title: Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells.
abstract: Embryonic stem cells are pluripotent and capable of unlimited self-renewal. Elucidation of the underlying molecular mechanism may contribute to the advancement of cell-based regenerative medicine. In the present work, we performed a large scale analysis of the phosphoproteome in mouse embryonic stem (mES) cells. Using multiplex strategies, we detected 4581 proteins and 3970 high confidence distinct phosphosites in 1642 phosphoproteins. Notably, 22 prominent phosphorylated stem cell marker proteins with 39 novel phosphosites were identified for the first time by mass spectrometry, including phosphorylation sites in NANOG (Ser-65) and RE1 silencing transcription factor (Ser-950 and Thr-953). Quantitative profiles of NANOG peptides obtained during the differentiation of mES cells revealed that the abundance of phosphopeptides and non-phosphopeptides decreased with different trends. To our knowledge, this study presents the largest global characterization of phosphorylation in mES cells. Compared with a study of ultimately differentiated tissue cells, a bioinformatics analysis of the phosphorylation data set revealed a consistent phosphorylation motif in human and mouse ES cells. Moreover, investigations into phosphorylation conservation suggested that phosphoproteins were more conserved in the undifferentiated ES cell state than in the ultimately differentiated tissue cell state. However, the opposite conclusion was drawn from this conservation comparison with phosphosites. Overall, this work provides an overview of phosphorylation in mES cells and is a valuable resource for the future understanding of basic biology in mES cells.
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Qing-Run
authors.initials: QR
authors.lastname: Li
authors.forename: Xiao-Bin
authors.initials: XB
authors.lastname: Xing
authors.forename: Tao-Tao
authors.initials: TT
authors.lastname: Chen
authors.forename: Rong-Xia
authors.initials: RX
authors.lastname: Li
authors.forename: Jie
authors.initials: J
authors.lastname: Dai
authors.forename: Quan-Hu
authors.initials: QH
authors.lastname: Sheng
authors.forename: Shun-Mei
authors.initials: SM
authors.lastname: Xin
authors.forename: Li-Li
authors.initials: LL
authors.lastname: Zhu
authors.forename: Ying
authors.initials: Y
authors.lastname: Jin
authors.forename: Gang
authors.initials: G
authors.lastname: Pei
authors.forename: Jiu-Hong
authors.initials: JH
authors.lastname: Kang
authors.forename: Yi-Xue
authors.initials: YX
authors.lastname: Li
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D000943:Antigens, Differentiation / Q000378:metabolism; D002454:Cell Differentiation; D002460:Cell Line; D030562:Databases, Protein; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D010749:Phosphoprotein Phosphatases / Q000378:metabolism; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D011494:Protein Kinases / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000378:metabolism*
chemical_list: D000943:Antigens, Differentiation; D010750:Phosphoproteins; D020543:Proteome; D011494:Protein Kinases; D010749:Phosphoprotein Phosphatases