The evolution of the GPCR signaling system in eukaryotes: modularity, conservation, and the transition to metazoan multicellularity

Abstract

The G-protein-coupled receptor (GPCR) signaling system is one of the main signaling pathways in eukaryotes. Here, we analyze the evolutionary history of all its components, from receptors to regulators, to gain a broad picture of its system-level evolution. Using eukaryotic genomes covering most lineages sampled to date, we find that the various components of the GPCR signaling pathway evolved independently, highlighting the modular nature of this system. Our data show that some GPCR families, G proteins, and regulators of G proteins diversified through lineage-specific diversifications and recurrent domain shuffling. Moreover, most of the gene families involved in the GPCR signaling system were already present in the last common ancestor of eukaryotes. Furthermore, we show that the unicellular ancestor of Metazoa already had most of the cytoplasmic components of the GPCR signaling system, including, remarkably, all the G protein alpha subunits, which are typical of metazoans. Thus, we show how the transition to multicellularity involved conservation of the signaling transduction machinery, as well as a burst of receptor diversification to cope with the new multicellular necessities.

Keywords: GRK; Ric8; arrestin; heterotrimeric G protein complex; phosducin.

Fig. 1.—

Schematic representation of the GPCR signaling pathway. Protein families belonging to similar functional categories are grouped as specified in the color legend.

Fig. 2.—

Distribution and abundance of GPCR signaling components in 78 eukaryotic genomes. Numbers and abundance of domain containing proteins are depicted according to the color legend in the upper left, being black absence of the given domain in a given species. Yellow color indicates smaller amounts, whereas the scale to purple indicates more abundance. The various domains are grouped into functional modules specified in figure 1, as shown in the schema at the bottom right. Species marked with an asterisk are only covered by RNA-seq data, therefore gene absence is not definitive. The original numbers of the heatmap are available at supplementary table S1, Supplementary Material online.

Fig. 3.—

Conservation of the domain architecture of different GPCR signaling components across eukaryotic genomes. A black dot indicates the presence of a given domain architecture. A white dot refers to similar domain architecture, Tyrosine Kinase instead of Serine/Threonine kinase in the case of Choanoflagellate GRK-like genes. For simplicity, only the most common architectures are shown. The percentage of genes found with a given architecture within a family is indicated at the bottom part of the table, as well as the total number of genes within the family. GPM in the first column of GoLoco motif containing proteins stands for G Protein Modulator/Rapsynoid. The complete domain architectures of the GPCR signaling system components are found in supplementary figures S3, S4, and S6, Supplementary Material online.

Fig. 4.—

Maximum likelihood (ML) phylogenetic tree inferred by the G protein alpha subunit. Different eukaryotic lineages are represented by a color code depicted in the legend. Within the gene family clades, the specific taxonomic groups which comprise eukaryotic lineages represented in that clade (i.e., eumetazoans and placozoans) are shown on the right. Nodal supports indicate 100-replicate ML bootstrap support and Bayesian posterior probability (BPP). Supports are only shown for nodes recovered by both ML and Bayesian inference, with BPP > 0.9.

Fig. 5.—

Schematic representation of the functional modules in eukaryotic lineages that were analyzed in the study. Green boxes indicate the presence, white the absence, and half-filled squares the presence with some simplification or uncertain affiliation. Asterisks in Arrestin and phosducin rows indicate the presence of orthologs of a subfamily (B-Arrestins and Phosducin-I clade), as discussed in the main text. In the upper part of the table, red dots indicate full reduction of GPCR signaling and green dots indicate severe simplifications but with some conserved functional modules.

Fig. 6.—

Cladogram representing the major patterns of evolution of GPCR signaling components in a eukaryotic phylogeny. Colored boxes with white text indicate specific components defined by a domain, whereas colored boxes with black text refer to specific gene family acquisitions. Green and red boxes depict gain and loss of domains, respectively, and blue boxes depict significant enrichments of the component shown, according to a Wilcoxon rank-sum test, with P value threshold of <0.01. Additionally, we show in the upper part a selected set of conserved GPCR architectures placed where they must have appeared according to Dollo Parsimony.

Fig. 7.—

Graphic depicts the median number of GPCR signaling components in opisthokont lineages. Total numbers of G protein alpha, beta, and gamma subunits are comprised in the heterotrimeric G proteins category; RGS and Go-Loco-motif containing proteins are comprised in regulators of G proteins category; and GPCR types presented in figure 3 are comprised in GPCR category. Median values were obtained using all taxa of a given clade as shown in the supplementary table S1, Supplementary Material online.