Editorial GuideSystems Biology

Focus Issue: Systems Analysis of Protein Phosphorylation

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Science Signaling  31 Aug 2010:
Vol. 3, Issue 137, pp. eg6
DOI: 10.1126/scisignal.3137eg6

Abstract

Kinases and phosphatases are key regulatory molecules that participate in most cell signaling pathways. Systems-level analyses are providing new insights into phosphorylation sites and kinase specificity, and phosphoproteomic analyses are creating not just a wealth of data, but are also revealing rich revelations about cellular behavior, cellular responses to changing environmental conditions, and mechanisms of disease. Phosphatases are not merely signal terminators, but play active roles in signal transduction and are especially important in redox signaling. In this Focus Issue, Science Signaling highlights protein phosphorylation as the center of the signaling universe.

Phosphorylation is central to most signaling networks. Indeed, the complexity of the human kinome is a testament to the extensive use that Nature has made of this posttranslational modification in building complex, highly regulated systems. Protein and lipid phosphorylation are common forms of phosphorylation that participate in cellular regulatory events. Phosphorylation is not a one-way street; the phosphorylation status of proteins and lipids is dynamic and reflects the balance in the activities of kinases and phosphatases. Furthermore, phosphorylation status is also modified by the amount of access that the kinase or phosphatase has to its substrate through scaffolding proteins or alterations in the subcellular localization of either the enzyme or its target. Phosphorylation status can also be affected by other posttranslational modifications. Research is turning to systems biology to gain insight into the phosphoproteome, its dynamics, and its regulation by other posttranslational events.

With the wealth of data available on kinase specificity and the identification of large numbers of phosphorylation sites, researchers have succeeded in building various tools that can predict the likelihood that a particular site is phosphorylated by a particular kinase (see the Web sites described in ST NetWatch). In the new Research Resources section in Science Signaling, Schwartz and Church have leveraged information in the literature to index phosphorylation sites in human viruses and predicted potential sites with motif-based prediction algorithms. This collection should improve our understanding of viral-host interactions and aid in the design of therapies to fight viral infections. In articles from the Archives, Mok et al. add to this rich collection of data regarding phosphorylation sites in a study that used a high-throughput peptide array approach to investigate kinase substrates and specificity in yeast. Tan et al. took advantage of data regarding the phosphoproteomes of multiple species to compare the human phosphoproteome to that of nonvertebrate model organisms, which produced insights into kinase evolution and human disease. Both of these studies represent launching points for the exploration of the biological functions of kinases.

In addition to available data about kinase specificity and phosphorylation sites, data are now rapidly emerging from studies of the phosphoproteome. Quantitative phosphoproteomic analysis, with methods such as mass spectrometry (see Collins et al. in the Archive) enables tens of thousands of phosphorylation sites to be monitored in cells under various conditions, providing insight into the dynamics of the phosphoproteome. Other proteomic technologies should enable processing of patient samples to determine the phosphorylation-dependent signals that occur in disease states (see Gujral and MacBeath in the Archives). Studies in the Archives by Olsen et al. and Wang et al. provide information on the dynamic changes in the phosphoproteome during the cell cycle and the interactions that occur during mitosis between protein phosphorylation and another posttranslational modification, O-GlcNAcylation (see the Perspective by Hall in the Archives). These studies provide a global perspective on the dynamics of protein modifications within the cell and how these dynamics are affected by the cellular environment.

Understanding phosphorylation-dependent signaling networks and the ability to integrate that information with information about transcriptional regulatory networks or protein interaction networks provides insight into cellular behavior and what occurs when those regulatory circuits become dysfunctional or how those circuits are modified in response to changing environmental conditions. Two studies investigated such questions in the nervous system: Michaelevski et al. integrated phosphoproteomic data with transcriptional expression data to understand the neuronal response to injury. Coba et al. explored the phosphorylation of the postsynaptic density and how the pattern of phosphorylation changed depending on the activity of different classes of neurotransmitter receptors. Turning to the immune system, Mayya et al. performed a systems-level phosphoproteomic analysis of the response to activation of the T cell receptor (TCR). Their work revealed an unanticipated role for serine and threonine phosphorylation in the modulation of protein-protein interactions in this system, which is dominated by tyrosine phosphorylation signaling events. Bertotti et al. and Moritz et al. explored the changes in phosphorylation-dependent signaling that occurred in cancer cells, which could point toward new therapies and help explain the mechanisms by which cells become resistant to currently available therapeutic agents.

The kinases that mediate phosphorylation make up only half of the picture; phosphatases provide the other half. Although a smaller family than the kinome, the phosphatome is no less critical for proper cellular behavior. Indeed, phosphatases are so important that pathogens modulate their activity to promote infection, as described in research by Gomez et al. Protein phosphatases also coordinate recovery from genotoxic stress, as revealed by the work of Li et al. In a proteomic screen, Zagórska et al. identified an interaction between a kinase, a phosphatase, and a regulatory subunit that controlled the phosphorylation of myosin and regulated cell adhesion.

Tyrosine phosphatases are unique among protein phosphatases in that their activity is inhibited by reversible oxidation, enabling redox signals to modulate phosphoprotein status. Kwon et al. describe one such example in the redox regulation of TCR signaling. In a Protocol in this issue, Boivin et al. present their methods for identifying which protein tyrosine phosphatases in a cell or tissue have been reversibly inactivated by oxidation. The Archives include another method that relies on labeling protein tyrosine phosphatases with a fluorescent dye that enables identification of changes in oxidative inactivation of these enzymes under varying conditions. Roy and Cyert describe the motifs that control the interactions between phosphatases and other proteins in a Review in the Archives. Understanding how those motifs control the interactions between these enzymes and their substrates is important, but equally important is knowing which phosphatases are present in a given cell at a particular time. Similar to data shared by Pelech and Zhang in the Archives on the tissue-specific expression of kinases, Arimura and Yagi present a comprehensive analysis of the expression of genes that encode protein tyrosine phosphatases in various immune cells (also in the new Research Resources section).

To understand the effects of phosphorylation and dephosphorylation events on signaling networks, a combination of systems-level, computational, and predictive analyses will likely be required. The articles and tools highlighted here are only a small part of rapidly expanding efforts to reveal further properties of the phosphoproteome.

Featured in This Focus Issue

Research Resources

Protocol

  • B. Boivin, M. Yang, N. K. Tonks, Targeting the reversibly oxidized protein tyrosine phosphatase superfamily. Sci. Signal. 3, pl2 (2010). [Abstract] [Full Text] [PDF]

Related Resources

Editorial Guides

  • L. B. Ray, N. R. Gough, Focus Issue: The kinome—Techniques and methods for analysis. Sci. STKE 2002, eg13 (2002). [Abstract] [Full Text] [PDF]

Research Articles

  • A. Bertotti, M. F. Burbridge, S. Gastaldi, F. Galimi, D. Torti, E. Medico, S. Giordano, S. Corso, G. Rolland-Valognes, B. P. Lockhart, J. A. Hickman, P. M. Comoglio, L. Trusolino, Only a subset of Met-activated pathways are required to sustain oncogene addiction. Sci. Signal. 2, ra80 (2009). [Abstract] [Full Text] [PDF]

  • M. P. Coba, A. J. Pocklington, M. O. Collins, M. V. Kopanitsa, R. T. Uren, S. Swamy, M. D. R. Croning, J. S. Choudhary, S. G. N. Grant, Neurotransmitters drive combinatorial multistate postsynaptic density networks. Sci. Signal. 2, ra19 (2009). [Abstract] [Full Text] [PDF]

  • M. A. Gomez, I. Contreras, M. Hallé, M. L. Tremblay, R. W. McMaster, M. Olivier, Leishmania GP63 alters host signaling through cleavage-activated protein tyrosine phosphatases. Sci. Signal. 2, ra58 (2009). [Abstract] [Full Text] [PDF]

  • J. Kwon, K. E. Shatynski, H. Chen, S. Morand, X. de Deken, F. Miot, T. L. Leto, M. S. Williams, The nonphagocytic NADPH oxidase Duox1 mediates a positive feedback loop during T cell receptor signaling. Sci. Signal. 3, ra59 (2010). [Abstract] [Full Text] [PDF]

  • X. Li, H. H. Lin, H. Chen, X. Xu, H.-M. Shih, D. K. Ann, SUMOylation of the transcriptional co-repressor KAP1 is regulated by the serine and threonine phosphatase PP1. Sci. Signal. 3, ra32 (2010). [Abstract] [Full Text] [PDF]

  • V. Mayya, D. H. Lundgren, S.-I. Hwang, K. Rezaul, L. Wu, J. K. Eng, V. Rodionov, D. K. Han, Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci. Signal. 2, ra46 (2009). [Abstract] [Full Text] [PDF]

  • I. Michaelevski, Y. Segal-Ruder, M. Rozenbaum, K. F. Medzihradszky, O. Shalem, G. Coppola, S. Horn-Saban, K. Ben-Yaakov, S. Y. Dagan, I. Rishal, D. H. Geschwind, Y. Pilpel, A. L. Burlingame, M. Fainzilber, Signaling to transcription networks in the neuronal retrograde injury response. Sci. Signal. 3, ra53 (2010). [Abstract] [Full Text] [PDF]

  • M. L. Miller, L. J. Jensen, F. Diella, C. Jørgensen, M. Tinti, L. Li, M. Hsiung, S. A. Parker, J. Bordeaux, T. Sicheritz-Ponten, M. Olhovsky, A. Pasculescu, J. Alexander, S. Knapp, N. Blom, P. Bork, S. Li, G. Cesareni, T. Pawson, B. E. Turk, M. B. Yaffe, S. Brunak, R. Linding, Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal. 1, ra2 (2008). [Abstract] [Full Text] [PDF]

  • J. Mok, P. M. Kim, H. Y. K. Lam, S. Piccirillo, X. Zhou, G. R. Jeschke, D. L. Sheridan, S. A. Parker, V. Desai, M. Jwa, E. Cameroni, H. Niu, M. Good, A. Remenyi, J.-L. N. Ma, Y.-J. Sheu, H. E. Sassi, R. Sopko, C. S. M. Chan, C. De Virgilio, N. M. Hollingsworth, W. A. Lim, D. F. Stern, B. Stillman, B. J. Andrews, M. B. Gerstein, M. Snyder, B. E. Turk, Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal. 3, ra12 (2010). [Abstract] [Full Text] [PDF]

  • A. Moritz, Y. Li, A. Guo, J. Villén, Y. Wang, J. MacNeill, J. Kornhauser, K. Sprott, J. Zhou, A. Possemato, J. M. Ren, P. Hornbeck, L. C. Cantley, S. P. Gygi, J. Rush, M. J. Comb, Akt–RSK–S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci. Signal. 3, ra64 (2010). [Abstract] [Full Text] [PDF]

  • 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). [Abstract] [Full Text] [PDF]

  • C. S. H. Tan, B. Bodenmiller, A. Pasculescu, M. Jovanovic, M. O. Hengartner, C. Jørgensen, G. D. Bader, R. Aebersold, T. Pawson, R. Linding, Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci. Signal. 2, ra39 (2009). [Abstract] [Full Text] [PDF]

  • Z. Wang, N. D. Udeshi, C. Slawson, P. D. Compton, K. Sakabe, W. D. Cheung, J. Shabanowitz, D. F. Hunt, G. W. Hart, Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci. Signal. 3, ra2 (2010). [Abstract] [Full Text] [PDF]

  • A. Zagórska, M. Deak, D. G. Campbell, S. Banerjee, M. Hirano, S. Aizawa, A. R. Prescott, D. R. Alessi, New roles for the LKB1-NUAK pathway in controlling myosin phosphatase complexes and cell adhesion. Sci. Signal. 3, ra25 (2010). [Abstract] [Full Text] [PDF]

Perspectives

  • T. S. Gujral, G. MacBeath, Emerging miniaturized proteomic technologies to study cell signaling in clinical samples. Sci. Signal. 2, pe65 (2009). [Abstract] [Full Text] [PDF]

  • M. C. Hall, Proteomics modifies our understanding of cell cycle complexity. Sci. Signal. 3, pe4 (2010). [Abstract] [Full Text] [PDF]

  • S. Pelech, H. Zhang, Plasticity of the kinomes in monkey and rat tissues. Sci. STKE 2002, pe50 (2002). [Abstract] [Full Text] [PDF]

Review

  • J. Roy, M. S. Cyert, Cracking the phosphatase code: Docking interactions determine substrate specificity. Sci. Signal. 2, re9 (2009). [Gloss] [Abstract] [Full Text] [PDF]

Protocols

  • M. O. Collins, L. Yu, H. Husi, W. P. Blackstock, J. S. Choudhary, S. G. N. Grant, Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry. Sci. STKE 2005, pl6 (2005). [Abstract] [Full Text] [PDF]

  • G. Firaguay, J. A. Nunès, Analysis of signaling events by dynamic phosphoflow cytometry. Sci. Signal. 2, pl3 (2009). [Abstract] [Full Text] [PDF]

  • Y. Wang, S.-J. Ding, W. Wang, F. Yang, J. M. Jacobs, D. Camp II, R. D. Smith, R. L. Klemke, Methods for pseudopodia purification and proteomic analysis. Sci. STKE 2007, pl4 (2007). [Abstract] [Full Text] [PDF]

  • R. F. Wu, L. S. Terada, Oxidative modification of protein tyrosine phosphatases. Sci. STKE 2006, pl2 (2006). [Abstract] [Full Text] [PDF]

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