A5002095126- Enzyme Production and Characterization
- Enzyme Structure and Function
- Biofuel production and bioconversion
- Microbial Metabolites in Food Biotechnology
- Carbohydrate Chemistry and Synthesis
- Probiotics and Fermented Foods
- Diet, Metabolism, and Disease
- Infant Nutrition and Health
- Digestive system and related health
- Polysaccharides and Plant Cell Walls
- Amino Acid Enzymes and Metabolism
- Gut microbiota and health
- Metal-Catalyzed Oxygenation Mechanisms
- Anaerobic Digestion and Biogas Production
- Microbial Fuel Cells and Bioremediation
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Catalysis and Immobilization
- Biochemical and Molecular Research
- Fungal Biology and Applications
- Metalloenzymes and iron-sulfur proteins
- Genomics and Phylogenetic Studies
- Metal Extraction and Bioleaching
- Lysosomal Storage Disorders Research
- Cancer Research and Treatments
- Tannin, Tannase and Anticancer Activities
Meiji University
2023-2025
The University of Tokyo
2013-2023
Kyoto University
2008-2018
Collaborative Research Group
2018
Abstract Gut microbiota of breast-fed infants are generally rich in bifidobacteria. Recent studies show that infant gut-associated bifidobacteria can assimilate human milk oligosaccharides (HMOs) specifically among the gut microbes. Nonetheless, little is known about how bifidobacterial-rich communities shaped gut. Interestingly, HMOs assimilation ability not related to dominance each species. Bifidobacterium longum susbp. and breve commonly found as dominant species stools; however, they...
Abstract The early life human gut microbiota exerts life-long health effects on the host, but mechanisms underpinning its assembly remain elusive. Particularly, colonization of Clostridiales from Roseburia - Eubacterium group, associated with protection colorectal cancer, immune- and metabolic disorders is enigmatic. Here, we describe catabolic pathways that support growth members distinct milk oligosaccharides (HMOs). HMO pathways, which include enzymes a previously unknown structural fold...
Feruloyl esterase (FAE) catalyzes the hydrolysis of ferulic and diferulic acids present in plant cell wall polysaccharides, tannase tannins to release gallic acid. The fungal family ESTHER database contains various enzymes, including FAEs tannases. Despite importance tannases bioindustrial applications, three-dimensional structures members have been unknown. Here, we determined crystal structure FAE B from Aspergillus oryzae (AoFaeB), which belongs family, at 1.5 Å resolution. AoFaeB...
Three thermophilic methanogens (Methanothermobacter thermautotrophicus, Methanosaeta thermophila, and Methanosarcina thermophila) were investigated for their ability to reduce poorly crystalline Fe(III) oxides (ferrihydrite) the inhibitory effects of ferrihydrite on methanogenesis. This study demonstrated that Fe(II) generation from occurs in cultures three only when H2 was supplied as source reducing equivalents, even Mst. thermophila do not grow produce CH4 H2/CO2. While supplementation...
Fructooligosaccharides and their anhydrides are widely used as health-promoting foods prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been to produce functional compounds. However, that hydrolyze form α-D-fructofuranosyl less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase difructose dianhydride I synthase/hydrolase [αFFase1]) an enzyme with α-D-fructofuranosidase...
Abstract The recent discovery of zinc‐dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on Zn‐coordinated cysteine nucleophile and passing through thioglycosyl enzyme intermediate, remains controversial. This is primarily due to expected stability intermediate C−S bond. To facilitate study this atypical we report synthesis...
Acetyl xylan esterase plays a crucial role in the degradation of xylan, major plant hemicellulose, by liberating acetic acid from backbone polysaccharides. B Aspergillus oryzae , designated Ao AxeB, was biochemically and structurally investigated. The AxeB‐encoding gene with native signal peptide successfully expressed Pichia pastoris as an active extracellular protein. purified recombinant protein had pH temperature optima 8.0 30 °C, respectively, stable up to 35 °C. optimal substrate for...
The addition of ferrihydrite to methanogenic microbial communities obtained from a thermophilic anaerobic digester suppressed methanogenesis in dose-dependent manner. amount reducing equivalents consumed by the reduction iron was significantly smaller than that expected decrease production CH4, which suggested competition between iron-reducing microorganisms and methanogens not most significant cause for suppression methanogenesis. Microbial community analyses revealed presence markedly...
p-Hydroxybenzoate hydroxylase (PHBH) is a flavoprotein monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (p-OHB) to 3,4-dihydroxybenzoate (3,4-DOHB). PHBH can bind other benzoate derivatives in addition p-OHB; however, does not occur on 3,4-DOHB. Replacement Tyr385 with Phe forms mutant, which enables production 3,4,5-trihydroxybenzonate (gallic acid) from 3,4-DOHB, although catalytic activity mutant quite low. In this study, we report how L199V/Y385F double exhibits for...
The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis leprae, contain lipoarabinomannan arabinogalactan. These components are composed D-arabinose, the enantiomer typical L-arabinose found in plants. unique glycan structures mycobacteria contribute to their ability evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-D-arabinanases, GH172 exo-α-D-arabinofuranosidase, GH116 exo-β-D-arabinofuranosidase) from...
N-Linked glycans play important roles in various cellular and immunological events. Endo-β-N-acetylglucosaminidase (ENGase) can release or transglycosylate N-glycans is a promising tool for the chemoenzymatic synthesis of glycoproteins with homogeneously modified glycans. The ability ENGases to act on core-fucosylated key factor determining their therapeutic utility because mammalian are frequently α-1,6-fucosylated. Although biochemistries structures have been studied extensively,...
Enzymes acting on α-L-arabinofuranosides have been extensively studied; however, the structures and functions of β-L-arabinofuranosidases are not fully understood. Three enzymes an ABC transporter in a gene cluster Bifidobacterium longum JCM 1217 constitute degradation import system β-L-arabinooligosaccharides plant hydroxyproline-rich glycoproteins. An extracellular β-L-arabinobiosidase (HypBA2) belonging to glycoside hydrolase (GH) family 121 plays key role pathway by releasing...
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At active site of HypBA1, a cysteine residue (Cys417) coordinates with Zn2+ atom and functions as catalytic nucleophile for anomer-retaining hydrolytic reaction. In this study, role ion in catalysis well substrate-bound structure were studied based on biochemical crystallographic approaches. The enzymatic activity decreased after dialysis presence EDTA guanidine hydrochloride was then...
Pyruvyl modification of oligosaccharides is widely seen in both prokaryotes and eukaryotes. Although the biosynthetic mechanisms pyruvylation have been investigated, enzymes that metabolize degrade pyruvylated are not well known. Here, we searched for a galactose (PvGal)-releasing enzyme by screening soil samples. We identified Bacillus strain, as confirmed 16S ribosomal RNA gene analysis, exhibited PvGal-ase activity toward p-nitrophenyl-β-D-pyruvylated galactopyranose (pNP-β-D-PvGal)....
Two thermophilic bacterial strains, Bacillus thermoamylovorans NB501 and NB502, were isolated from a high-temperature aerobic fermentation reactor system that processes tofu refuse (okara) in the presence of used soybean oil. We cloned lipase gene strain NB501, which secretes lipase. The biochemical characteristics recombinant enzyme (Lip501r) elucidated. Lip501r is monomeric solution with an apparent molecular mass 38 kDa on SDS-PAGE. optimal pH temperature 8 60°C, respectively....
Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea bacteria, catalyze oxygen-dependent oxygenation disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure reactions take place at active sites inside the chamber. The crystal structures SORs from Acidianus species have been reported. However, states site components (mononuclear iron cysteines) entry exit paths substrate products still dispute. Here, we report biochemical...
Glycoside hydrolase family 136 (GH136) was established after the discovery and structural analysis of lacto-N-biosidase (LNBase) from infant gut bacterium Bifidobacterium longum subsp. JCM1217 (BlLnbX). Homologous genes BlLnbX are widely distributed in genomes human bacteria monkey spp., although only 2 crystal structures were reported GH136 family. Cell suspensions saguini, Tyzzerella nexilis, Ruminococcus lactaris exhibited LNBase activity. Recombinant LNBases these 3 species functionally...
Abstract The recent discovery of zinc‐dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on Zn‐coordinated cysteine nucleophile and passing through thioglycosyl enzyme intermediate, remains controversial. This is primarily due to expected stability intermediate C−S bond. To facilitate study this atypical we report synthesis...
A novel actinobacterial strain, designated YM16-381T, was isolated from sediments of Lake Nakaumi in Shimane Prefecture, Japan. The cell the strain motile, non-spore-forming and Gram-positive. colony gray-pink circular on marine agar 2216 medium. Phylogenetic analysis based 16S rRNA gene sequences indicated that belongs to family Dermatophilaceae suborder Micrococcineae. highest sequence similarity value isolate 96.2% against Kineosphaera limosa. diaminopimelic acid wall meso-A2pm. major...