Journal Article

Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Furches, Anna, Teixeira Prates, Erica, Zhao, Nan, Galanie, Stephanie, Saint-Vincent, Patricia M. B., Kalluri, Udaya C., Muchero, Wellington, Ranjan, Priya, Jones, Piet, Aldridge, Jessa L., Jacobson, Daniel A., Tschaplinski, Timothy J., Kainer, David, Martin, Madhavi Z., Chen, Jin-Gui, Labbe, Audrey

2023

Overview

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme–substrate relationships. We focus on uridine diphosphate–glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa , presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: Biofuels / Biosynthesis / Candidates / Cell walls / Cellular stress response / Crop production / Energy crops / Enzymatic activity / Enzymes / Flavonoids / Flowers & plants / functional genomics / Genes / Genetics / Genome-wide association studies / Genomes / Genomics / Glycosylation / glycosyltransferase / GWAS / high throughput / Lignans / Mass spectrometry / Metabolism / metabolite-gene validation / Metabolites / Metabolomics / Phenotypes / Phylogenetics / Plant hormones / Plant Science / Plant species / Populus / Populus trichocarpa / Salicylic acid / Scientific imaging / Secondary metabolites / Substrate specificity / Substrates / Uridine / Woody plants