Abstract: ABSTRACT: BACKGROUND: Considerable interest in the bioconversion of lignocellulosic biomass into ethanol has led metabolic engineering of Saccharomyces cerevisiae for fermentation of xylose. In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose. RESULTS: Genes encoding respiratory proteins, proteins of the tricarboxylic acid and glyoxylate cycles, and gluconeogenesis were only partially repressed by xylose, similar to the genes encoding their transcriptional regulators HAP4, CAT8 and SIP1-2 and 4. Also several other genes that are repressed via the Snf1p/Mig1p-pathway during growth on glucose had higher expression in the cells grown on xylose than in the glucose repressed cells but lower than in the glucose derepressed cells. On the other hand, some genes normally repressed by glucose had their highest expression in cells grown on xylose. The observed expression profiles of the transcription repressor RGT1 and its target genes HXT2-3, encoding hexose transporters suggested that extracellular xylose was sensed by the glucose sensors Rgt2p and Snf3p. Proteome analyses revealed distinct patterns in phosphorylation of hexokinase 2, glucokinase and enolase isoenzymes in the xylose- and glucose-grown cells. CONCLUSIONS: The results of the present study show that xylose triggers only part of the regulatory responses of glucose, but is also able to onset specific responses. The results indicated that xylose poses only a mild repressive effect and that the metabolism of yeast cultured on xylose was neither fully glucose repressed nor derepressed. This may be one of the major reasons for the suboptimal fermentation of xylose by recombinant S. cerevisiae strains. Phosphorylation of different isoforms of glycolytic enzymes suggested that regulation of glycolysis also occurred at post-translational level, supporting prior findings.