Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Sci. Signal., 15 March 2011
Vol. 4, Issue 164, p. rs3
[DOI: 10.1126/scisignal.2001570]


System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

Kristoffer T. G. Rigbolt1*, Tatyana A. Prokhorova1*, Vyacheslav Akimov1, Jeanette Henningsen1,2, Pia T. Johansen3, Irina Kratchmarova1, Moustapha Kassem3,4, Matthias Mann5,6, Jesper V. Olsen6{dagger}, and Blagoy Blagoev1{dagger}

1 Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
2 Centre of Inflammation and Metabolism, University of Copenhagen, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.
3 Molecular Endocrinology Laboratory, Department of Endocrinology, Odense University Hospital and Medical Biotechnology Center, Winslowsparken 25, DK-5000 Odense, Denmark.
4 Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, 11461 Riyadh, Kingdom of Saudi Arabia.
5 Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.
6 Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.

* These authors contributed equally to this work.

Abstract: To elucidate cellular events underlying the pluripotency of human embryonic stem cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic analyses of hESCs during differentiation initiated by a diacylglycerol analog or transfer to media that had not been conditioned by feeder cells. We profiled 6521 proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic changes in phosphorylation status during 24 hours of differentiation. These data are a resource for studies of the events associated with the maintenance of hESC pluripotency and those accompanying their differentiation. From these data, we identified a core hESC phosphoproteome of sites with similar robust changes in response to the two distinct treatments. These sites exhibited distinct dynamic phosphorylation patterns, which were linked to known or predicted kinases on the basis of the matching sequence motif. In addition to identifying previously unknown phosphorylation sites on factors associated with differentiation, such as kinases and transcription factors, we observed dynamic phosphorylation of DNA methyltransferases (DNMTs). We found a specific interaction of DNMTs during early differentiation with the PAF1 (polymerase-associated factor 1) transcriptional elongation complex, which binds to promoters of the pluripotency and known DNMT target genes encoding OCT4 and NANOG, thereby providing a possible molecular link for the silencing of these genes during differentiation.

{dagger} To whom correspondence should be addressed. E-mail: bab{at} (B.B.); jesper.olsen{at} (J.V.O.)

Citation: K. T. G. Rigbolt, T. A. Prokhorova, V. Akimov, J. Henningsen, P. T. Johansen, I. Kratchmarova, M. Kassem, M. Mann, J. V. Olsen, B. Blagoev, System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation. Sci. Signal. 4, rs3 (2011).

Read the Full Text

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells.
J. Munoz, T. Y. Low, Y. J. Kok, A. Chin, C. K. Frese, V. Ding, A. Choo, and A. J. R. Heck (2014)
Mol Syst Biol 7, 550
   Abstract »    Full Text »    PDF »
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.
V. van Noort, J. Seebacher, S. Bader, S. Mohammed, I. Vonkova, M. J. Betts, S. Kuhner, R. Kumar, T. Maier, M. O'Flaherty, et al. (2014)
Mol Syst Biol 8, 571
   Abstract »    Full Text »    PDF »
Evolution and functional cross-talk of protein post-translational modifications.
P. Beltrao, P. Bork, N. J. Krogan, and V. van Noort (2014)
Mol Syst Biol 9, 714
   Abstract »    Full Text »    PDF »
Dynamic Regulation of the COP9 Signalosome in Response to DNA Damage.
M. G. Fuzesi-Levi, G. Ben-Nissan, E. Bianchi, H. Zhou, M. J. Deery, K. S. Lilley, Y. Levin, and M. Sharon (2014)
Mol. Cell. Biol. 34, 1066-1076
   Abstract »    Full Text »    PDF »
Signaling regulates activity of DHCR24, the final enzyme in cholesterol synthesis.
W. Luu, E. J. Zerenturk, I. Kristiana, M. P. Bucknall, L. J. Sharpe, and A. J. Brown (2014)
J. Lipid Res. 55, 410-420
   Abstract »    Full Text »    PDF »
Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue.
M. Marcilla, A. Alpizar, M. Lombardia, A. Ramos-Fernandez, M. Ramos, and J. P. Albar (2014)
Mol. Cell. Proteomics 13, 462-474
   Abstract »    Full Text »    PDF »
Comprehensive Quantitative Comparison of the Membrane Proteome, Phosphoproteome, and Sialiome of Human Embryonic and Neural Stem Cells.
M. N. Melo-Braga, M. Schulz, Q. Liu, A. Swistowski, G. Palmisano, K. Engholm-Keller, L. Jakobsen, X. Zeng, and M. R. Larsen (2014)
Mol. Cell. Proteomics 13, 311-328
   Abstract »    Full Text »    PDF »
A Proteomic Perspective of Sirtuin 6 (SIRT6) Phosphorylation and Interactions and Their Dependence on Its Catalytic Activity.
Y. V. Miteva and I. M. Cristea (2014)
Mol. Cell. Proteomics 13, 168-183
   Abstract »    Full Text »    PDF »
Alpha-synuclein Post-translational Modifications as Potential Biomarkers for Parkinson Disease and Other Synucleinopathies.
A. W. Schmid, B. Fauvet, M. Moniatte, and H. A. Lashuel (2013)
Mol. Cell. Proteomics 12, 3543-3558
   Abstract »    Full Text »    PDF »
Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry.
J. V. Olsen and M. Mann (2013)
Mol. Cell. Proteomics 12, 3444-3452
   Abstract »    Full Text »    PDF »
Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development.
M. R. Facette, Z. Shen, F. R. Bjornsdottir, S. P. Briggs, and L. G. Smith (2013)
PLANT CELL 25, 2798-2812
   Abstract »    Full Text »    PDF »
A RANKL-PKC{beta}-TFEB signaling cascade is necessary for lysosomal biogenesis in osteoclasts.
M. Ferron, C. Settembre, J. Shimazu, J. Lacombe, S. Kato, D. J. Rawlings, A. Ballabio, and G. Karsenty (2013)
Genes & Dev. 27, 955-969
   Abstract »    Full Text »    PDF »
Role of serine-threonine phosphoprotein phosphatases in smooth muscle contractility.
T. Butler, J. Paul, N. Europe-Finner, R. Smith, and E.-C. Chan (2013)
Am J Physiol Cell Physiol 304, C485-C504
   Abstract »    Full Text »    PDF »
Lamin A tail modification by SUMO1 is disrupted by familial partial lipodystrophy-causing mutations.
D. N. Simon, T. Domaradzki, W. A. Hofmann, and K. L. Wilson (2013)
Mol. Biol. Cell 24, 342-350
   Abstract »    Full Text »    PDF »
Posttranslational Modifications of the Retinoblastoma Tumor Suppressor Protein as Determinants of Function.
J. I. MacDonald and F. A. Dick (2013)
Genes & Cancer
   Abstract »    Full Text »    PDF »
Poly(ADP-ribose) polymerase 1 regulates nuclear reprogramming and promotes iPSC generation without c-Myc.
S.-H. Chiou, B.-H. Jiang, Y.-L. Yu, S.-J. Chou, P.-H. Tsai, W.-C. Chang, L.-K. Chen, L.-H. Chen, Y. Chien, and G.-Y. Chiou (2013)
J. Exp. Med. 210, 85-98
   Abstract »    Full Text »    PDF »
Mediator Phosphorylation Prevents Stress Response Transcription During Non-stress Conditions.
C. Miller, I. Matic, K. C. Maier, B. Schwalb, S. Roether, K. Strasser, A. Tresch, M. Mann, and P. Cramer (2012)
J. Biol. Chem. 287, 44017-44026
   Abstract »    Full Text »    PDF »
Extracellular Phosphorylation and Phosphorylated Proteins: Not Just Curiosities But Physiologically Important.
G. Yalak and V. Vogel (2012)
Science Signaling 5, re7
   Abstract »    Full Text »    PDF »
A Novel Method for the Simultaneous Enrichment, Identification, and Quantification of Phosphopeptides and Sialylated Glycopeptides Applied to a Temporal Profile of Mouse Brain Development.
G. Palmisano, B. L. Parker, K. Engholm-Keller, S. E. Lendal, K. Kulej, M. Schulz, V. Schwammle, M. E. Graham, H. Saxtorph, S. J. Cordwell, et al. (2012)
Mol. Cell. Proteomics 11, 1191-1202
   Abstract »    Full Text »    PDF »
Phosphorylation of Serine 51 Regulates the Interaction of Human DNA Ligase I with Replication Factor C and Its Participation in DNA Replication and Repair.
Z. Peng, Z. Liao, B. Dziegielewska, Y. Matsumoto, S. Thomas, Y. Wan, A. Yang, and A. E. Tomkinson (2012)
J. Biol. Chem. 287, 36711-36719
   Abstract »    Full Text »    PDF »
The where, when and how of microtubule nucleation - one ring to rule them all.
N. Teixido-Travesa, J. Roig, and J. Luders (2012)
J. Cell Sci. 125, 4445-4456
   Abstract »    Full Text »    PDF »
Dynactin's pointed-end complex is a cargo-targeting module.
T.-Y. Yeh, N. J. Quintyne, B. R. Scipioni, D. M. Eckley, and T. A. Schroer (2012)
Mol. Biol. Cell 23, 3827-3837
   Abstract »    Full Text »    PDF »
Novel PKC{alpha}-mediated phosphorylation site(s) on cofilin and their potential role in terminating histamine release.
M. Sakuma, Y. Shirai, K.-i. Yoshino, M. Kuramasu, T. Nakamura, T. Yanagita, K. Mizuno, I. Hide, Y. Nakata, and N. Saito (2012)
Mol. Biol. Cell 23, 3707-3721
   Abstract »    Full Text »    PDF »
TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics.
J. Zhong, M.-S. Kim, R. Chaerkady, X. Wu, T.-C. Huang, D. Getnet, C. J. Mitchell, S. M. Palapetta, J. Sharma, R. N. O'Meally, et al. (2012)
Mol. Cell. Proteomics 11, M112.017764
   Abstract »    Full Text »    PDF »
PTMScan Direct: Identification and Quantification of Peptides from Critical Signaling Proteins by Immunoaffinity Enrichment Coupled with LC-MS/MS.
M. P. Stokes, C. L. Farnsworth, A. Moritz, J. C. Silva, X. Jia, K. A. Lee, A. Guo, R. D. Polakiewicz, and M. J. Comb (2012)
Mol. Cell. Proteomics 11, 187-201
   Abstract »    Full Text »    PDF »
Computational Approaches for Analyzing Information Flow in Biological Networks.
B. Kholodenko, M. B. Yaffe, and W. Kolch (2012)
Science Signaling 5, re1
   Abstract »    Full Text »    PDF »
Proteomic Analysis of Stem Cell Differentiation and Early Development.
D. van Hoof, J. Krijgsveld, and C. Mummery (2012)
Cold Spring Harb Perspect Biol 4, a008177
   Abstract »    Full Text »    PDF »
Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins.
T. Geiger, A. Wehner, C. Schaab, J. Cox, and M. Mann (2012)
Mol. Cell. Proteomics 11, M111.014050
   Abstract »    Full Text »    PDF »
Phosphosite Mapping of P-type Plasma Membrane H+-ATPase in Homologous and Heterologous Environments.
E. L. Rudashevskaya, J. Ye, O. N. Jensen, A. T. Fuglsang, and M. G. Palmgren (2012)
J. Biol. Chem. 287, 4904-4913
   Abstract »    Full Text »    PDF »
Dynamics of the G Protein-coupled Vasopressin V2 Receptor Signaling Network Revealed by Quantitative Phosphoproteomics.
J. D. Hoffert, T. Pisitkun, F. Saeed, J. H. Song, C.-L. Chou, and M. A. Knepper (2012)
Mol. Cell. Proteomics 11, M111.014613
   Abstract »    Full Text »    PDF »
Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells.
A. Pines, C. D. Kelstrup, M. G. Vrouwe, J. C. Puigvert, D. Typas, B. Misovic, A. de Groot, L. von Stechow, B. van de Water, E. H. J. Danen, et al. (2011)
Mol. Cell. Biol. 31, 4964-4977
   Abstract »    Full Text »    PDF »
GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data.
K. T. G. Rigbolt, J. T. Vanselow, and B. Blagoev (2011)
Mol. Cell. Proteomics 10, O110.007450
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882