Large scale analysis of the tomato membrane proteome during fruit ripening

As a step towards understanding the role of membrane proteins in tomato fruit ripening, a subcellular proteomic study was undertaken to provide a qualitative global analysis of total microsomes obtained from tomato mature green (MG) and red ripe (RR) fruit. Microsomes were fractionated using self-generating iodixanol gradient and a shotgun LC-MS/MS approach was used to identify tryptic peptide fragments of the collected fractions. About 2000 proteins from both MG and RR microsomes were identified, many of which are unique and developmental stage specific. Gene Ontology term analysis, used to categorize the proteomes with respect to subcellular localization, molecular functions and biological processes, showed that proteins related to response to biotic and abiotic stress, protein metabolism, cell developmental processes and transport were the most abundant. Moreover, several cell wall proteins that are known to be localized in the Golgi or other compartments of the secretory pathway, were identified. The relevance of some proteins belonging to the classes of signalling and response to stress, cellular trafficking and cell wall synthesis and modification is discussed.