Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease.
complexome profiling
disease
mass spectrometry
mitochondria
oxidative phosphorylation
protein complex
protein-protein interaction (PPI)
proteomics
Journal
Frontiers in cell and developmental biology
ISSN: 2296-634X
Titre abrégé: Front Cell Dev Biol
Pays: Switzerland
ID NLM: 101630250
Informations de publication
Date de publication:
2021
2021
Historique:
received:
15
10
2021
accepted:
08
12
2021
entrez:
31
1
2022
pubmed:
1
2
2022
medline:
1
2
2022
Statut:
epublish
Résumé
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
Identifiants
pubmed: 35096826
doi: 10.3389/fcell.2021.796128
pii: 796128
pmc: PMC8790184
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
796128Informations de copyright
Copyright © 2022 Cabrera-Orefice, Potter, Evers, Hevler and Guerrero-Castillo.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Am J Hum Genet. 2016 Jul 7;99(1):208-16
pubmed: 27374773
Biochim Biophys Acta. 2016 Jul;1857(7):980-90
pubmed: 27040506
Nat Protoc. 2020 Aug;15(8):2341-2386
pubmed: 32690956
Adv Microb Physiol. 2000;43:165-224
pubmed: 10907557
Cell Rep. 2016 Apr 5;15(1):197-209
pubmed: 27052170
Nucleic Acids Res. 2019 Sep 26;47(17):9386-9399
pubmed: 31396629
EMBO Mol Med. 2020 Nov 6;12(11):e12619
pubmed: 32969598
Eur J Hum Genet. 2011 Apr;19(4):394-9
pubmed: 21189481
Nucleic Acids Res. 2019 Jan 8;47(D1):D559-D563
pubmed: 30357367
EMBO J. 2020 Feb 3;39(3):e102817
pubmed: 31912925
Methods. 2020 Jun 1;178:72-82
pubmed: 31586594
Am J Hum Genet. 2013 Apr 4;92(4):605-13
pubmed: 23541340
Am J Hum Genet. 2016 Jul 7;99(1):217-27
pubmed: 27374774
Biochim Biophys Acta Bioenerg. 2021 Sep 1;1862(9):148448
pubmed: 34015258
Biochim Biophys Acta Bioenerg. 2019 Sep 1;1860(9):734-744
pubmed: 31376363
Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11591-11596
pubmed: 27671629
Cell. 2012 Aug 31;150(5):1068-81
pubmed: 22939629
EMBO J. 2020 Jul 15;39(14):e103912
pubmed: 32511785
Mol Cell Proteomics. 2012 Apr;11(4):M111.010587
pubmed: 22186715
Cell Mol Life Sci. 2018 Aug;75(16):3051-3067
pubmed: 29464284
Nat Protoc. 2011 Feb;6(2):147-57
pubmed: 21293456
Cold Spring Harb Perspect Biol. 2010 Dec;2(12):a000752
pubmed: 20961978
J Mass Spectrom. 2010 Aug;45(8):892-9
pubmed: 20635431
Cell Metab. 2014 Aug 5;20(2):226-40
pubmed: 25088301
Cell. 2019 Jan 10;176(1-2):391-403.e19
pubmed: 30528433
Mol Cell Proteomics. 2016 Mar;15(3):878-91
pubmed: 26714524
J Proteomics. 2008 Aug 21;71(3):265-76
pubmed: 18602503
Biochim Biophys Acta Mol Basis Dis. 2018 Nov;1864(11):3650-3658
pubmed: 30251684
J Proteome Res. 2020 Jan 3;19(1):327-336
pubmed: 31746214
Nat Rev Microbiol. 2018 Mar;16(3):156-170
pubmed: 29355852
J Anal Methods Chem. 2016;2016:8183656
pubmed: 27668122
Anal Bioanal Chem. 2014 Feb;406(6):1629-37
pubmed: 24281322
J Biol Chem. 2016 Jul 8;291(28):14851-60
pubmed: 27226634
Nat Commun. 2020 Nov 26;11(1):6008
pubmed: 33243981
Ann Rev Mar Sci. 2015;7:403-23
pubmed: 25560607
Cell Metab. 2012 Oct 3;16(4):538-49
pubmed: 22982022
EMBO J. 2011 Oct 18;30(21):4356-70
pubmed: 22009199
Elife. 2015 Sep 24;4:
pubmed: 26402457
Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8247-8252
pubmed: 28720701
Mol Cell Proteomics. 2019 Jul;18(7):1345-1362
pubmed: 31023727
Biochim Biophys Acta Bioenerg. 2017 Mar;1858(3):197-207
pubmed: 27940020
EMBO J. 2021 Feb 15;40(4):e106174
pubmed: 33459420
Cell Rep. 2019 Aug 6;28(6):1635-1647.e5
pubmed: 31390575
RNA. 2009 Feb;15(2):277-86
pubmed: 19096045
J Neurol Sci. 1983 Dec;62(1-3):327-55
pubmed: 6142097
Mol Cell Proteomics. 2014 Sep;13(9):2503-12
pubmed: 24938287
Electrophoresis. 1999 Dec;20(18):3551-67
pubmed: 10612281
Plant Methods. 2005 Nov 16;1(1):11
pubmed: 16287510
F1000Res. 2016 Mar 31;5:
pubmed: 27092249
Life Sci Alliance. 2020 Aug 11;3(10):
pubmed: 32788226
Mol Cell Neurosci. 2013 Jul;55:1-12
pubmed: 22986124
Am J Hum Genet. 2017 Feb 2;100(2):216-227
pubmed: 28065471
Methods Mol Biol. 2013;977:289-98
pubmed: 23436371
Front Mol Biosci. 2021 Apr 07;8:661448
pubmed: 33898526
Cell Rep. 2020 Apr 21;31(3):107541
pubmed: 32320651
PLoS One. 2016 Aug 01;11(8):e0160258
pubmed: 27479602
Mitochondrion. 2011 Nov;11(6):954-63
pubmed: 21945727
Nucleic Acids Res. 2019 Nov 4;47(19):10267-10281
pubmed: 31665743
Nat Rev Mol Cell Biol. 2020 Jun;21(6):327-340
pubmed: 32235894
Biochim Biophys Acta Bioenerg. 2020 Aug 1;1861(8):148202
pubmed: 32275929
PLoS Pathog. 2021 Mar 2;17(3):e1009301
pubmed: 33651838
Biochim Biophys Acta. 2016 Oct;1857(10):1694-704
pubmed: 27461995
Nucleic Acids Res. 2016 Jan 4;44(D1):D7-19
pubmed: 26615191
Nat Commun. 2020 Apr 2;11(1):1643
pubmed: 32242014
Cell. 2006 Apr 7;125(1):187-99
pubmed: 16615899
Proteomics. 2010 Sep;10(18):3379-87
pubmed: 20687061
Hum Mol Genet. 2017 Jul 1;26(13):2541-2550
pubmed: 28449065
Mol Cell Proteomics. 2016 Feb;15(2):669-81
pubmed: 26598645
Plant Methods. 2021 Jul 23;17(1):82
pubmed: 34301293
PLoS One. 2015 Mar 17;10(3):e0120213
pubmed: 25781180
Proc Natl Acad Sci U S A. 2015 May 5;112(18):5685-90
pubmed: 25902503
BMC Bioinformatics. 2017 Oct 23;18(1):457
pubmed: 29061110
Nat Commun. 2021 Jun 21;12(1):3820
pubmed: 34155201
Proteomics. 2016 Mar;16(6):973-88
pubmed: 26792001
Nucleic Acids Res. 2021 Jan 8;49(D1):D437-D451
pubmed: 33211854
Nat Methods. 2012 Sep;9(9):907-9
pubmed: 22863883
Annu Rev Biochem. 2013;82:551-75
pubmed: 23527692
Nature. 2010 Mar 25;464(7288):543-8
pubmed: 20336137
RNA. 2004 Nov;10(11):1692-4
pubmed: 15388877
Bioessays. 2006 Mar;28(3):316-24
pubmed: 16479579
PLoS Comput Biol. 2010 Jun 24;6(6):e1000807
pubmed: 20589078
Biochim Biophys Acta Bioenerg. 2021 Jan 1;1862(1):148308
pubmed: 33002447
J Clin Invest. 2021 Mar 15;131(6):
pubmed: 33465056
Am J Hum Genet. 2020 Jan 2;106(1):92-101
pubmed: 31866046
Anal Chem. 2014 Jul 15;86(14):7150-8
pubmed: 24927332
Biochim Biophys Acta Bioenerg. 2021 Aug 1;1862(8):148444
pubmed: 33940038
J Am Soc Mass Spectrom. 2020 Feb 5;31(2):196-206
pubmed: 32031400
Proteomics. 2009 Jan;9(1):205-9
pubmed: 19053139
Mitochondrion. 2021 Sep;60:70-84
pubmed: 34339868
Nucleic Acids Res. 2009 Jan;37(Database issue):D539-43
pubmed: 18957442
Cell. 2019 Nov 27;179(6):1357-1369.e16
pubmed: 31761533
Methods Mol Biol. 2013;954:583-93
pubmed: 23150422
Proteomes. 2021 Mar 23;9(1):
pubmed: 33806881
Nucleic Acids Res. 2020 Feb 28;48(4):1969-1984
pubmed: 31863585
Mol Biol Cell. 2017 Aug 9;:
pubmed: 28794267
Mol Cell Proteomics. 2010 Oct;9(10):2149-61
pubmed: 20173216
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717
pubmed: 22261725
Nat Rev Mol Cell Biol. 2022 Feb;23(2):141-161
pubmed: 34621061
Proteomics. 2018 Jun;18(11):e1700427
pubmed: 29655301
Pediatrics. 1979 Jul;64(1):24-9
pubmed: 572031
Sci Adv. 2016 Mar 04;2(3):e1501502
pubmed: 26973877
Arch Dis Child. 2010 Apr;95(4):296-301
pubmed: 20335238
Science. 2013 Jun 28;340(6140):1567-70
pubmed: 23812712
Protein Sci. 2005 Jun;14(6):1438-46
pubmed: 15883184
Mol Cell. 2017 Jul 6;67(1):96-105.e4
pubmed: 28673544
Proteomics. 2015 Sep;15(18):3175-92
pubmed: 26097186
Curr Protoc Protein Sci. 2012 Apr;Chapter 29:Unit 29.5.1-12
pubmed: 22470129
EMBO Rep. 2021 Oct 5;22(10):e51991
pubmed: 34351705
J Inherit Metab Dis. 2020 Nov;43(6):1382-1391
pubmed: 32418222
J Biol Chem. 2006 Dec 22;281(51):39217-24
pubmed: 17082194
Cell. 2021 Jul 22;184(15):4073-4089.e17
pubmed: 34214469
Anal Chem. 2018 Apr 17;90(8):5032-5039
pubmed: 29522331
Genet Med. 2021 Sep;23(9):1705-1714
pubmed: 34140661
Nat Methods. 2016 Aug 30;13(9):741-8
pubmed: 27575624
Biotechniques. 2004 Dec;37(6):961-9
pubmed: 15597545
Cell Metab. 2012 Sep 5;16(3):378-86
pubmed: 22902835
Nature. 2016 Nov 24;539(7630):579-582
pubmed: 27775717
Cell. 2011 Mar 18;144(6):986-98
pubmed: 21414488
Nature. 2003 Dec 4;426(6966):570-4
pubmed: 14654843
Anal Biochem. 2016 Nov 15;513:21-27
pubmed: 27544650
Cell Rep. 2019 Oct 29;29(5):1351-1368.e5
pubmed: 31665645
Microb Cell. 2017 Jul 20;4(8):259-272
pubmed: 28845423
Nat Commun. 2019 Mar 1;10(1):990
pubmed: 30824702
Mol Syst Biol. 2019 Jan 14;15(1):e8438
pubmed: 30642884
Proteomics. 2015 Nov;15(21):3603-12
pubmed: 26223664
Am J Hum Genet. 2018 Apr 5;102(4):685-695
pubmed: 29576219
Biochim Biophys Acta Bioenerg. 2021 Jul 1;1862(7):148411
pubmed: 33722514
Nat Struct Mol Biol. 2018 Nov;25(11):1000-1008
pubmed: 30374081
BMC Biochem. 2004 Oct 01;5:14
pubmed: 15461782
Cell Rep. 2016 Aug 30;16(9):2387-98
pubmed: 27545886
Int J Mol Sci. 2021 Apr 24;22(9):
pubmed: 33923221
Mol Cell Biol. 2013 Jul;33(13):2623-34
pubmed: 23648483
Mol Cell. 2019 Jul 11;75(1):184-199.e10
pubmed: 31076284
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Mol Cell Proteomics. 2005 Aug;4(8):1194-204
pubmed: 15937296
Biochim Biophys Acta. 2016 Jan;1863(1):91-101
pubmed: 26477565
Nat Genet. 1996 Apr;12(4):385-9
pubmed: 8630491
Plant J. 2017 Mar;89(6):1079-1092
pubmed: 27943495
Bioinformatics. 2015 Feb 1;31(3):440-1
pubmed: 25301849
Science. 1989 Oct 27;246(4929):500-3
pubmed: 2814477
Front Mol Biosci. 2021 Apr 15;8:660542
pubmed: 33937337
Int J Mol Sci. 2021 Jul 21;22(15):
pubmed: 34360575
BMC Biol. 2013 Jun 13;11:67
pubmed: 23763941
Biochim Biophys Acta Bioenerg. 2021 Jun 1;1862(6):148395
pubmed: 33600785
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612
pubmed: 33237311
Nat Protoc. 2016 Dec;11(12):2301-2319
pubmed: 27809316
Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):
pubmed: 34548399
Plant J. 2011 Jul;67(1):181-94
pubmed: 21418111
Cells. 2021 Feb 10;10(2):
pubmed: 33578848
J Exp Bot. 2022 Jan 5;73(1):245-262
pubmed: 34436580
Nucleic Acids Res. 2017 Jun 2;45(10):5945-5957
pubmed: 28460002
Science. 2012 Sep 14;337(6100):1348-52
pubmed: 22984071
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5207-12
pubmed: 24706851
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
Mol Cell Proteomics. 2002 May;1(5):376-86
pubmed: 12118079
PLoS One. 2013 Jul 23;8(7):e68340
pubmed: 23935861
Methods Cell Biol. 2008;84:143-79
pubmed: 17964931
Elife. 2018 Aug 10;7:
pubmed: 30095066
Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):93-102
pubmed: 31848235
Mol Cell Proteomics. 2007 Jul;6(7):1215-25
pubmed: 17426019
Mol Cell. 2016 Oct 6;64(1):148-162
pubmed: 27642048
Biochim Biophys Acta Bioenerg. 2021 Jun 1;1862(6):148399
pubmed: 33592209
Nat Methods. 2013 Apr;10(4):332-4
pubmed: 23435260
Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18934-9
pubmed: 24191001
Mol Cell Proteomics. 2014 Sep;13(9):2513-26
pubmed: 24942700
Trends Biochem Sci. 2016 Mar;41(3):261-273
pubmed: 26857402
Nucleic Acids Res. 2020 Sep 18;48(16):9301-9319
pubmed: 32813020
Biochem Soc Trans. 2011 Jan;39(1):45-50
pubmed: 21265745
Methods Mol Biol. 2021;2192:147-158
pubmed: 33230772
EMBO Rep. 2020 Oct 5;21(10):e49585
pubmed: 32945072
Cell Mol Life Sci. 2021 Jul;78(13):5325-5339
pubmed: 34046695
Bioinformatics. 2019 Sep 1;35(17):3083-3091
pubmed: 30649188
Nat Protoc. 2007;2(8):1849-61
pubmed: 17703195
FEBS J. 2011 May;278(10):1634-42
pubmed: 21410645
Mol Cell Proteomics. 2018 Feb;17(2):216-232
pubmed: 29222160
Am J Hum Genet. 2018 Oct 4;103(4):592-601
pubmed: 30245030
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Mol Cell Proteomics. 2002 Jan;1(1):3-10
pubmed: 12096135
EMBO J. 2011 Sep 09;30(22):4652-64
pubmed: 21909073
Methods Mol Biol. 2020;2071:27-47
pubmed: 31758445
EMBO Rep. 2016 Dec;17(12):1844-1856
pubmed: 27737933
Hum Mol Genet. 2004 Oct 15;13(20):2461-72
pubmed: 15317750
Nat Methods. 2019 Aug;16(8):737-742
pubmed: 31308550
Cell Rep. 2017 Feb 14;18(7):1727-1738
pubmed: 28199844
Mol Cell. 2016 Aug 18;63(4):621-632
pubmed: 27499296
Proteomics. 2009 Sep;9(17):4221-8
pubmed: 19688755
Nature. 2011 May 19;473(7347):337-42
pubmed: 21593866
Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737
pubmed: 28130547
Biochim Biophys Acta. 2016 Jul;1857(7):938-45
pubmed: 26906428
Sci Adv. 2020 Jun 24;6(26):eaba7509
pubmed: 32637615
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
Nat Rev Mol Cell Biol. 2021 May;22(5):307-325
pubmed: 33594280
Front Plant Sci. 2013 Apr 15;4:84
pubmed: 23596449
Biochim Biophys Acta Bioenerg. 2017 Mar;1858(3):208-217
pubmed: 27988283
Nat Genet. 2008 Nov;40(11):1288-90
pubmed: 18953340
Protein Sci. 2021 Jan;30(1):187-200
pubmed: 33070389
Nucleic Acids Res. 2022 Jan 7;50(D1):D578-D586
pubmed: 34718729
FEMS Microbiol Rev. 2013 May;37(3):428-61
pubmed: 23210799
Methods Mol Biol. 2021;2192:269-285
pubmed: 33230779
Chem Rev. 2013 Apr 10;113(4):2343-94
pubmed: 23438204
RNA. 2020 Sep;26(9):1216-1233
pubmed: 32467309
Protein Expr Purif. 2018 Oct;150:81-85
pubmed: 29777748
Curr Biol. 2018 May 21;28(10):1606-1613.e4
pubmed: 29731306
Nat Commun. 2021 Aug 12;12(1):4900
pubmed: 34385433
J Proteomics. 2021 Jan 6;230:103990
pubmed: 32961344
Nat Protoc. 2018 Jan;13(1):293-306
pubmed: 29323663
EMBO J. 2021 Nov 2;40(21):e108648
pubmed: 34542926
Mol Omics. 2021 Feb 1;17(1):29-42
pubmed: 33034323
J Liq Chromatogr Relat Technol. 2012 Nov;35(20):2923-2950
pubmed: 23378719
Nat Rev Microbiol. 2021 May;19(5):319-330
pubmed: 33437024
PLoS One. 2013 May 21;8(5):e63683
pubmed: 23704930
J Med Genet. 2012 Sep;49(9):578-90
pubmed: 22972949
Mol Syst Biol. 2017 Jul 25;13(7):936
pubmed: 28743795
Cell Metab. 2017 Jan 10;25(1):128-139
pubmed: 27720676
Electrophoresis. 2006 Aug;27(16):3306-21
pubmed: 16858726
Nat Protoc. 2006;1(1):418-28
pubmed: 17406264
Biochim Biophys Acta Bioenerg. 2021 Jul 1;1862(7):148414
pubmed: 33727070