Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains

Abstract

Zona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. While some biomedically-relevant ZP modules are well-studied, little is known about the protein family’s broad-scale diversity and evolution. The increasing availability of sequenced genomes from “non-model” systems provides a valuable opportunity to address this issue, and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains—which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation—can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.

Form and function of the apical extracellular matrix: new insights from Caenorhabditis elegans, Drosophila melanogaster, and the vertebrate inner ear

“…Recent bioinformatic analysis has enumerated components of the C. elegans ECM (including aECMs), predicting a total “matrisome” of over 700 proteins 10 . The 43 C. elegans ZP proteins have been further classified by phylogenetic methods 11 , 12 . This “parts list” for C. elegans aECMs remains dauntingly complex, with functional or expression data lacking for many proteins.…”

A C. elegans Zona Pellucida domain protein functions via its ZPc domain

“…Initial surveys of ZP proteins across phyla suggested that some contain ZPn domains without ZPc domains, and yet are still capable of polymerization [36], while proteins with only ZPc domains were not thought to exist [30]. However, we and others found that C. elegans does have five predicted ZPc-only proteins [34,68]. In proteins like uromodulin that have polymerizing ZPn domains, ZPc domains are thought to inhibit the ZPn domain [30].…”

“…However, we and others found that C . elegans does have five predicted ZPc-only proteins [ 34 , 68 ]. In proteins like uromodulin that have polymerizing ZPn domains, ZPc domains are thought to inhibit the ZPn domain [ 30 ].…”

Characterization of thePristionchus pacificus“epigenetic toolkit” reveals the evolutionary loss of the histone methyltransferase complex PRC2

“…The nematode Pristionchus pacificus was established in the 1990's as a comparative system to the model nematode Caenorhabditis elegans (last sharing a common ancestor 80-200 mya) (Howard et al 2022). Having two divergent, experimentally tractable model organisms in the same Order has facilitated functional evolutionary and developmental (evo-devo) studies leading to several unexpected findings (Markov et al 2016;Rošić et al 2018;Beltran et al 2019;Bui and Ragsdale 2019;Hong et al 2019;Weadick 2020;Sun et al 2021;Lo et al 2022). For example, early studies on vulva development revealed the extent of developmental systems drift, whereby the genetic underpinnings of a trait diverge even as the trait itself is conserved (Wang and Sommer 2011;Sommer 2012).…”