Plant Proteomics

An understanding of gene function requires a complementation of gene and gene expression analysis by the systematic analysis of proteins. Progress in plant proteomics has been lagging behind animal and microbial proteomics due to the lack of plant genome data and the problems involved in successful protein extraction from plant material. With the sequencing of more and more plant genomes, this slow progress will soon be overcome. The moss Physcomitrella patens is a model organism in the field of plant functional genomics. P. patens is the first seedless plant for which the complete genome was sequenced. Genome annotation is currently in progress. While identification of proteins requires knowledge of all coding genes of the organism under study, gene annotation and functional characterization benefit greatly from the findings of proteome analysis. The proteome of P. patens is accessible and approaches are under way to increase the spectrum of proteomic methods applied to this plant. Here we provide a protocol for the extraction of proteins from P. patens and describe the basic and still most important method of proteome analysis, two-dimensional polyacrylamide electrophoresis of proteins. As this technique (not entirely unjustifiably) has the reputation of being unpredictably complicated, we provide a detailed protocol intended to reduce the reluctance that many scientists may have in using this technique.