Proteomic Analysis of Abiotic Stress in Grapevines

Proteomic studies in grapevines (Vitis vinifera) have become increasingly prevalent in recent years since the publication of the complete grape genome sequence. In our laboratory we have carried out a number of different studies involving analysis of differential protein expression in grape plants and cells, induced by exposure to different abiotic stress conditions. This has included detailed analysis of the response of grape cells to a wide range of temperature stresses, identification of proteins affected by changes in day length in riverbank grapes, and a detailed quantitative analysis of a series of different cultivars exposed to water deficit stress. This work was all performed using shotgun proteomics analysis with nanoLC-MS/MS, coupled with calculation and measurement of normalised spectral abundance factors using software developed in-house. This analytical pipeline enables the identification and quantitation of thousands of proteins simultaneously without the need for metabolic or chemical isotopic labelling. In this presentation we will present some highlights from these studies, focusing on the commonalities of the biological responses observed in these and other studies. We will also discuss statistical validation of protein expression changes, including recent work on the development of a procedure for estimation of false discovery at the protein quantitation level.