Ecologically Guided Searches for New Riboswitch Functions

Riboswitches are structured RNA elements that regulate gene expression by directly binding ligands. Bioinformatics approaches have greatly accelerated the discovery of candidate riboswitches by searching for conserved RNA structures. However, discovering the ligand that binds to a conserved element remains challenging. Traditional approach search for clues to the binding partners of riboswitches by analyzing the function of downstream genes. This approach has proven highly successful, but poses challenges in poorly annotated genomes, such as from metagenomic samples, and may miss important environmentally delivered ligands. Here we propose to use ecological interactions to search for riboswitch functions. For our model system we will use herbivores which feed on sagebrush, highly defended by toxic chemicals known as plant secondary metabolites (PSM). We hypothesize that the microbial communities from these gut environments will contain riboswitches responding to the plant chemicals. Our collaborative research will produce shotgun metagenomics data from the fecal samples collected from animals ingesting sagebrush, bioinformatics searches for candidate riboswitch variants in the samples, and biochemical and biophysical validation of riboswitches using plant extracted chemicals. If successful, the research will produce new antibiotic candidates and targets, and will advance our understanding of how microbial communities contribute to the plant-herbivore arms race that drives biodiversity across the planet.