Chloroform-assisted phenol extraction improving proteome profiling of maize embryos through selective depletion of high-abundance storage proteins

PLoS One. 2014 Nov 11;9(11):e112724. doi: 10.1371/journal.pone.0112724. eCollection 2014.

Abstract

The presence of abundant storage proteins in plant embryos greatly impedes seed proteomics analysis. Vicilin (or globulin-1) is the most abundant storage protein in maize embryo. There is a need to deplete the vicilins from maize embryo extracts for enhanced proteomics analysis. We here reported a chloroform-assisted phenol extraction (CAPE) method for vicilin depletion. By CAPE, maize embryo proteins were first extracted in an aqueous buffer, denatured by chloroform and then subjected to phenol extraction. We found that CAPE can effectively deplete the vicilins from maize embryo extract, allowing the detection of low-abundance proteins that were masked by vicilins in 2-DE gel. The novelty of CAPE is that it selectively depletes abundant storage proteins from embryo extracts of both monocot (maize) and dicot (soybean and pea) seeds, whereas other embryo proteins were not depleted. CAPE can significantly improve proteome profiling of embryos and extends the application of chloroform and phenol extraction in plant proteomics. In addition, the rationale behind CAPE depletion of abundant storage proteins was explored.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Chemical Fractionation / methods*
  • Chloroform / chemistry*
  • Electrophoresis, Gel, Two-Dimensional
  • Glycine max / chemistry
  • Molecular Sequence Data
  • Phenol / chemistry
  • Proteomics / methods*
  • Seed Storage Proteins / chemistry*
  • Seeds / chemistry*
  • Tandem Mass Spectrometry
  • Zea mays / chemistry*

Substances

  • Seed Storage Proteins
  • Phenol
  • Chloroform
  • vicilin protein, plant

Grants and funding

This work was supported by National Natural Science Foundation of China (http://www.nsfc.gov.cn/; grant no. 31371543, to WW), Plan for Scientific Innovation Talent of Henan Province (http://www.hnkjt.gov.cn/; grant no. 144200510012, to WW) and State Key Laboratory of Crop Biology in Shandong Agricultural University (http://klab.sdau.edu.cn/; grant no. 2012KF01, to WW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.