Article
Biochemistry & Molecular Biology
Hiroto Hirayama, Tadashi Suzuki
Summary: Cytosolic peptide:N-glycanase (NGLY1 in mammals) is a conserved enzyme that plays a role in the deglycosylation of N-glycans attached to glycopeptide/glycoproteins. NGLY1 deficiency is an autosomal recessive disorder related to the NGLY1 gene, characterized by motor deficits and neurological problems. The intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 has been shown to partially restore motor functions in Ngly1(-/-) rats, suggesting a possible therapeutic intervention. Therefore, the development of robust assay methods for NGLY1 activity and the identification of NGLY1 deficiency-specific biomarkers are critical for early diagnosis and evaluation of treatment efficacy.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Cell Biology
Zhen Wu, Zhijie Cao, Han Yao, Xiaojun Yan, Wenbin Xu, Mi Zhang, Zishan Jiao, Zijing Zhang, Jianyuan Chen, Yajing Liu, Meng Zhang, Donglai Wang
Summary: This study describes the crosstalk between deglycosylation and ubiquitination in regulating the stability of programmed death-1 (PD-1). MDM2 is identified as an E3 ligase involved in the deglycosylation and subsequent degradation of PD-1. Additionally, interferon-alpha (IFN-a) reduces PD-1 levels in T cells by stimulating the p53-MDM2 axis, which enhances the effectiveness of anti-PD-1 immunotherapy. These findings provide insights into a potential strategy for boosting cancer immunotherapy by targeting the T cell-specific MDM2-PD-1 regulatory axis.
Article
Chemistry, Multidisciplinary
Tsuyoshi Takahashi, Tatsuya Uchibayashi, Nozomi Ishii, Ichiro Matsuo, Yukiko Yoshida, Tadashi Suzuki
Summary: A split intein-based method has been developed to detect PNGase activity in live cells. The method utilizes protein trans-splicing between N-intein peptides and C-intein to generate an active luciferase, resulting from the cleavage of the N,N '-diacetylchitobiose linkage by PNGase.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ruijie Liu, Jingjing Gu, Yilin Ye, Yuxin Zhang, Shaoxing Zhang, Qiange Lin, Shuying Yuan, Yanwen Chen, Xinrong Lu, Yongliang Tong, Shaoxian Lv, Li Chen, Guiqin Sun
Summary: This study used structure-based virtual analysis to screen for NGLY1 inhibitor candidates from natural compounds. Three natural compounds with significant inhibitory activity were identified, and their core structure was revealed. This finding could guide future drug development.
Article
Multidisciplinary Sciences
Yukiko Yoshida, Makoto Asahina, Arisa Murakami, Junko Kawawaki, Meari Yoshida, Reiko Fujinawa, Kazuhiro Iwai, Ryuichi Tozawa, Noriyuki Matsuda, Keiji Tanaka, Tadashi Suzuki
Summary: Mutation in the NGLY1 gene leads to a recessive disorder in humans. Findings in this study suggest that dysfunction of the proteasome caused by accumulation of N-glycoproteins, particularly NRF1 ubiquitinated by SCFFBS2, contributes to the pathogenesis resulting from NGLY1 deficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kristyna Slamova, Jakub Cerveny, Zuzana Meszaros, Tereza Friede, David Vrbata, Vladimir Kren, Pavla Bojarova
Summary: Gal-4 is a carbohydrate-binding lectin expressed in the epithelial cells of the gastrointestinal tract, regulating cell proliferation, apoptosis, adhesion, and migration by cross-linking glycans on cell membranes or extracellular matrix components. Its altered expression in tumor tissue is associated with various cancers, and this study provides insights into its binding preferences and the influence of multivalency. These findings may contribute to the design of efficient ligands for Gal-4 with diagnostic or therapeutic potential.
Biographical-Item
Biochemistry & Molecular Biology
Naoyuki Taniguchi, Ernesto Carafoli
Summary: This article expresses gratitude and admiration for Dr. William Lennarz for his contributions and accomplishments in the field of life science during his tenure as Editor-in-Chief of Biochemical and Biophysical Research Communications.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Chihiro Honda, Ryo Katsuta, Mariko Yamada, Yusuke Kojima, Ayane Mamiya, Nanako Okada, Takuya Kawamura, Akira Totsuka, Hitoshi Shindo, Masaru Hosaka, Tomoo Nukada, Masafumi Tokuoka
Summary: This study identified novel isomeric structures in oligosaccharides from sake, containing double branches that had not been identified in starch. These isomers showed poor digestion by fungal glucoamylase, possibly due to the presence of adjacent double branches at the non-reducing end.
CARBOHYDRATE POLYMERS
(2021)
Article
Veterinary Sciences
Ling Chang, Yanan Ding, Yushi Wang, Zehe Song, Fei Li, Xi He, Haihan Zhang
Summary: This study investigated the effects of different oligosaccharides on the growth performance and intestinal function in broilers. The results showed that dietary supplementation with raffinose oligosaccharide and chitooligosaccharide significantly improved the growth and feed intake of broilers, enhanced immune function and antioxidant capacity, and improved intestinal health.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Juan Ventura, Clara Uriel, Ana M. Gomez, J. Cristobal Lopez
Summary: Convergent synthetic routes to PI-88 tetra-and pentasaccharide-component analogues have been developed using regioselective glycosylations of mannose-polyol n-pentenyl glycosides (NPG) acceptors with 1,2-methyl orthoesters (MeOE) glycosyl donors.
CARBOHYDRATE RESEARCH
(2022)
Review
Nutrition & Dietetics
Xiangguang Miao, Jin Wu, Hongping Chen, Guanting Lu
Summary: This review examines the structure and functions of cytosolic PNGase, highlighting its crucial role in ER-associated degradation and its association with NGLY1 deficiency, a genetic disorder related to deglycosylation.
Article
Chemistry, Multidisciplinary
Farong Ye, Jie Zhao, Peng Xu, Xinliang Liu, Jing Yu, Wei Shangguan, Jiazhi Liu, Xiaosheng Luo, Cheng Li, Tianlei Ying, Jing Wang, Biao Yu, Ping Wang
Summary: Investigating the role of carbohydrate domains in RBD glycoproteins is crucial for the development of neutralizing antibodies and vaccines against SARS-CoV-2, but the high heterogeneity of glycoforms may result in incomplete neutralization effects. This study presents an efficient and scalable strategy for preparing six glycosylated RBDs with defined structure glycoforms, providing insights into the structure-function relationships of carbohydrates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Food Science & Technology
Naveen Kango, Uttam K. Jana, Ritumbhara Choukade, Suresh Nath
Summary: This article presents the latest developments related to the production and applications of prebiotic mannooligosaccharides (MOS), highlighting the health benefits they provide, including antineoplastic, immunomodulatory, and hypolipidemic effects. The article also explores the potential usage of MOS as functional food ingredients for humans.
CURRENT OPINION IN FOOD SCIENCE
(2022)
Article
Food Science & Technology
Jie-Hua Chen, Yiyuan Wang, Jialiang Pan, Louise Weiwei Lu, Jianfeng Yu, Bin Liu, Feng Chen, Hong Deng
Summary: This study investigates the mechanism of how GOS/FOS affect iron absorption in an iron-deficient rat model and determines the optimum dose of GOS.
MOLECULAR NUTRITION & FOOD RESEARCH
(2022)
Article
Plant Sciences
Naoko Okamoto, Megumi Maeda, Chiharu Yamamoto, Reo Kodama, Koichi Sugimoto, Yoshihito Shinozaki, Hiroshi Ezura, Yoshinobu Kimura
Summary: Through CRISPR/Cas9 technology, researchers have established tomato mutants with suppressed ENGase activity. These mutants lack ENGase activity, resulting in the production of GN2-HMT-FNGs with a different structure instead of the ubiquitous GN1-HMT-FNGs. However, there is no significant difference between the mutants and the wild type during fruit maturation.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Yuki Sasaki, Masahiro Komeno, Akihiro Ishiwata, Ayako Horigome, Toshitaka Odamaki, Jin-Zhong Xiao, Katsunori Tanaka, Yukishige Ito, Kanefumi Kitahara, Hisashi Ashida, Kiyotaka Fujita
Summary: Gum arabic arabinogalactan protein (AGP) can be effectively degraded by the cooperative action of GAfase, exo-beta 1,3-galactanase (Bl1,3Gal), and BlArafE, leading to the production of alpha-L-Rhap-(1 -> 4)-beta-D-GlcpA-(1-6)-beta-D-Galp-(1 -> 6)-D-Gal tetrasaccharide. This oligosaccharide can be utilized by commensal bacteria, potentially facilitating cross-feeding interactions between bifidobacteria and other gut microbial groups.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Midori Ikezaki, Kazuchika Nishitsuji, Ko Matsumura, Shino Manabe, Yukinao Shibukawa, Yoshinao Wada, Yukishige Ito, Yoshito Ihara
Summary: This study investigated the effects of C-mannosylation on the biological function of WSPW peptides and found that C-mannosylated WSPW peptides could interact with actinin-4, influencing the expression and subcellular localization of E-cadherin in cells.
Article
Biochemistry & Molecular Biology
Wataru Miyanishi, Makoto Ojika, Dai Akase, Misako Aida, Yasuhiro Igarashi, Yukishige Ito, Yu Nakagawa
Summary: The study found that attachment of 2-aminoethanol to the carboxy group of PRM-A significantly suppressed aggregation, and the prepared amide derivatives not only bound to Man without aggregation but also exhibited antifungal activity.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Kazuchika Nishitsuji, Midori Ikezaki, Shino Manabe, Kenji Uchimura, Yukishige Ito, Yoshito Ihara
Summary: C-Mannosylation affects the biological functions of proteins, especially in thrombospondin 1 repeats. C-Mannosylated WSPW peptide inhibits TGF-beta-mediated synaptogenesis by suppressing Smad 2 activation. The molecular details of how C-mannosylation affects the biological functions of WxxW motifs require further study for clarification.
GLYCOCONJUGATE JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Takashi Kikuma, Haruka Ibuki, Masaya Nakamoto, Akira Seko, Yukishige Ito, Yoichi Takeda
Summary: It has been discovered that EDEM3 plays a significant role in the protein quality control in the endoplasmic reticulum (ER), by converting specific glycans into other types of glycans. Additionally, the activity of EDEM3 is enhanced through interaction with ERp46. This study provides new insights into the enzymatic properties of EDEM3 and the use of artificial glycan substrates to study ERAD mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Yu Nakagawa, Yuzuka Oya, Makoto Ojika, Yasuhiro Igarashi, Yukishige Ito
Summary: This study discovered that the modified derivatives of C4'-N-formyl PRM-A and C4'-N-acetyl PRM-A showed significant antifungal activities without forming aggregates or precipitates, providing a new strategy for the therapeutic application of PRM-A.
Article
Chemistry, Multidisciplinary
Hak Park, Soo Kyung Seo, Ju-Ri Sim, Su Jin Hwang, Ye Jin Kim, Dong Hoon Shin, Dong Geon Jang, Shin Hye Noh, Pil-Gu Park, Si Hwan Ko, Mi Hwa Shin, Jae Young Choi, Yukishige Ito, Chung-Min Kang, Jae Myun Lee, Min Goo Lee
Summary: This study reveals the critical role of TMED proteins in the Golgi-independent unconventional secretion of transmembrane proteins under ER stress. TMED3 is able to recognize ER core-glycosylated protein cargos and the TMED2/3/9/10 complex mediates their unconventional secretion. These findings provide evidence for a common role of TMED3 and related TMED proteins in the ER stress-associated unconventional secretion of transmembrane proteins.
Article
Biochemistry & Molecular Biology
Sayaka Higashi, Yuki Imamura, Takashi Kikuma, Takahiro Matoba, Saya Orita, Yoshiki Yamaguchi, Yukishige Ito, Yoichi Takeda
Summary: The details of the complex formation between SelenoF and HUGT1 in the endoplasmic reticulum glycoprotein quality control system are still unclear. This study used co-transfection and crosslinking experiments to reveal the binding position of SelenoF to HUGT1, further elucidating the function of SelenoF.
Article
Chemistry, Multidisciplinary
Junpei Abe, Yoichi Takeda, Takashi Kikuma, Yasuhiko Kizuka, Hiroyuki Kajiura, Yasuhiro Kajihara, Yukishige Ito
Summary: UDP-Glc：glycoprotein glucosyltransferase (UGGT) plays a central role in maintaining the quality control of correctly folded N-glycoproteins in the endoplasmic reticulum (ER). However, a selective and potent inhibitor against UGGT has not been identified. In this study, we report squaryl group-modified UDP analogs as potential UGGT inhibitors, with one compound showing the highest potency and suggesting a candidate for further optimization.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yasuto Hoshikawa, Yasuyuki Kanno, Hanako Tawata, Takuya Sagae, Takafumi Ishii, Shuhei Imoto, Shinya Hagihara, Takehiko Wada, Fumi Nagatsugi, Alex Aziz, Hirotomo Nishihara, Takashi Kyotani, Tetsuji Itoh
Summary: Water-dispersible carbon nano-test tubes (CNTTs) were prepared using the template technique, with inner and outer diameters of approximately 25 and 35 nm, respectively. The inner carbon surface of these CNTTs was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was studied in the presence of Ca2+ cations, revealing that Ox-CNTTs can selectively attract DNA molecules based on Ca2+-mediated electrostatic interactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Editorial Material
Chemistry, Multidisciplinary
Yasuto Hoshikawa, Yasuyuki Kanno, Hanako Tawata, Takuya Sagae, Takafumi Ishii, Shuhei Imoto, Shinya Hagihara, Takehiko Wada, Fumi Nagatsugi, Alex Aziz, Hirotomo Nishihara, Takashi Kyotani, Tetsuji Itoh
Summary: Water-dispersible carbon nano-test tubes (CNTTs) with selective oxidation of the inner carbon surface were prepared and their adsorption behavior of DNA molecules in the presence of Ca2+ cations was studied. The electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface attracted many DNA molecules to the inner space of the oxidized CNTTs (Ox-CNTTs). The selective adsorption was attributed to the stronger electrostatic interaction on the inner concave surface compared to the outer convex surface, and the DNA could easily desorb when Ca2+ cations were removed.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Sheng-Tao Li, Hiroto Hirayama, Chengcheng Huang, Tsugiyo Matsuda, Ritsuko Oka, Takahiro Yamasaki, Daisuke Kohda, Tadashi Suzuki
Summary: It is known that oligosaccharyltransferase (OST) has hydrolytic activity toward dolichol-linked oligosaccharides, but the functional importance of this activity remains unknown. In this study, we found that the hydrolytic activity of OST is enhanced in yeast under conditions related to the biosynthesis of dolichol-linked oligosaccharides and ubiquitin ligase, but is canceled under conditions promoting protein unfolding. These results suggest a possible role of free N-glycans in protein folding.
Article
Biochemistry & Molecular Biology
Shun Maruyama, Kota Sawano, Satoko Amaki, Takehiro Suzuki, Satoru Narita, Kenta Kimura, Takatoshi Arakawa, Chihaya Yamada, Yukishige Ito, Naoshi Dohmae, Kiyotaka Fujita, Akihiro Ishiwata, Shinya Fushinobu
Summary: This study investigated the catalytic mechanism and substrate binding structure of the beta-l-arabinofuranosidase HypBA1 from Bifidobacterium longum. Zn2+ ion and cysteine were found to play key roles in catalysis, and the mode of substrate binding affected the catalytic activity.
Article
Biochemistry & Molecular Biology
Hiroto Hirayama, Yuriko Tachida, Junichi Seino, Tadashi Suzuki
Summary: The deficiency of cytosolic peptide N-glycanase (NGLY1) is a rare genetic disorder with common symptoms exhibited by patients, however, there is currently a lack of a reliable method to quantify NGLY1 activity.
Article
Biochemistry & Molecular Biology
Chengcheng Huang, Junichi Seino, Haruhiko Fujihira, Keiko Sato, Reiko Fujinawa, Zeynep Sumer-Bayraktar, Nozomi Ishii, Ichiro Matsuo, Shuichi Nakaya, Tadashi Suzuki
Summary: Recent studies have shown the presence of sialyl free N-glycans in animal sera, with a variety of neutral and sialylated FNGs. The formation mechanism of these FNGs remains unclear, and different species have varying ratios of Gn1-type sialyl FNGs. The discovery of small sialylated glycans similar to milk oligosaccharides in sera indicates a complex mechanism behind the formation of free oligosaccharides.
