Submitted to: Applied Microbiology and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2020
Publication Date: 2/20/2020
Citation: Liu, Z.L., Ma, M. 2020. Pathway-based signature transcriptional profiles as tolerant phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF. Applied Microbiology and Biotechnology. 104:3473–3492. https://doi.org/10.1007/s00253-020-10434-0.
DOI: https://doi.org/10.1007/s00253-020-10434-0

Interpretive Summary: Previously, ARS scientists developed a tolerant industrial yeast strain able to detoxify inhibitory compounds liberated from plant biomass during conversion to ethanol. Understanding mechanisms of the yeast tolerance is essential for development of the next-generation biocatalyst. An induced stress response by a chemical treatment is commonly regarded to be a phenotype supported by various identifiable genes contributing to tolerance. Recent studies demonstrated that such individual genes were poorly associated with cell survival. The yeast tolerance is believed to be evolved in various mechanisms at the genomic level. The system-level response of the yeast tolerance remains only partially understood. Identification of more useful system-based phenotypes is needed. In this research, we distinguished four tolerance phenotypes by monitoring pathway-based gene transcription during a stress response. Characterizations of the acquired tolerant components of the adapted defensive system have led to a better understanding of tolerance and adaptation mechanisms of the yeast. This research provided an advancement in foundational knowledge needed for the development of more robust next-generation biocatalysts for low-cost lignocellulose-to-biofuels conversion.

Technical Abstract: The industrial yeast Saccharomyces cerevisiae has a plastic genome with great flexibility to adapt to diverse conditions of nutrition, temperature, chemistry, osmolarity and pH. A strain tolerant to 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) was successfully obtained previously by adaptation through environmental engineering toward development of the next-generation biocatalyst. Using a time-course comparative transcriptome analysis in response to a synergistic challenge of furfural-HMF, tolerant phenotypes were shown to have altered pathway-based transcriptional profiles as components of the adapted defensive system for the tolerant strain NRRL Y-50049. The newly identified tolerant phenotypes included an enabled biosynthesis superpathway of sulfur amino acids, an adapted cell wall response, a strengthened defensive reduction-oxidation reaction, and an extended capability of endogenous and exogenous cellular detoxification. Key transcription factors closely related to these pathway-based components, such as Yap1, Met4, Met31/32, Msn2/4 and Pdr1/3, were also indicated by the results. Many important genes acquired an enhanced background increased in transcription abundance and showed continued increased expressions during the entire lag phase in the presence of furfural-HMF. Such signature expressions distinguished the adapted tolerant components in Y-50049 from the innate stress response of its progenitor NRRL Y-12632, an industrial type strain. The acquired yeast tolerance is believed to have evolved via mechanisms at the genomic level. Identification of these tolerant phenotypes provides a basis for investigation of copy number variants, and the insight into the pathway-based interactions aids dissection of molecular mechanisms of the yeast tolerance and adaptation.