Skip to main content

Tyrosine-Phosphoproteome Dynamics

  • Chapter
  • First Online:
Systems Biology for Signaling Networks

Part of the book series: Systems Biology ((SYSTBIOL))

  • 1921 Accesses

Abstract

Signal transduction systems are known to widely regulate complex biological events such as cell proliferation, differentiation, and apoptosis. Since numerous biological analyses have revealed phosphotyrosine-dependent networks play a key role in transmitting signals, a comprehensive and fine description of their dynamic behavior would contribute substantially toward system-level understanding of the regulatory mechanisms that result in each biological effect. Recent technological advances in mass spectrometry-based proteomics have enabled us to obtain a network-wide description of signaling dynamics through the comprehensive identification and quantification of tyrosine-phosphorylated molecules within a cell. This chapter introduces the current status of quantitative proteomics technology for temporal studies of signal transduction and the application of their dynamics data to mathematical analyses of the regulatory networks.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bose R, Molina H, Patterson AS et al (2006) Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci USA 103:9773–9778

    Article  CAS  PubMed  Google Scholar 

  • Blagoev B, Ong SE, Kratchmarova I et al (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22:1139–1145

    Article  CAS  PubMed  Google Scholar 

  • Dengjel J, Akimov V, Olsen JV et al (2007) Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 25:566–568

    Article  CAS  PubMed  Google Scholar 

  • Guha U, Chaerkady R, Marimuthu A et al (2008) Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci USA 105:14112–14117

    Article  CAS  PubMed  Google Scholar 

  • Guo A, Villen J, Kornhauser J et al (2008) Signaling networks assembled by oncogenic EGFR and c-Met. Proc Natl Acad Sci USA 105:692–697

    Article  CAS  PubMed  Google Scholar 

  • Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  CAS  PubMed  Google Scholar 

  • Han DK, Eng J, Zhou H et al (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 19: 946–951

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Huang PH, Mukasa A, Bonavia R et al (2007) Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci USA 104:12867–12872

    Article  CAS  PubMed  Google Scholar 

  • Hunter T (2000) Signaling–2000 and beyond. Cell 100:113–127

    Article  CAS  PubMed  Google Scholar 

  • Kratchmarova I, Blagoev B, Haack-Sorensen M et al (2005) Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 308:1472–1477

    Article  CAS  PubMed  Google Scholar 

  • Kumar N, Wolf-Yadlin A, White FM et al (2007) Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol 3:e4

    Article  PubMed Central  PubMed  Google Scholar 

  • Mawuenyega KG, Kaji H, Yamuchi Y et al (2003) Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res 2:23–35

    Article  CAS  PubMed  Google Scholar 

  • Morandell S, Stasyk T, Skvortsov S et al (2008) Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network. Proteomics 8:4383–4401

    Article  CAS  PubMed  Google Scholar 

  • Nagashima T, Shimodaira H, Ide K et al (2007) Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J Biol Chem 282:4045–4056

    Article  CAS  PubMed  Google Scholar 

  • Nagashima T, Oyama M, Kozuka-Hata H et al (2008) Phosphoproteome and transcriptome analyses of ErbB ligand-stimulated MCF-7 cells. Cancer Genomics Proteomics 5:161–168

    CAS  PubMed  Google Scholar 

  • Natsume T, Yamauchi Y, Nakayama H et al (2002) A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics. Anal Chem 74:4725–4733

    Article  CAS  PubMed  Google Scholar 

  • Oda K, Matsuoka Y, Funahashi A et al (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1:0010

    Article  PubMed  Google Scholar 

  • Olsen JV, Blagoev B, Gnad F et al (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635–648

    Article  CAS  PubMed  Google Scholar 

  • Ong SE, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386

    Article  CAS  PubMed  Google Scholar 

  • Ong SE, Kratchmarova I, Mann M (2003) Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2:173–181

    Article  CAS  PubMed  Google Scholar 

  • Oyama M, Itagaki C, Hata H et al (2004) Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res 14:2048–2052

    Article  CAS  PubMed  Google Scholar 

  • Oyama M, Kozuka-Hata H, Suzuki Y et al (2007) Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics 6:1000–1006

    Article  CAS  PubMed  Google Scholar 

  • Oyama M, Kozuka-Hata H, Tasaki S et al (2009) Temporal perturbation of tyrosine-phosphoproteome dynamics reveals the system-wide regulatory networks. Mol Cell Proteomics 8:226–231

    Article  CAS  PubMed  Google Scholar 

  • Rikova K, Guo A, Zeng Q et al (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131:1190–1203

    Article  CAS  PubMed  Google Scholar 

  • Ross PL, Huang YN, Marchese J et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3: 1154–1169

    Article  CAS  PubMed  Google Scholar 

  • Rush J, Moritz A, Lee KA et al (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 23:94–101

    Article  CAS  PubMed  Google Scholar 

  • Saito A, Nagasaki M, Oyama M et al (2007) AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics 8:15

    Article  PubMed Central  PubMed  Google Scholar 

  • Schlessinger J (2000) Cell signaling by receptor tyrosine kinases. Cell 103:211–225

    Article  CAS  PubMed  Google Scholar 

  • Schulze WX, Mann M (2004) A novel proteomic screen for peptide-protein interactions. J Biol Chem 279:10756–10764

    Article  CAS  PubMed  Google Scholar 

  • Stokes MP, Rush J, MacNeill J et al (2007) Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci USA 104:19855–19860

    Article  CAS  PubMed  Google Scholar 

  • Tasaki S, Nagasaki M, Oyama M et al (2006) Modeling and estimation of dynamic egfr pathway by data assimilation approach using time series proteomic data. Genome Inform 17:226–238

    CAS  PubMed  Google Scholar 

  • Thelemann A, Petti F, Griffin G et al (2005) Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells. Mol Cell Proteomics 4: 356–376

    Article  CAS  PubMed  Google Scholar 

  • Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242–247

    Article  CAS  PubMed  Google Scholar 

  • Wolf-Yadlin A, Kumar N, Zhang Y et al (2006) Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol 2:54

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhang Y, Wolf-Yadlin A, Ross PL et al (2005) Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics 4:1240–1250

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Masaaki Oyama .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Oyama, M., Tasaki, S., Kozuka-Hata, H. (2010). Tyrosine-Phosphoproteome Dynamics. In: Choi, S. (eds) Systems Biology for Signaling Networks. Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5797-9_18

Download citation

Publish with us

Policies and ethics