. 2019 Sep 27;12(10):
pubmed: 31562251
Cells. 2019 Jul 03;8(7):
pubmed: 31277291
PLoS One. 2017 Mar 15;12(3):e0173602
pubmed: 28296955
Bioinformatics. 2017 Dec 15;33(24):4049
pubmed: 29028934
Genome Biol. 2002;3(12):RESEARCH0080
pubmed: 12537569
BMC Genomics. 2008 Oct 07;9:461
pubmed: 18840285
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
J Mol Biol. 2020 Jan 3;432(1):80-103
pubmed: 31310766
Fly (Austin). 2012 Oct-Dec;6(4):246-53
pubmed: 23222005
Genetics. 2017 Sep;207(1):9-27
pubmed: 28874452
PLoS One. 2009 Jun 29;4(6):e6068
pubmed: 19562034
Genome Res. 2005 Mar;15(3):376-84
pubmed: 15710747
Genetics. 2017 Jul;206(3):1227-1236
pubmed: 28684603
Autophagy. 2008 Jan;4(1):37-45
pubmed: 17952025
Nucleic Acids Res. 2021 Jan 8;49(D1):D899-D907
pubmed: 33219682
Genome Biol. 2002;3(12):RESEARCH0079
pubmed: 12537568
Methods Enzymol. 2014;545:181-99
pubmed: 25065891
Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63
pubmed: 24234451
Cell Rep. 2022 Jan 25;38(4):110286
pubmed: 35081354
Nature. 2012 Jul 26;487(7408):491-5
pubmed: 22810586
PLoS One. 2011 Apr 01;6(4):e17796
pubmed: 21483780
Science. 2010 Dec 24;330(6012):1787-97
pubmed: 21177974
Autophagy. 2016 Oct 2;12(10):1945-1953
pubmed: 27484196
Cells. 2021 Sep 06;10(9):
pubmed: 34571985
Nature. 2010 Jul 1;466(7302):68-76
pubmed: 20562859
Trends Biochem Sci. 1999 Jan;24(1):34-6
pubmed: 10087920
Genetics. 2018 Mar;208(3):937-949
pubmed: 29284660
Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1514-1523
pubmed: 31915294
Cell Rep. 2016 Sep 13;16(11):3062-3074
pubmed: 27626673
Cell. 2011 Oct 28;147(3):690-703
pubmed: 22036573
Nat Methods. 2009 Jan;6(1):55-61
pubmed: 19079254
Genome Biol. 2004;5(12):R96
pubmed: 15575970
BMC Bioinformatics. 2011 Aug 31;12:357
pubmed: 21880147
Wiley Interdiscip Rev Dev Biol. 2021 Sep;10(5):e396
pubmed: 32940008
FEBS Lett. 2014 Jan 3;588(1):8-14
pubmed: 24211836
Science. 2008 Oct 3;322(5898):104-10
pubmed: 18719252
Genetics. 2018 Mar;208(3):853-874
pubmed: 29487145
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Nat Cell Biol. 2001 Dec;3(12):1114-9
pubmed: 11781573
Nat Methods. 2009 Jan;6(1):91-7
pubmed: 19060903
Nat Methods. 2009 Jan;6(1):83-90
pubmed: 19060904
Science. 2016 Sep 23;353(6306):
pubmed: 27708008
Methods Mol Biol. 2011;723:257-72
pubmed: 21370071
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nature. 2020 Apr;580(7803):402-408
pubmed: 32296183
Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541
pubmed: 30476227
Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6
pubmed: 22121220
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Front Plant Sci. 2019 Nov 14;10:1437
pubmed: 31803201
Nucleic Acids Res. 2011 Jan;39(Database issue):D736-43
pubmed: 21036869
Cell Syst. 2016 Jun 22;2(6):412-21
pubmed: 27237738
Science. 2000 Mar 24;287(5461):2185-95
pubmed: 10731132
Science. 2003 Dec 5;302(5651):1727-36
pubmed: 14605208
Nucleic Acids Res. 2018 Jan 4;46(D1):D567-D574
pubmed: 29155944
Sci Signal. 2013 Feb 26;6(264):rs5
pubmed: 23443684
Cell Metab. 2018 May 01;27(5):1040-1054.e8
pubmed: 29606597
Nat Commun. 2019 Mar 18;10(1):1240
pubmed: 30886144
Nature. 2014 Aug 28;512(7515):393-9
pubmed: 24670639
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Methods. 2014 Jun 15;68(1):134-9
pubmed: 24667416
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7
pubmed: 17517783
Genome Res. 2014 Jul;24(7):1209-23
pubmed: 24985915
Nat Methods. 2009 Jan;6(1):39-46
pubmed: 19116613
BMC Bioinformatics. 2014 Jun 10;15:177
pubmed: 24913703
Curr Biol. 2007 Jan 9;17(1):1-11
pubmed: 17208179
Cell Rep. 2019 Apr 16;27(3):955-970.e7
pubmed: 30995488
Cell Death Differ. 2009 Jan;16(1):21-30
pubmed: 19079286
Genome Res. 2011 Feb;21(2):301-14
pubmed: 21177962
BMC Syst Biol. 2011 May 06;5:65
pubmed: 21548953
Methods Mol Biol. 2015;1278:447-55
pubmed: 25859968
Genome Biol. 2014 Aug 28;15(8):R70
pubmed: 25262759