S. cerevisiae YSX3 (MATalpha, leu2::LEU2-XYL1, ura3::URA3-XYL2, Ty3::NEO-XYL3) was used in this study. Cells were grown under aerobic or oxygen-limited conditions with glucose or xylose (four conditions). Cells were cultivated aerobically in 200 ml of YP medium with either 20 g/L of glucose or xylose in 1000 ml flasks shaken at 300 rpm and harvested at OD600 = 1. Oxygen-limited cells were cultivated in 50 ml of YP medium with either 40 g/L of glucose or xylose in 125 ml flasks shaken at 100 rpm and harvested at OD600 = 30. For monitoring transcripts in the respiration-deficient mutant, FPL-YSX3P, cells were first grown on YP medium with glucose and harvested at OD600 = 1. The harvested cells were transferred into YP medium with xylose and then RNA was extracted after 24 hours incubation. GeneChip arrays (Affymetrix, Santa Clara, CA) were used to monitor mRNA transcripts of putative S. cerevisiae open reading frames (ORFs). Quantitative RT-PCR was used to measure expression of P. stipitis XYL1, XYL2, and XYL3 transcripts. Total RNA from yeast cells was isolated as described in Holstege et al. cDNA was synthesized with a T7-(dT)24 primer (GENSET Corp). Labeling of RNA transcripts, hybridization, and scanning were performed according to the manufacturer’s instructions (Affymetrix). Keywords = xylose Keywords = glucose Keywords = aerobic Keywords = oxygen limited
