Genome and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae

Authors: ZHOU, QIAN - Chinese Academy Of Sciences; Liu, Zonglin; NING, KANG - Chinese Academy Of Sciences; WANG, ANHUI - Three Gorges University; ZENG, XIAOWEI - Chinese Academy Of Sciences; XU, JIAN - Chinese Academy Of Sciences

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2014
Publication Date: 10/9/2014
Publication URL: http://handle.nal.usda.gov/10113/62289
Citation: Zhou, Q., Liu, Z., Ning, K., Wang, A., Zeng, X., Xu, J. 2014. Genome and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae. Scientific Reports. doi:10.1038/srep06556.

Interpretive Summary: Results on research and development to improve yeast performance obtained from using laboratory model strains and industrial strains for biofuels application are often inconsistent. The lack of knowledge on genomic origins of different responses between model lab strain and industrial strain hinders R&D progress for the next-generation biocatalyst development. This research characterized genomic sequence variation and transcriptome profiling of an industrial yeast type (strain NRRL Y-12632) from a worldwide collection that distinguished its robust characteristics from a model laboratory strain of yeast (Saccharomyces cerevisiae. This work revealed the first insights into the unique industrial genomic background, especially the signaling system in overcoming common toxic compounds liberated from biomass pretreatment. It provided a new knowledge base and rationale for necessary increased utilization of industrial yeast as a workhorse, as well as a research model towards a practical renewable and sustainable bio-based economy.

Technical Abstract: The industrial ethanologenic yeast Saccharomyces cerevisiae is a promising biocatalyst for next-generation advanced biofuels applications including lignocellulose-to-ethanol conversion. Here we present the first insight into the genomic background of NRRL Y-12632, a type strain from a worldwide collection, and its transcriptomic response to 5-hydroxymethyl-2-furaldehyde (HMF), a commonly encountered toxic compound liberated from lignocellulosic-biomass pretreatment, in dissecting the underlying genomic mechanisms of yeast stress tolerance. Compared with the laboratory model S288C genome, we identified more than 32,000 single-nucleotide variations (SNPs) in Y-12632 with 23,000 missense and nonsense SNPs associated with many protein-coding genes. Higher levels of sequence mutations occurred for genes involved in mitogen-activated protein kinase (MAPK)- and phosphatidylinositol (PI)- signaling pathways, each with at least 41 and 13 genes harboring non-synonymous SNPs, respectively. Most of the mutated genes in these pathways displayed consistent up-regulated signature expression in response to 30 mM HMF, which suggests a potential sequence structure-function relationship for the yeast tolerance. Failure to grow on a HMF-containing medium by selective single-gene deletion mutants suggested important roles of those candidate genes in overcoming the HMF challenge through the PI-signaling system and at least three MAPK-signaling pathways, especially the cell-wall integrity pathway, due to its critical bridging functions between the closely related MAPK- and PI- pathways. The comprehensive global sequence variations and more adaptive signaling pathways in Y-12632 distinguished its robust characteristics from the model strain. Findings of this research suggest the use of industrial yeast is necessary as a workhorse as well as a research model for future advanced biofuels applications.