Proteomics assisted studies of the host nuclear proteome identifies candidate regulators of immunity modified during Phytophthora capsici-tomato interactions

In this study we have combined nuclei enrichment with quantitative proteomics to study tomato nuclear proteome dynamics during early infection with the devastating broad host-range oomycete pathogen Phytophthora capsici. Using this method we have identified hundreds of host nuclear proteins that show specific changes in abundance during P. capsici infection including proteins implicated in nucleic acid binding, oxidoreductase activity, helicase activity, RNA binding and transcription regulator activity. A number of these proteins have known links to plant immunity or defence signalling. We have confirmed the nuclear localisation of a selection of proteins which show P. capsici infection dependant changes in abundance and have examined the impact of their expression on resistance. As direct proof of biological relevance we demonstrate that in planta overexpression of an AT-hook family protein which decreased in abundance during infection, causes enhanced resistance to P. capsici. We conclude that organelle enrichment combined with quantitative proteomics represents a valuable strategy, suited to interrogate dynamic proteomes during stress, and allows the identification of promising targets to bolster immunity in crops.