Additional file 1: Figure S1. Construction of synthetic xylose metabolic pathways in Shewanella oneidensis MR-1. (A) Schematic of the plasmid with a synthesized functional fragment of genes. The restriction sites EcoRI and XbaI with the ribosome binding site (RBS) are located upstream of each codon-optimized gene sequence, while the restrictions SpeI and PstI are located downstream of the gene. (B) Four plasmid constructs with xylose utilization pathways. To construct the multigene assembly in S. oneidensis, a Biobrick compatible expression vector pYYDT was adopted, which was previously constructed in our laboratory. Layout of the four plasmid constructs containing gene components in the xylose pathway examined in this study. Figure S2. Xylose consumption rate by E. coil (BL21) and by the recombinant S. oneidensis strain. The error bars were calculated from triplicate experiments. Figure S3. Metabolic pathway of riboflavin synthesis from xylose fermentation in S. oneidensis. A synthetic intracellular xylose metabolic pathway, i.e. the oxidoreductase pathway including genes XYL1, XYL2 and XKS1 from S. stipites, is incorporated into S. oneidensis MR-1 to enable the direct utilization of xylose. Xylulose 5-phosphate, as a metabolite in the oxidoreductase pathway, was converted to ribulose-5-P by ribulose-phosphate 3-epimerase (encoded by the rpe gene) in the pentose phosphate pathway, which was a crucial precursor for the biosynthesis of riboflavin via the riboflavin synthesis pathway. Figure S4. Xylose consumption under anaerobic conditions with 10 mM and 50 mM fumarate. The error bars were calculated from triplicate experiments
