Article
Biochemistry & Molecular Biology
Jun Katahira, Tatsuya Ohmae, Mayo Yasugi, Ryosuke Sasaki, Yumi Itoh, Tomoko Kohda, Miki Hieda, Masami Yokota Hirai, Toru Okamoto, Yoichi Miyamoto
Summary: To facilitate replication, viruses can block host gene expression by targeting processes such as mRNA nuclear export. In this study, it was found that Nsp14, a viral replicase subunit, inhibits mRNA nuclear export, leading to accumulation of RNA in the cell nucleus and disruption of nuclear speckles. Dysregulation of splicing and mRNA processing was observed in SARS-CoV-2-infected cells. The inhibitory activities of Nsp14 were diminished by a mutation in its guanine-N7-methyltransferase active site. The compromise of the nuclear cap-binding complex (NCBC) function by N7-methyl-GTP, produced in Nsp14-expressing cells, leads to defects in mRNA processing and export, representing a novel viral strategy to block host gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Jianzhen Lei, Jingheng Ye, Rong She, Ruyi Zhang, Yanan Wang, Guocui Yang, Jie Yang, Lan Luo
Summary: The study found that L-theanine significantly hindered cholesterol accumulation in macrophages and inhibited foam cell formation by promoting the degradation of scavenger receptor A protein.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Environmental Sciences
Jianwei Zhao, Jing Zhang, Dalei Zhang, Zhanbo Hu, Yingjie Sun
Summary: The study revealed that the impact of fluoxetine (FLX) on excess sludge (ES) anaerobic digestion is dose-dependent, with higher concentrations of FLX inhibiting methane production from ES digestion. Mechanistically, the presence of FLX was found to inhibit key enzyme activity in the hydrolysis, acidification, and methanogenesis processes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Vinay K. Nagarajan, Catherine J. Stuart, Anna T. DiBattista, Monica Accerbi, Jeffrey L. Caplan, Pamela J. Green
Summary: In plants, cytoplasmic mRNA decay controlled by DNE1 is crucial for gene expression and RNA homeostasis. Using RNA degradome approaches, this study identified over 200 DNE1 substrates, primarily cleaved within coding regions. While most DNE1 targets were NMD-insensitive, some were NMD-sensitive, indicating its role in turnover of diverse mRNAs. Mutations in the endoribonuclease domain of DNE1 abolished the cleavage, demonstrating its requirement for activity. This work provides important insights into DNE1-mediated mRNA decay.
Article
Biochemistry & Molecular Biology
Yi Rao, Seth T. Gammon, Margie N. Sutton, Niki M. Zacharias, Pratip Bhattacharya, David Piwnica-Worms
Summary: This study reveals that high concentrations of exogenous pyruvate inhibit intracellular LDH activity and glycolytic ECAR, with the extent of inhibition being highly dependent on pyruvate influx mediated by monocarboxylate transporter-1. These findings suggest that maintaining plasma pyruvate at submillimolar concentrations could minimize transient metabolic perturbations and enhance the accuracy of metabolic studies using hyperpolarized [1-C-13]pyruvate magnetic resonance spectroscopic imaging and stable isotope tracer experiments.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Agricultural Engineering
Ying Gao, Jianwei Zhao, Chengzhi Qin, Qingjiang Yuan, Jiangwei Zhu, Yingjie Sun, Chenggang Lu
Summary: Fluoxetine inhibits biohydrogen production in anaerobic dark fermentation, even at low concentrations. High levels of fluoxetine reduce every step associated with biohydrogen production, including decreasing concentrations of ammonia nitrogen and phosphate and having a significant negative effect on enzyme activity.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Physical
Ke Zhang, Tingze Pan, Yangyang Sun, Zhuzhu Tang, Yuhong Ren, Hualei Wang, Dongzhi Wei
Summary: This study developed a rational in silico strategy to accurately identify CP-NLases with significant hydration activity. A key motif, LNCXE, responsible for the catalytic promiscuity in nitrilases was identified by mimicking active site architectural features. Utilizing this strategy, six CP-NLases with significant hydration activity were discovered, and one nitrilase (NitPC) exhibited the highest promiscuous activity ever reported, producing 89.7% mandelamide.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nana Sakata, Ayumi Ogata, Mai Takegawa, Nagisa Tajima, Misaki Nishimura, Teruki Hagiwara, Mitsuhiro Miyazawa, Shigeru Shimamoto, Yuji Hidaka
Summary: This study investigates the activation and folding mechanism of cocoonase by overexpressing recombinant cocoonase and prococoonase in E. coli cells. The results suggest that cocoonase becomes trapped in a molten globule-like state during folding without the assistance of the propeptide region. The propeptide region kinetically accelerates the folding of cocoonase to adopt the correct conformation at the final step of the folding pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Pranas Grigaitis, Bas Teusink
Summary: Using computational modeling, it is suggested that yeast maintains an excess of glycolytic enzymes at low specific growth rates, which helps in adapting to sugar fluctuations in the environment.
Article
Chemistry, Organic
Blazej A. Wojtczak, Marcelina Bednarczyk, Pawel J. Sikorski, Anna Wojtczak, Piotr Surynt, Joanna Kowalska, Jacek Jemielity
Summary: Chemical modifications of the mRNA cap structure can improve the therapeutic properties of synthetic mRNA by enhancing stability, translational properties, and half-life. The Suzuki-Miyaura cross-coupling reaction is a useful approach for modifying cap structures, and two methods for synthesizing C8-modified cap structures using this reaction were described. The modified cap structures were successfully used to study the interaction with cap-binding proteins.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Scott Mazurkewich, Andrea Seveso, Johan Larsbrink
Summary: Copper radical oxidases (CROs) are redox enzymes that oxidize alcohols or aldehydes using a single copper atom as cofactor. This study characterized an AA5 enzyme from the bacterial pathogen Burkholderia pseudomallei that was fused with a carbohydrate esterase family 3 domain. The enzyme showed promiscuous primary alcohol oxidase activity similar to enzymes from subfamily 2, while the esterase domain was inactive due to substitutions in the active site residues.
Article
Cell Biology
Nicola D. Roverato, Carolin Sailer, Nicola Catone, Annette Aichem, Florian Stengel, Marcus Groettrup
Summary: Parkin is a key protein associated with familial Parkinson's disease, and its degradation by FAT10ylation inhibits mitophagy progression, potentially exacerbating the disease. Targeting FAT10ylation pathways may offer new therapeutic opportunities for Parkinson's disease.
Article
Environmental Sciences
Jianwei Zhao, Chengzhi Qin, Meiping Sui, Siyi Luo, Huanyun Zhang, Jiangwei Zhu
Summary: This study investigated the effect of PBDEs on methane production during anaerobic co-digestion of excess sludge and kitchen waste. The results showed that PBDEs reduced methane yield and the proportion of methane in the biogas. PBDEs also inhibited volatile fatty acid production and key enzyme activities related to methane production.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Genetics & Heredity
Fengchao Zhang, Yao Chen, Jie Shen, Junzheng Zhang
Summary: The Notch signaling pathway plays crucial roles in animal development, with protein ubiquitination regulating the stability and activity of major signaling components. Multiple ubiquitin ligases and deubiquitinating enzymes have been identified in Drosophila that modify Notch ligand and receptor proteins. UbcD1 has been found to be required for Notch signaling activation during Drosophila wing development, suggesting a novel role for UbcD1 in development.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Lillian F. Schmaltz, Julia E. Ceniceros, Seongmin Lee
Summary: The human oxoG DNA glycosylase hOGG1 plays a crucial role in sensing and repairing oxidative DNA damage, and its crystal structure provides insights into the enzyme's catalytic mechanism.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Baerbel S. Blaum, Martin Frank, Ross C. Walker, Ursula Neu, Thilo Stehle
Article
Virology
Luisa J. Stroeh, Melissa S. Maginnis, Baerbel S. Blaum, Christian D. S. Nelson, Ursula Neu, Gretchen V. Gee, Bethany A. O'Hara, Nasim Motamedi, Daniel DiMaio, Walter J. Atwood, Thilo Stehle
JOURNAL OF VIROLOGY
(2015)
Article
Microbiology
Michael H. C. Buch, A. Manuel Liaci, Samantha D. O'Hara, Robert L. Garcea, Ursula Neu, Thilo Stehle
Article
Biochemistry & Molecular Biology
Nicole L. Kallewaard, Davide Corti, Patrick J. Collins, Ursula Neu, Josephine M. McAuliffe, Ebony Benjamin, Leslie Wachter-Rosati, Frances J. Palmer-Hill, Andy Q. Yuan, Philip A. Walker, Matthias K. Vorlaender, Siro Bianchi, Barbara Guarino, Anna De Marco, Fabrizia Vanzetta, Gloria Agatic, Mathilde Foglierini, Debora Pinna, Blanca Fernandez-Rodriguez, Alexander Fruehwirth, Chiara Silacci, Roksana W. Ogrodowicz, Stephen R. Martin, Federica Sallusto, JoAnn A. Suzich, Antonio Lanzavecchia, Qing Zhu, Steven J. Gamblin, John J. Skehel
Article
Virology
Zaigham Mahmood Khan, Yan Liu, Ursula Neu, Michel Gilbert, Bernhard Ehlers, Ten Feizi, Thilo Stehle
JOURNAL OF VIROLOGY
(2014)
Article
Virology
Luisa J. Stroeh, Ursula Neu, Baerbel S. Blaum, Michael H. C. Buch, Robert L. Garcea, Thilo Stehle
JOURNAL OF VIROLOGY
(2014)
Article
Multidisciplinary Sciences
Donald J. Benton, Andrea Nans, Lesley J. Calder, Jack Turner, Ursula Neu, Yi Pu Lin, Esther Ketelaars, Nicole L. Kallewaard, Davide Corti, Antonio Lanzavecchia, Steven J. Gamblin, Peter B. Rosenthal, John J. Skehel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Microbiology
Ursula Neu, Zaigham Mahmood Khan, Benjamin Schuch, Angelina S. Palma, Yan Liu, Michael Pawlita, Ten Feizi, Thilo Stehle
Article
Microbiology
Ursula Neu, Stacy-ann A. Allen, Baerbel S. Blaum, Yan Liu, Martin Frank, Angelina S. Palma, Luisa J. Stroeh, Ten Feizi, Thomas Peters, Walter J. Atwood, Thilo Stehle
Review
Biochemical Research Methods
Baerbel S. Blaum, Ursula Neu, Thomas Peters, Thilo Stehle
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2018)
Article
Microbiology
Ursula Neu, Bernardo A. Mainou
Article
Biochemistry & Molecular Biology
Johann J. Roske, Sunbin Liu, Bernhard Loll, Ursula Neu, Markus C. Wahl
Summary: The study revealed complex interactions between Mitomycin repair factor A, DNA, and ATP, with an analysis of the enzyme's structure uncovering unique structural and functional features.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Virology
Giulia Glorani, Max Ruwolt, Nicole Holton, Bernhard Loll, Ursula Neu
Summary: In this study, we investigated the stability and conformation of the reovirus attachment protein sigma 1 at different pH values. We found that sigma 1 is remarkably thermostable, especially at low pH. The optimal pH for stability was determined to be between pHs 5 and 6, which is close to the pH of the endosome and jejunum. We identified the role of the aspartic acid cluster in maintaining sigma 1 thermostability, trimeric organization, and binding to JAM-A receptor, especially at the gastric pH reovirus has to withstand while passing the stomach.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sebastian Goetze, Regine Herbst-Irmer, Martin Klapper, Helmar Goerls, Kilian R. A. Schneider, Robert Barnett, Thomas Burks, Ursula Neu, Pierre Stallforth
ACS CHEMICAL BIOLOGY
(2017)