Construction of PDZ domain-ligand interaction network and comparative interactomics study to understand phenotypic differences between species

DoctorPDZ domains are one of the most common protein-protein interaction domains found in bacteria to humans, facilitating cell signaling or determination of receptor localization in key biological processes. By recognizing specific C-terminal residues on ligands, PDZ domains play critical roles in key biological processes such as signal transduction, synapse formation, protein trafficking, and cell polarity maintenance. Despite the extensive experimental and computational efforts to identify PDZ domain-ligand interactions, a quantitative PDZ domain-ligand selectivity map on a genome-wide scale is still absent. First, we developed a method that predicts the binding strength of PDZ domain-ligand interactions by combining a position weight matrix with a machine learning algorithm. Our predictions were validated through experimentally determined sets of PDZ ligands and correlated well with their binding affinities. By using this method, we constructed the first human PDZ domain-ligand interaction network (PDZNet) together with binding motif sequences and interaction strengths of ligands. PDZNet includes 1,213 interactions between 97 human PDZ proteins and 591 ligands that connect most PDZ protein-mediated interactions (98%) in a large single network via shared ligands. PDZNet will be a valuable resource to further characterize the organization of the PDZ domain-mediated signaling proteome. We implemented a web service at http://sbi.postech.ac.kr/pdz, which takes a PDZ domain sequence to provide the rank list of potential ligands. Second, we performed a comparative interactomics analysis of PDZ domain-ligand interactions by tracing changes in the C-terminal binding motif sequences of the PDZ ligands, which cause interaction rewiring in signaling circuits. Rewiring of interactions provides a simple mechanism for the development of new signaling circuits by redirecting information flows without a gain or loss of genes. Particularly, interactions mediated by short linear motifs can be easily changed by mutations, resulting in a rewiring of interactions. It is of great interest to understand how PDZ domain-ligand interactions emerged and how they become rewired across different species. We found that interaction rewiring by sequence mutation frequently occurred across species. The rewiring of PDZ domain-ligand interactions provided an effective means of functional innovations in nervous system development. We also found that components of PDZNet are highly associated with neurological diseases. Our findings provide empirical evidence for a network model that highlights the rewiring of interactions as a mechanism for the development of new protein functions and prompt new approach to study relationship of specific traits and phenotypic differences between species