The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics.
Despite many decades of study, mitotic chromosome structure and composition remain poorly characterized. Here, we have integrated quantitative proteomics with bioinformatic analysis to generate a series of independent classifiers that describe the approximately 4,000 proteins identified in isolated mitotic chromosomes. Integrating these classifiers by machine learning uncovers functional relationships between protein complexes in the context of intact chromosomes and reveals which of the approximately 560 uncharacterized proteins identified here merits further study. Indeed, of 34 GFP-tagged predicted chromosomal proteins, 30 were chromosomal, including 13 with centromere-association. Of 16 GFP-tagged predicted nonchromosomal proteins, 14 were confirmed to be nonchromosomal. An unbiased analysis of the whole chromosome proteome from genetic knockouts of kinetochore protein Ska3/Rama1 revealed that the APC/C and RanBP2/RanGAP1 complexes depend on the Ska complex for stable association with chromosomes. Our integrated analysis predicts that up to 97 new centromere-associated proteins remain to be discovered in our data set.
Ohta
Shinya
S
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
Bukowski-Wills
Jimi-Carlo
JC
Sanchez-Pulido
Luis
L
Alves
Flavia de Lima
Fde L
Wood
Laura
L
Chen
Zhuo A
ZA
Platani
Melpi
M
Fischer
Lutz
L
Hudson
Damien F
DF
Ponting
Chris P
CP
Fukagawa
Tatsuo
T
Earnshaw
William C
WC
Rappsilber
Juri
J
D000818:Animals; D002460:Cell Line; D002868:Chromosomal Proteins, Non-Histone / Q000032:analysis* / Q000378:metabolism; D002875:Chromosomes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D018386:Kinetochores / Q000378:metabolism; D008938:Mitosis; D040901:Proteomics / Q000379:methods*; D008941:Spindle Apparatus / Q000378:metabolism
D002868:Chromosomal Proteins, Non-Histone
Genes Cells. 2007 Mar;12(3):269-84
17352734
Chromosoma. 2005 Feb;113(7):385-97
15609038
Nat Rev Mol Cell Biol. 2008 Jan;9(1):33-46
18097444
Genome Biol. 2004;5(10):R80
15461798
Anal Chem. 2003 Feb 1;75(3):663-70
12585499
EMBO J. 2009 May 20;28(10):1442-52
19360002
J Cell Biol. 2002 May 27;157(5):749-60
12034769
Curr Biol. 2004 Apr 6;14(7):611-7
15062103
BMC Genomics. 2008 Feb 27;9:102
18304323
Chromosoma. 2005 Dec;114(6):377-88
16136320
Cell. 2008 Dec 12;135(6):1039-52
19070575
Mol Cell Biol. 1993 Aug;13(8):4884-93
8336724
Annu Rev Biophys Biomol Struct. 2000;29:291-325
10940251
Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
19920124
J Cell Biol. 2009 Jul 27;186(2):173-82
19620631
Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10484-9
20483991
Dev Cell. 2003 Aug;5(2):323-36
12919682
Nature. 2008 Oct 30;455(7217):1251-4
18820680
J Mol Biol. 2000 May 5;298(3):521-37
10772867
Mol Cell. 2009 Oct 23;36(2):290-301
19854137
J Mol Biol. 2000 Sep 8;302(1):205-17
10964570
Cell. 1997 Nov 14;91(4):491-500
9390558
J Biol Chem. 2010 Mar 26;285(13):9322-9326
20129925
Mol Biol Cell. 2008 May;19(5):2300-10
18305100
Mol Cell. 1999 Jul;4(1):21-33
10445024
Nature. 2010 Apr 1;464(7289):721-7
20360735
Cell. 2009 Jan 9;136(1):175-86
19135898
Dev Cell. 2009 Mar;16(3):374-85
19289083
Mol Biol Cell. 2009 May;20(9):2371-80
19261808
Nat Biotechnol. 2008 Dec;26(12):1367-72
19029910
J Biol Chem. 2005 Apr 29;280(17):16994-7004
15687487
BMC Bioinformatics. 2005 Apr 27;6:108
15857510
J Cell Sci. 2010 May 15;123(Pt 10):1623-33
20392738
Dev Cell. 2009 Jan;16(1):105-17
19154722
J Cell Sci. 2009 Jul 15;122(Pt 14):2436-45
19549680
Nat Cell Biol. 2004 Nov;6(11):1135-41
15502821
J Mol Evol. 2003 May;56(5):527-39
12698291
Nature. 2003 Dec 4;426(6966):570-4
14654843
J Chromatogr A. 2002 Dec 6;979(1-2):233-9
12498253
Bioinformatics. 2004 Oct 12;20(15):2479-81
15073010
Science. 2010 Apr 30;328(5978):593-9
20360068
BMC Bioinformatics. 2007 Mar 05;8:73
17338813
Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41
11517324
Science. 2003 Sep 5;301(5638):1380-2
12958361
J Cell Biol. 2007 Oct 22;179(2):187-97
17938248
Nat Struct Mol Biol. 2005 Dec;12(12):1064-71
16299513
Nat Cell Biol. 2006 May;8(5):458-69
16622419
Proc Natl Acad Sci U S A. 2003 May 13;100(10):5813-8
12724530
Mol Cell Proteomics. 2002 May;1(5):376-86
12118079
Nature. 2006 Sep 7;443(7107):101-5
16943775
Nucleic Acids Res. 2002 Dec 1;30(23):5318-27
12466558
Nat Protoc. 2006;1(6):2856-60
17406544
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D142-4
14681379
Proteins. 2003 Feb 1;50(2):177-83
12486711
Proteomics. 2007 Dec;7(24):4511-27
18022940
EMBO J. 2009 May 20;28(10):1453-65
19387489
Cell. 1982 May;29(1):171-81
7105181
Mol Cell Proteomics. 2005 Sep;4(9):1265-72
15958392
J Biol Chem. 2010 May 21;285(21):15966-77
20332092
Curr Biol. 2009 Sep 15;19(17):1467-72
19646878
J Cell Biol. 2010 May 17;189(4):739-54
20479470
Nat Cell Biol. 2006 May;8(5):446-57
16622420
Genome Res. 2002 Aug;12(8):1231-45
12176931
Chromosoma. 1985;91(3-4):313-21
2579778