Relationship between perturbation specificity and functional dispensability in yeast phosphoproteome

Protein phosphorylation is crucial in many cellular functions. Although the existence of functionally dispensable phosphosites is well recognized, previous estimation of dispensable content in the phosphoproteome has not quantitatively assessed how functional dispensability of a phosphosite is related to the degree of its perturbation specificity, i.e., the number of environmental perturbations where the phosphosite is phosphorylated. Here, we address this question by integrating a high-quality, perturbation-specific yeast phosphoproteome with site-specific evolutionary rate relative to adjacent residues of the site in the protein sequence (denoted "relative evolutionary rate"), a proxy for functional dispensability. We observe extreme heterogeneity in perturbation specificity among phosphosites, where the majority of phosphosites are phosphorylated either under only a few perturbations (denoted "conditional phosphosites") or across nearly all perturbations (denoted "near-universal phosphosites"), yielding a bimodal distribution of perturbation specificity. Our evolutionary analyses reveal that, in disordered regions, perturbation specificity is a key correlate of functional dispensability of phosphosites. Conditional and near-universal phosphosites exhibit significantly higher and lower average relative evolutionary rate than all other experimental and literature-curated phosphoproteome data sets considered, respectively. These trends remain robust even when residue burial is controlled, suggesting that conditional and near-universal phosphosites contain the highest and the lowest levels of dispensable content in disordered regions, respectively, among all phosphoproteome data sets considered. Using the near-universal phosphosites and serine/threonine sites not known to be phosphorylated to set the lower and upper bounds of the dispensable content spectrum, we estimate that ∼30-40% of phosphosites in disordered regions of the yeast phosphoproteome are functionally dispensable.