Phosphoproteomic Analysis of Potato Tuber Reveals a Possible Correlation Between Phosphorylation Site Occupancy and Protein Attributes

Protein phosphorylation is a critical post-translational modification in all aspects of plant biology. The position of the phosphorylated site is an essential characteristic of phosphoproteins. The distribution of phosphosites is associated with both protein sequences and functions. Proteomics and multivariate data analysis were performed on phosphorylated proteins to investigate the relationship between phosphosites and protein attributes in potato tubers. A total of 488 phosphoproteins were identified. In total, 1028 of serine and threonine phosphorylation sites contained 676 phosphorylation sites outside of the predicted homology domain. All phosphoproteins shared 7 common phosphorylation motifs ([SP], [RxxSP], [GSP], [SSP], [RxxS], [SDxE], and [TP]). These motifs participated in a variety of metabolic processes. Phosphorylated proteins were classified into some important pathways by GO and KEGG enrichment analysis, including glucose metabolism, mRNA production, and the MAPK pathway. OPLS models were employed to identify a correlation between the phosphosites and various protein attributes. Phosphorylation sites of transcription and translation protein were located at 13% and 98% positions in the proteins, respectively. The position was a vital region of signal transduction protein at 89% in the phosphoprotein. Moreover, the C-terminal region was closely correlated with phosphoproteins of protein biogenesis and storage. These results suggest that the frequency distribution of phosphosites remained stable along the sequences of proteins. The phosphorylation of serine/threonine residues occurs readily in disordered regions at N- and C-termini of proteins. N- and C-termini of proteins represent a possible vital region of phosphorylation for the three types of protein functions in potato tubers.