Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression.
Reversible phosphorylation of proteins is an important process modulating cellular activities from upstream, which mainly involves sequential phosphorylation of signaling molecules, to downstream where phosphorylation of transcription factors regulates gene expression. In this study, we combined quantitative labeling with multidimensional liquid chromatography-mass spectrometry to monitor the proteome and phosphoproteome changes in the initial period of adipocyte differentiation. The phosphorylation level of a specific protein may be regulated by a kinase or phosphatase without involvement of gene expression or as a phenomenon that accompanies the alteration of its gene expression. Concurrent quantification of phosphopeptides and non-phosphorylated peptides makes it possible to differentiate cellular phosphorylation changes at these two levels. Furthermore, on the system level, certain proteins were predicted as the targeted gene products regulated by identified transcription factors. Among them, several proteins showed significant expression changes along with the phosphorylation alteration of their transcription factors. This is to date the first work to concurrently quantify proteome and phosphoproteome changes during the initial period of adipocyte differentiation, providing an approach to reveal the system-wide association of protein phosphorylation and gene expression.
Wu
Yi-Bo
YB
Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Dai
Jie
J
Yang
Xing-Lin
XL
Li
Su-Jun
SJ
Zhao
Shi-Lin
SL
Sheng
Quan-Hu
QH
Tang
Jia-Shu
JS
Zheng
Guang-Yong
GY
Li
Yi-Xue
YX
Wu
Jia-Rui
JR
Zeng
Rong
R
D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid; D003907:Dexamethasone / Q000494:pharmacology; D005786:Gene Expression Regulation / Q000187:drug effects; D007328:Insulin / Q000494:pharmacology; D013058:Mass Spectrometry; D051379:Mice; D008969:Molecular Sequence Data; D009862:Online Systems; D010748:Phosphopeptides / Q000032:analysis / Q000737:chemistry; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism*; D010766:Phosphorylation / Q000187:drug effects; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism; D014970:Xanthines / Q000494:pharmacology
D007328:Insulin; D010748:Phosphopeptides; D010750:Phosphoproteins; D020543:Proteome; D014157:Transcription Factors; D014970:Xanthines; C008514:methylxanthine; D003907:Dexamethasone
Plant Cell. 2008 Aug;20(8):2238-51
18682547
Nat Methods. 2007 Mar;4(3):207-14
17327847
Nat Methods. 2007 Oct;4(10):798-806
17901869
Biochem Biophys Res Commun. 1999 Nov 30;265(3):664-8
10600478
Biotechniques. 2006 Jun;40(6):790-8
16774123
Science. 2003 Jul 4;301(5629):102-5
12843395
J Proteome Res. 2007 Jan;6(1):250-62
17203969
Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9766-71
15985551
Cell. 1993 Apr 23;73(2):395-406
8477450
Obesity (Silver Spring). 2007 Nov;15(11):2571-82
18070748
Mol Cell Proteomics. 2005 Sep;4(9):1240-50
15951569
Trends Biotechnol. 2002 Jun;20(6):261-8
12007495
FEBS Lett. 1994 Oct 10;353(1):33-6
7926017
Cell Death Differ. 2007 Sep;14(9):1688-99
17572661
J Immunol. 2007 Jan 1;178(1):416-27
17182580
Mol Cell Proteomics. 2003 Nov;2(11):1234-43
14506206
Cell. 1994 Sep 9;78(5):799-811
8087847
Cell. 1994 Jul 15;78(1):137-47
8033205
Mol Cell. 2008 Aug 8;31(3):438-48
18691976
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7
16723010
Mol Cell Proteomics. 2008 Apr;7(4):684-96
18056256
J Biol Chem. 2003 Jul 18;278(29):27096-104
12734206
Oncogene. 2008 Apr 7;27(16):2276-88
18391970
Immunol Rev. 1998 Feb;161:129-41
9553770
Br J Pharmacol. 2008 Apr;153(8):1669-77
18297106
Eur J Biochem. 2001 Oct;268(19):5001-10
11589691
Proteomics. 2004 May;4(5):1433-8
15188412
Cell Cycle. 2004 Jun;3(6):774-8
15197340
Cell Mol Life Sci. 1999 Dec;56(11-12):894-907
11212324
Biochem Biophys Res Commun. 1996 Nov 21;228(3):709-15
8941343
Exp Cell Res. 2005 Apr 1;304(2):443-56
15748890
Cancer Cell. 2003 Mar;3(3):219-31
12676581
Mol Cell Biochem. 2004 May;260(1-2):49-53
15228085
Science. 2008 Mar 28;319(5871):1785-6
18369135
J Biol Chem. 1996 May 17;271(20):11858-64
8662682
Nat Cell Biol. 2007 Aug;9(8):970-7
17643114
Mol Cell Proteomics. 2007 Feb;6(2):283-93
17114649
J Proteome Res. 2003 Mar-Apr;2(2):173-81
12716131
J Proteome Res. 2008 Nov;7(11):4743-55
18823140
Nat Genet. 2005 Apr;37(4):382-90
15778709
J Biol Chem. 1993 Feb 5;268(4):2899-903
8428963
Nat Methods. 2008 Apr;5(4):319-22
18345006
Bioinformatics. 2008 Oct 15;24(20):2416-7
18713790
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2451-6
18268350
Cell. 2006 Nov 3;127(3):635-48
17081983
J Proteome Res. 2009 Jan;8(1):133-41
19053533
J Biol Chem. 2001 Jul 27;276(30):28098-105
11356826
Endocrinology. 2006 Oct;147(10):4950-9
16825321
Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1800-4
17264204
Nat Biotechnol. 2004 Sep;22(9):1139-45
15314609
Gene. 2004 Mar 31;329:167-85
15033539
Nat Cell Biol. 2002 May;4(5):E127-30
11988757
Mol Cell Proteomics. 2005 Jul;4(7):873-86
15858219
Mol Cell Biol. 2004 Apr;24(7):3025-35
15024089
FEBS J. 2007 Mar;274(5):1235-45
17286578
BMC Bioinformatics. 2008 Jun 16;9:282
18554421
Biochem Cell Biol. 2007 Dec;85(6):649-62
18059524