title: Phytophthora infestans specific phosphorylation patterns and new putative control targets.
abstract: In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation.
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. Electronic address: itziar.frades@gmail.com.
authors.forename: Itziar
authors.initials: I
authors.lastname: Frades
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Andreasson
mesh_terms: D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D010750:Phosphoproteins / Q000032:analysis*; D010766:Phosphorylation; D055750:Phytophthora infestans / Q000737:chemistry*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000032:analysis*
chemical_list: D010750:Phosphoproteins; D020543:Proteome
keywords: Crinklers; Discriminative n-grams; Pesticide targets; Phosphoproteomics; small RNA