Evolutionary rate covariation analysis of E-cadherin identifies Raskol as regulator of cell adhesion and actin dynamics inDrosophila

Abstract

The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link cortical actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies genes with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify genes with evolutionary histories similar to shotgun (shg), which encodes the Drosophila E-cadherin (DE-Cad) ortholog. Core adherens junction components α-catenin and p120-catenin displayed strong ERC correlations with shg, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the shg ERC profile revealed a collection of genes not previously associated with shg function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidate genes by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-Cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol (“to split” in Russian) and show that it regulates DE-Cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-Cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.Author SummaryThe establishment of intercellular adhesions facilitated the genesis of multicellular organisms. The adherens junction, which links the actin cytoskeletons of neighboring cells, arose early in the evolution of multicellularity and selective pressures have shaped its function and molecular composition over time. In this study, we used evolutionary rate covariation (ERC) analysis to examine the evolutionary history of the adherens junction and to identify genes that coevolved with the adherens junction gene shotgun, which encodes the Drosophila E-cadherin (DE-Cad). ERC analysis of shotgun revealed a collection of genes with similar evolutionary histories. We then tested the role of these genes in border cell migration in the fly egg chamber, a process that requires the coordinated regulation of cell-cell adhesion and cell motility. Among these, we found that a previously uncharacterized gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates the collective cell migration of border cells, stabilizes cell-cell adhesions and regulates the actin dynamics. Our results demonstrate that components of the adherens junction share an evolutionary history and that ERC analysis is a powerful method to identify novel components of cell adhesion complexes in Drosophila.

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter

“…In the course of the present studies, we used ERC, a bioinformatics assay, to predict the localization of a poorly understood ion transporter. While ERC has been described and tested before [23,[25][26][27][28][29][30], our approach utilized a novel idea that tracking evolutionary histories of functionally linked proteins may inform their functional context, such as localization. Therefore, using this approach we were able to predict protein localization in the absence of obvious clearly defined functional domains.…”

“…It is also important to note that many, but not all, recognized functional relationships between genes are reflected by high ERC correlations. Because of its predictive capability in some pathways, ERC has been used to identify the functions of uncharacterized genes, including novel DNA damage-induced apoptosis suppressor, sex peptide network components, regulators of cell adhesion, mitochondrial components and ion and aminoacid transporters [23,[25][26][27][28][29][30]. ERC is calculated as correlation between evolutionary rates throughout a phylogeny.…”

Complex basis of hybrid female sterility and Haldane’s rule inHeliconiusbutterflies: Z-linkage and epistasis

“…Within the proximal epistatic Z-linked QTL at 4.65 cM, we identified only one candidate gene, magu , mutants of which are known to cause defective border cell migration in D. melanogaster (Raza et al ., 2019). Within the distal Z-linked QTL at 55.08 cM, 8 candidate genes were identified.…”

ADrosophilaRNAi screen reveals conserved glioblastoma-related adhesion genes that regulate collective cell migration

“…Cell-cell adhesion is essential for cells to stay connected during cohesive collective migration (Friedl and Mayor 2017). Reduction (or loss) of adhesion genes, such as E-cadherin ( Drosophila shotgun [ shg ]), disrupts the integrity of the cluster and blocks the migration of the border cell cluster to the oocyte (Figure 1, D and E) (Niewiadomska et al 1999; Sarpal et al 2012; Desai et al 2013; Cai et al 2014; Chen et al 2020, Raza et al 2019). Many adhesion genes are conserved from flies to humans and could contribute to both border cell migration and GBM invasion (Figure 1F).…”