Skip to main content

Proteome Analysis of Arabidopsis Roots

  • Protocol
  • First Online:
Root Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1761))

Abstract

Plant health and development are directly depending on a plant’s ability to react to a constantly changing environment. Sensing of water and nutrition levels and of the biotic environment is vital for a plant, making the root one of the key plant organs. Proteins are the key molecules that play numerous roles in a cell’s everyday life. Quantitative proteome profiling of roots can provide a global overview on the molecular regulatory mechanisms and networks involved in plant growth and development and abiotic and biotic stress responses. Here, we provide a detailed proteomics workflow on Arabidopsis thaliana roots from plant growth up to proteomics data analysis.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Pacifici E, Polverari L, Sabatini S (2015) Plant hormone cross-talk: the pivot of root growth. J Exp Bot 66:1113–1121

    Article  CAS  PubMed  Google Scholar 

  2. Stahl Y, Simon R (2012) Peptides and receptors controlling root development. Philos Trans R Soc Lond Ser B Biol Sci 367:1453–1460

    Article  CAS  Google Scholar 

  3. Tian H, De Smet I, Ding Z (2014) Shaping a root system: regulating lateral versus primary root growth. Trends Plant Sci 19:426–431

    Article  CAS  PubMed  Google Scholar 

  4. Lavenus J, Goh T, Roberts I et al (2013) Lateral root development in arabidopsis: fifty shades of auxin. Trends Plant Sci 18:1360–1385

    Article  CAS  Google Scholar 

  5. Sozzani R, Iyer-Pascuzzi A (2014) Postembryonic control of root meristem growth and development. Curr Opin Plant Biol 17:7–12

    Article  PubMed  Google Scholar 

  6. De Smet I, Beeckman T (2011) Asymmetric cell division in land plants and algae: the driving force for differentiation. Nat Rev Mol Cell Biol 12:273–273

    Article  CAS  Google Scholar 

  7. Feder ME, Walser JC (2005) The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol 18:901–910

    Article  CAS  PubMed  Google Scholar 

  8. Jorrín-Novo JV, Pascual J, Sánchez-Lucas R et al (2015) Fourteen years of plant proteomics reflected in proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 15:1089–1112

    Article  CAS  PubMed  Google Scholar 

  9. Cox J, Hein MY, C a L et al (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13:2513–2526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Smaczniak C, Li N, Boeren S et al (2012) Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues. Nat Protoc 7:2144–2158

    Article  CAS  PubMed  Google Scholar 

  11. Zhang H, Zhou H, Berke L et al (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 

  12. Qian H, Lu H, Ding H et al (2015) Analyzing Arabidopsis Thaliana root proteome provides insights into the molecular bases of enantioselective imazethapyr toxicity. Sci Rep 5:11975

    Article  PubMed  PubMed Central  Google Scholar 

  13. Fromm S, Senkler J, Eubel H et al (2016) Life without complex I: proteome analyses of an Arabidopsis mutant lacking the mitochondrial NADH dehydrogenase complex. J Exp Bot 67:3079–3093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Walton A, Stes E, Goeminne G et al (2016) The response of the root proteome to the synthetic strigolactone GR24 in Arabidopsis. Mol Cell Proteomics 15:2744–2755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Tyanova S, Temu T, Sinitcyn P et al (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 13:731–740

    Article  CAS  PubMed  Google Scholar 

  16. LD V, Stes E, Van Bel M et al (2016) Up-to-date workflow for plant (Phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves. J Proteome Res 15:4304–4317

    Article  CAS  Google Scholar 

  17. LD V, Verstraeten I, Stes E et al (2017) Proteome profiling of wheat shoots from different cultivars. Front Plant Sci 8:1–11

    Google Scholar 

  18. Noble JE, Bailey MJAA (2009) Chapter 8 quantitation of protein. In: Methods Enzymol, 1st edn. Elsevier Inc., Amsterdam, pp 73–95

    Google Scholar 

  19. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11:2301–2319

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

L.D.V. is the recipient of a VIB International Ph.D. program fellowship. E.S. was a postdoctoral fellow of the Research Foundation-Flanders. Kris Gevaert and Ive De Smet contributed equally to this work.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ive De Smet .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Nikonorova, N., Vu, L.D., Stes, E., Gevaert, K., De Smet, I. (2018). Proteome Analysis of Arabidopsis Roots. In: Ristova, D., Barbez, E. (eds) Root Development. Methods in Molecular Biology, vol 1761. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7747-5_20

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7747-5_20

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7746-8

  • Online ISBN: 978-1-4939-7747-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics