Applied Microbiology and Biotechnology

, Volume 92, Issue 6, pp 1237–1249

RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose

Genomics, transcriptomics, proteomics

DOI: 10.1007/s00253-011-3607-6

Cite this article as:
Yuan, T., Ren, Y., Meng, K. et al. Appl Microbiol Biotechnol (2011) 92: 1237. doi:10.1007/s00253-011-3607-6

Abstract

Xylose is the second most abundant lignocellulosic component besides glucose, but it cannot be fermented by the widely used ethanol-producing yeast Saccharomyces cerevisiae. The yeast Scheffersomyces stipitis, however, is well known for its high native capacity to ferment xylose. Here, we applied next-generation sequencing technology for RNA (RNA-Seq) to generate two high-resolution transcriptional maps of the S. stipitis genome when this yeast was grown using glucose or xylose as the sole carbon source. RNA-Seq revealed that 5,176 of 5,816 annotated open reading frames had a uniform transcription and that 214 open reading frames were differentially transcribed. Differential expression analysis showed that, compared with other biological processes, carbohydrate metabolism and oxidation-reduction reactions were highly enhanced in yeast grown on xylose. Measurement of metabolic indicators of fermentation showed that, in yeast grown on xylose, the concentrations of cysteine and ornithine were twofold higher and the concentrations of unsaturated fatty acids were also increased. Analysis of metabolic profiles coincided with analysis of certain differentially expressed genes involved in metabolisms of amino acid and fatty acid. In addition, we predicted protein–protein interactions of S. stipitis through integration of gene orthology and gene expression. Further analysis of metabolic and protein–protein interactions networks through integration of transcriptional and metabolic profiles predicted correlations of genes involved in glycolysis, the tricarboxylic acid cycle, gluconeogenesis, sugar uptake, amino acid metabolism, and fatty acid β-oxidation. Our study reveals potential target genes for xylose fermentation improvement and provides insights into the mechanisms underlying xylose fermentation in S. stipitis.

Keywords

Scheffersomyces stipitisXylose fermentationTranscriptomeRNA-SeqMetabolic networksProtein–protein interactions

Supplementary material

253_2011_3607_MOESM1_ESM.doc (1.5 mb)
ESM 1(DOC 1.54 mb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research InstituteChinese Academy of Agricultural SciencesBeijingChina
  2. 2.TEDA School of Biological Sciences and BiotechnologyNankai UniversityTianjinChina
  3. 3.Tianjin Research Center for Functional Genomics and BiochipTianjinChina
  4. 4.School of Biological SciencesTsinghua UniversityBeijingChina