Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Rui Pereira; Yongjun Wei; Elsayed Mohamed; Mohammad Radi; Carl Malina; Markus J Herrgård; Adam M Feist; Jens Nielsen; Yun Chen

doi:10.1016/j.ymben.2019.09.008

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Metab Eng. 2019 Dec:56:130-141. doi: 10.1016/j.ymben.2019.09.008. Epub 2019 Sep 21.

Authors

Rui Pereira¹, Yongjun Wei², Elsayed Mohamed³, Mohammad Radi³, Carl Malina², Markus J Herrgård³, Adam M Feist⁴, Jens Nielsen⁵, Yun Chen⁶

Affiliations

¹ Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden.
² Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
³ The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark.
⁴ The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; Department of Bioengineering, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093, USA.
⁵ Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen N, Denmark.
⁶ Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden. Electronic address: yunc@chalmers.se.

PMID: 31550508
DOI: 10.1016/j.ymben.2019.09.008

Abstract

Improving the growth phenotypes of microbes in high product concentrations is an essential design objective in the development of robust cell factories. However, the limited knowledge regarding tolerance mechanisms makes rational design of such traits complicated. Here, adaptive laboratory evolution was used to explore the tolerance mechanisms that Saccharomyces cerevisiae can evolve in the presence of inhibiting concentrations of three dicarboxylic acids: glutaric acid, adipic acid and pimelic acid. Whole-genome sequencing of tolerant mutants enabled the discovery of the genetic changes behind tolerance and most mutations could be linked to the up-regulation of multidrug resistance transporters. The amplification of QDR3, in particular, was shown to confer tolerance not only to the three dicarboxylic acids investigated, but also towards muconic acid and glutaconic acid. In addition to increased acid tolerance, QDR3 overexpression also improved the production of muconic acid in the context of a strain engineered for producing this compound.

Keywords: Adaptive laboratory evolution; Dicarboxylic acid; Multidrug resistance transporter.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Dicarboxylic Acids / pharmacology*
Directed Molecular Evolution*
Gene Expression Regulation, Fungal*
Saccharomyces cerevisiae Proteins* / biosynthesis
Saccharomyces cerevisiae Proteins* / genetics
Saccharomyces cerevisiae* / genetics
Saccharomyces cerevisiae* / metabolism

Substances

Dicarboxylic Acids
Saccharomyces cerevisiae Proteins