Fig. 4

Venn diagram showing the JGI numbers, CAZy classifications and (determined or predicted) enzyme activities encoded by differentially expressed genes (DEGs) expected to be involved in plant cell wall degradation. The CAZy genes that are up-regulated (> twofold, p value > 0.01) in the 2 h d-xylose or l-arabinose samples compared to the 2 h d-glucose samples of the M. thermophila wild-type strain are designated ‘d-xylose induced’ or ‘l-arabinose induced’ genes. The MtXyr1 dependent genes are genes down-regulated (> twofold, p value > 0.01) in the ΔMtxyr1 strain on d-xylose or l-arabinose compared to the wild-type strain on d-xylose or l-arabinose. The genes containing an asterisk are genes that were up-regulated in the ΔMtxyr1 strain. The graphs show the gene expression patterns for the genes of each of the seven groups. DEGs were grouped and of each group the average RPKM per conditions was calculated and plotted in a graph (y-axis: RPKM value and x-axis: strain and substrate. W = wild-type strain, Δ = ΔMtxyr1 strain, G = 2 h d-glucose, X = 2 h d-xylose and A = 2 h l-arabinose). The enzyme activities were predicted based on manual annotation and phylogenetic analysis (see Additional file 2 for annotation results and enzyme abbreviations). In bold, the enzymes that have been characterized in the M. thermophila C1 strain. The color scheme (see legend) represents the specific plant polysaccharide the enzyme is predicted to act on in pink, orange, yellow, blue, green and purple. In gray (various), the enzymes that act on more than one specific plant polysaccharide. If there is no color assigned, the substrate of which the enzyme is active on remains unknown