Membrane proteomics: Use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties

Abstract

Recent efforts at the proteomic level were employed to describe the protein equipment of the plasma membrane of the model plant Arabidopsis thaliana. These studies had revealed that the plasma membrane is rich in extrinsic proteins but came up against two major problems: (i) few hydrophobic proteins were recovered in two-dimensional electrophoresis gels, and (ii) many plasma membrane proteins had no known function or were unknown in the database despite extensive sequencing of the Arabidopsis genome. In this paper, several methods expected to enrich a membrane sample in hydrophobic proteins were compared. The optimization of solubilization procedures revealed that the detergent to be used depends on the lipid content of the sample. The corresponding proteomes were compared with the statistical model AMMI (additive main effects with multiplicative interaction) that aimed at regrouping proteins according to their solubility and electrophoretic properties. Distinct groups emerged from this analysis and the identification of proteins in each group allowed us to assign specific features to several of them. For instance, two of these groups regrouped very hydrophobic proteins, one group contained V-ATPase subunits, another group contained proteins with one transmembrane domain as well as proteins known to interact with membrane proteins. This study provides methodological tools to study particular classes of plasma membrane proteins and should be applicable to other cellular membranes.

Proteomic Approach to Identify Novel Mitochondrial Proteins in Arabidopsis

“…To analyze gene functions, new approaches have been started, including the establishment of large Arabidopsis "knock out" pop- ulations and the development of DNA chips to monitor gene expression. Meanwhile, proteome projects were initiated to systematically characterize gene products of defined subproteomes from Arabidopsis (Robertson et al, 1997;Santoni et al, 1998Santoni et al, , 2000Peltier et al, 2000). The present paper reports the initiation of an Arabidopsis mitochondrial proteome project.…”

“…Hence, proteome research often is based on a subset of proteins of eukaryotic cells called "subproteome" (Cordewell et al, 2000;Jung et al, 2000). In plant biology, very successful subproteomic analyses were carried out for the cell wall, the plasma membrane, and the thylakoids (Robertson et al, 1997;Santoni et al, 1998Santoni et al, , 2000Peltier et al, 2000;Prime et al, 2000;van Wijk, 2000). During these investigations, hundreds of proteins were separated, several of which were identified for the first time.…”

A Plasma Membrane Syntaxin Is Phosphorylated in Response to the Bacterial Elicitor Flagellin

“…However, biochemical research on its protein composition is challenged by the low abundance and difficulty in handling of hydrophobic membrane proteins. Proteomic studies have identified a small number of true transmembrane proteins on two-dimensional gels (28,29). Using established protocols for the analysis of hydrophobic proteins, we obtained well resolved two-dimensional gels of carbonatewashed plasma membranes from cell cultures.…”

Proteomics for Protein Expression Profiling in Neuroscience

“…For neuroscientists, this represents a challenge because many proteins of interest in the brain are expressed at relatively low levels and are hydrophobic proteins. The effectiveness of 2-DE to examine membrane proteins is limited due to poor solubilization of hydrophobic proteins (99,100). New detergents and electrophoresis methods can aid in examining hydrophobic proteins, but more improvements are needed (101).…”