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., 12 January 2010
Vol. 3, Issue 104, p. ra3
[DOI: 10.1126/scisignal.2000475]

RESEARCH ARTICLES

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

Jesper V. Olsen1,2*, Michiel Vermeulen1,3*, Anna Santamaria4*, Chanchal Kumar1,5*, Martin L. Miller2,6, Lars J. Jensen2, Florian Gnad1, Jürgen Cox1, Thomas S. Jensen7, Erich A. Nigg4, Søren Brunak2,7, and Matthias Mann1,2{dagger}

1 Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany.
2 Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
3 Department of Physiological Chemistry and Cancer Genomics Centre, University Medical Centre Utrecht, 3584 CG Utrecht, the Netherlands.
4 Biozentrum, Universität Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.
5 Lilly Singapore Centre for Drug Discovery, 8A Biomedical Grove #02-05, Immunos, Biopolis, Singapore 138648, Singapore.
6 Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
7 Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.

* These authors contributed equally to this work.

Abstract: Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry–based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.

{dagger} To whom correspondence should be addressed. E-mail: mmann{at}biochem.mpg.de

Citation: J. V. Olsen, M. Vermeulen, A. Santamaria, C. Kumar, M. L. Miller, L. J. Jensen, F. Gnad, J. Cox, T. S. Jensen, E. A. Nigg, S. Brunak, M. Mann, Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis. Sci. Signal. 3, ra3 (2010).

Read the Full Text

THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Cyclin-Dependent Kinase 16/PCTAIRE Kinase 1 Is Activated by Cyclin Y and Is Essential for Spermatogenesis.
P. Mikolcevic, R. Sigl, V. Rauch, M. W. Hess, K. Pfaller, M. Barisic, L. J. Pelliniemi, M. Boesl, and S. Geley (2012)
Mol. Cell. Biol. 32, 868-879
   Abstract »    Full Text »    PDF »
Phosphorylation of the Transcription Factor YY1 by CK2{alpha} Prevents Cleavage by Caspase 7 during Apoptosis.
S. Riman, R. Rizkallah, A. Kassardjian, K. E. Alexander, B. Luscher, and M. M. Hurt (2012)
Mol. Cell. Biol. 32, 797-807
   Abstract »    Full Text »    PDF »
Cytoplasmic Metadherin (MTDH) Provides Survival Advantage under Conditions of Stress by Acting as RNA-binding Protein.
X. Meng, D. Zhu, S. Yang, X. Wang, Z. Xiong, Y. Zhang, P. Brachova, and K. K. Leslie (2012)
J. Biol. Chem. 287, 4485-4491
   Abstract »    Full Text »    PDF »
Cdc14 Phosphatases Preferentially Dephosphorylate a Subset of Cyclin-dependent kinase (Cdk) Sites Containing Phosphoserine.
S. C. Bremmer, H. Hall, J. S. Martinez, C. L. Eissler, T. H. Hinrichsen, S. Rossie, L. L. Parker, M. C. Hall, and H. Charbonneau (2012)
J. Biol. Chem. 287, 1662-1669
   Abstract »    Full Text »    PDF »
The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator.
S. Jungmichel, J. A. Clapperton, J. Lloyd, F. J. Hari, C. Spycher, L. Pavic, J. Li, L. F. Haire, M. Bonalli, D. H. Larsen, et al. (2012)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Characterization of kinase inhibitors using different phosphorylation states of colony stimulating factor-1 receptor tyrosine kinase.
D. Kitagawa, M. Gouda, Y. Kirii, N. Sugiyama, Y. Ishihama, I. Fujii, Y. Narumi, K. Akita, and K. Yokota (2012)
J. Biochem. 151, 47-55
   Abstract »    Full Text »    PDF »
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.
T. Kim, M. S. Tyndel, H. Huang, S. S. Sidhu, G. D. Bader, D. Gfeller, and P. M. Kim (2011)
Nucleic Acids Res.
   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 »
Interaction of Sororin Protein with Polo-like Kinase 1 Mediates Resolution of Chromosomal Arm Cohesion.
N. Zhang, A. K. Panigrahi, Q. Mao, and D. Pati (2011)
J. Biol. Chem. 286, 41826-41837
   Abstract »    Full Text »    PDF »
Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network.
N. Jailkhani, S. Ravichandran, S. R. Hegde, Z. Siddiqui, S. C. Mande, and K. V. S. Rao (2011)
Genome Res. 21, 2067-2081
   Abstract »    Full Text »    PDF »
Two Ancient Bacterial-like PPP Family Phosphatases from Arabidopsis Are Highly Conserved Plant Proteins That Possess Unique Properties.
R. G. Uhrig and G. B. Moorhead (2011)
Plant Physiology 157, 1778-1792
   Abstract »    Full Text »    PDF »
Systematic Phosphorylation Analysis of Human Mitotic Protein Complexes.
B. Hegemann, J. R. A. Hutchins, O. Hudecz, M. Novatchkova, J. Rameseder, M. M. Sykora, S. Liu, M. Mazanek, P. Lenart, J.-K. Heriche, et al. (2011)
Science Signaling 4, rs12
   Abstract »    Full Text »    PDF »
Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis.
S. B. Ficarro, Y. Zhang, M. J. Carrasco-Alfonso, B. Garg, G. Adelmant, J. T. Webber, C. J. Luckey, and J. A. Marto (2011)
Mol. Cell. Proteomics 10, O111.011064
   Abstract »    Full Text »    PDF »
KIBRA Protein Phosphorylation Is Regulated by Mitotic Kinase Aurora and Protein Phosphatase 1.
L. Xiao, Y. Chen, M. Ji, D. J. Volle, R. E. Lewis, M.-Y. Tsai, and J. Dong (2011)
J. Biol. Chem. 286, 36304-36315
   Abstract »    Full Text »    PDF »
Phosphoproteomic Analysis of Salmonella-Infected Cells Identifies Key Kinase Regulators and SopB-Dependent Host Phosphorylation Events.
L. D. Rogers, N. F. Brown, Y. Fang, S. Pelech, and L. J. Foster (2011)
Science Signaling 4, rs9
   Abstract »    Full Text »    PDF »
Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes.
R. Wu, N. Dephoure, W. Haas, E. L. Huttlin, B. Zhai, M. E. Sowa, and S. P. Gygi (2011)
Mol. Cell. Proteomics 10, M111.009654
   Abstract »    Full Text »    PDF »
Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation.
B. T. Weinert, S. A. Wagner, H. Horn, P. Henriksen, W. R. Liu, J. V. Olsen, L. J. Jensen, and C. Choudhary (2011)
Science Signaling 4, ra48
   Abstract »    Full Text »    PDF »
Characterization of the Mechanisms Controlling Greatwall Activity.
S. Vigneron, A. Gharbi-Ayachi, A.-A. Raymond, A. Burgess, J.-C. Labbe, G. Labesse, B. Monsarrat, T. Lorca, and A. Castro (2011)
Mol. Cell. Biol. 31, 2262-2275
   Abstract »    Full Text »    PDF »
S1P lyase: a novel therapeutic target for ischemia-reperfusion injury of the heart.
P. Bandhuvula, N. Honbo, G.-Y. Wang, Z.-Q. Jin, H. Fyrst, M. Zhang, A. D. Borowsky, L. Dillard, J. S. Karliner, and J. D. Saba (2011)
Am J Physiol Heart Circ Physiol 300, H1753-H1761
   Abstract »    Full Text »    PDF »
System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation.
K. T. G. Rigbolt, T. A. Prokhorova, V. Akimov, J. Henningsen, P. T. Johansen, I. Kratchmarova, M. Kassem, M. Mann, J. V. Olsen, and B. Blagoev (2011)
Science Signaling 4, rs3
   Abstract »    Full Text »    PDF »
T Cell Receptor (TCR)-induced Tyrosine Phosphorylation Dynamics Identifies THEMIS as a New TCR Signalosome Component.
C. Brockmeyer, W. Paster, D. Pepper, C. P. Tan, D. C. Trudgian, S. McGowan, G. Fu, N. R. J. Gascoigne, O. Acuto, and M. Salek (2011)
J. Biol. Chem. 286, 7535-7547
   Abstract »    Full Text »    PDF »
Negative Regulation of the Endocytic Adaptor Disabled-2 (Dab2) in Mitosis.
D. Chetrit, L. Barzilay, G. Horn, T. Bielik, N. I. Smorodinsky, and M. Ehrlich (2011)
J. Biol. Chem. 286, 5392-5403
   Abstract »    Full Text »    PDF »
Cyclin-dependent Kinase-mediated Phosphorylation of RBP1 and pRb Promotes Their Dissociation to Mediate Release of the SAP30{middle dot}mSin3{middle dot}HDAC Transcriptional Repressor Complex.
R. Suryadinata, M. Sadowski, R. Steel, and B. Sarcevic (2011)
J. Biol. Chem. 286, 5108-5118
   Abstract »    Full Text »    PDF »
Overview: The Maturing of Proteomics in Cardiovascular Research.
J. E. Van Eyk (2011)
Circ. Res. 108, 490-498
   Abstract »    Full Text »    PDF »
Divide and Conquer: The Application of Organelle Proteomics to Heart Failure.
G. Agnetti, C. Husberg, and J. E. Van Eyk (2011)
Circ. Res. 108, 512-526
   Abstract »    Full Text »    PDF »
Temporal changes in Hec1 phosphorylation control kinetochore-microtubule attachment stability during mitosis.
(2011)
J. Cell Sci. 124, 622-634
Effective Representation and Storage of Mass Spectrometry-Based Proteomic Data Sets for the Scientific Community.
J. V. Olsen and M. Mann (2011)
Science Signaling 4, pe7
   Abstract »    Full Text »    PDF »
Setting the Standards for Signal Transduction Research.
J. Saez-Rodriguez, L. G. Alexopoulos, and G. Stolovitzky (2011)
Science Signaling 4, pe10
   Abstract »    Full Text »    PDF »
Science Signaling Podcast: 4 January 2011.
M. B. Yaffe and A. M. VanHook (2011)
Science Signaling 4, pc1
   Abstract »    Full Text »
PHOSIDA 2011: the posttranslational modification database.
F. Gnad, J. Gunawardena, and M. Mann (2011)
Nucleic Acids Res. 39, D253-D260
   Abstract »    Full Text »    PDF »
The Plk1-dependent Phosphoproteome of the Early Mitotic Spindle.
A. Santamaria, B. Wang, S. Elowe, R. Malik, F. Zhang, M. Bauer, A. Schmidt, H. H. W. Sillje, R. Korner, and E. A. Nigg (2011)
Mol. Cell. Proteomics 10, M110.004457
   Abstract »    Full Text »    PDF »
Evolutionary Constraints of Phosphorylation in Eukaryotes, Prokaryotes, and Mitochondria.
F. Gnad, F. Forner, D. F. Zielinska, E. Birney, J. Gunawardena, and M. Mann (2010)
Mol. Cell. Proteomics 9, 2642-2653
   Abstract »    Full Text »    PDF »
O-GlcNAc Transferase Regulates Mitotic Chromatin Dynamics.
K. Sakabe and G. W. Hart (2010)
J. Biol. Chem. 285, 34460-34468
   Abstract »    Full Text »    PDF »
Pathway-Based Identification of Biomarkers for Targeted Therapeutics: Personalized Oncology with PI3K Pathway Inhibitors.
J. N. Andersen, S. Sathyanarayanan, A. Di Bacco, A. Chi, T. Zhang, A. H. Chen, B. Dolinski, M. Kraus, B. Roberts, W. Arthur, et al. (2010)
Science Translational Medicine 2, 43ra55
   Abstract »    Full Text »    PDF »
Transient ATM Kinase Inhibition Disrupts DNA Damage-Induced Sister Chromatid Exchange.
J. S. White, S. Choi, and C. J. Bakkenist (2010)
Science Signaling 3, ra44
   Abstract »    Full Text »    PDF »
Dissecting the M Phase-specific Phosphorylation of Serine-Proline or Threonine-Proline Motifs.
C. F. Wu, R. Wang, Q. Liang, J. Liang, W. Li, S. Y. Jung, J. Qin, S. H. Lin, and J. Kuang (2010)
Mol. Biol. Cell 21, 1470-1481
   Abstract »    Full Text »    PDF »
Proteomics Modifies Our Understanding of Cell Cycle Complexity.
M. C. Hall (2010)
Science Signaling 3, pe4
   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