Article
Chemistry, Physical
Jorick Franceus, Jolien Lormans, Lore Cools, Matthias D'hooghe, Tom Desmet
Summary: The study demonstrates significant phosphorylase activity can be established in GH3 glycoside hydrolases through single-site substitutions and further optimized through mutational paths. These findings suggest new insights into developing phosphorylases and provide a novel approach for future research in this field.
Article
Biochemistry & Molecular Biology
Emma De Beul, Alana Jongbloet, Jorick Franceus, Tom Desmet
Summary: The study focuses on the sequence diversity of Glycoside Hydrolase Family 65 (GH65) and identified specificity-determining positions through in-silico analysis of correlated mutations. By searching for amino acid motifs that differ from previously characterized enzymes, several new clades with potential new functions were identified. Three new enzymes were expressed in E. coli, with one enzyme showing high specificity in hydrolyzing specific substrates.
Article
Chemistry, Physical
Jonathan C. K. Quirke, David Crich
Summary: Carbohydrate side chain conformation plays a crucial role in controlling reactivity at the anomeric center during glycosidic bond formation and cleavage. Enzymes such as glycosyltransferases restrict substrate side chains to achieve optimal stabilization of the transition state for glycosyl transfer. Insights into side chain preferences of different types of enzymes will aid in the design of improved GT inhibitors.
Article
Biochemistry & Molecular Biology
Kedar Sharma, Carlos M. G. A. Fontes, Shabir Najmudin, Arun Goyal
Summary: The alpha-L-arabinofuranosidase from Clostridium thermocellum displays a modular architecture, enhancing catalytic efficiency. Molecular dynamics simulation analysis reveals higher flexibility in its C-terminal module. Small angle X-ray scattering analysis indicates an elongated structure of the enzyme.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Marc De Doncker, Chloe De Graeve, Jorick Franceus, Koen Beerens, Vladimir Kren, Helena Pelantova, Ronny Vercauteren, Tom Desmet
Summary: The study delves into the sequence-function space of glycoside hydrolase family 94, identifying a novel enzyme GGalP that can be used for synthesizing rare disaccharides. This highlights the potential of rational sequence space exploration in discovering new enzyme specificities for rare disaccharide synthesis.
Article
Biochemistry & Molecular Biology
Casey Crooks, Nathan J. Bechle, Franz J. St John
Summary: This study characterized a non-reducing terminal (NRT)-specific xylobiohydrolase AcXbh30A, which strictly cleaves xylobiose from the NRT with minimal other hydrolysis products under optimized reaction conditions. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Alexander Sigg, Mario Klimacek, Bernd Nidetzky
Summary: This study demonstrates the use of (mechanistic-empirical) hybrid modeling for optimizing the sucrose phosphorylase-catalyzed glycosylation of glycerol to synthesize the cosmetic ingredient GG. The hybrid model includes microscopic terms of the reverse reaction to account for the full-time course of GG synthesis, enabling comprehensive window-of-operation analysis and constrained optimization of GG production. The hybrid model is shown to be a powerful tool for process decision making and rational selection of enzyme catalysts.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Chemistry, Medicinal
Dianyi Li, Zheng Wang, Yong Yu, Huirong Li, Wei Luo, Bo Chen, Guoqing Niu, Haitao Ding
Summary: A novel GH2 beta-galactosidase from Marinomonas sp. BSi20584 was successfully expressed in E. coli and showed stable soluble form. The purified enzyme had a specific activity of 96.827 U mg(-1) at 30 degrees C using ONPG as a substrate. It had an optimum pH of 7.0 and an optimum temperature of 50 degrees C. The enzyme's activity was enhanced by some divalent cations and inhibited by EDTA. Despite being derived from a cold-adapted strain, the enzyme exhibited considerable stability against various physical and chemical elements. It also showed activity towards rare substrates. The enzyme is a promising candidate for the industrial application of beta-galactosidase.
Article
Biochemistry & Molecular Biology
Huitang Qi, Xi Jiang, Yi Ding, Tian Liu, Qing Yang
Summary: Kasugamycin, an aminoglycoside antibiotic, has been found to be a competitive inhibitor of glycoside hydrolase family 18 (GH18) chitinases in various organisms. It was discovered that the electrostatic interaction between kasugamycin and a conserved aspartate in GH18 chitinase is vital for its inhibitory activity. This research not only identifies new molecular targets of kasugamycin but also expands the understanding of GH inhibitor design by utilizing a scaffold unrelated to the substrate.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Agriculture, Multidisciplinary
Laura Plaza-Vinuesa, Oswaldo Hernandez-Hernandez, Ana Sanchez-Arroyo, Jose M. Cumella, Nieves Corzo, Ana M. Munnoz-Labrador, F. Javier Moreno, Blanca de las Rivas, Rosario Munoz
Summary: This study confirmed the myrosinase-like activity of Lactiplantibacillus plantarum WCFS1, indicating that glucosinolates in this strain may undergo phosphorylation and the glycosidases belonging to the GH1 family are involved in the hydrolysis of phosphorylated glucosinolates.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Anders Lonstrup Hansen, Johanna M. Koivisto, Signe Simonsen, Zehui Dong, Ramon Crehuet, Dennis K. Hansen, Martin Willemoes
Summary: The study identified the importance of Asp-682 and a conserved water molecule in the activation of the catalytic nucleophile in endo-alpha-N-acetylgalactosaminidase EngBF. Mutagenesis experiments showed that His-685, His-718, and the catalytic water molecule are also crucial for catalytic activity.
Article
Plant Sciences
Naoki Shinohara, Kazuhiko Nishitani
Summary: This study reveals that the non-plant origin of the XTH family is from ExoKs in Alphaproteobacteria, not licheninases in Firmicutes as previously believed, with the relevant HGT event traced back to the Cryogenian geological period, supporting the adaptation of plants and fungi to the ancient icy environment.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Alexandre M. Sorlin, Marina Lopez-Alvarez, Sarah J. Rabbitt, Aryn A. Alanizi, Rebecca Shuere, Kondapa Naidu Bobba, Joseph Blecha, Sasank Sakhamuri, Michael J. Evans, Kenneth W. Bayles, Robert R. Flavell, Oren S. Rosenberg, Renuka Sriram, Tom Desmet, Bernd Nidetzky, Joanne Engel, Michael A. Ohliger, James S. Fraser, David M. Wilson
Summary: Chemoenzymatic techniques have been widely used in pharmaceutical development, especially when routine synthetic methods fail. The regioselective and stereoselective construction of complex glycans is a rarely applied elegant application in positron emission tomography (PET) tracers. This study successfully dimerized [F-18]FDG to form [F-18]-labeled disaccharides for detecting microorganisms based on their bacteria-specific glycan incorporation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Shubha Singh, Jebin Ahmed, Parmeshwar Vitthal Gavande, Carlos M. G. A. Fontes, Arun Goyal
Summary: This study investigated the structure and function of family 30 glycoside hydrolase from Ruminococcus flavefaciens. The results revealed the catalytic residues and ligand binding characteristics of the enzyme. Experimental techniques were used to validate the structural features and stability of the enzyme, providing various conformational information in solution.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Review
Biochemistry & Molecular Biology
Xi Jiang, Qing Yang
Summary: Glycoside hydrolase family 20 (GH20) and GH84 are involved in glycoprotein modification, metabolism, and degradation, with potential applications in disease treatment and plant protection. The challenges lie in designing highly selective inhibitors due to the similarity of their active sites. Understanding the catalytic mechanism and substrate binding mode of Hex and OGA provides crucial information for inhibitor design.
BIOORGANIC CHEMISTRY
(2024)
Article
Biotechnology & Applied Microbiology
Miriam N. Ojima, Yuya Asao, Aruto Nakajima, Toshihiko Katoh, Motomitsu Kitaoka, Aina Gotoh, Junko Hirose, Tadasu Urashima, Satoru Fukiya, Atsushi Yokota, Maher Abou Hachem, Mikiyasu Sakanaka, Takane Katayama
Summary: In this study, the authors examined the HMO consumption phenotypes of two bifidobacterial species and found that the diversity of the FL transporter led to uptake specificities of fucosylated sugars ranging from simple trisaccharides to complex hexasaccharides. These findings explain the adaptation and proliferation of bifidobacteria in the competitive and HMO-rich infant gut environment.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kazuhiro Chiku, Mitsuru Yoshida, Hiroshi Ono, Motomitsu Kitaoka
Summary: The study investigated the behavior of maltose and maltulose during heating in a phosphate buffer solution at pH 7.5, revealing that maltose was isomerized into maltulose which then underwent degradation and tautomerization to form 3-deoxy-D-glycero-pent-2-ulose. The formation of different products under varying acid-base conditions was also observed.
CARBOHYDRATE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Toma Kashima, Kouki Okumura, Akihiro Ishiwata, Machika Kaieda, Tohru Terada, Takatoshi Arakawa, Chihaya Yamada, Kentaro Shimizu, Katsunori Tanaka, Motomitsu Kitaoka, Yukishige Ito, Kiyotaka Fujita, Shinya Fushinobu
Summary: A novel glycoside hydrolase family member, alpha-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase, was identified in Bifidobacterium dentium. This enzyme has unique activities and is not homologous with known enzymes, indicating its novelty in the field of glycoside hydrolases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Wataru Saburi, Takanori Nihira, Hiroyuki Nakai, Motomitsu Kitaoka, Haruhide Mori
Summary: Glycoside phosphorylases are promising enzymes for efficient glycoside production. In this study, a new glycoside phosphorylase, solabiose phosphorylase, was characterized from an uncharacterized protein. The enzyme showed specific activity towards d-galactose, producing solabiose through a sequential bi-bi mechanism. Solabiose was successfully produced from lactose and sucrose without the need for chromatographic procedures.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Applied
Mitsuru Yoshida, Ayane Tabata, Takumi Niino, Kazuhiro Chiku, Rumiko Nakashita, Yaeko Suzuki
Summary: This study discovered that the geographical origin of Japanese and Mexican kabocha pumpkins can be differentiated using the δ13C and δ18O values. The extraction of crude fiber eliminates the influence of seasoning after cooking or processing, enabling geographical origin verification even after cooking and processing. The use of δ13C and δ18O in crude fiber extends the application possibilities of stable isotope analysis in geographical origin verification of various cooked and processed vegetables and fruits.
Article
Biochemistry & Molecular Biology
Shuntaro Machida, Katsuichi Saito, Mamoru Nishimoto, Motomitsu Kitaoka
Summary: This study reports a method to produce Lacto-N-biose I (LNB) without the use of genetically modified enzymes. By selectively inactivating interfering enzymes, GlcNAc was successfully converted into LNB.
JOURNAL OF APPLIED GLYCOSCIENCE
(2022)
Article
Chemistry, Applied
Asako Narai-Kanayama, Kazuhiro Chiku, Hiroshi Ono, Takamitsu Momoi, Miho Hiwatashi-Kanno, Akiko Kobayashi, Hiroko Matsuda, Mitsuru Yoshida, Tsutomu Nakayama
Summary: Theaflavin, the polyphenol responsible for the orange color and bioactivities of black tea, can undergo autoxidation to change its color to brown under neutral and mild alkaline conditions. The presence of thiol compounds such as cysteine, glutathione, or N-acetyl cysteine can inhibit the browning of theaflavin solution and lead to a decrease in the concentrations of both theaflavin and thiol group over time. LC-MS analysis revealed the formation of novel adducts of thiol compounds. The chemical structures of theaflavin-cysteine and theaflavin-glutathione adducts were determined using NMR, showing the addition of a new cyclic structure to the theaflavin-cysteine adduct.
Article
Ecology
Miriam N. Ojima, Lin Jiang, Aleksandr A. Arzamasov, Keisuke Yoshida, Toshitaka Odamaki, Jinzhong Xiao, Aruto Nakajima, Motomitsu Kitaoka, Junko Hirose, Tadasu Urashima, Toshihiko Katoh, Aina Gotoh, Douwe van Sinderen, Dmitry A. Rodionov, Andrei L. Osterman, Mikiyasu Sakanaka, Takane Katayama
Summary: This study applied assembly theory to investigate the formation of bifidobacterial communities in the infant gut. The results showed that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis dominated through inhibitory priority effects, while Bifidobacterium breve benefited from facilitative priority effects and utilized a specific degradant to dominate. This study highlights the importance of initial community assembly and its impact on the maturation trajectory of the infant gut microbiota.
Article
Biochemistry & Molecular Biology
Kazuhiro Chiku, Ayaka Ohfuji, Nozomi Ohtake, Mitsuru Yoshida, Hiroshi Ono, Motomitsu Kitaoka
Summary: Isomaltose and isomaltulose undergo isomerization and release of glucose upon heating in sodium phosphate buffer. The concentration of these disaccharides decreases with heating time, but this decrease is not directly correlated with the release of glucose or fructose. The reaction also leads to a slight decrease in pH and the formation of organic acids, along with the presence of formic acid and species resulting from hydroxyl group elimination. The released glucose is likely generated through tautomerization and cleavage of the glycosidic linkage.
CARBOHYDRATE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Motomitsu Kitaoka
Summary: We developed a Microsoft Excel file called Enzyme Kinetics_Calculator, which contains macro programs that can automatically calculate kinetic parameters and their standard errors for typical enzymatic reactions. The file also includes functionalities to generate [S]-v plots and 1/[S]-1/v plots with theoretical lines. Enzyme Kinetics_Calculator is available as a supplementary file on the J. Appl. Glycosci. website.
JOURNAL OF APPLIED GLYCOSCIENCE
(2023)
Article
Food Science & Technology
Xin Huang, Yue Sun, Suhong Li, Motomitsu Kitaoka, Tuoping Li
Summary: To enhance the thermal stability of Lacto-N-biose (LNB), it was encapsulated within OVA-CMC microparticles. With a mass ratio of OVA:CMC:LNB as 1.5:1:1, the microparticles exhibited a particle size of 623 +/- 4 nm, encapsulation efficiency of 83 +/- 1.38%, and loading efficiency of 45 +/- 0.92%. Characterization techniques such as SEM, FT-IR, and XRD confirmed the spherical and uniform distribution of the OVA-CMC-LNB microparticles. Hydrogen bonding and electrostatic interactions were identified as the main forces responsible for the microparticles' assembly. Thermal analysis revealed that the microparticles remained structurally stable at 240 degrees C, greatly improving the thermal stability of LNB. In vitro digestion experiments demonstrated a release rate of LNB from the microparticles of 95 +/- 1.31%. These findings provide a theoretical and technological framework for enhancing the thermal stability of LNB delivery systems.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Junichi Mano, Hirotoshi Sushida, Tsuyoshi Tanaka, Ken Naito, Hiroshi Ono, Masakazu Ike, Ken Tokuyasu, Motomitsu Kitaoka
Summary: By extensively screening microbial strains, we discovered that the BS15 strain efficiently produces PEFAs with high titer. The strain was able to produce high concentrations of PEFA and dry cells in batch fermentation. Additionally, the genome sequence of the BS15 strain was analyzed and a high-quality reference genome was generated.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Gastroenterology & Hepatology
Rika Hirano, Mikiyasu Sakanaka, Kazuto Yoshimi, Naohisa Sugimoto, Syogo Eguchi, Yuko Yamauchi, Misaki Nara, Shingo Maeda, Yuta Ami, Aina Gotoh, Takane Katayama, Noriho Iida, Tamotsu Kato, Hiroshi Ohno, Satoru Fukiya, Atsushi Yokota, Mamoru Nishimoto, Motomitsu Kitaoka, Hiroyuki Nakai, Shin Kurihara
Summary: The study identified Gal-beta 1,4-Rha as a next-generation prebiotic candidate that selectively promotes the growth of beneficial bacteria like Bifidobacterium without stimulating the growth of other prominent bacteria and pathogens. This prebiotic was found to suppress the growth of the enteric pathogen Clostridioides difficile, indicating its potential for preventing infections and improving gut health.