title: Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production.
abstract: Xylose is one of the most abundant lignocellulosic components, but it cannot be used by R. oryzae for fumaric acid production. Here, we applied high-throughput RNA sequencing to generate two transcriptional maps of R. oryzae following fermentation in glucose or xylose. The differential expression analysis showed that, genes involved in amino acid metabolism, fatty acid metabolism, and gluconeogenesis, were up-regulated in response to xylose. Moreover, we discovered the potential presence of oxidative stress in R. oryzae during xylose fermentation. To adapt to this unfavorable condition, R. oryzae displayed reduced growth and induce of a number of antioxidant enzymes, including genes involved in glutathione, trehalose synthesis, and the proteasomal pathway. These responses might divert the flow of carbon required for the accumulation of fumaric acid. Furthermore, using high-throughput RNA sequencing, we identified a large number of novel transcripts and a substantial number of genes that underwent alternative splicing. Our analysis provides remarkable insight into the mechanisms underlying xylose fermentation by R. oryzae. These results may reveal potential target genes or strategies to improve xylose fermentation.
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.|College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xu
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Li
authors.affiliation: College of Food Science and Light Industry, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Jiang
authors.affiliation: School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816, China. biotech@njtech.edu.cn.
authors.forename: He
authors.initials: H
authors.lastname: Huang
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. jpwen@tju.edu.cn.
authors.forename: Jianping
authors.initials: J
authors.lastname: Wen
mesh_terms: D017398:Alternative Splicing; D018533:Biomass; D005285:Fermentation; D005650:Fumarates / Q000378:metabolism*; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D012329:RNA, Bacterial; D012233:Rhizopus / Q000235:genetics*; D059467:Transcriptome; D014994:Xylose / Q000378:metabolism*
chemical_list: D005650:Fumarates; D012329:RNA, Bacterial; C032005:fumaric acid; D014994:Xylose; D005947:Glucose
keywords: Fumaric acid; Glucose; Rhizopus oryzae; Transcriptome analysis; Xylose