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. 2014 Jan 29;4:3926. doi: 10.1038/srep03926

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(A) The metabolic pathway for xylose fermentation in lactic acid bacteria. (B) Schematic gene maps of the xylose-utilization genes found in the B. coagulans strains examined in this study. Genes, that were not filled, are pseudogenes. xylR: DNA-binding transcriptional activator; xylAI: xylose isomerase Type I; xylB: xylulokinase; xylT: Xylose H⁺-symporter; xylAIII: xylose isomerase Type III; P1: quinolinate synthetase; P2: iron-containing alcohol dehydrogenase; P3: peptidase; P4: hypothetical protein; P5: PfkB domain-containing protein; P6: LacI family transcriptional regulator; P7: beta-ketoacyl reductase; P8: hypothetical protein; P9: breakpoint of contigs; P10: hypothetical protein; P11: hypothetical protein; P12: 6-phospho-3-hexuloisomerase; (C) Maximum likelihood tree of xylA genes. The genes marked by filled circles () are from B. coagulans strains and are homologs of xylA in B. subtilis. The genes marked with squares () are from B. coagulans strains, and are the novel xylose isomerases discovered in this study. (D) Maximum likelihood tree of xylB genes. The genes marked with filled circle () are from B. coagulans strains. The accession numbers of these genes downloaded from the NCBI database are shown in the parentheses. A scale bar for the genetic distance is shown at the bottom.

Inline graphic — (A) The metabolic pathway for xylose fermentation in lactic acid bacteria. (B) Schematic gene maps of the xylose-utilization genes found in the B. coagulans strains examined in this study. Genes, that were not filled, are pseudogenes. xylR: DNA-binding transcriptional activator; xylAI: xylose isomerase Type I; xylB: xylulokinase; xylT: Xylose H⁺-symporter; xylAIII: xylose isomerase Type III; P1: quinolinate synthetase; P2: iron-containing alcohol dehydrogenase; P3: peptidase; P4: hypothetical protein; P5: PfkB domain-containing protein; P6: LacI family transcriptional regulator; P7: beta-ketoacyl reductase; P8: hypothetical protein; P9: breakpoint of contigs; P10: hypothetical protein; P11: hypothetical protein; P12: 6-phospho-3-hexuloisomerase; (C) Maximum likelihood tree of xylA genes. The genes marked by filled circles () are from B. coagulans strains and are homologs of xylA in B. subtilis. The genes marked with squares () are from B. coagulans strains, and are the novel xylose isomerases discovered in this study. (D) Maximum likelihood tree of xylB genes. The genes marked with filled circle () are from B. coagulans strains. The accession numbers of these genes downloaded from the NCBI database are shown in the parentheses. A scale bar for the genetic distance is shown at the bottom.