Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene)

Some genes encoding proteins within the co-evolved pre- and postsynaptic compartments are present in genomes long preceding the origination of the synapse within the animal kingdom. DLG4, gene encoding PSD-95, is one of the most abundant synaptic proteins. It is a MAGUK family member that shares a conserved domain structure comprised of one or multiple PDZ domains, a Src homology 3 (SH3), and a guanylate kinase (GK) domain. Here, we construct the phylogeny of the tri-PDZ domains in DLG4 to its deep ancestral origin in Filozoa, which includes animals and their nearest unicellular relatives. PDZ domain architecture appears to be a strong organizing feature of this gene lineage that originated with a single ancestral PDZ3-like domain in Capsaspora owczarzaki from which PDZ1 and PDZ2 were derived. The strong conservation of individual PDZ domain identities was captured by Evolutionary Scale Modeling (ESM2) across the boundary to the animal kingdom, corroborating distinct clades formed by the divergence of PDZ1, PDZ2, and PDZ3 in the phylogeny. CRIPT, PDZ3 ligand, is present in all Filozoa genomes studied here. AlphaFold2 Multimer demonstrates conserved binding function; however, conserved binding does not completely depend on either sequence motifs or hydrophobicity profiles. Rather, the most conserved feature is hydrogen bonds at the 0 and -2 positions of the ligand as an ancient foundational innovation for PDZ3 ligand interaction. Hydrogen bonds may loosen the sequence requirements for binding to allow a more extensive search space for protein-protein interactions that enhance fitness before the mutations that secure those interactions occur.