Differential isolation and identification of PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana using an agarose-phosphatidylinositol-phosphate affinity chromatography

J Proteomics. 2013 Oct 8;91:580-94. doi: 10.1016/j.jprot.2013.08.020. Epub 2013 Sep 2.

Abstract

A phosphatidylinositol-phosphate affinity chromatographic approach combined with mass spectrometry was used in order to identify novel PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana suspension cell extracts. Most of the phosphatidylinositol-phosphate interacting candidates identified from this differential screening are characterized by lysine/arginine rich patches. Direct phosphoinositide binding was identified for important membrane trafficking regulators as well as protein quality control proteins such as the ATG18p orthologue involved in autophagosome formation and the lipid Sec14p like transfer protein. A pentatricopeptide repeat (PPR) containing protein was shown to directly bind to PI(3,5)P2 but not to PI(3)P. PIP chromatography performed using extracts obtained from high salt (0.4M and 1M NaCl) pretreated suspensions showed that the association of an S5-1 40S ribosomal protein with both PI(3)P and PI(3,5)P2 was abolished under salt stress whereas salinity stress induced an increase in the phosphoinositide association of the DUF538 domain containing protein SVB, associated with trichome size. Additional interacting candidates were co-purified with the phosphoinositide bound proteins. Binding of the COP9 signalosome, the heat shock proteins, and the identified 26S proteasomal subunits, is suggested as an indirect effect of their interaction with other proteins directly bound to the PI(3)P and the PI(3,5)P2 phosphoinositides.

Biological significance: PI(3,5)P2 is of special interest because of its low abundance. Furthermore, no endogenous levels have yet been detected in A. thaliana (although there is evidence for its existence in plants). Therefore the isolation of novel interacting candidates in vitro would be of a particular importance since the future study and localization of the respective endogenous proteins may indicate possible targeted compartments or tissues where PI(3,5)P2 could be enriched and thereafter identified. In addition, PI(3,5)P2 is a phosphoinositide extensively studied in mammalian and yeast systems. However, our knowledge of its role in plants as well as a list of its effectors from plants is very limited.

Keywords: ARM; Arabidopsis thaliana; Armadillo repeat; COP9 signalosome complex subunit 3/FUSCA11; COP9 signalosome complex subunit 4; CSN3; CSN4; HEAT; HSF; HSP; Huntingtin–EF3–PP2A–TOR1; PCaP; PI(3)P; PI(3,4,5)P(3); PI(3,5)P(2); PIP; PPIase; PPR; Plant; SUMO; Stress; heat shock factor; heat shock protein; pentatricopeptide repeat; peptidyl prolyl-cis-trans isomerase; phosphatidylinositol-3,4,5-trisphosphate; phosphatidylinositol-3,5-bisphosphate; phosphatidylinositol-3-phosphate; phosphatidylinositol-phosphate; plasma membrane-associated cation-binding protein; small ubiquitin-like modifier.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / metabolism
  • Chromatography, Affinity / methods*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Glutathione Transferase / metabolism
  • Lipids / chemistry
  • Molecular Sequence Data
  • Phosphatidylinositol Phosphates / chemistry*
  • Phosphatidylinositols / chemistry
  • Protein Binding
  • Proteome
  • Proteomics
  • Sepharose / chemistry*

Substances

  • Arabidopsis Proteins
  • Lipids
  • Phosphatidylinositol Phosphates
  • Phosphatidylinositols
  • Proteome
  • phosphatidylinositol 3,5-diphosphate
  • phosphatidylinositol 3-phosphate
  • Sepharose
  • Glutathione Transferase