Biology subjects

Hashimoto, W.

Publications and source records attributed to Hashimoto, W..

3 recordsLinked to original sources

bioRxiv2025

Molecular evolution and diversity of isomerase-reductase operons involved in bacterial metabolism of glycosaminoglycans

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. 4-Deoxy-L-threo-5-hexosulose uronate (DHU) is produced during the degradation of GAGs. Pectin, abundant in plants, is also degraded into DHU. DHU is metabolized in a stepwise manner by the isomerase KduI or DhuI, followed by the reductase KduD or DhuD. Previous studies have shown that the two genes encoding isomerase and reductase (kduI-kduD and dhuD-dhuI, respectively) are designated in an operon. Therefore, it was believed that dhuD-dhuI and kduI-kduD operons evolved independently. Nevertheless, the discovery of a hybrid kduI-dhuD operon raised questions regarding the evolution of these operons. This study was conducted to investigate the factors driving the diversity of operons through a pan-genomic phylogenetic analysis across 3550 bacterial strains. Seven types of DHU metabolism-related operons were identified. The phylum Bacteroidota possesses a hybrid-type kduI-dhuD operon rather than kduI-kduD or kduD-kduI operon. The phylum Bacillota, but not Pseudomonadota or Bacteroidota, possesses the dhuD-dhuI operon; however, dhuI-dhuD operon was not detected in any bacterial strain. Although DHU is generated from the degradation of oligomerized GAG by an unsaturated glucuronyl hydrolase (UGL), the UGL gene was found in strains positive for kduD-kduI, dhuD-dhuI, kduI-dhuD, and dhuD-kduI operons at high ratios, indicating that the acquisition of these operons is advantageous for colonization on human hosts. (230 words) IMPORTANCEGlycosaminoglycans (GAGs), crucial components of the extracellular matrix, play a vital role in host infection by pathogenic bacteria as well as in the colonization of the host by commensal bacteria. The isomerases KduI and DhuI are nonhomologous isofunctional enzymes. The dhuD-dhuI operon is well conserved within certain phyla and appears to have a strong association with GAG metabolism. In contrast, the kduI system is more widely distributed across various species. Based on the possession ratios of genes encoding each enzyme that produces 4-deoxy-L-threo-5-hexosulose uronate, this study indicated that the substrates targeted by each metabolic system vary depending on the specific operon type.

microbiology↗

bioRxiv2020

Mutually Beneficial Symbiosis Between Human and Gut-Dominant Bacteroides Species Through Bacterial Assimilation of Host Mucosubstances

The composition of gut microbiota is influenced by the quantity and type of nutrients in host. Even with some Bacteroides species being categorized as pathogens, Bacteroides is one of the most dominant gut bacteria. Here we indicate the physiological determinants of the species of Bacteroides for being dominant in human gut microbiota. Each of the host extracellular mucosubstances including glycosaminoglycans (GAGs) and mucin has grown human gut microbiota. In spite of the differences among initial microbiota profiles, Bacteroides species dominated the community when GAG (e.g., chondroitin sulfate or hyaluronan) was used as a sole carbon source. In fact, GAGs and the Bacteroides genes which are vital for the degradation of GAGs were commonly detected in human feces. Mucin has encouraged the growth of Bacteroides and several other genera. A comprehensive analysis on the degradation and assimilation of mucosubstances by the genus Bacteroides using around 30 species has shown that most species degrade and assimilate GAGs and mucin, showing that Bacteroides species can survive even in the undernutrition condition including the fasting state. In the assimilation of GAG or mucin, Bacteroides species significantly secreted essential amino acids, {gamma}-amino butyrate (GABA), and/or short-chain fatty acids which are needed for human health. This is the first report as regards mutually beneficial interaction between human and Bacteroides species via bacterial assimilation of host mucosubstances and secretion of metabolites for host health promotion. SignificanceThe genus Bacteroides is one of the most dominant gut bacteria, although its beneficial effects on human health have not been well understood. Here, we show modes of action in human-Bacteroides interrelationship. Mucosubstances including GAGs and mucin secreted by human host are abundant in gut for microbiota to grow well. Bacteroides species are dominant in the community in the presence of GAGs, and provide human host with a considerable amount of essential amino acids, {gamma}-amino butyrate, and short-chain fatty acids produced from mucosubstances. These results postulate mutually beneficial symbiosis system between human and Bacteroides through bacterial assimilation of host mucosubstances and secretion of metabolites for human body and mental health promotion even in the undernutrition condition including the fasting state.

microbiology↗

bioRxiv2018

Streptococcal phosphotransferase system imports unsaturated hyaluronan disaccharide derived from host extracellular matrices

Certain bacterial species target the polysaccharide glycosaminoglycans (GAGs) of animal extracellular matrices for colonization and/or infection. GAGs such as hyaluronan and chondroitin sulfate consist of repeating disaccharide units of uronate and amino sugar residues, and are depolymerized to unsaturated disaccharides by bacterial extracellular or cell-surface polysaccharide lyase. The disaccharides are degraded and metabolized by cytoplasmic enzymes such as unsaturated glucuronyl hydrolase, isomerase, and reductase. The genes encoding these enzymes are assembled to form a GAG genetic cluster. Here, we demonstrate the Streptococcus agalactiae phosphotransferase system (PTS) for import of unsaturated hyaluronan disaccharide. S. agalactiae NEM316 was found to depolymerize and assimilate hyaluronan, whereas its mutant with a disruption in PTS genes included in the GAG cluster was unable to grow on hyaluronan, while retaining the ability to depolymerize hyaluronan. Using toluene-treated wild-type cells, the PTS import activity of unsaturated hyaluronan disaccharide was significantly higher than that observed in the absence of the substrate. In contrast, the PTS mutant was unable to import unsaturated hyaluronan disaccharide, indicating that the corresponding PTS is the only importer of fragmented hyaluronan, which is suitable for PTS to phosphorylate the substrate at the C-6 position. The three-dimensional structure of streptococcal EIIA, one of the PTS components, was found to contain a Rossman-fold motif by X-ray crystallization. Docking of EIIA with another component EIIB by modeling provided structural insights into the phosphate transfer mechanism. This study is the first to identify the substrate (unsaturated hyaluronan disaccharide) recognized and imported by the streptococcal PTS.\n\nIMPORTANCE (118/120 words)The PTS identified in this work imports sulfate group-free unsaturated hyaluronan disaccharide as a result of the phosphorylation of the substrate at the C-6 position. S. agalactiae can be indigenous to animal hyaluronan-rich tissues owing to the bacterial molecular system for fragmentation, import, degradation, and metabolism of hyaluronan. Distinct from hyaluronan, most GAGs, which are sulfated at the C-6 position, are unsuitable for PTS due to its inability to phosphorylate the substrate. More recently, we have identified a solute-binding protein-dependent ABC transporter in a pathogenic Streptobacillus moniliformis as an importer of sulfated and non-sulfated fragmented GAGs without any substrate modification. Our findings regarding PTS and ABC transporter shed light on bacterial clever colonization/infection system targeting various animal GAGs.

microbiology↗