Skip to main content

Phosphoproteomics Analysis for Probing Plant Stress Tolerance

  • Protocol
  • First Online:
Plant Stress Tolerance

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1631))

Abstract

Protein phosphorylation is a key signaling mechanism during the plant biotic and abiotic stress response. Signaling cascades communicate between the cell surface, where the stress is perceived, and the nucleus, where a response can be enacted. Many of these signals involve the specific, transient phosphorylation of proteins by kinases, a signal which is usually amplified through cascades. The advent of high-throughput phosphoproteomics, pioneered mainly in yeast and mammalian cells, has made it possible to discover novel phosphorylation events rapidly and efficiently in a data-dependent manner and this has greatly enlarged our understanding of the plant’s response to stress. This chapter describes a simple gel-free protocol for high-throughput phosphoproteomics, which is amenable to most labs engaged in plant stress research.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
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

  1. Engholm-Keller K, Larsen M (2013) Technologies and challenges in large-scale phosphoproteomics. Proteomics 13:910–931

    Article  CAS  PubMed  Google Scholar 

  2. Nilsson CL (2011) Advances in quantitative phosphoproteomics. Anal Chem 84:735–746

    Article  PubMed  Google Scholar 

  3. Silva-Sanchez C, Li H, Chen S (2015) Recent advances and challenges in plant phosphoproteomics. Proteomics 15:1127–1141

    Article  CAS  PubMed  Google Scholar 

  4. Rampitsch C, Bykova NV (2012) The beginnings of crop phosphoproteomics: exploring early warning systems of stress. Front Plant Sci 3:144

    Article  PubMed  PubMed Central  Google Scholar 

  5. Schulze B, Mentzel T, Jehle AK, Mueller K, Beeler S, Boller T, Felix G, Chinchilla D (2010) Rapid heteromerization and phosphorylation of ligand-activated plant transmembrane receptors and their associated kinase BAK1. J Biol Chem 285:9444–9451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Mann M, Ong S-E, Grønborg M, Jensen ON, Pandey A (2002) Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 6:261–268

    Article  Google Scholar 

  7. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A 104:2199–2204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Mughal W, Nguyen L, da Silva Rosa SC, Piotrowski S, Chapman D, Du M, Alli NS, Grigull J, Halayko AJ, Aliani M, Topham MK, Epand RM, Hatch GM, Kereliuk S, McDermott JC, Rampitsch C, Dolinsky VW, Gordon JW (2015) A conserved MADS-box phosphorylation motif regulates differentiation and mitochondrial function in skeletal, cardiac, and smooth muscle cells. Cell Death Dis 6:e1944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mazanek M, Mituloviæ G, Herzog F, Stingl C, Hutchins JR, Peters JM, Mechtler K (2007) Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis. Nat Protoc 2:1059–1069

    Article  CAS  PubMed  Google Scholar 

  10. Ficarro SB, Salomon AR, Brill LM, Mason DE, Stettler-Gill M, Brock A, Peters EC (2005) Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. Rapid Commun Mass Spectrom 19:57–71

    Article  CAS  PubMed  Google Scholar 

  11. Thingholm TE, Jensen ON, Robinson PJ, Larsen MR (2007) SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 7:661–671

    Article  PubMed  Google Scholar 

  12. Zhang H, Zhou H, Berke L, Heck AJR, Mohammed S, Scheres B, Menke FLH (2013) Quantitative phosphoproteomics after Auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth. Mol Cell Proteomics 12:1158–1169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Damerval C (1986) Technical improvements in two-dimensional electrophoresis increases the level of genetic variation detected in wheat seedling proteins. Electrophoresis 7:52–54

    Article  CAS  Google Scholar 

  14. Rampitsch C, Bykova NV (2009) Methods for functional proteomic analyses. In: Somers D et al (eds) Methods in molecular biology, vol 513. Humana press, Totowa NJ, pp 93–110

    Google Scholar 

  15. Kollipara L, Zahedi RP (2013) Protein carbamylation: in vivo modification or in vitro artefact? Proteomics 13:941–944

    Google Scholar 

  16. Boja ES, Fales HM (2001) Overalkylation of a protein digest with iodoacetamide. Anal Chem 73:3576–3582

    Article  CAS  PubMed  Google Scholar 

  17. Villén J, Gygi S (2008) The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 3:1630–1638

    Article  PubMed  PubMed Central  Google Scholar 

  18. Kalli A, Smith GT, Sweredoski MJ, Hess S (2013) Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res 12:3071–3086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Perkins D, Pappin D, Creasy D, Cottrell J (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567

    Article  CAS  PubMed  Google Scholar 

  20. Eng JK, McCormak AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989

    Article  CAS  PubMed  Google Scholar 

  21. Craig R, Cortens JP, Beavis RC (2004) Open source system for analyzing, validating and storing protein identification data. J Proteome Res 3:1234–1242

    Article  CAS  PubMed  Google Scholar 

  22. Keller BO, Sui J, Young AB, Whittal RM (2008) Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta 627:71–81

    Article  CAS  PubMed  Google Scholar 

  23. Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24:1285–1292

    Article  CAS  PubMed  Google Scholar 

  24. Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B (2011) Confident phosphorylation site localization using the Mascot delta score. Mol Cell Proteomics 10:M110.003830

    Article  PubMed  Google Scholar 

  25. Rampitsch C, Subramaniam R, Djuric-Ciganovic S, Bykova NV (2010) The phosphoproteome of Fusarium graminearum at the onset of nitrogen starvation. Proteomics 10:124–140

    Article  CAS  PubMed  Google Scholar 

  26. Villén J, Beausoleil SA, Gygi SP (2008) Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics 8:4444–4452

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

Funding for proteomics research to CR originates from Agriculture and Agrifood Canada. I thank Slavica Djuric-Ciganovic for critical comments on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Christof Rampitsch .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Rampitsch, C. (2017). Phosphoproteomics Analysis for Probing Plant Stress Tolerance. In: Sunkar, R. (eds) Plant Stress Tolerance. Methods in Molecular Biology, vol 1631. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7136-7_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7136-7_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7134-3

  • Online ISBN: 978-1-4939-7136-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics