BioE3 identifies specific substrates of ubiquitin E3 ligases.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
23 Nov 2023
23 Nov 2023
Historique:
received:
16
05
2023
accepted:
07
11
2023
medline:
27
11
2023
pubmed:
24
11
2023
entrez:
23
11
2023
Statut:
epublish
Résumé
Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
Identifiants
pubmed: 37996419
doi: 10.1038/s41467-023-43326-8
pii: 10.1038/s41467-023-43326-8
pmc: PMC10667490
doi:
Substances chimiques
Ubiquitin-Protein Ligases
EC 2.3.2.27
Ubiquitin
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7656Subventions
Organisme : European Cooperation in Science and Technology (COST)
ID : CA20113
Organisme : European Cooperation in Science and Technology (COST)
ID : CA20113
Organisme : European Cooperation in Science and Technology (COST)
ID : CA20113
Organisme : European Cooperation in Science and Technology (COST)
ID : CA20113
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
ID : 765445-EU
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
ID : 765445-EU
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
ID : 765445-EU
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)
ID : 765445-EU
Informations de copyright
© 2023. The Author(s).
Références
Nat Cell Biol. 2022 Jan;24(1):62-73
pubmed: 35013556
Mol Cell. 2013 Jul 11;51(1):20-34
pubmed: 23727017
J Virol. 2010 Aug;84(16):8181-92
pubmed: 20519395
Biomolecules. 2020 Oct 31;10(11):
pubmed: 33142801
Mol Cell. 2015 Jan 8;57(1):150-64
pubmed: 25557546
Nat Commun. 2015 Jun 02;6:7112
pubmed: 26033541
Life (Basel). 2022 Feb 16;12(2):
pubmed: 35207587
Mol Cell Biol. 2009 Jun;29(12):3307-18
pubmed: 19364824
Front Genet. 2021 Nov 12;12:753535
pubmed: 34868226
Cell Cycle. 2016;15(6):787-98
pubmed: 26766492
Nucleic Acids Res. 2016 Dec 15;44(22):11033
pubmed: 27683222
Commun Biol. 2020 Oct 20;3(1):592
pubmed: 33082525
Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
pubmed: 10982861
Nat Rev Drug Discov. 2022 Mar;21(3):181-200
pubmed: 35042991
Mech Dev. 2005 Oct;122(10):1106-17
pubmed: 16061358
Semin Cell Dev Biol. 2022 Dec;132:109-119
pubmed: 35181195
J Cell Sci. 2018 Mar 13;131(5):
pubmed: 29535154
BMC Bioinformatics. 2015 May 22;16:169
pubmed: 25994840
EMBO Rep. 2015 Dec;16(12):1699-712
pubmed: 26508657
Nucleic Acids Res. 2021 Jan 8;49(D1):D1541-D1547
pubmed: 33174596
Cell Rep. 2013 Nov 14;5(3):826-38
pubmed: 24210823
Front Cell Dev Biol. 2020 Feb 04;8:39
pubmed: 32117970
Semin Cell Dev Biol. 2012 Jun;23(4):429-36
pubmed: 22306180
Genes Cells. 2014 Oct;19(10):743-54
pubmed: 25205350
Dev Cell. 2012 Jun 12;22(6):1299-312
pubmed: 22658936
Methods Mol Biol. 2012;832:173-83
pubmed: 22350885
Cell Death Differ. 2013 Jan;20(1):21-30
pubmed: 22722335
Nature. 2009 Mar 26;458(7237):461-7
pubmed: 19325626
Proteomics. 2019 Nov;19(21-22):e1900185
pubmed: 31566917
Science. 1995 Dec 22;270(5244):1999-2002
pubmed: 8533093
Mol Cell Biol. 2012 Sep;32(17):3585-93
pubmed: 22751931
Cell Rep. 2019 May 7;27(6):1657-1665.e4
pubmed: 31067453
Front Genet. 2018 Feb 14;9:29
pubmed: 29491882
Mol Cell. 2018 Feb 1;69(3):517-532.e11
pubmed: 29395067
J Cell Biol. 2023 Apr 3;222(4):
pubmed: 36880596
J Cell Sci. 2020 Apr 7;133(7):
pubmed: 32265230
Nat Commun. 2021 Nov 18;12(1):6671
pubmed: 34795231
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Trends Cell Biol. 2016 Nov;26(11):804-817
pubmed: 27667171
Sci Rep. 2017 Jan 18;7:40756
pubmed: 28098257
J Biol Chem. 2011 Mar 25;286(12):10238-47
pubmed: 21247896
J Biochem. 2022 Dec 27;173(1):1-11
pubmed: 36346121
Nat Struct Mol Biol. 2013 Jun;20(6):696-701
pubmed: 23644597
Nat Rev Mol Cell Biol. 2016 Oct;17(10):626-42
pubmed: 27485899
Development. 2005 Aug;132(15):3459-70
pubmed: 16000382
EMBO J. 2021 Sep 15;40(18):e107413
pubmed: 34346517
Science. 1999 Aug 6;285(5429):895-8
pubmed: 10436159
Curr Biol. 2014 Mar 17;24(6):664-70
pubmed: 24613305
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Methods Mol Biol. 2015;1266:171-84
pubmed: 25560075
EMBO J. 2009 Nov 18;28(22):3534-48
pubmed: 19779455
J Biol Chem. 2007 Jun 15;282(24):17375-86
pubmed: 17426036
Biochem J. 2010 Oct 1;431(1):23-9
pubmed: 20681948
Mol Cell. 2015 Mar 5;57(5):912-924
pubmed: 25747658
EMBO J. 2006 Apr 19;25(8):1710-9
pubmed: 16601690
J Cell Sci. 2015 May 1;128(9):1674-82
pubmed: 25795303
Trends Biochem Sci. 2015 Apr;40(4):233-42
pubmed: 25778614
EMBO J. 2012 Jun 29;31(13):3008-19
pubmed: 22635276
Nat Commun. 2017 Nov 27;8(1):1809
pubmed: 29180619
J Biol Chem. 2019 Oct 18;294(42):15218-15234
pubmed: 31285264
EMBO Rep. 2014 May;15(5):601-8
pubmed: 24714598
FASEB J. 2023 Feb;37(2):e22757
pubmed: 36607310
Mol Biol Cell. 2002 Nov;13(11):4060-73
pubmed: 12429846
Genes Dev. 2012 Jun 1;26(11):1179-95
pubmed: 22661229
Elife. 2016 May 05;5:
pubmed: 27146717
Nat Rev Mol Cell Biol. 2016 Sep;17(9):581-95
pubmed: 27435506
Mol Cell Proteomics. 2011 May;10(5):M110.002188
pubmed: 20861518
Elife. 2020 Jun 02;9:
pubmed: 32484436
Methods Mol Biol. 2023;2602:177-189
pubmed: 36446975
J Transl Int Med. 2020 Jun 30;8(2):71-79
pubmed: 32983929
J Am Chem Soc. 2008 Jul 23;130(29):9251-3
pubmed: 18582056
Curr Biol. 2017 Jul 24;27(14):2123-2136.e7
pubmed: 28712572
Sci Rep. 2019 Aug 28;9(1):12471
pubmed: 31462741
EMBO Rep. 2023 Jun 5;24(6):e56317
pubmed: 37074924
Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9
pubmed: 27098042
Structure. 2014 Nov 4;22(11):1639-49
pubmed: 25438670
BMC Bioinformatics. 2003 Jan 13;4:2
pubmed: 12525261
Nat Cell Biol. 2008 May;10(5):547-55
pubmed: 18408733
J Biochem. 2014 May;155(5):273-9
pubmed: 24616159
Sci Adv. 2023 Aug 2;9(31):eadh2073
pubmed: 37531430
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
Mol Biol Cell. 2009 Mar;20(6):1816-32
pubmed: 19158374
Cell Metab. 2020 Sep 1;32(3):479-497.e9
pubmed: 32877691
Mol Cell. 2019 Oct 17;76(2):268-285
pubmed: 31585693
Cells. 2019 Oct 29;8(11):
pubmed: 31671755
Nat Cell Biol. 2008 May;10(5):538-46
pubmed: 18408734
Biomol Eng. 1999 Dec 31;16(1-4):119-25
pubmed: 10796994
Trends Biochem Sci. 2019 Jul;44(7):599-615
pubmed: 30819414
Nat Rev Mol Cell Biol. 2009 Jun;10(6):398-409
pubmed: 19436320
J Cell Sci. 2019 Jan 22;132(2):
pubmed: 30584065
Nucleic Acids Res. 2022 Jun 10;50(10):5672-5687
pubmed: 35640614
Nat Genet. 2016 Nov;48(11):1349-1358
pubmed: 27694961