Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae

Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize xylodextrins in aerobic condtions but not anaerobic conditions. We sequenced mRNA from anaerobically fed-batch cultures of the engineered S. cerevisiae grown on xylodextrins with or without the continuous feeding of xylose in biological duplicate. Dynamic changes of gene expression during xylose feeding experiment revealed by RNA deep sequencing indicated that xylose helps anaerobically xylodextrin-grown cells to recover mithondrial function thereby resuming xylodextrin consumption. Furthermore, different portions of genes involved in ribosome biogenesis showed either decreased or increased transcriptions. The underlying mechanism remains to be elucidated. The mRNA levels of fed-batch cultures anaerobically grown on xylodextrins with or without the continuous feeding of xylose were examined by deep sequencing, in duplicate, using Illumina Genome Analyzer-II. After inoculation, cells were cultured as follows: without xylose feeding for 20 h, with xylose feeding for 24 h, and without xylose feeding until total 72 h of fermentation. Samples were taken as follows: right before xylose feeding (0 h); 0.5 h, 1 h, 2 h, 4 h and 24 h with xylose feeding; 8 h and 24 h after stopping xylose feeding.