Transcriptome and metabolome analysis of Pichia stipitis to three representative lignocellulosic inhibitors

  • Yuanyuan Zhu
  • Lu Wu
  • Junjun Zhu
  • Yong Xu
  • Shiyuan Yu
Original Paper


During the bioconversion of xylose to ethanol, Pichia stipitis cells are often inhibited by substances generated in the lignocellulosic hydrolysate. However, the response mechanism of P. stipitis to inhibitors has not been completely understood till date. With this aim, integrated transcriptomic and metabolomic analyses were performed on P. stipitis to investigate the interactive effects of three representative inhibitors [vanillin, 5-hydroxymethylfurfural (5-HMF), and acetic acid] present in lignocellulosic hydrolysates. The genes involved in carbohydrate metabolism were observed to significantly down-regulated in the presence of the three combined inhibitors in both lag and middle exponential phases. In addition, inhibitor addition induced amino acid metabolism (e.g., glutamine and asparagine syntheses), since the yeast cells required more amino acids in stressful conditions. The metabolomic analysis yielded similar results, particularly those related with the analysis of metabolic biomarkers including fatty acids, amino acids, and sugars. 70 intracellular metabolites were detected by gas chromatography coupled with mass spectrometry (GC–MS), and samples from different phases were clearly separated by principal component analysis (PCA). The large amount of specific responsive genes and metabolites highlighted the complex regulatory mechanisms involved in the fermentation process in the presence of the three combined inhibitors.


Inhibitor Pichia stipitis Metabolomic Transcriptomic Bioethanol 



Gas chromatography coupled with mass spectrometry


Principal component analysis






High-performance liquid chromatography


Optical density


Internal standard


Pentose phosphate pathway





The authors acknowledge the financial support from the National Key Research and Development Program of China (2017YFD0601001), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Jiangsu Oversea Research & Training Program for University Prominent Young & Middle-aged Teachers and Presidents, and Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX17_0850).

Compliance with ethical standards

Conflict of interest

The authors declare that no conflicting financial interests exist.

Supplementary material

203_2018_1600_MOESM1_ESM.tif (7.7 mb)
Supplementary material 1 (TIF 7919 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest ResourcesNanjing Forestry UniversityNanjingChina
  2. 2.College of Chemical EngineeringNanjing Forestry UniversityNanjingChina
  3. 3.Jiangsu Key Lab of Biomass-based Green Fuel and ChemicalsNanjingChina

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