Article
Agriculture, Multidisciplinary
Xuanwei Mei, Yuying Zhang, Xiaoxiao Jiang, Guanchen Liu, Jingjing Shen, Changhu Xue, Hang Xiao, Yaoguang Chang
Summary: A novel agarose-binding CBM, WfCBM101, was discovered and characterized in this study. This research provides important insights into the study of agarose.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Biochemistry & Molecular Biology
Libo Zhang, Hai Yu, Yuanyuan Bai, Bijoyananda Mishra, Xiaoxiao Yang, Jing Wang, Evan B. Yu, Riyao Li, Xi Chen
Summary: Carbohydrate-protein conjugates have diverse applications, from vaccines to high-throughput assays. A process combining chemoenzymatic synthesis, squarate linker conjugation, and neoglycoprotein immobilization on fluorescent magnetic beads was developed for a suspension multiplex array platform. This platform allowed for analysis of glycan and GBP interactions, providing useful insights into human galectins' multivalent glycan-binding properties.
Article
Chemistry, Multidisciplinary
Jon I. Quintana, Sandra Delgado, Reyes Nunez-Franco, F. Javier Canada, Gonzalo Jimenez-Oses, Jesus Jimenez-Barbero, Ana Arda
Summary: Gal-4 consists of two different domains that preferentially bind to A and B histo blood group antigens with different affinities. The study used NMR, ITC, and molecular modeling to investigate the binding of the N-terminal domain of Gal-4 to a group of differently presented A and B oligosaccharide antigens in solution, providing a structural-based rationale for the observed binding preferences.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Dixita Chettri, Manswama Boro, Lija Sarkar, Anil Kumar Verma
Summary: Lectins are non-enzymatic carbohydrate binding proteins found in all domains of life, functioning to recognize, interact, and bring about reversible binding with specific sugar moieties in molecules. Studying lectins helps understand the characteristics of glycan molecules and their important roles in biological processes.
CARBOHYDRATE RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Hamed I. Hamouda, Yi-Xuan Fan, Mohnad Abdalla, Hang Su, Ming Lu, Fu-Li Li
Summary: Lam16A is a GH16 beta-1,3-1,4-lichenase with potential in promoting the availability of beta-1,3-glucan oligosaccharides for health benefits. The six carbohydrate-binding modules (CBMs) in its catalytic module, particularly Lam16A-1CBM, play a crucial role in substrate specificity, thermal stability, and binding affinity. The full-length Lam16A with six CBMs exhibits excellent thermostability and high activity against certain polysaccharides, such as barley beta-glucan and laminarin.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Fisheries
Nongnuch Singrang, Thassanai Sitthiyotha, Nusara Chomanee, Chaninat Watthanasak, Surasak Chunsrivirot, Kittikhun Wangkanont
Summary: By studying zebrafish intelectin-2, we have gained insights into its basic biochemical properties and bacterial binding specificities, providing essential knowledge for the aquaculture industry and laying a foundation for further application of DrIntL-2 in bacteria detection and identification.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Federico Tidu, Marco De Zuani, Shyam Sushama Jose, Kamila Bendickova, Lukas Kubala, Frank Caruso, Francesca Cavalieri, Giancarlo Forte, Jan Fric
Summary: MSCs respond to fungal component zymosan by phagocytosing it, leading to Syk phosphorylation, increased cytosolic calcium levels, and ultimately NFAT1 nuclear translocation.
Article
Materials Science, Paper & Wood
Olanrewaju Raji, Vincent G. H. Eijsink, Emma Master, Zarah Forsberg
Summary: In this study, a fluorescent labeling technique was used to track the action of lytic polysaccharide monooxygenases (LPMOs) on microcrystalline cellulose and evaluate the impact of carbohydrate-binding modules (CBMs) on the distribution of LPMO activity.
Article
Fisheries
Angelica Lizeth Toiber-Estrella, Adrian Quintero-Martinez, Adela Rodriguez-Romero, Hector Riveros-Rosas, Alejandra Hernandez-Santoyo
Summary: Galectins are a family of lectins that have ancient evolutionary origins and can recognize and bind to beta-galactosides. In this study, a galectin called HrGal was identified and characterized from the mollusk Haliotis rufescens. HrGal has four tandem-repeat CRDs and showed specificity for galactosides. It belongs to a monophyletic group of tetradomain galectins unrelated to vertebrate galectins. The sulfated sugars heparin and iota-carrageenan were the only ones that inhibited its hemagglutinating activity.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Microbiology
Viviana G. Correia, Filipa Trovao, Benedita A. Pinheiro, Joana L. A. Bras, Lisete M. Silva, Claudia Nunes, Manuel A. Coimbra, Yan Liu, Ten Feizi, Carlos M. G. A. Fontes, Barbara Mulloy, Wengang Chai, Ana Luisa Carvalho, Angelina S. Palma
Summary: A multi-gene polysaccharide utilization locus (PUL) targeting mixed-linkage beta 1,3-1,4-glucans has been identified in prominent members of Bacteroidetes in the human gut, which plays a crucial role in promoting a healthy microbiota and as potential prebiotics. The BoSGBP(MLG)-A protein shows unique binding specificity towards beta 1,3-1,4-gluco-oligosaccharides, with interactions characterized by a complex hydrogen bonding network and specific interactions with ordered water molecules. Understanding the molecular mechanisms of carbohydrate recognition by commensal bacteria like Bacteroidetes can provide insights into modulating the microbiome for promoting human health.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Zijia Lu, Alma Kvammen, He Li, Mengshu Hao, Annie R. Inman, Vincent Bulone, Lauren S. McKee
Summary: This study shows that the soil bacterium Chitinophaga pinensis can degrade two different polysaccharides found in fungal cell walls using multi-modular carbohydrate-active enzymes. It reveals the complexity of polysaccharide deconstruction in nature and demonstrates how one enzymatic cascade can access multiple different glycans.
Article
Chemistry, Applied
Gilvan Pessoa Furtado, Sibeli Carli, Luana Parras Meleiro, Jose Carlos Santos Salgado, Richard John Ward
Summary: A RtCBM11-BglS chimera was created and showed increased hydrolytic efficiency against purified barley beta-glucan, making it potentially useful for treatment of crude barley extracts in the brewing industry.
Article
Biotechnology & Applied Microbiology
James Li, Ethan D. Goddard-Borger, Olanrewaju Raji, Hirak Saxena, Laleh Solhi, Yann Mathieu, Emma R. Master, Warren W. Wakarchuk, Harry Brumer
Summary: Cellulomonas flavigena is a bacterium that plays an important role in cellulose degradation and has been found to produce a chitin-active LPMO enzyme, providing new insights into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nozomi Oka, Sota Mori, Marina Ikegaya, Enoch Y. Park, Takatsugu Miyazaki
Summary: N-glycans are modified by glycosyltransferases in the endoplasmic reticulum and Golgi apparatus, with N-acetylglucosaminyltransferase IV (GnT-IV) being an important enzyme in synthesizing complex-type N-glycans. The study identified CBML as potential novel CBM family proteins with GlcNAc-binding ability, suggesting a conserved role among isozymes.
Article
Biochemistry & Molecular Biology
Sonal Mahajan, Thirumalai Nallan Chakravarthy Ramya
Summary: Alginate lyases, such as CaAly, have the potential to disrupt alginate-rich biofilms in cystic fibrosis patients' infected lungs. CaAly demonstrates effective degradation of polyM and polyG alginates, as well as binding to fucosylated glycans. Moreover, it shows strong inhibition of biofilm formation by Pseudomonas aeruginosa on both plastic surfaces and lung epithelial cell monolayers.
Review
Biochemistry & Molecular Biology
Naoyuki Taniguchi, Yuki Ohkawa, Kento Maeda, Yoichiro Harada, Masamichi Nagae, Yasuhiko Kizuka, Hideyuki Ihara, Yoshitaka Ikeda
Summary: Cancer-related changes in glycans on cell surface proteins are regulated by glycosyltransferases and related genes, which play key roles in cancer metastasis and invasion. The significance of EMT and N-glycan branching glycosyltransferases needs to be reconsidered for potential therapeutic strategies. Specific glycosyltransferases involved in EMT or MET pathways may be difficult to define due to their roles in intermediate states.
MOLECULAR ASPECTS OF MEDICINE
(2021)
Article
Biophysics
Saeko Yanaka, Yoshiki Yamaguchi, Takeshi Takizawa, Yohei Miyanoiri, Rina Yogo, Ichio Shimada, Koichi Kato
Summary: The N-glycosylation at the Fc portion of IgG plays a critical role in defensive effector functions. Degalactosylation was found to structurally perturb the Fc region in a solution-based analysis.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)
Article
Biochemistry & Molecular Biology
Sushil K. Mishra, Yoshiki Yamaguchi, Makoto Higuchi, Naruhiko Sahara
Summary: This study utilized molecular modeling to investigate the binding of PET probes to tau filaments from patients with Pick's disease, identifying binding sites, modes, and energies. Among the probes tested, PM-PBB3 showed the strongest binding affinity, suggesting potential for the rational design of PET tracers specific to Pick's disease in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Masamichi Nagae, Kei Suzuki, Norihisa Yasui, Terukazu Nogi, Takao Kohno, Mitsuharu Hattori, Junichi Takagi
Summary: Reelin is a glycoprotein that regulates embryonic brain development and adult brain functions. Its N-terminal region is crucial for multimer formation and efficient signal transduction.
JOURNAL OF BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shiho Ohno, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, Yoshiki Yamaguchi
Summary: Ribitol, an acyclic sugar alcohol found in mammalian alpha-dystroglycan, exhibits conformational asymmetry influenced by hydrogen bonds and steric hinderance. Solid-state and solution NMR spectra show differences in chemical shifts. Molecular dynamics simulations reveal the presence of asymmetric conformations in ribitol.
Article
Biochemistry & Molecular Biology
Kyoka Hoshi, Hiromi Ito, Eriko Abe, Takashi J. Fuwa, Mayumi Kanno, Yuta Murakami, Mitsunari Abe, Takenobu Murakami, Akioh Yoshihara, Yoshikazu Ugawa, Takashi Saito, Takaomi C. Saido, Kana Matsumoto, Yoshiki Yamaguchi, Katsutoshi Furukawa, Hiroyuki Arai, Mitsuyasu Kanai, Masakazu Miyajima, Hajime Arai, Norihiro Ogawa, Hiroyasu Akatsu, Yoshio Hashizume, Hiroaki Tateno, Takashi Honda, Yasuhiro Hashimoto
Summary: The study explored glycan-biomarkers on Tf in cerebrospinal fluid, finding that Man-Tf levels were significantly increased in patients with AD and MCI, correlating well with p-tau levels. Man-Tf could be a new biomarker for AD.
Review
Biochemistry & Molecular Biology
Shunli Pan, Noriyoshi Manabe, Yoshiki Yamaguchi
Summary: IgG is the most studied immunoglobin class currently, while IgA and IgM play a crucial role in mucosal immunity. These immunoglobulins have complex structures, but with emerging technologies, there is increasing understanding of the 3D structures and structure-function relationships of IgA and IgM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Reina F. Osuka, Tetsuya Hirata, Masamichi Nagae, Miyako Nakano, Hiroyuki Shibata, Ryo Okamoto, Yasuhiko Kizuka
Summary: The N-terminal domain of N-acetylglucosaminyltransferase-V (GnT-V) is crucial for efficient glycosylation and plays a key role in the recognition of glycoprotein substrates. This study revealed that the N domain interacts directly with the substrate polypeptide, providing new insights into the mechanism of substrate-selective biosynthesis of N-glycans.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Immunology
Xiuyuan Lu, Yuki Hosono, Masamichi Nagae, Shigenari Ishizuka, Eri Ishikawa, Daisuke Motooka, Yuki Ozaki, Nicolas Sax, Yuichi Maeda, Yasuhiro Kato, Takayoshi Morita, Ryo Shinnakasu, Takeshi Inoue, Taishi Onodera, Takayuki Matsumura, Masaharu Shinkai, Takashi Sato, Shota Nakamura, Shunsuke Mori, Teru Kanda, Emi E. Nakayama, Tatsuo Shioda, Tomohiro Kurosaki, Kiyoshi Takeda, Atsushi Kumanogoh, Hisashi Arase, Hironori Nakagami, Kazuo Yamashita, Yoshimasa Takahashi, Sho Yamasaki
Summary: Through single-cell TCR and RNA sequencing, researchers identified public cTfh clonotypes expanded in recovered COVID-19 patients, determined their epitopes in the conserved regions of spike protein, and found that these epitopes may be valuable candidates for booster antigens to enhance adaptive immunity against the virus.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Amol M. Vibhute, Hide-nori Tanaka, Sushil K. Mishra, Reina F. Osuka, Masamichi Nagae, Chizuko Yonekawa, Hiroaki Korekane, Robert J. Doerksen, Hiromune Ando, Yasuhiko Kizuka
Summary: This study aims to design novel inhibitors for GnT-V by chemically synthesizing a series of UDP-GlcNAc analogs and testing their inhibitory effects on GnT-V. The results show that although these analogs have modest inhibition potency, they exhibit a certain selectivity for GnT-V. Additionally, the docking models provide insights into the interactions and inhibitory mechanisms between these analogs and GnT-V.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Biochemistry & Molecular Biology
Kyoka Hoshi, Mayumi Kanno, Mitsunari Abe, Takenobu Murakami, Yoshikazu Ugawa, Aya Goto, Takashi Honda, Takashi Saito, Takaomi C. Saido, Yoshiki Yamaguchi, Masakazu Miyajima, Katsutoshi Furukawa, Hiroyuki Arai, Yasuhiro Hashimoto
Summary: CSF protein levels may be associated with neurodegenerative diseases, particularly Alzheimer's disease. Increased CSF protein levels in CN subjects are positively correlated with AD markers, while correlations decline in MCI and AD patients with AD markers.
Article
Biology
Masamichi Nagae, Tetsuya Hirata, Hiroaki Tateno, Sushil K. Mishra, Noriyoshi Manabe, Naoko Osada, Yuko Tokoro, Yoshiki Yamaguchi, Robert J. Doerksen, Toshiyuki Shimizu, Yasuhiko Kizuka
Summary: X-ray crystallography, NMR, and computer modeling were used to investigate the structure and catalytic mechanism of GnTIVa, an enzyme involved in the synthesis of GlcNAc branches. The enzyme contains a C-terminal lectin domain that regulates its activity. The lectin domain was found to interact selectively with N-glycans having a beta 1-4 GlcNAc branch. Our findings provide insights into the biosynthesis of branching structures in N-glycans.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Naoko Osada, Masamichi Nagae, Miyako Nakano, Tetsuya Hirata, Yasuhiko Kizuka
Summary: In this study, the authors found that GnT-IVa and GnT-IVb have different preferences for glycoprotein substrates in both cells and in vitro. They discovered that the noncatalytic C-terminal lectin domain regulates the substrate selectivity of these enzymes, providing a new mechanism for the formation of N-glycan branches on glycoproteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Noriyoshi Manabe, Shiho Ohno, Kana Matsumoto, Taiji Kawase, Kenji Hirose, Katsuyoshi Masuda, Yoshiki Yamaguchi
Summary: The determination of glycan structures is crucial for understanding the relationship between structure and function of glycans and glycoconjugates. Mass spectrometry is an effective method for analyzing glycan structures due to its high sensitivity and mass resolution. In this study, we propose a rapid and precise method for identifying N-glycan structures using ultraperformance liquid chromatography-connected ion mobility mass spectrometry (UPLC/IM-MS). We validate this methodology by examining 71 pyridylaminated (PA-) N-linked oligosaccharides, including isomeric pairs. By establishing a database of m/z, CCS index, and normalized retention time (GU), we provide a practical strategy for structural analysis of N-linked glycans.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Multidisciplinary Sciences
Kensuke Shibata, Chihiro Motozono, Masamichi Nagae, Takashi Shimizu, Eri Ishikawa, Daisuke Motooka, Daisuke Okuzaki, Yoshihiro Izumi, Masatomo Takahashi, Nao Fujimori, James B. Wing, Takahide Hayano, Yoshiyuki Asai, Takeshi Bamba, Yoshihiro Ogawa, Makoto Furutani-Seiki, Mutsunori Shirai, Sho Yamasaki
Summary: By studying a Bcl11b-deficient mouse model, the authors found that MR1-reactive T cells have pathogenic potential and that MR1 functions as an antigen presenting protein on cells other than MAIT cells.
NATURE COMMUNICATIONS
(2022)
