Article
Biochemistry & Molecular Biology
Xuefei Chen, Wei Wei, Wei Xiong, Shen Wu, Quanchao Wu, Peng Wang, Guoping Zhu
Summary: This study provides a foundation for understanding the evolution and function of two NADP-IDHs in the pathogenic bacterium P. aeruginosa.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mingjie Bian, Jiaxin Zhao, Wenqiang Xu, Xueyang Han, Xuefei Chen, Peng Wang, Guoping Zhu
Summary: This study identified and characterized a dual coenzyme-dependent isocitrate dehydrogenase (UmIDH) from Umbonibacter Marinipuiceus for the first time. UmIDH is a homodimer with a molecular weight of 84.7 kDa. It exhibits higher affinity for NAD(+) than NADP(+) in the presence of Mn2+. The study also achieved bidirectional modification of UmIDH's coenzyme dependence for the first time, providing insights into the coenzyme-specific evolutionary mechanisms of isocitrate dehydrogenase.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shiping Huang, Jiaxin Zhao, Wenjing Li, Peng Wang, Zhenglian Xue, Guoping Zhu
Summary: PtIDH2 is a novel type III IDH subfamily member from marine microalga Phaeodactylum tricornutum, showing high homology with marine bacterial monomeric IDHs. PtIDH2 is a homotetramer enzyme depending on bivalent metal ions, with Mn2+ as the optimal activator.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Plant Sciences
Maria Begona Gonzalez-Moro, Itziar Gonzalez-Moro, Marlon de la Pena, Jose Maria Estavillo, Pedro M. Aparicio-Tejo, Daniel Marino, Carmen Gonzalez-Murua, Izargi Vega-Mas
Summary: Nitrate and ammonium are the main nitrogen sources in agricultural soils, with ammonium playing a diverse role in plant metabolism. Different plant species have varying strategies to maintain NH4+ balance, and the study analyzed metabolic responses in seven plant species and discussed the role of different anaplerotic enzymes in ammonium nutrition.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Ryan A. Herold, Christopher J. Schofield, Fraser A. Armstrong
Summary: The study utilizes a nanoporous electrode material, the e-Leaf, to control enzyme cascades and gain detailed kinetic insight into an anti-cancer drug mechanism. The e-Leaf allows for the quantification of IDH1 R132H inhibition kinetics and reveals factors underlying inhibitor residence time. The study highlights the importance of this method in obtaining detailed kinetic and mechanistic information that is difficult to obtain using conventional techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Agriculture, Dairy & Animal Science
T. Larsen, R. Rupp, N. C. Friggens, J. A. A. Pires
Summary: This study presents a novel method for quantifying the activity of the enzyme isocitrate dehydrogenase (IDH) in ruminant milk without pretreatment of the sample. The results show that IDH activity significantly increases during a period of nutritional restriction, accompanied by an increase in the metabolite isocitrate concentration and somatic cell count, and returns to the initial level shortly after the restriction period.
Article
Biochemical Research Methods
Kamil Kaminski, Jan Ludwiczak, Maciej Jasinski, Adriana Bukala, Rafal Madaj, Krzysztof Szczepaniak, Stanislaw Dunin-Horkawicz
Summary: Rossmann fold enzymes play important roles in biochemical pathways such as nucleotide and amino acid metabolism. This study used deep learning models based on the sequence and structural features of the beta alpha beta motif to predict the specificity of enzymes towards cofactors. The results showed highly accurate predictions, demonstrating the significance of this research for studying enzyme functions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Li Yi, Qingying Fan, Yuxin Wang, Chenlong Mao, Jinpeng Li, Manyu Jin, Xiaoling Zhang, Ke Ding, Yang Wang
Summary: The study demonstrated that recombinant PDH protein induced high levels of antibodies in mice, enhancing the immune response and protecting pathological organs from damage. Additionally, PDH antiserum significantly inhibited the growth of S. suis and the formation of biofilm in vitro.
VETERINARY MICROBIOLOGY
(2021)
Review
Cell Biology
Matthew J. Merrins, Barbara E. Corkey, Richard G. Kibbey, Marc Prentki
Summary: This review focuses on recent developments in the understanding of nutrient-induced insulin secretion. It challenges the canonical model of ATP production and K-ATP channels. The study discusses the importance of beta cell metabolic oscillations, the alignment of metabolic cycles with insulin secretion, and the regulatory roles of metabolic signaling components. A refined model of the signaling process is proposed for evaluation by the field.
Review
Biochemical Research Methods
Liliana Calzadiaz-Ramirez, Anne S. Meyer
Summary: New measures are urgently needed to reduce atmospheric CO2 levels. Formate dehydrogenases (FDHs) have the potential to catalyze the conversion of CO2 to formate, providing a novel first step approach for biocatalytic carbon capture and utilization. However, improvements are needed in the efficacy of the electron donor, enzyme stabilization, and enhancing the desired reverse FDH reactivity. Recent research has shown that the commonly used cofactor NADH is inefficient for FDH catalyzed CO2 conversion. Understanding the details of the redox reactions and structure-function relations of both metal dependent and metal-independent FDHs is crucial for promoting enzymatic CO2 utilization.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Veterinary Sciences
April A. Estrada, Marcelo Gottschalk, Connie J. Gebhart, Douglas G. Marthaler
Summary: Pan-genome analysis of Streptococcus suis identified novel candidate virulence-associated genes (VAGs) and proposed a genotyping scheme for predicting pathogenicity. Mobile genetic elements carrying antimicrobial resistance genes (ARGs) were also identified.
VETERINARY RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Raluca-Ioana Stefan-van Staden, Catalina Cioates Negut, Sorin Sebastian Gheorghe, Paula Sfirloaga
Summary: Two three-dimensional stochastic microsensors based on single-walled carbon nanotubes (SWCNT) and multi-walled carbon nanotubes (MWCNT) were designed to recognize and quantify IDH1 and IDH2 in biological samples. The microsensor using MWCNT demonstrated the highest sensitivity and recovery rate compared to the ELISA standard method.
Review
Pharmacology & Pharmacy
Giorgia Colombo, Edoardo Luigi Maria Gelardi, Federica Carolina Balestrero, Marianna Moro, Cristina Travelli, Armando A. Genazzani
Summary: Tumor cells modify their cellular metabolism in order to sustain uncontrolled proliferation, requiring adequate amounts of NAD and NADPH to support overexpressed enzymes. This review explores the rationale for targeting key enzymes that maintain the cellular NAD/NADPH pool in colorectal cancer and enzymes that consume or use NADP(H).
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Veterinary Sciences
Yumin Zhang, Guoqing Zhao, Yangjing Xiong, Feiyu Li, Yifan Chen, Yuqiang Cheng, Jingjiao Ma, Henan Wang, Yaxian Yan, Zhaofei Wang, Jianhe Sun
Summary: A multi-epitope subunit vaccine against multiple serotypes of Streptococcus suis was designed and evaluated using immunoinformatics. The vaccine showed high antigenicity, non-toxicity, and non-allergenicity, and demonstrated strong immune responses and worldwide population coverage.
VETERINARY SCIENCES
(2023)
Review
Microbiology
Muriel Dresen, Peter Valentin-Weigand, Yenehiwot Berhanu Weldearegay
Summary: This review focuses on the role of Streptococcus suis metabolism in adapting to different in vivo host niches, as well as its link to virulence. The potential of targeting metabolic pathways for new therapeutic strategies is also discussed.
Article
Biochemistry & Molecular Biology
Youming Zhu, Peng Wang, Li Zhang, Guo Bai, Chi Yang, Yuanying Wang, Jiacai He, Zhiyuan Zhang, Guoping Zhu, Duohong Zou
CELL DEATH AND DIFFERENTIATION
(2019)
Article
Biochemistry & Molecular Biology
Peng Wang, Tingting Liu, Xinxin Zhou, Guoping Zhu
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Peng Wang, Xuefei Chen, Jing Yang, Yunyun Pei, Mingjie Bian, Guoping Zhu
Article
Biochemistry & Molecular Biology
Peng Wang, Yuan Wang, Xiuxiu Guo, Shiping Huang, Guoping Zhu
Article
Biochemical Research Methods
Ya-Dong Ge, Lu-Lu Jiang, Shao-Lin Hou, Feng-Zhi Su, Peng Wang, Gen Zhang
PROTEIN EXPRESSION AND PURIFICATION
(2020)
Article
Biochemistry & Molecular Biology
Shi-Ping Huang, Lu-Chun Zhou, Bin Wen, Peng Wang, Guo-Ping Zhu
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Ping Song, Meng-li Wang, Qing-yang Zheng, Peng Wang, Guo-ping Zhu
Summary: Acinetobacter baumannii encodes enzymes for the TCA cycle and glyoxylate bypass, with its IDH1 potentially phosphorylated by E. coli IDHKP to regulate intracellular carbon flux. AbIDH1 is a fully active enzyme, with Ser113 identified as a phosphorylation site.
Article
Biochemistry & Molecular Biology
Xin Chang, Shuang Wu, Jie Chen, Shengqi Xiong, Peng Wang, Xueqin Shi, Ao Wang, Baojuan Wang
Summary: The study presented the synthesis and characterization of a gene from Streptomyces lividans TK24 in Escherichia coli, which encoded an enzyme with high thermal and alkali stability, and showed remarkable catalytic efficiency towards pNPA2.
Article
Biochemistry & Molecular Biology
Wanggang Tang, Minhao Wu, Na Qin, Li Liu, Rui Meng, Chengliang Wang, Peng Wang, Jianye Zang, Guoping Zhu
Summary: This study elucidated the crystal structures and catalytic mechanism of OtIDH, revealing its novel interactions with NAD+ and conserved substrate binding mode. The findings demonstrated that OtIDH could be evolutionary ancestors of eukaryotic NADP-IDHs in the type II subfamily.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Peng Wang, Liying Han, Moxin Yu, Zhengyu Cao, Xiaoning Li, Yunxia Shao, Guoping Zhu
Summary: The study found that PERK is differentially expressed in various cancers, with high expression associated with poor prognosis in KIRP, LGG, BRCA, and THCA, but favorable prognosis in HNSC. GSEA results indicated that PERK is mainly enriched in immune-related signaling pathways in BRCA, HNSC, and THCA. Additionally, PERK expression is significantly correlated with infiltrating levels of macrophages and dendritic cells, and with various immune markers, especially macrophage mannose receptor 1 (MRC1, also called CD206) and T-helper cells (Th).
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shiping Huang, Jiaxin Zhao, Wenjing Li, Peng Wang, Zhenglian Xue, Guoping Zhu
Summary: PtIDH2 is a novel type III IDH subfamily member from marine microalga Phaeodactylum tricornutum, showing high homology with marine bacterial monomeric IDHs. PtIDH2 is a homotetramer enzyme depending on bivalent metal ions, with Mn2+ as the optimal activator.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Microbiology
Zhengyu Cao, Jie Liu, Rui Meng, Peng Wang, Guoping Zhu
Summary: In this study, the soluble pyridine nucleotide transhydrogenase (STH) from Gram-positive bacterium Streptomyces avermitilis was successfully expressed and purified, revealing its characteristics for the first time. SaSTH showed optimal activity at lower temperatures and slightly acidic pH, with higher affinity for NADPH compared to NADH, and its activity was regulated by divalent ions and nucleotides.
CURRENT MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Changqing Tian, Bin Wen, Mingjie Bian, Mingming Jin, Peng Wang, Lei Xu, Guoping Zhu
Summary: The study successfully constructed a chimeric monomeric isocitrate dehydrogenase, demonstrating the potential of dimeric IDHs to evolve into monomeric ones. The evolution of the IDH family was also discussed in the research.
Article
Biochemistry & Molecular Biology
Baojuan Wang, Shuang Wu, Xin Chang, Jie Chen, Jinxue Ma, Peng Wang, Guoping Zhu
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Peipei Lv, Wanggang Tang, Peng Wang, Zhengyu Cao, Guoping Zhu
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Siva Santhiya Arul, Brinda Balakrishnan, Savithri S. Handanahal, Sangita Venkataraman
Summary: Viral nanoparticles are self-assembling delivery systems used for vaccines and therapeutic agents. They have improved biocompatibility and are widely used in various biomedical applications. However, large-scale production of VNPs still faces challenges.
Article
Biochemistry & Molecular Biology
Wisely Chua, Carl O. Marsh, Si En Poh, Winston LC. Koh, Melody Li Ying Lee, Li Fang Koh, Xin-Zi Emily Tang, Peter See, Zheng Ser, Shi Mei Wang, Radoslaw M. Sobota, Thomas L. Dawson Jr, Yik Weng Yew, Steven Thng, Anthony J. O'Donoghue, Hazel H. Oon, John E. Common, Hao Li
Summary: In this study, the gene expression of enzymes secreted by Malassezia globosa in the skin was investigated using targeted RNA sequencing. The study found that the expression of these enzymes is regulated by the fungus's environment and differs significantly from healthy skin sites. Additionally, a pseudoprotease MGL_3331 was identified to elicit an immune reaction in patients with atopic dermatitis. This highlights the importance of studying fungal proteins in physiologically relevant environments and their role in host immunity.
Article
Biochemistry & Molecular Biology
Belisa Parmeggiani, Marian Flores Signori, Cristiane Cecatto, Marina Rocha Frusciante, Manuela Bianchin Marcuzzo, Debora Guerini Souza, Rafael Teixeira Ribeiro, Bianca Seminotti, Diogo Onofre Gomes de Souza, Cesar Augusto Joa o Ribeiro, Moacir Wajner, Guilhian Leipnitz
Summary: Non ketotic hyperglycinemia (NKH) is a disorder caused by mutations in the genes encoding glycine cleavage system proteins, leading to severe neurodegeneration and white matter alterations. The study found that glycine affects myelin structure, glutamatergic system, and induces oxidative stress in neonatal rats and MO3.13 oligodendroglial cells.
Review
Biochemistry & Molecular Biology
Marie Rose Ndella Thiaw, Pascal Gantet
Summary: Mini zinc fingers play important roles in plant development, including control of cell division and expansion, meristem state transition, and growth and organ development. They have diverse modes of action, such as direct gene activation, interaction with specific transcription factors, and aggregation of protein complexes for chromatin remodeling. Further research is needed to explore their wider range of biological functions and their involvement in biotic and abiotic stress responses.
Article
Biochemistry & Molecular Biology
Shao-Jui Lai, Takahiro Kameda, Maasa Morita, Yuka Yamagata, Kaoruko Nishizaka, Yuna Horiuchi, Yukihiro Kobayashi, Yoko Usami, Jun-Jen Liu, Takeshi Kasama, Minoru Tozuka, Ryunosuke Ohkawa
Summary: In this study, the co-modification and impact of chymase and MPO on HDL were investigated. Sequential treatment with MPO and chymase generated two novel apoA-I fragments from HDL, one of which has a specific immunological property and can be used to predict patients with normal HDL-C levels and cardiovascular diseases.
Article
Biochemistry & Molecular Biology
Xiao-Mi Sun, Asami Yoshida, Takuya Ishii, Yan-Rong Jiang, Yi-Li Gao, Mikinori Ueno, Katsuya Hirasaka, Kiyoshi Osatomi
Summary: This study found that infection with the causative bacteria of edwardsiellosis, Edwardsiella tarda NUF251, leads to the production of superoxide radicals, causing oxidative stress. The research on the Jfsod1 gene suggests that the transcription factor NF-IL6 plays a significant role in upregulating the transcriptional activity of the gene in response to oxidative stress induced by NUF251 infection.
Article
Biochemistry & Molecular Biology
Shane M. Carey, Sean P. Kearns, Matthew E. Millington, Gregory S. Buechner, Beda E. Alvarez Jr, Leily Daneshian, Brendan Abiskaroon, Maksymilian Chruszcz, Edward L. D'Antonio
Summary: The importance of F337 in TcGlcK was investigated using the hole mutagenesis approach, revealing its key interactions with aromatic tail groups in inhibitor molecules. Mutants retaining activity and structural similarity were obtained, suggesting the possibility of TcHxK existing as a monomer lacking the F337 residue. Similar D-glucosamine inhibitors may bind less strongly to TcHxK due to the absence of van der Waals contacts from residue side chains.
Article
Biochemistry & Molecular Biology
Catia Barria, Diogo Athayde, Guillem Hernandez, Leonor Fonseca, Jorge Casinhas, Tiago N. Cordeiro, Margarida Archer, Cecilia M. Arraiano, Jose A. Brito, Rute G. Matos
Summary: Ribonucleases play a crucial role in RNA regulation by processing, degrading, and quality controlling cellular transcripts. Campylobacter jejuni, the main cause of human gastroenteritis, relies on the exoribonuclease PNPase (CjPNP) for low-temperature survival, virulence factor synthesis, and swimming, cell adhesion/invasion, and chick colonization abilities. The crystallographic structure of CjPNP, along with SAXS analysis, confirms its trimeric arrangement and provides insight into domain arrangement and flexibility. Mutations in highly conserved residues reveal unexpected RNA degradation activity even under conditions favoring polymerization. These findings have significant implications for the development of strategies to combat C. jejuni infections.
Article
Biochemistry & Molecular Biology
Elvira R. Shaykhutdinova, Maria S. Severyukhina, Inna V. Kholoshenko, Elena A. Gondarenko, Irina V. Shelukhina, Elena V. Kryukova, Alina M. Ismailova, Elena S. Sadovnikova, Igor A. Dyachenko, Arkady N. Murashev, Victor I. Tsetlin, Yuri N. Utkin
Summary: Evidence suggests that activating nicotinic acetylcholine receptors (nAChRs) can reduce cardiac injury caused by ischemia and reperfusion. In this study, the expression of a4, a6, and a132 nAChR subunits in the rat heart's left ventricle was demonstrated. The nAChR agonists cytisine and varenicline, commonly used for nicotine addiction treatment, were found to significantly reduce myocardial ischemia-reperfusion injury, with varenicline showing greater protection. The presence of a4132, a7, and/or a6132-containing receptors suggests that the protective effect of varenicline may be mediated by these subunits. These findings indicate a potential new use for cytisine and varenicline as cardioprotective agents.
Article
Biochemistry & Molecular Biology
Xinhai Xiong, Wenjie Chen, Cheng Chen, Qi Wu, Chaopeng He
Summary: This article summarizes the important roles of Cx43 in disease development from the perspective of subcellular localization and provides new ideas for Cx43 as a therapeutic target and the search for related pathological mechanisms.
Article
Biochemistry & Molecular Biology
Veronica Bastos, Simone Pascoal, Kamila Lopes, Marcia Mortari, Helena Oliveira
Summary: Cancer, especially melanoma, is a major global health problem due to its metastatic capacity, treatment resistance, and high mortality rates. The Chartergellus-CP1 peptide isolated from Chartergellus communis wasp venom showed selective cytotoxicity towards melanoma cell lines, inducing apoptosis, cell cycle impairment, and intracellular ROS increase.
Article
Biochemistry & Molecular Biology
Charlotte Claeyssen, Nathan Bulangalire, Bruno Bastide, Onnik Agbulut, Caroline Cieniewski-Bernard
Summary: Maintenance of striated muscle tissue relies on a dynamic network of protein-protein interactions. Desmin intermediate filaments play a crucial role in heart and skeletal muscle by maintaining cell structure and contributing to various cellular processes. The assembly of desmin intermediate filaments requires aB-crystallin, which is involved in multiple cellular functions.
Article
Biochemistry & Molecular Biology
Dhritiman Dey, Adhiraj Dasgupta, Dipanjan Ghosh, Oindrila Bhattacharjee, Abhrajyoti Ghosh, Ayae Honda, Dhrubajyoti Chattopadhyay
Summary: This study successfully identified host factors that interact with Chandipura Virus (CHPV) and play a critical role in infection, including A2M, LRP1, and GRP78. Knocking out A2M has a severe effect on viral infection, indicating the potential role of these host proteins in viral entry into host cells.
Article
Biochemistry & Molecular Biology
Anna Dotsenko, Igor Sinelnikov, Aleksandra Rozhkova, Ivan Zorov, Arkady Sinitsyn
Summary: Xylanases play important roles in various industrial applications, such as feed additives, pulp and paper bleaching, and the production of bread, food, and drinks. Xylanases from the GH10 family show high thermostability and resistance to protein inhibitors, making them promising candidates for these processes. This study successfully improved the thermostability and enzymatic activity of GH10 xylanase, which could enhance its effectiveness as a feed additive and during pulp and paper bleaching.
Article
Biochemistry & Molecular Biology
M. Jaquet, M. Bengue, K. Lambert, G. Carnac, D. Misse, C. Bisbal
Summary: Changes to our environment have led to the emergence of human pathogens such as chikungunya virus, which is now a major public health concern. In this study, the interconnection between skeletal muscle cells metabolism, their differentiation stage, and the infectivity of chikungunya virus was investigated. The results showed that chikungunya virus infectivity is dependent on cell differentiation and metabolism and that the virus interferes with cellular metabolism.