Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast
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Biotechnology for Biofuels Open Access
RESEARCH
Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast Li Wang1,2†, Xin Wang3†, Zhi‑Qiang He1,2, Si‑Jie Zhou1,2, Li Xu1,2, Xiao‑Yu Tan1,2, Tao Xu1,2, Bing‑Zhi Li1,2* and Ying‑Jin Yuan1,2
Abstract Background: Stress tolerance is one of the important desired microbial traits for industrial bioprocesses, and global regulatory protein engineering is an efficient approach to improve strain tolerance. In our study, IrrE, a global regula‑ tory protein from the prokaryotic organism Deinococcus radiodurans, was engineered to confer yeast improved toler‑ ance to the inhibitors in lignocellulose hydrolysates or high temperatures. Results: Three IrrE mutations were developed through directed evolution, and the expression of these mutants could improve the yeast fermentation rate by threefold or more in the presence of multiple inhibitors. Subsequently, the tolerance to multiple inhibitors of single-site mutants based on the mutations from the variants were then evalu‑ ated, and 11 mutants, including L65P, I103T, E119V, L160F, P162S, M169V, V204A, R244G, Base 824 Deletion, V299A, and A300V were identified to be critical for the improved representative inhibitors, i.e., furfural, acetic acid and phenol (FAP) tolerance. Further studies indicated that IrrE caused genome-wide transcriptional perturbation in yeast, and the mutant I24 led to the rapid growth of Saccharomyces cerevisiae by primarily regulating the transcription level of tran‑ scription activators/factors, protecting the intracellular environment and enhancing the antioxidant capacity under inhibitor environments, which reflected IrrE plasticity. Meanwhile, we observed that the expression of the wild-type or mutant IrrE could also protect Saccharomyces cerevisiae from the damage caused by thermal stress. The recombinant yeast strains were able to grow with glucose at 42 ℃. Conclusions: IrrE from Deinococcus radiodurans can be engineered as a tolerance-enhancer for Saccharomyces cerevisiae. Systematic research on the regulatory model and mechanism of a prokaryotic global regulatory factor IrrE to increase yeast tolerance provided valuable insights for the improvements in microbial tolerance to complex industrial stress conditions. Keywords: IrrE, Global regulatory protein engineering, Lignocellulose-derived inhibitors, Genome-wide transcriptional perturbation, Thermal tolerance Background Concerns about energy supplies and global climate change have led to growing attention worldwide for producing biochemicals, biofuels, and biomaterials from *Correspondence: [email protected] † Li Wang and Xin Wang contributed equally to this work 1 Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China Full list of author information is available at the end of the article
lignocellulosic biomass [1, 2]. To officially ferment lignocellulosic hydrolysat
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