Starvation resistance in the nematodePristionchus pacificusrequires a conserved supplementary nuclear receptor

Abstract

Nuclear hormone receptors (NHRs) are a deeply-conserved superfamily of metazoan transcription factors, which fine-tune the expression of their regulatory target genes in response to a plethora of sensory inputs. In nematodes, NHRs underwent an explosive expansion and many species have hundreds ofnhrgenes, most of which remain functionally uncharacterized. However, recent studies elucidated that two sister receptors,Ppa-NHR-1 andPpa-NHR-40, are crucial down-stream regulators of feeding plasticity in the diplogastrid model organismPristionchus pacificus. In this study, we functionally characterizePpa-NHR-10, the closest paralog toPpa-NHR-1 andPpa-NHR-40, aiming to demonstrate that it too regulates aspects of feeding plasticity. We used CRISPR/CAS9-mediated mutagenesis to create knock-out mutations of this receptor and applied a combination of geometric morphometrics and unsupervised clustering to characterize potential mutant phenotypes. Surprisingly, we found thatPpa-NHR-10 is not involved in the regulation of plasticity in feeding structures. Instead, multiple RNA-seq experiments revealed that many of the target genes of this receptor are crucial for lipid catabolism. We hypothesized that their mis-regulation could affect the survival of mutant worms during starvation, where lipid catabolism is often essential. Using survival assays, we found that mutant worms indeed show drastically decreased starvation resistance, both as young adults and as dauer larvae. We also characterized genome-wide changes to the transcriptional landscape inP. pacificuswhen exposed to 24hrs of acute starvation, and found thatPpa-NHR-10 partially regulates some of these responses. Taken together, we were able to demonstrate thatPpa-NHR-10 is broadly required for starvation resistance and regulates different biological processes than its closest paralogsPpa-NHR-1 andPpa-NHR-40 and its one-to-one ortholog inCaenorhabditis elegans.This shows that, amongst distantly-related model nematodes, even deeply-conserved NHRs can regulate vastly distinct biological processes and that neither paralogs, nor one-to-one orthologs, may be adequate predictors of their biological functions.Author summaryWhen predicting the biological function of a gene (or the protein it encodes) we usually use its homologs for reference since it is likely that our gene or protein of interest has homologs in a different organism (orthologs) or in the same organism (paralogs), whose biological roles have already been characterized via molecular genetic interventions. However, predicting biological functions from homologs can have its limitations. In this study, we functionally characterized a conserved nuclear receptor,Ppa-NHR-10, in the nematodePristionchus pacificusand found that both dauer larvae (a specialized dispersal stage) and adult worms are less resistant to starvation if this receptor is experimentally rendered non-functional. Not only did these findings reveal thatPpa-NHR-10 is crucial for the worms to survive harsh conditions they would frequently encounter in the wild, they also demonstrated thatPpa-NHR-10’s homologs would not have been adequate predictors of its biological role: its homolog inCaenorhabditis elegansregulates a metabolic shunt pathway; its paralogs inP. pacificusregulate feeding plasticity. Thus, our data suggests that conserved nuclear receptors can functionally diversify across distantly-related nematodes, and that we cannot categorically infer their biological roles from well-studied homologs.