Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast

作者：Douglas A. Higgins, Megan K. M. Young, Mary Tremaine, Maria Sardi, Jenna M Fletcher, M. Dorothy Agnew, Lisa Liu, Quinn Dickinson, David Peris, Russell L. Wrobel, Chris Todd Hittinger, Audrey P. Gasch, Steven W. Singer, Blake A. Simmons, Robert Landick, Michael P. Thelen, Trey K. Sato · 发表于：Genetics · 年份：2018 · DOI：10.1534/genetics.118.301161 · 被引用次数：42 · 研究领域：Biofuel production and bioconversion、Ionic liquids properties and applications、Microbial Metabolic Engineering and Bioproduction

Abstract Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affe...