Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis

Abstract

In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.

Modular metabolite assembly in C. elegans depends on carboxylesterases and formation of lysosome-related organelles

“…3c, S15b). These results indicate that CEST-2.2 is required specifically for biosynthesis of the amide linkage between the carboxy terminus of ascr#7 and PABA derivatives, in contrast to the implied functions of UAR-1, CEST-8, CEST-3, and CEST- 9.2, which are involved in the formation of ester bonds between various head groups and the 4′- hydroxy group of ascarylose 26, 28 .…”

“…Similarly, tiglic acid is preferentially attached to indole and tyramine glucosides but not to anthranilic acid glucosides (Table 1). Given that 4′- modification of ascarosides in P. pacificus and C. elegans require cest homologs, we hypothesized that the biosynthesis of other modular ascarosides as well as the newly identified glucosides may be under the control of cest family enzymes 26, 28 . From a list of 44 uar-1 homologs from BLAST analysis (Table 2), we selected seven for further study (Fig.…”

“…Parallel studies of other Caenorhabditis species 23–25 and Pristionchus pacificus 26 , a nematode species being developed as a satellite model system to C. elegans 27 , revealed that production of modular ascarosides is widely conserved among nematodes. Leveraging the high genomic diversity of sequenced P. pacificus isolates, genome-wide association studies coupled to metabolomic analysis revealed that uar-1 , a carboxylesterase from the α/ß-hydrolase superfamily with homology to cholinesterases (AChEs), is required for 4′-attachment of an ureidoisobutyryl moiety to a subset of ascarosides, e.g.…”

“…ubas#3 ( 4 , Fig. 1c) 26 . Homology searches revealed a large expansion of c arboxyl est erase ( cest ) homologs in P. pacificus as well as C. elegans (Fig.…”

Adult Influence on Juvenile Phenotypes by Stage-Specific Pheromone Production

“…Subsequent studies revealed that specific NDMMs also regulate other life history traits, such as mating ( Chasnov et al., 2007 , Izrayelit et al., 2012 ), social behavior ( Srinivasan et al., 2012 ), and developmental speed ( Ludewig et al., 2017 ). Although NDMMs are broadly conserved ( Choe et al., 2012 , Dong et al., 2018 , Markov et al., 2016 ), inter- and intraspecific competition have driven the evolution of distinct response regimes (different levels of sensitivity to the same pheromone, or sensitivity to different pheromones) for the same phenotypes ( Bose et al., 2014 , Choe et al., 2012 , Diaz et al., 2014 , Falcke et al., 2018 , Greene et al., 2016 ). In addition, distinct plastic phenotypes have evolved that are regulated by more complex ascaroside structures ( Bose et al., 2012 ).…”