System-wide mapping of neuropeptide-GPCR interactions inC. elegans

Abstract

Neuropeptides are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many neuropeptides remain elusive, as our insight into neuropeptide-receptor interactions is limited and many peptide GPCRs in animal models and humans are still orphan receptors. Here we report a genome-wide neuropeptide-GPCR interaction map in C. elegans. By reverse pharmacology screening of over 55,384 possible interactions, we identify 461 cognate peptide-GPCR couples that uncover a broad signaling network with specific and complex combinatorial interactions encoded across and within single peptidergic genes. These interactions provide insights into neuropeptide functions and evolution. Combining our dataset with phylogenetic analysis supports peptide-receptor co-evolution and conservation of at least 14 bilaterian peptidergic systems in C. elegans. This resource lays a foundation for system-wide analysis of the peptidergic network.

The neuropeptidergic connectome ofC. elegans

“…(A) Datasets used to build the network in silico. Left: biochemical neuropeptide-GPCR interaction dataset defining 91 neuropeptide - G protein-coupled receptor (GPCR) pairs below 500 nM EC 50 affinity, coupling 51 GPCRs to 48 neuropeptides 64 . Neuropeptides from the same precursor gene (NPP) are considered the same.…”

“…For each dataset, it was necessary to threshold for biologically relevant interactions. For biochemical interactions, the raw dataset contained 461 neuropeptide-receptor pairs that showed dose-dependent activation with a half-maximal effective concentration (EC 50 ) ranging between 0.1 pM to 22 μM 64 . At the gene level, these pairs were encoded by 55 neuropeptide and 56 GPCR genes, with 148 unique gene-gene interactions.…”

“…By this criterion, we defined 91 individual neuropeptide-receptor gene couples, with a large number (51) of the predicted neuropeptide GPCRs having at least one identified ligand. The ligand-receptor interactions were complex, with several peptides activating more than one receptor (promiscuous receptors) and several receptors being activated by multiple peptides encoded by distinct precursor genes (versatile peptides) 64 .…”

“…The neuropeptide network used in this work was made using a similar approach to that used for the monoamines. The interactions between ligands and receptors were identified using a large-scale in vitro reverse pharmacology pipeline in which over 87% of the predicted peptide GPCRs were challenged with FMRFamide related peptides (FLP) and non-insulin non-FLP like peptides (NLP) 64 . Neuropeptide precursor and GPCR gene expression for the 302 neurons was extracted from the single-cell transcriptome data of the CeNGEN project (https://www.cengen.org) 40 .…”

“…The strains used in this study are listed in Supplementary Tables 1 and 2. 500 nM EC50 affinity, coupling 51 GPCRs to 48 neuropeptides 64 . Neuropeptides from the same precursor gene (NPP) are considered the same.…”