PYR1 biosensor-driven genome-wide CRISPR screens for improved monoterpenoid production in Kluyveromyces marxianus

Abstract

Monoterpenoids are valued for their roles as flavors, fragrances, insecticides, and energy-dense fuels. Microbial biosynthesis offers sustainable biosynthesis routes for these important molecules, but production levels remain limited. Here, we introduce a biosensor-driven microbial engineering strategy to enhance monoterpenoid production, specifically targeting geraniol. Using mutagenized libraries of the PYR1 receptor--a versatile biosensor from plant ABA signaling pathways with a malleable binding pocket--we screened 24 monoterpenoids and identified PYR1 variants responsive to eight, including geraniol. A low background, highly selective geraniol-sensitive PYR1 variant was expressed in the thermotolerant yeast Kluyveromyces marxianus as a growth-based biosensor circuit, allowing for rapid strain engineering. By coupling the geraniol-sensitive PYR1 sensor with a genome-wide CRISPR-Cas9 mutagenesis approach, we identified six gene knockouts that enhance geraniol production, achieving up to a 2-fold increase in titer. This study demonstrates the power of the PYR1 biosensor platform to enable rapid strain engineering and the identification of mutants that improve titer of a desired metabolite.