Molecular evolution and diversity of isomerase–reductase clusters involved in the bacterial metabolism of glycosaminoglycans

Authors:
Open Access
Publisher website
Google Scholar
Abstract
Glycosaminoglycans (GAGs), comprising uronic acids and amino sugars, are widely distributed in human tissues such as the intestine and oral cavity. Various bacteria colonize these tissues by assimilating GAGs. During GAG degradation, 4-deoxy- l - threo -5-hexosulose uronate (DHU) is produced. Pectin, an abundant plant component, is also degraded into DHU. DHU is metabolized in a stepwise manner by the isomerase KduI or its nonhomologous isofunctional enzyme DhuI, followed by the reductase KduD or DhuD, belonging to the same reductase–dehydrogenase family. Previous studies have found that the genes encoding isomerase and reductase ( kduI–kduD and dhuD–dhuI , respectively) are usually organized in clusters. Therefore, it was believed that the kduI–kduD and dhuD–dhuI clusters evolved independently. However, the discovery of a hybrid kduI–dhuD cluster raised questions regarding the evolution of these clusters. This study investigated the diversity of clusters through a pan-genomic phylogenetic analysis across 3,550 bacterial strains. Among 16 possible cluster structures, 10 types were involved in DHU metabolism. Bacteroidota possessed a hybrid-type kduI–dhuD cluster, while Bacillota, but not Pseudomonadota or Bacteroidota, possessed the cluster dhuD–dhuI . Using public data sets from the human fecal microbiome and environmental habitats, we detected the prevalence of kduI–dhuD and dhuD–dhuI clusters in gut microbes. Although DHU is generated from oligomerized GAG degradation by unsaturated glucuronyl hydrolase (UGL), the UGL gene was frequently found in pathogenic strains containing kduD–kduI , dhuD–dhuI , kduI–dhuD , or dhuD–kduI , indicating that the acquisition of these clusters is advantageous for human colonization. IMPORTANCE: Glycosaminoglycans (GAGs), crucial components of the extracellular matrix, play vital roles in host infection by pathogenic bacteria and host colonization by commensal bacteria. The dhuD–dhuI cluster is well conserved within certain phyla, and it appears to have a strong association with GAG metabolism. In contrast, kduI -containing clusters are more widely distributed across bacterial species. Based on the possession ratios of genes encoding the enzymes involved in the production of 4-deoxy- l - threo -5-hexosulose uronate, this study indicates that the substrates differ depending on the specific cluster type.
Funding Information
  • Japan Society for the Promotion of Science (25K01979)
  • Japan Society for the Promotion of Science (21H02156)
  • Kyoto University Foundation

This publication has 62 references indexed in Scilit: