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Genetics. 2018 Sep;210(1):219-234. doi: 10.1534/genetics.118.301161. Epub 2018 Jul 25.

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

Author information

1
Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608.
2
Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550.
3
Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.
4
Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726.
5
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California 94720.
6
Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53726.
7
Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53726.
8
Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608 thelen1@llnl.gov tksato@glbrc.wisc.edu.
9
Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726 thelen1@llnl.gov tksato@glbrc.wisc.edu.

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 affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.

KEYWORDS:

Saccharomyces cerevisiae; biofuels; ionic liquid; major facilitator superfamily; natural variation; toxin tolerance; yeast

PMID:
30045857
PMCID:
PMC6116967
DOI:
10.1534/genetics.118.301161
[Indexed for MEDLINE]
Free PMC Article

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