Journal of Bioprocessing & Biotechniques

Fermentation Monitoring of a Co-Culture Process with Saccharomyces cerevisiae and Scheffersomyces stipitis Using Shotgun Proteomics

Abstract

Eric L Huang, Mark G Lefsrud

Co-culture processes present the opportunity to produce value-added products from economical raw materials, but there lacks a high-throughput fermentation monitoring technique to study the temporal physiology of fermentation organisms in co-culture processes. In this study, we applied shotgun proteomics to investigate a co-culture process of Saccharomyces cerevisiae and Scheffersomyces stipitis, and we monitored the fermentation until glucose depletion. Three time points were taken for proteomics analysis at 11.5 hour, 18.5 hour and 32 hour, representing transition into diauxic shift. Using label-free quantitation, we observed cellular dynamic within 20-hour time frame. We distinguished the proteome between two yeasts, and the most abundant proteins of S. stipitis and S. cerevisiae contained expected processes of glycolytic enzymes, histones, heat shock proteins, ribosomal proteins and F1F0-ATPase. After glucose depletion, we identified up-regulations of S. stipitis malate synthase and isocitrate lyase as key enzymes in glyoxylate cycle and gluconeogenesis. Increased expression of S. stipitis histone 2B was observed in diauxic shift, and histone acetylation was suggested by up-regulation of acetyl-CoA synthetase. Without the presence of xylose, we observed induction of NAD(P)H-dependent D-xylose reductase (Xyl1p) as early as 11.5-hour before glucose depletion. We also observed the expression of D-xylulose reductase after glucose depletion without xylose induction. Further study is needed to investigate the cause of derepression signals for xylose oxo-reductive pathway. Without cellulose induction, the up-regulation of S. stipitis endo-1,4-beta-glucanase suggested S. stipites’ strategy in diversifying carbon choices after glucose repression. This research demonstrated the application of shotgun proteomics in high-throughput monitoring of complex co-culture system and able to elucidate the temporal physiology of S. stipitis.