Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study

Abstract

Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with phosphorylated residues discovered through phosphoproteomic surveys. As a ubiquitous form of post-translational modification, phosphorylation by protein kinases is a crucial form of both discrete protein and whole metabolic or signaling pathway regulation. Despite the importance of protein phosphorylation, the relationships between these modifications are poorly understood at the proteomic scale. Through this work, a variety of phosphorylation site network visualization formats were developed to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, indicative of protein kinases acting on multiple targets within the pathway and playing an important regulatory role in quickly modulating different steps in the pathway in response to extra- or intra-cellular signals. Overall, this work may lead to streamlined workflows to connect tens of thousands of experimentally supported phosphorylation sites to thousands of protein kinases.