Article
Immunology
Xin Tan, Jun Qiao, Hedan Li, Danyang Huang, Xiaoqing Hu, Xiaoyuan Wang
Summary: This study investigated the metabolic regulation profile of Vibrio parahaemolyticus under polymyxin B stimulation, revealing significant changes in gene transcription and activation of cellular antioxidant systems to prevent bacteria from oxidant stress. The findings suggest new insights into polymyxin B-related stress response in V. parahaemolyticus, which could be beneficial for developing novel drugs for infection.
MICROBIAL PATHOGENESIS
(2021)
Review
Plant Sciences
Bing Yang, Chenyun Xu, Yuting Cheng, Ting Jia, Xueyun Hu
Summary: Iron-sulfur (Fe-S) clusters are ancient protein cofactors that exist ubiquitously in organisms and play important roles in various life processes. Plastids, semi-autonomous organelles believed to originate from cyanobacterial endosymbionts, have a Fe-S cluster biosynthesis and delivery pathway similar to cyanobacteria. Fe-S clusters are crucial for the normal functioning of downstream Fe-S proteins in plastids. Recent research has made significant progress in understanding this pathway and this review summarizes these findings as well as the remaining scientific challenges.
PLANT CELL REPORTS
(2023)
Article
Multidisciplinary Sciences
Olabisi Flora Davies-Bolorunduro, Bharkbhoom Jaemsai, Wuthiwat Ruangchai, Worakorn Phumiphanjarphak, Pakorn Aiewsakun, Prasit Palittapongarnpim
Summary: Mutations in whiB7 gene are associated with antibiotic resistance in Mycobacterium tuberculosis. Specific mutations affect the structure of WhiB7 protein and result in the deletion of AT-hook. These findings provide important insights into understanding the antibiotic resistance of tuberculosis and offer potential for the development of new treatments.
SCIENTIFIC REPORTS
(2023)
Review
Microbiology
Michal Wojcicki, Olga Swider, Kamila J. Daniluk, Paulina Srednicka, Monika Akimowicz, Marek L. Roszko, Barbara Sokolowska, Edyta Juszczuk-Kubiak
Summary: The widespread use of antibiotics has led to the development of multidrug resistance in many bacterial strains, including Salmonella. Salmonella, a common pathogen causing intoxication from contaminated food and water, is pharmacologically treated with antibiotics like fluoroquinolones, ceftriaxone, and azithromycin. Understanding the molecular mechanisms behind antibiotic resistance in Salmonella is essential for choosing effective treatment and addressing the significant global concern of increasing antibiotic resistance.
Article
Engineering, Environmental
Da Lin, Lin Zhu, Yanlai Yao, Lizhong Zhu, Meizhen Wang
Summary: Fermentation broth from fruit and vegetable waste (FFVW) can effectively reduce the pollution of antibiotic resistance genes (ARGs) by inhibiting the growth of Actinobacteria and reducing the transfer frequency of genes. It shows a remarkable ability to decrease the resistance of genes to sulfonamide, macrolide-lincosamide-streptogramin, chloramphenicol, and tetracycline.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Jing Du, Zhaoyang Huang, Yanchun Li, Xueying Ren, Chaoting Zhou, Ruolan Liu, Ping Zhang, Guojie Lei, Jianxin Lyu, Jianghui Li, Guoqiang Tan
Summary: Copper is a necessary mineral nutrient but excess copper is cytotoxic. Wilson's disease is an autosomal recessive hereditary disease characterized by pathological copper accumulation in organs. The molecular mechanism of Wilson's disease is not fully understood and further research is needed to develop therapeutic strategies.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Darwin Linardi, Weiyi She, Qian Zhang, Yi Yu, Pei-Yuan Qian, Henry Lam
Summary: The study developed a high throughput proteomics-based method to complement genome mining methods for the identification of biosynthetic pathways in Streptomyces species.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tao Wan, Magdalena Horova, Daisy Guiza Beltran, Shanren Li, Huey-Xian Wong, Li-Mei Zhang
Summary: WhiB7 is a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, interacting with the primary sigma factor (sigma(A)(4)) in RNA polymerase holoenzyme to regulate gene expression through its DNA-binding motif, the AT-hook. This study reveals the structural basis of functional divergence between the two subclasses of Wbl proteins in Mycobacterium tuberculosis through high-resolution structural analysis and molecular approaches.
Article
Multidisciplinary Sciences
Francesca Sartor, Xinming Xu, Tanja Popp, Antony N. Dodd, Akos T. Kovacs, Martha Merrow
Summary: This study investigates the circadian clock in Bacillus subtilis and discovers its complexity. The circadian rhythm in B. subtilis can be regulated by blue and red light, exhibiting characteristics of circadian entrainment. These findings suggest that circadian rhythms are a common feature in this prokaryotic species and its circadian system responds to the environment in a similar way to multicellular eukaryotic circadian systems.
Article
Biotechnology & Applied Microbiology
Zhe-Chong Wang, I-Wen Lo, Kuan-Hung Lin, An Ning Cheng, Saeid Malek Zadeh, Yen-Hua Huang, Tsung-Lin Li
Summary: This study elucidates the biosynthetic gene cluster of albofungin and the functions of two key genes, orfA and orfL, in vivo, revealing their roles in antimicrobial detoxification/resistance mechanisms.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Xingju Song, Xu Yang, Zhu Ying, Kaijian Wu, Jing Liu, Qun Liu
Summary: Iron-sulfur [Fe-S] clusters are ancient and important prosthetic groups that play key roles in various metabolic processes. In this study, we investigated the role of mitochondrial glutaredoxin 5 (NcGRX5) in Neospora caninum, a parasite belonging to the phylum Apicomplexa. We found that deficiency of NcGRX5 led to abnormal mitochondrial structure and significantly reduced parasite proliferation and virulence. Comparative proteomics and energy metabolomics revealed that disruption of NcGRX5 downregulated expression of mitochondrial electron transport chain and tricarboxylic acid cycle proteins, affecting corresponding metabolic fluxes. We also identified proteins interacting with NcGRX5, including iron-sulfur cluster synthesis proteins ISCS and ISCU1. Our findings highlight the importance of NcGRX5 in parasite growth and mitochondrial energy metabolism through mediating iron-sulfur cluster biosynthesis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Jing Zhang, Zechen Bai, Min Ouyang, Xiumei Xu, Haibo Xiong, Qiang Wang, Bernhard Grimm, Jean-David Rochaix, Lixin Zhang
Summary: Fe-S clusters are ancient and important for life processes. The biogenesis of Fe-S clusters involves iron acquisition, sulfur mobilization, and cluster formation. Two Arabidopsis DnaJ proteins, DJA6 and DJA5, play a crucial role in facilitating iron incorporation into Fe-S clusters during chloroplast Fe-S cluster biogenesis. Loss of these proteins leads to defects in chloroplast Fe-S protein accumulation and photosynthesis dysfunction. Evolutionary analysis shows that DJA6 and DJA5 are highly conserved in photosynthetic organisms and have a strong evolutionary relationship with SUFE1, SUFC, and SUFD.
Article
Environmental Sciences
Yan He, Xin Zhao, Siman Zhu, Long Yuan, Xinyi Li, Zhihan Feng, Xuan Yang, Ling Luo, Yinlong Xiao, Yan Liu, Lilin Wang, Ouping Deng
Summary: Livestock manure amendment can worsen antibiotic resistance gene (ARG) pollution, while manure biochar can reduce ARGs in soil. This study explored the effects of swine manure and its biochar on ARGs and microbial communities in soil. The results showed that biochar amendments significantly reduced ARG abundance and diversity compared to manure amendments, suggesting that converting manure to biochar can help control the spread of manure ARGs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Chemistry, Inorganic & Nuclear
Jason C. Crack, Nick E. Le Brun
Summary: Iron-sulfur (FeS) clusters are protein cofactors essential for various biological functions such as electron transfer, catalysis, and gene regulation. Recent progress in using mass spectrometry has provided new insights into FeS cluster assembly and chemistry, particularly in transcriptional regulators coordinating cellular responses to changing conditions.
COORDINATION CHEMISTRY REVIEWS
(2021)
Review
Oncology
Jaewang Lee, Jong-Lyel Roh
Summary: Iron dysregulation is a characteristic of cancer, characterized by increased expression of genes involved in iron metabolism and iron-sulfur cluster (ISC) biogenesis. Dysregulated iron homeostasis leads to elevated intracellular labile iron, which can result in the formation of excessive cytotoxic radicals and susceptibility to regulated cell death, including ferroptosis. Various strategies, such as redox operations, iron chelation, and replacement of iron with redox-inert metals, can destabilize or restrict ISC formation and function, providing potential therapeutic approaches for cancer treatment. Targeting ISCs to induce ferroptosis shows promise in cancer therapy. This review provides a comprehensive overview of iron metabolism, ferroptosis, and the role of ISC modulation in cancer cells, as well as the potential of targeting ISCs for ferroptosis induction in cancer treatment. Further research and clinical trials are needed to validate these strategies for various cancers, with the goal of developing novel and effective cancer treatments.
Article
Ophthalmology
Lucas Janeschitz-Kriegl, Dhryata Kamdar, Mathieu Quinodoz, Karolina Kaminska, Marc Folcher, Bence Gyoergy, Peter Meyer, Andreas Wild, Pascal Escher, Hendrik P. N. Scholl, Carlo Rivolta, David Goldblum
Summary: This study investigated the clinical and genetic features of a man and his daughter with posterior polymorphous corneal dystrophy (PPCD). The results showed that both patients carried a mutation in the OVOL2 gene, which is associated with the disease. This study provides important evidence for understanding the genetic mechanism and pathophysiology of PPCD.
Article
Economics
Laurenske A. Visser, Marc Folcher, Claudia Delgado Simao, Biotza Gutierrez Arechederra, Encarna Escudero, Carin A. Uyl-de Groot, William Ken Redekop
Summary: The Optogenerapy consortium is developing a novel bioelectronic cell-based implant for controlled release of beta-interferon protein into the body, which has shown to be a cost-effective therapy for multiple sclerosis patients. The innovative technology of the Optoferon implant may potentially revolutionize treatment administration for MS patients and other disease areas.
Review
Biochemical Research Methods
Megan E. Wolf, Daniel J. Hinchen, Jennifer L. DuBois, John E. McGeehan, Lindsay D. Eltis
Summary: The valorization of lignin is crucial in the transition to sustainable biorefineries, and microbial cell factories are offering new possibilities for upgrading lignin-derived aromatic compounds (LDACs). Cytochromes P450, due to their catalytic versatility and involvement in lignin metabolism, are attractive enzymes for engineering such biocatalysts. This review highlights P450s that catalyze aromatic O-demethylation and their potential in developing biocatalysts for the conversion of LDACs to valuable chemicals. The intersection of biochemistry, structure-guided enzyme engineering, and metabolic engineering offers broader opportunities for the application of P450s in microbial lignin valorization.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ji Hoon Han, Gavin Ryan, Alyson Guy, Lu Liu, Mathieu Quinodoz, Ingrid Helbling, Joey E. Lai-Cheong, Julian Barwell, Marc Folcher, John A. McGrath, Celia Moss, Carlo Rivolta
Summary: The study identified LIPHAK as a previously unrecognized ribosomopathy, where variants in the LTV1 gene result in abnormal splicing and premature termination of the protein it encodes.
HUMAN MOLECULAR GENETICS
(2022)
Article
Chemistry, Physical
Allan R. E. Hansen, Kasper Enemark-Rasmussen, Frans A. A. Mulder, Pernille R. Jensen, Sebastian Meier
Summary: Electrochemical reduction allows for the capture and utilization of CO2 by converting it into small chemicals and fuels. However, there is a lack of well-established analytical standard operating procedures for accurately quantifying short-chain acids, aldehydes, and alcohols. The smallest organic compounds produced through electrochemical reduction of CO2 require slow NMR quantifications, which can be improved by using paramagnetic contrast agents or cooling water/DMSO for T-1-optimized measurements. H-1 NMR experiments commonly used in the study of biological mixtures are not suitable for quantitative analysis of T-1-optimized samples.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Microbiology
Kirstin L. Brown, Kaley M. Wilburn, Christine R. Montague, Jason C. Grigg, Olalla Sanz, Esther Perez-Herran, David Barros, Lluis Ballell, Brian C. VanderVen, Lindsay D. Eltis
Summary: GSK286 acts as an agonist of Rv1625c, a membrane-bound adenylyl cyclase, to inhibit the growth of Mycobacterium tuberculosis and increase intracellular cAMP levels. However, the detailed mechanism of action of these compounds still needs to be elucidated.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Chemistry, Physical
Francesca Sannelli, Sanni Gao, Pernille Rose Jensen, Sebastian Meier
Summary: By mixing glucose and furfural in suitable ratios, novel strategies for C-C bond formation on furfural can be achieved with the help of low-cost biological catalysts. The presence of furfural is shown to modulate glucose metabolism and favor the accumulation of acetaldehyde, redirecting glucose carbons towards C-C bond formation. This strategy allows for a relative influx of at least 80% of glucose carbons into the C-C bond formation on furfural in non-engineered yeasts, showing potential for the upgrading of lignocellulosic biomass.
Article
Chemistry, Multidisciplinary
Feng-Jie Wu, Pascal S. Rieder, Layara Akemi Abiko, Philip Roessler, Alvar D. Gossert, Daniel Haeussinger, Stephan Grzesiek
Summary: The method presented in this study utilizes antibodies tagged with lanthanoid DOTA chelators to efficiently assign nuclei of biomacromolecules, providing insights into their chemical shift changes during functional dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Allison Z. Werner, Lindsay D. Eltis
Summary: In 2014, Linger et al. proposed a tandem process that combines chemical and biological catalysis for lignin valorization. Chemical pretreatment of corn stover produced mixed lignocellulose-derived monomers, which were further converted to a single product, polyhydroxyalkanoates, by Pseudomonas putida. Since then, tandem processes have been developed for various feedstocks to promote the bioeconomy.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Allan R. E. Hansen, Pernille R. Jensen, Sebastian Meier
Summary: The conversion of lignocellulosic biomass and its components to precursor chemicals offers great potential in expanding the range of industrial chemicals and reducing reliance on fossil resources. However, challenges in this green transition include the multifunctionality of biosourced reactants and the search for highly selective conversion processes. Recent research has shown that chemocatalytic conversion of carbohydrates to lactate and its ester variants using concentrated aqueous solutions of barium hydroxide is highly selective. This study used sensitive enhanced NMR to track the reaction cascade and identified key intermediates in the pathway, providing valuable insights into the process.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Sebastian Meier, Allan R. Hansen, Pernille Rose Jensen
Summary: Carbohydrates are expected to play a central role in future organic chemical production, but the understanding of accessible pathways for carbohydrate upgrading is still inadequate. The complex structure of carbohydrates, with various functional groups and stereochemistries, can result in a diverse range of isomers during the conversion process. In this study, the conversion of C5 carbohydrates using Lewis acidic SnCl4 in dimethyl sulfoxide (DMSO)/water system was investigated. The effects of removing individual functional groups on the pathways of carbohydrate conversion were evaluated. The removal of the hydroxy group at C5 was found to enhance the selectivity of carbohydrate conversion through an acyclic pathway, rather than the formation of furanic compounds or humins. Blocking the primary alcohol in xylose may be beneficial for biomass conversion strategies. Additionally, the conversion of pentose followed second-order kinetics, even without intermolecular reactions leading to humin formation.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Infectious Diseases
Lara Munoz-Munoz, Jose A. Ainsa, Santiago Ramon-Garcia
Summary: This study evaluated the in vitro activity of various beta-lactam antibiotics against Mycobacterium kansasii (Mkn), a tuberculosis-like lung infection. Penicillins plus clavulanate and first- and third-generation cephalosporins were found to be the most active beta-lactams against Mkn. Combinatorial time-kill assays also showed favorable interactions of amoxicillin-clavulanate and cefadroxil with the standard Mkn treatment, making them potential alternative options for Mkn therapy.
Article
Chemistry, Analytical
Francesca Sannelli, Pernille Rose Jensen, Sebastian Meier
Summary: The central carbon metabolism of microbes has potential applications in sustainable bioproduction. A deeper understanding of central metabolism could enhance the control of activity and selectivity in whole-cell catalysis. NMR spectroscopy can be used to track cellular pathways and optimize pathway usage, allowing for the design of conditions for glucose influx into specific industrial precursors. By inducing overflow at the pyruvate level, glucose conversion to 2,3-butanediol can be significantly increased. This study suggests a reassessment of canonical metabolism using in-cell spectroscopy may be warranted.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Francesca Sannelli, Ke-Chuan Wang, Pernille Rose Jensen, Sebastian Meier
Summary: Changes in metabolism are a common feature of many diseases, and in-cell NMR assays can provide real-time insights into disease metabolism. This study aimed to improve in-cell NMR assays by developing a comprehensive collection of spectral data for central carbon metabolites and intracellular pH. Using enriched glucose as a probe molecule, early glycolytic intermediates and intracellular pH were detected in prostate cancer cell lines. The addition of non-enriched pyruvate as an adjuvant allowed for the detection of reactions in the pentose phosphate pathway. The findings suggest a rerouting of cancer cell metabolism in response to pyruvate in the tumor environment.
ANALYTICAL METHODS
(2023)
Article
Multidisciplinary Sciences
Gara N. Dexter, Laura E. Navas, Jason C. Grigg, Harbir Bajwa, David J. Levy-Booth, Jie Liu, Nathan A. Louie, Seyed A. Nasseri, Soo-Kyeong Jang, Scott Renneckar, Lindsay D. Eltis, William W. Mohn
Summary: This study describes a pathway for catabolism of acetovanillone and identifies key enzymes and reaction mechanisms. The findings provide a theoretical basis for designing bacterial strains for the degradation of acetovanillone.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
