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Additional file 1: Table S1. Concentration of glucose in various medium. Table S2. Primers used in this study. Table S3. Concentration of amino acids in various medium (expressed as mM). Figure S1. M9-yeast extract medium supplemented with (A) blank, (B) 10 mM glucose, or (C) 50 mM glucose was incubated by E. coli DH10B for 1–26.5 hours, and the amino acid concentrations were compared. Values are given as mean ± SD (n = 3).

Pathway analysis of glycolysis. Glycolysis pathway was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon sources. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; green, galactomannan; pectin, blue) (PDF 563 kb)

Pathway analysis of tricarboxylic acid cycle. Tricarboxylic acid cycle was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 708 kb)

Pathway analysis of xylan degradation and metabolism. Pathway of xylan degradation and metabolism was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 344 kb)

Pathway analysis of galactomannan degradation and metabolism. (a) Pathway of mannan degradation and metabolism; (b) galactose degradation and metabolism pathway A. Each pathway was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 699 kb)

Pathway analysis of pectin degradation and metabolism. Pathway of pectin degradation and metabolism was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 656 kb)

Hypoxia has critical effects on the physiology of organisms. In the yeast Saccharomyces cerevisiae, glycolytic enzymes, including enolase (Eno2p), formed cellular foci under hypoxia. Here, we investigated the regulation and biological functions of these foci. Focus formation by Eno2p was inhibited temperature independently by the addition of cycloheximide or rapamycin or by the single substitution of alanine for the Val22 residue. Using mitochondrial inhibitors and an antioxidant, mitochondrial reactive oxygen species (ROS) production was shown to participate in focus formation. Focus formation was also inhibited temperature dependently by an SNF1 knockout mutation. Interestingly, the foci were observed in the cell even after reoxygenation. The metabolic turnover analysis revealed that [U-(13)C]glucose conversion to pyruvate and oxaloacetate was accelerated in focus-forming cells. These results suggest that under hypoxia, S. cerevisiae cells sense mitochondrial ROS and, by the involvement of SNF1/AMPK, spatially reorganize metabolic enzymes in the cytosol via de novo protein synthesis, which subsequently increases carbon metabolism. The mechanism may be important for yeast cells under hypoxia, to quickly provide both energy and substrates for the biosynthesis of lipids and proteins independently of the tricarboxylic acid (TCA) cycle and also to fit changing environments.

Additional file 1: Fig S1. Oligosaccharide assimilation by C. cellulovorans. C. cellulovorans was grown in media containing 6 g/L glucose, 6 g/L cellobiose, and 6 g/L xylooligosaccharides mixture (a), 10 g/L glucose and 10 g/L xylooligosaccharides (b), 10 g/L cellobiose and 10 g/L xylooligosaccharides (c). Residual sugar amount was normalized to that of 0 h (set to 100%). Closed circles, glucose; open triangles, cellobiose; open squares, xylooligosaccharide. All points were measured in triplicate. Error bars represent means Âą SEs.

Additional file 1. List of primers used in this study (Table S1). Box plots showing the ratio of sum of pixel values for (A) rabbit, (B) chicken, (C) horse, and (D) swine erythrocytes (Fig. S1). Sequence alignment of hHAsÎą2,6 and hHAsÎą2,6* (Fig. S2).