title: Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae.
abstract: The industrial yeast Saccharomyces cerevisiae is a traditional ethanologenic agent and a promising biocatalyst for advanced biofuels production using lignocellulose materials. Here we present the genomic background of type strain NRRL Y-12632 and its transcriptomic response to 5-hydroxymethyl-2-furaldehyde (HMF), a commonly encountered toxic compound liberated from lignocellulosic-biomass pretreatment, in dissecting the genomic mechanisms of yeast tolerance. Compared with the genome of laboratory model strain S288C, we identified more than 32,000 SNPs in Y-12632 with 23,000 missense and nonsense SNPs. Enriched sequence mutations occurred for genes involved in MAPK- and phosphatidylinositol (PI)- signaling pathways in strain Y-12632, with 41 and 13 genes containing non-synonymous SNPs, respectively. Many of these mutated genes displayed consistent up-regulated signature expressions in response to challenges of 30 mM HMF. Analogous single-gene deletion mutations of these genes showed significantly sensitive growth response on a synthetic medium containing 20 mM HMF. Our results suggest at least three MAPK-signaling pathways, especially for the cell-wall integrity pathway, and PI-signaling pathways to be involved in mediation of yeast tolerance against HMF in industrial yeast Saccharomyces cerevisiae. Higher levels of sequence variations were also observed for genes involved in purine and pyrimidine metabolism pathways.
authors.affiliation: 1] Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China 266101 [2].
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: 1] Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL, USA 61604-3902 [2].
authors.forename: Z Lewis
authors.initials: ZL
authors.lastname: Liu
authors.affiliation: 1] Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China 266101 [2].
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.affiliation: College of Computer and Information Technology, China Three Gorges University, Yichang, Hubei, China.
authors.forename: Anhui
authors.initials: A
authors.lastname: Wang
authors.affiliation: Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China 266101.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zeng
authors.affiliation: Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China 266101.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
mesh_terms: D002473:Cell Wall / Q000187:drug effects / Q000235:genetics; D025141:Drug Resistance, Fungal / Q000235:genetics; D005662:Furaldehyde / Q000008:administration & dosage / Q000031:analogs & derivatives; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects*; D023281:Genomics; D020935:MAP Kinase Signaling System / Q000187:drug effects / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics*
chemical_list: C008046:5-hydroxymethylfurfural; D005662:Furaldehyde