Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies

  • Eman Elagamey
  • Kanika Narula
  • Niranjan Chakraborty
  • Subhra Chakraborty
Part of the Methods in Molecular Biology book series (MIMB, volume 2057)


Understanding molecular mechanisms and cellular metabolism in varied plant processes necessitates knowledge of the expressed proteins and their subcellular distribution. Spatial partitioning of organelles generates an enclosed milieu for physiochemical reactions designed and tightly linked to a specific organelle function. Of which, extracellular matrix (ECM)/cell wall (CW) is a dynamic and chemically active compartment. The ECM proteins are organized into complex structural and functional networks involved in several metabolic processes, including carbon and nitrogen metabolism. Organellar proteomics aim for comprehensive identification of resident proteins that rely on the isolation of highly purified organelle free from contamination by other intracellular components. Extraction and isolation of plant ECM proteins features key caveats due to the lack of adjoining membrane, the presence of a polysaccharide–protein network that traps contaminants, and the existence of high phenolic content. Furthermore, due to diverse biochemical forces, including labile, weakly bound and strongly bound protein in the protein–polysaccharide matrix different elution procedures are required to enrich ECM proteins. Here, we describe a method that allows efficient fractionation of plant ECM, extraction of ECM proteins and protein profiling from variety of crop plants, including rice, chickpea and potato. This method can easily be adapted to other plant species for varied experimental conditions.

Key words

Plant Organellar proteomics Extracellular matrix Cell wall Protein enrichment Gel electrophoresis Mass spectrometry 



This work was supported by grants from National Institute of Plant Genome Research, New Delhi, India and Department of Biotechnology, Govt. of India (No. BT/PR10796/BRB/10/621/2008, BT/HRD/35/01/05/2013 and BT/PR23748/BPA/118/345/2017) to S.C. E.E. was the recipient of postdoctoral fellowship from DBT-TWAS. K.N. is the recipient of postdoctoral fellowship from Department of Biotechnology (DBT), Govt. of India. The authors also thank Jasbeer Singh for illustrations and graphical representations in the manuscript.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Eman Elagamey
    • 1
    • 2
  • Kanika Narula
    • 1
  • Niranjan Chakraborty
    • 1
  • Subhra Chakraborty
    • 1
  1. 1.National Institute of Plant Genome ResearchNew DelhiIndia
  2. 2.Plant Pathology Research InstituteAgricultural Research Center (ARC)GizaEgypt

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