title: Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis.
abstract: BACKGROUND
  How protein phosphorylation relates to kingdom/phylum divergence is largely unknown and the amino acid residues surrounding the phosphorylation site have profound importance on protein kinase-substrate interactions. Standard motif analysis is not adequate for large scale comparative analysis because each phophopeptide is assigned to a unique motif and perform poorly with the unbalanced nature of the input datasets.
  
  
  RESULTS
  First the discriminative n-grams of five species from five different kingdom/phyla were identified. A signature with 5540 discriminative n-grams that could be found in other species from the same kingdoms/phyla was created. Using a test data set, the ability of the signature to classify species in their corresponding kingdom/phylum was confirmed using classification methods. Lastly, ortholog proteins among proteins with n-grams were identified in order to determine to what degree was the identity of the detected n-grams a property of phosphosites rather than a consequence of species-specific or kingdom/phylum-specific protein inventory. The motifs were grouped in clusters of equal physico-chemical nature and their distribution was similar between species in the same kingdom/phylum while clear differences were found among species of different kingdom/phylum. For example, the animal-specific top discriminative n-grams contained many basic amino acids and the plant-specific motifs were mainly acidic. Secondary structure prediction methods show that the discriminative n-grams in the majority of the cases lack from a regular secondary structure as on average they had 88% of random coil compared to 66% found in the phosphoproteins they were derived from.
  
  
  CONCLUSIONS
  The discriminative n-grams were able to classify organisms in their corresponding kingdom/phylum, they show different patterns among species of different kingdom/phylum and these regions can contribute to evolutionary divergence as they are in disordered regions that can evolve rapidly. The differences found possibly reflect group-specific differences in the kinomes of the different groups of species.
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. 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. svante.resjo@slu.se.
authors.forename: Svante
authors.initials: S
authors.lastname: Resjö
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. erik.andreasson@slu.se.
authors.forename: Erik
authors.initials: E
authors.lastname: Andreasson
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D017360:Arabidopsis / Q000378:metabolism; D016000:Cluster Analysis; D016002:Discriminant Analysis; D056890:Eukaryota / Q000378:metabolism*; D019143:Evolution, Molecular; D006801:Humans; D010748:Phosphopeptides / Q000032:analysis / Q000737:chemistry; D010766:Phosphorylation; D010838:Phytophthora / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000378:metabolism
chemical_list: D010748:Phosphopeptides; D011506:Proteins