From neuropeptide and receptor annotation to ligand-receptor pairing: a sequence- and structure-based framework for mapping the neuropeptide-receptor interactome in Gryllus bimaculatus

Neuropeptides and their G protein-coupled receptors (GPCRs) play a vital role in controlling various aspects of insect physiology and behavior. However, in Gryllus bimaculatus, an insect model organism and edible insect, mapping which peptide each receptor activates is challenging due to receptor sequence similarity. The researchers re-annotated a chromosome-scale genome with a BUSCO completeness score of 95.3% (up from 86.7% in a previous dataset) and curated 48 neuropeptide precursor families, comprising 51 loci, including seven previously unidentified.

Additionally, they curated 134 candidate GPCRs, encompassing 66 rhodopsin-class and 68 secretin-class receptors. By modeling all 15,946 peptide-receptor pairs using AlphaFold3 and Boltz-2, and scoring each interface with pLDDT and ipSAE, the researchers were able to create a comprehensive neuropeptide-receptor interactome catalogue.

Subsequently, they ranked these scores and cross-checked the top candidates for each family against a receptor phylogeny of known ligand specificity, resulting in a confident and phylogenetically related receptor for 27 out of 35 curated receptor groups. These matches were validated with existing deorphanization data and offered receptors for peptides previously lacking functional evidence.

All the annotation, curated peptide and receptor sets, as well as the ranked complexes, are now accessible through CricketBase (https://cricket.annotation.jp), a genome browser equipped with a structure viewer of peptide-receptor complexes. This resource will prove invaluable for G. bimaculatus endocrinology research and will serve as a model workflow for deorphanizing GPCRs in other non-model insects.