Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture.
Deubiquitination
Mass spectrometry
Post-translational modification
Ubiquitination
Journal
Cell & bioscience
ISSN: 2045-3701
Titre abrégé: Cell Biosci
Pays: England
ID NLM: 101561195
Informations de publication
Date de publication:
12 Aug 2022
12 Aug 2022
Historique:
received:
11
05
2022
accepted:
02
08
2022
entrez:
12
8
2022
pubmed:
13
8
2022
medline:
13
8
2022
Statut:
epublish
Résumé
Ubiquitination is a versatile post-translational modification (PTM), which regulates diverse fundamental features of protein substrates, including stability, activity, and localization. Unsurprisingly, dysregulation of the complex interaction between ubiquitination and deubiquitination leads to many pathologies, such as cancer and neurodegenerative diseases. The versatility of ubiquitination is a result of the complexity of ubiquitin (Ub) conjugates, ranging from a single Ub monomer to Ub polymers with different length and linkage types. To further understand the molecular mechanism of ubiquitination signaling, innovative strategies are needed to characterize the ubiquitination sites, the linkage type, and the length of Ub chain. With advances in chemical biology tools, computational methodologies, and mass spectrometry, protein ubiquitination sites and their Ub chain architecture have been extensively revealed. The obtained information on protein ubiquitination helps to crack the molecular mechanism of ubiquitination in numerous pathologies. In this review, we summarize the recent advances in protein ubiquitination analysis to gain updated knowledge in this field. In addition, the current and future challenges and barriers are also reviewed and discussed.
Identifiants
pubmed: 35962460
doi: 10.1186/s13578-022-00870-y
pii: 10.1186/s13578-022-00870-y
pmc: PMC9373315
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
126Subventions
Organisme : Science and Technology Planning Project of Guangdong Province
ID : 2018B030306047
Organisme : Science and Technology Planning Project of Guangdong Province
ID : 2020B1212060052
Organisme : Guangzhou Science and Technology Project
ID : 201904010469
Organisme : Guangzhou Regenerative Medicine and Health Guangdong Laboratory project
ID : 2018GZR110104003
Organisme : National Natural Science Foundation
ID : 22004021
Organisme : GuangDong Basic and Applied Basic Research Foundation
ID : 2020A1515110119
Organisme : National Key R&D Program of China
ID : 2020YFE0202200
Informations de copyright
© 2022. The Author(s).
Références
Trends Cell Biol. 2019 Sep;29(9):704-716
pubmed: 31300189
Mol Cell. 2016 Oct 20;64(2):251-266
pubmed: 27746020
Proteomics. 2007 Mar;7(6):868-74
pubmed: 17370265
BMC Bioinformatics. 2008 Jul 15;9:310
pubmed: 18625080
J Proteomics. 2016 Apr 29;139:45-59
pubmed: 26972027
J Proteomics. 2020 Mar 20;215:103634
pubmed: 31918034
Curr Drug Targets. 2019;20(5):565-578
pubmed: 30246637
Immunol Rev. 2019 Sep;291(1):123-133
pubmed: 31402498
FASEB J. 2010 Apr;24(4):981-93
pubmed: 19940261
Proteomics. 2020 May;20(9):e1900100
pubmed: 31930661
FEBS J. 2018 Aug;285(15):2746-2761
pubmed: 29679476
J Am Soc Mass Spectrom. 2020 May 6;31(5):1132-1139
pubmed: 32297515
Mol Oncol. 2021 Feb;15(2):487-502
pubmed: 33188726
Proteomics. 2016 Jul;16(14):1961-9
pubmed: 27037516
Biotechnol Genet Eng Rev. 2013;29:73-109
pubmed: 24568254
J Proteome Res. 2019 Jan 4;18(1):309-318
pubmed: 30489083
J Proteome Res. 2018 Jan 5;17(1):296-304
pubmed: 29091453
Proteomics. 2008 Jul;8(14):2885-96
pubmed: 18655026
Trends Cell Biol. 2004 Mar;14(3):103-6
pubmed: 15055197
Nat Biotechnol. 2010 Aug;28(8):868-73
pubmed: 20639865
Neuropharmacology. 2021 Sep 15;196:108690
pubmed: 34197891
Curr Opin Chem Biol. 2021 Aug;63:95-104
pubmed: 33813043
Anal Chem. 2020 Jan 7;92(1):1074-1080
pubmed: 31820937
Methods Mol Biol. 2005;301:255-70
pubmed: 15917637
Methods Enzymol. 2019;626:323-346
pubmed: 31606081
Nat Struct Mol Biol. 2019 Feb;26(2):137-146
pubmed: 30723328
Pharmaceuticals (Basel). 2020 Jun 23;13(6):
pubmed: 32585960
Curr Opin Chem Biol. 2013 Feb;17(1):49-58
pubmed: 23298953
Plant Cell. 2016 Jan;28(1):6-16
pubmed: 26744219
Signal Transduct Target Ther. 2021 Jan 13;6(1):16
pubmed: 33436547
J Proteome Res. 2017 Sep 1;16(9):3363-3369
pubmed: 28737031
Nat Rev Mol Cell Biol. 2012 Jul 23;13(8):508-23
pubmed: 22820888
Biochem Soc Trans. 2008 Oct;36(Pt 5):823-7
pubmed: 18793144
Cell Biosci. 2021 Jul 27;11(1):146
pubmed: 34315543
Nat Struct Mol Biol. 2015 Feb;22(2):116-23
pubmed: 25622294
Methods Mol Biol. 2021;2365:185-202
pubmed: 34432245
Autophagy. 2021 Apr;17(4):961-979
pubmed: 32164484
Nat Rev Mol Cell Biol. 2005 Aug;6(8):610-21
pubmed: 16064137
Cell. 2008 Aug 22;134(4):668-78
pubmed: 18724939
Immunobiology. 2020 Nov;225(6):152026
pubmed: 33190004
Cell Res. 2016 Apr;26(4):399-422
pubmed: 27012465
Anal Chem. 2017 Apr 4;89(7):3840-3846
pubmed: 28260372
Nature. 2019 Aug;572(7770):533-537
pubmed: 31413367
Cell Death Differ. 2021 Feb;28(2):685-699
pubmed: 32895487
Nat Struct Mol Biol. 2013 May;20(5):555-65
pubmed: 23563141
Nat Cell Biol. 2006 Jul;8(7):700-10
pubmed: 16799550
Mol Cell. 2011 Oct 21;44(2):325-40
pubmed: 21906983
Structure. 2013 May 7;21(5):727-40
pubmed: 23562397
Nat Methods. 2011 Jul 10;8(8):691-6
pubmed: 21743460
J Proteomics. 2021 Jan 16;231:103996
pubmed: 33017648
Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15247-52
pubmed: 23986494
Nat Biotechnol. 2003 Aug;21(8):921-6
pubmed: 12872131
Annu Rev Biochem. 2017 Jun 20;86:159-192
pubmed: 28498721
Nat Protoc. 2015 Feb;10(2):349-361
pubmed: 25633630
Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4630-5
pubmed: 25827227
Mol Cell Proteomics. 2012 Dec;11(12):1578-85
pubmed: 22790023
Mol Cell Proteomics. 2011 Oct;10(10):M111.013284
pubmed: 21890473
Methods Mol Biol. 2016;1449:161-75
pubmed: 27613034
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2371-2376
pubmed: 29463763
PLoS One. 2021 Jul 12;16(7):e0254386
pubmed: 34252134
J Proteome Res. 2014 Sep 5;13(9):4192-204
pubmed: 25093938
J Am Soc Mass Spectrom. 2021 Sep 1;32(9):2334-2345
pubmed: 33900069
Mol Cell Proteomics. 2011 Mar;10(3):M110.003590
pubmed: 21139048
Nat Rev Mol Cell Biol. 2009 Oct;10(10):659-71
pubmed: 19773779
J Mol Biol. 2012 May 4;418(3-4):134-44
pubmed: 22227388
Nat Commun. 2021 Jan 11;12(1):254
pubmed: 33431886
Mol Omics. 2021 Dec 6;17(6):948-955
pubmed: 34515266
Nat Struct Mol Biol. 2018 Jul;25(7):631-640
pubmed: 29967540
EMBO Rep. 2009 Nov;10(11):1250-8
pubmed: 19798103
J Mass Spectrom. 2016 Aug;51(8):629-637
pubmed: 28239975
Biomolecules. 2020 Apr 07;10(4):
pubmed: 32272761
Mol Cell. 2017 Oct 5;68(1):233-246.e5
pubmed: 28943312
J Proteomics. 2012 Jun 6;75(10):2998-3014
pubmed: 22178446
J Biomed Sci. 2019 Oct 21;26(1):80
pubmed: 31630678
Cell. 2017 Nov 2;171(4):918-933.e20
pubmed: 29033132
Front Mol Biosci. 2020 Feb 27;7:21
pubmed: 32175328
Mol Cell Proteomics. 2016 Apr;15(4):1381-96
pubmed: 27037361
Nat Commun. 2021 Jul 29;12(1):4608
pubmed: 34326324
Brief Funct Genomics. 2018 Jul 22;18(4):220-229
pubmed: 30576418
Int J Mol Sci. 2020 Apr 28;21(9):
pubmed: 32354117
Data Brief. 2015 May 21;4:130-4
pubmed: 26217776
Curr Protein Pept Sci. 2020;21(8):821-830
pubmed: 32504500
J Biol Chem. 2011 Dec 30;286(52):45186-96
pubmed: 22072716
J Proteome Res. 2014 Jun 6;13(6):3107-13
pubmed: 24816145
Nature. 2022 Jan;601(7893):460-464
pubmed: 34937942
Biochemistry. 2014 Aug 5;53(30):4979-89
pubmed: 25023374
Cell Death Dis. 2018 Feb 14;9(2):246
pubmed: 29445146
BMC Syst Biol. 2018 Nov 22;12(Suppl 6):109
pubmed: 30463553
J Biol Chem. 2013 Jun 28;288(26):18784-8
pubmed: 23696636
NPJ Precis Oncol. 2021 Mar 2;5(1):14
pubmed: 33654169
Brief Bioinform. 2015 Jul;16(4):640-57
pubmed: 25212598
Nucleic Acids Res. 2008 Jan;36(Database issue):D202-5
pubmed: 17998252
Neurosci Lett. 2019 Jun 11;703:53-57
pubmed: 30885635
Anal Chem. 2019 Dec 17;91(24):15890-15898
pubmed: 31774262
Biochem Soc Trans. 2019 Dec 20;47(6):1949-1962
pubmed: 31829417
Cancers (Basel). 2020 Oct 07;12(10):
pubmed: 33036368
J Biol Chem. 2021 Sep;297(3):101077
pubmed: 34391779
Int J Mol Sci. 2021 Jul 02;22(13):
pubmed: 34281220
Nat Cell Biol. 2016 May 27;18(6):579-86
pubmed: 27230526
Trends Biochem Sci. 2019 Jul;44(7):599-615
pubmed: 30819414
Nat Methods. 2008 Jun;5(6):459-60
pubmed: 18511913
Annu Rev Biochem. 1998;67:425-79
pubmed: 9759494
Anal Chem. 2017 Apr 18;89(8):4428-4434
pubmed: 28291339
Nat Chem Biol. 2018 Sep;14(9):831
pubmed: 30120356