Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast

Abstract

Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.