Pathway-based signature transcriptional profiles as tolerance phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF

Authors: Liu, Zonglin; MA, MENGGEN - Former ARS Employee

Submitted to: Applied Microbiology and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2020
Publication Date: 2/26/2020
Citation: Liu, Z., Ma, M. 2020. Distinctive expressions of transposable element genes impact adaptation of the industrial yeast Saccharomyces cerevisiae. 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: Development of tolerant industrial yeast is a significant challenge toward a low-cost and sustainable bio-based economy. Yeast gene expression response against toxic chemicals associated with lignocellulosic biomass conversion has been identified for many genes in a wide range of functional categories. However, nothing is known about the involvement of transposable element (TE) genes. Using an ARS patent tolerant yeast strain and an updated gene expression platform, this study revealed distinctive expressions of many TEs in response to the presence of inhibitory compounds from biomass-derived sugars. This research also found many genes initially repressed, but recovered during the lag phase, were significant for the yeast adaptation. New insight into the characteristics of the adapted industrial yeast obtained by this research opens a window for in-depth understanding mechanisms of the yeast adaptation to tolerance. The new knowledge achieved in this study aid the development of the next-generation biocatalyst for low-cost lignocellulose-to-biofuels conversion.

Technical Abstract: The industrial yeast Saccharomyces cerevisiae has a plastic genome with a great flexibility in adaptation to varied conditions of nutrition, temperature, chemistry, osmolarity, and pH in diversified applications. A tolerant strain against 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, here we report tolerance phenotypes of pathway-based transcriptional profiles as components of the adapted defensive system for the tolerant strain NRRL Y-50049. The newly identified tolerance phenotypes were involved in biosynthesis superpathway of sulfur amino acids, defensive reduction-oxidation reaction process, cell wall response, and 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 presented. Many important genes in Y-50049 acquired an enhanced transcription background and showed continued increased expressions during the entire lag phase against furfural-HMF. Such signature expressions distinguished tolerance phenotypes of Y-50049 from the innate stress response of its progenitor NRRL Y-12632, an industrial type strain. The acquired yeast tolerance is believed to be evolved in various mechanisms at the genomic level. Identification of legitimate tolerance phenotypes provides a basis for continued investigations on pathway interactions and dissection of mechanisms of yeast tolerance and adaptation at the genomic level.