A High Content in Lipid-modified Peripheral Proteins and Integral Receptor Kinases Features in the Arabidopsis Plasma Membrane Proteome

Anne Marmagne,Myriam Ferro,Thierry Meinnel,Christophe Bruley,Lauriane Kuhn,Jérome Garin,Hélène Barbier-Brygoo,Geneviève Ephritikhine

doi:10.1074/mcp.m700099-mcp200

Abstract

The proteomics of plasma membrane has brought to date only scarce and partial information on the actual protein repertoire. In this work, the plant plasma membrane proteome of Arabidopsis thaliana was investigated. A highly purified plasma membrane fraction was washed by NaCl and Na2CO3 salts, and the insoluble fractions were further analyzed by nano-LC-MS/MS. With 446 proteins identified, we hereby describe the largest plasma membrane proteome diversity reported so far. Half of the proteins were predicted to display transmembrane domains and/or to be anchored to the membrane, validating a posteriori the pertinence of the approach. A fine analysis highlighted two main specific and novel features. First, the main functional category is represented by a majority of as yet unreported signaling proteins, including 11% receptor-like kinases. Second, 16% of the identified proteins are predicted to be lipid-modified, specifically involving double lipid linkage through N-terminal myristoylation, S-palmitoylation, C-terminal prenylation, or glycosylphosphatidylinositol anchors. Thus, our approach led for the first time to the identification of a large number of peripheral proteins as part of the plasma membrane and allowed the functionality of the plasma membrane in the cell context to be reconsidered.

Highlights

The proteomics of plasma membrane has brought to date only scarce and partial information on the actual protein repertoire
A plasma membrane (PM) Proteome Derived from Salt Treatment-based Enrichment: Identification of Proteins Located in the Plasma Membrane
PM and Endomembranes—Proteins participating in the sequential steps of endocellular trafficking and secretion were identified: (i) subunits Sec5, Sec6, Sec8, and Sec10 of the exocyst complex involved in polarized exocytosis at the PM [85], (ii) several SNARE proteins, such as VAMP721 and SYP111, involved in specific vesicle fusion with the PM, (iii) dynamin-like proteins (ADL2b and ADL3) that might be involved in clathrin-mediated vesicle trafficking together with some of the new proteins identified in the present proteome, such as clathrin small chain (At4g08520), ␤-adaptin (At4g23460), and clathrin heavy chain (At3g11130), and (iv) other proteins such as Sec12-2 and SARA1B involved in vesicle formation from the ER to the Golgi compartments [54, 86]

Summary

Introduction

The proteomics of plasma membrane has brought to date only scarce and partial information on the actual protein repertoire. About 100 putative proteins were identified as part of the hydrophobic plasma membrane proteome isolated from Arabidopsis cell suspensions, 95% of which were yet unidentified proteins [9].

Results

Conclusion