Article
Biotechnology & Applied Microbiology
Zhuang Yao, Yu Meng, Huong Giang Le, Se Jin Lee, Hye Sung Jeon, Ji Yeon Yoo, Jeong Hwan Kim
Summary: In this study, the aprE3-5 promoter in Bacillus subtilis CH3-5 was replaced with stronger promoters, leading to increased fibrinolytic activity. The use of the P10 promoter resulted in the highest fibrinolytic activity, and changing the initiation codon from GTG to ATG further enhanced this activity. These results suggest that significant overproduction of fibrinolytic enzymes can be achieved through appropriate promoter modification.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Atziri Corin Chavez Alvarez, Chahrazed Bouzriba, Emmanuel Moreau, Philippe Auzeloux, Sophie Besse, Vincent Ouellette, Mitra Zarifi Khosroshahi, Marie-France Cote, Sylvie Pilote, Elisabeth Miot-Noirault, Jean-Michel Chezal, Chantale Simard, Rene C-Gaudreault, Sebastien Fortin
Summary: PAIB-SOs are new antimitotic prodrugs bioactivated in breast cancer cells expressing CYP1A1. Homologation of the alkyl side chain of PAIB-SOs improves their stability and selectivity, and n-pentyl PAIB-SOs show significant antitumor activity and low toxicity. The study confirms the suitability of homologation to enhance the hepatic stability of PAIB-SOs.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tzu-Ping Ko, Yu-Chuan Wang, Chia-Ling Tsai, Chia-Shin Yang, Mei-Hui Hou, Yeh Chen
Summary: The study presents the crystal structures of CD-NTase EcCdnD from Enter-obacter cloacae, showing significant structural variations compared to other CD-NTases. The enzyme is active on ATP or a mixture of ATP and GTP, with Mg2+ as the preferred metal cofactor. Based on structural analysis and comparison with other enzymes, a tentative catalytic pathway for EcCdnD in producing CTN is proposed.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Akihiro Kuno, Yoshihisa Ikeda, Shinya Ayabe, Kanako Kato, Kotaro Sakamoto, Sayaka R. Suzuki, Kento Morimoto, Arata Wakimoto, Natsuki Mikami, Miyuki Ishida, Natsumi Iki, Yuko Hamada, Megumi Takemura, Yoko Daitoku, Yoko Tanimoto, Tra Thi Huong Dinh, Kazuya Murata, Michito Hamada, Masafumi Muratani, Atsushi Yoshiki, Fumihiro Sugiyama, Satoru Takahashi, Seiya Mizuno
Summary: Genome editing can introduce designed mutations, but it can also lead to unintended variations. Existing genotyping methods are unable to comprehensively analyze diverse mutations. We developed a genotyping method with the software DAJIN, which can automatically identify and classify various mutations. This approach is highly adaptable and convenient, making DAJIN a potential new standard for validating genome editing outcomes.
Article
Biochemistry & Molecular Biology
Rachel O'Dea, Nafizul Kazi, Alicia Hoffmann-Benito, Zhou Zhao, Sarah Recknagel, Kim Wendrich, Petra Janning, Malte Gersch
Summary: Ubiquitin and ubiquitin-like proteins are involved in various functions and are regulated by distinct machineries. In this study, the researchers discovered that the immunosuppressive ubiquitin-like protein Fubi is processed by the nucleolar deubiquitinase USP36, which is essential for the formation of functional ribosomes. They also found that another deubiquitinase, USP16, has dual cleavage activity for both ubiquitin and Fubi. The crystal structures of USP36 with Fubi and ubiquitin provided insights into the substrate recognition mechanism and the specificity of deubiquitinases for Fubi. The findings shed light on the molecular mechanisms underlying the Fubi system and pave the way for future investigations.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Sandip Kumar Das, Subrata Das, Supratim Ghosh, Satyajit Roy, Monika Pareek, Brindaban Roy, Raghavan B. Sunoj, Buddhadeb Chattopadhyay
Summary: A new iron-porphyrin based catalytic system has been developed for intramolecular C-H amination of substituted tetrazolopyridines. This method exhibits high regioselectivity and excellent functional group tolerance, enabling the synthesis of three different classes of high-value N-heterocyclic scaffolds. The study also reveals the metalloradical activation mechanism of this catalytic system.
Article
Chemistry, Analytical
Cathrin Klopp, Michel A. A. Struwe, Christoph Plieth, Bernd Clement, Axel J. J. Scheidig
Summary: A fluorescence-based assay using NADH has been developed for rapid detection of substrates and potential inhibitors of mARC. This assay allows for high-sensitivity and high-precision recording of mARC-catalyzed reactions. It can be applied for high-throughput screening of substance libraries and detection of novel mARC substrate candidates. The normalization of enzyme activities to the standard benzamidoxime enables reproducible classification of substrates.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Toshiki Mikami, Sohei Majima, Haewon Song, Jeffrey W. W. Bode
Summary: In order to study the emerging functions of heterotypic and branched ubiquitin chains, new strategies for their preparation with defined lengths and connectivity are needed. The combination of K48- and K63-biased E2-conjugating enzymes and two new protecting groups allows the synthesis of heterotypic and branched ubiquitin chains. These protecting groups can be selectively removed from folded ubiquitin chains and monomers. By incorporating a cleavable C-terminal His-tag on the ubiquitin acceptor, the entire process can be conducted on a resin support, eliminating the need for intermediate oligomer handling and purification.
ACS CENTRAL SCIENCE
(2023)
Review
Chemistry, Inorganic & Nuclear
R. David Britt, Thomas B. Rauchfuss
Summary: This article discusses the biosynthesis mechanism of the H-cluster of [Fe-Fe] hydrogenase and the role of HydG in it, proposes a synthon model, and explores the importance of further validation.
DALTON TRANSACTIONS
(2021)
Review
Materials Science, Paper & Wood
Salla Hiltunen, Janak Sapkota, Eleni Ioannou, Majid Haddad Momeni, Emma Master, Matti Ristolainen
Summary: Cellulose activation plays a crucial role in various industrial processes, and expansin-related proteins have the potential to enhance enzymatic hydrolysis of cellulosic substrates for biofuel production. This review compares conventional and emerging technologies for cellulose activation and evaluates the potential of expansin-related proteins, while also presenting future applications.
Article
Biochemistry & Molecular Biology
He Liu, Zixia Hu, Ningning Han, Yi Yang, Guode Zhao, Mengdie Su, Yue Zhang, Weiwei Li, Ying Peng, Jiang Zheng
Summary: The study aimed to investigate the metabolic activation of MTX and its possible correlation with cytotoxicity. An oxidative metabolite (M1) and a GSH conjugate (M2) were observed in S9 fraction incubations and rat primary hepatocyte culture after MTX exposure. M1 and M2 were also detected in the bile of MTX-treated rats. CYP2A6 was found to be the dominant enzyme responsible for the oxidation of MTX. Inhibition of CYP2A6 and sulfotransferase significantly decreased the formation of M2. Pretreatment of primary hepatocytes with inhibitors reduced the susceptibility to MTX-induced cytotoxicity.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Pharmacology & Pharmacy
Joseph M. Collins, Rong Lu, Xinwen Wang, Hao-Jie Zhu, Danxin Wang
Summary: This study identified NR1H3 as a key factor regulating the expression of CES1 and demonstrated that its effect is splice isoform-specific and ligand independent.
DRUG METABOLISM AND DISPOSITION
(2022)
Article
Biology
Leonie Schnell, Alina Zubrod, Nicola Catone, Johanna Bialas, Annette Aichem
Summary: The ubiquitin-like modifier FAT10 plays an important role in protein degradation and is up-regulated in various cell types. While USE1 was previously thought to be the sole E2 enzyme for FAT10ylation, we identified additional E2 conjugating enzymes that are involved in FAT10 conjugation. This finding expands the field of FAT10 research and provides new possibilities for pharmacological interventions to regulate FAT10 conjugation under inflammatory conditions and/or viral infections.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemical Research Methods
Adam Gayoso, Zoe Steier, Romain Lopez, Jeffrey Regier, Kristopher L. Nazor, Aaron Streets, Nir Yosef
Summary: totalVI is a framework for end-to-end joint analysis of CITE-seq data which probabilistically represents data as a composite of biological and technical factors, providing a cohesive solution for common analysis tasks. It demonstrates strong performance in tasks such as dimensionality reduction, dataset integration, correlation estimation, and differential expression testing.
Article
Engineering, Environmental
Yan Lin, Hanxiyue Zhang, Yiqun Han, Xinghua Qiu, Xing Jiang, Zhen Cheng, Yanwen Wang, Xi Chen, Yunfei Fan, Weiju Li, Junfeng Zhang, Tong Zhu
Summary: In this study, the researchers found that the level of 2-PHECA in urine could be a biomarker for methylated PAH exposure, and the ratio of 2-PHECA/Sigma OH-PHEs in urine could indicate the relative importance of petrogenic or pyrogenic sources.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
