Article
Geosciences, Multidisciplinary
Wenyue Liang, Tiantian Yu, Liang Dong, Zhongjun Jia, Fengping Wang
Summary: Bathyarchaeota has been found to have the ability to fix carbon, as its abundance increased 15.3 times after long-term cultivation with lignin and sodium bicarbonate. Through DNA separation, it was confirmed that Bathyarchaeota DNA contained C-13, indicating its carbon fixation capacity.
SCIENCE CHINA-EARTH SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Hannah S. Shafaat, Anastasia C. Manesis, Alina Yerbulekova
Summary: This paper summarizes the research field of artificial metalloenzymes and describes the development of a functional metalloprotein-based model that replicates the acetyl coenzyme A synthase enzyme. Through the use of a nickel-substituted azurin protein and various spectroscopic and computational techniques, the model was able to mimic the active site and catalytic mechanism of the natural enzyme.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Qinhua Gu, Yujie Qi, Junnan Chen, Ming Lu, Bingsen Zhang
Summary: This study reveals the catalytic process of Co/Ti2C for the conversion of LiPSs and identifies the optimization of chemical adsorption, catalytic activity, and lithium-ion transfer behaviors as the reasons for its outstanding performance, along with sufficient interfaces between the catalyst and electrolyte.
Article
Chemistry, Multidisciplinary
Weijie Yu, Shengchun Wang, Meng He, Zhou Jiang, Yi Yu, Jinping Lan, Jin Luo, Pengjie Wang, Xiaotian Qi, Tao Wang, Aiwen Lei
Summary: Introducing two similar functional groups into bulk chemical alkenes is a challenging method to synthesize complex molecules. In this study, a redox-mediated electrolysis using aryl nitriles as both aryl radical precursors and redox-mediators is demonstrated to enable intermolecular alkene 1,2-diarylation with high regioselectivity, without the need for transition-metal catalysts. This reaction utilizes cyanoarene radical anions to activate various aryl halides and produces 1,2-diarylation adducts in up to 83% yield and >20:1 regioselectivity with over 80 examples, providing a feasible approach to complex bibenzyl derivatives.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Qiang Wang, Chong Sha, Hongcheng Wang, Kesen Ma, Juergen Wiegle, Abd El-Fatah Abomohra, Weilan Shao
Summary: Hyperthermophilic Thermotoga spp. are potential candidates for producing cellulosic ethanol, with Fe-AAdh identified as a key bifunctional enzyme that plays a crucial role in ethanol production at 80-85 degrees Celsius.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Yue Lu, Qing Bu, Mingli Chuan, Xiaoyun Cui, Yu Zhao, Dao-Xiu Zhou
Summary: Chromatin modifications play a crucial role in shaping the epigenome and regulating gene expression during plant development and adaptation to environmental changes. The activities of chromatin modification enzymes are influenced by cellular metabolites, such as S-adenosyl-methionine, acetyl-CoA, alpha-ketoglutarate, and NAD(+). On the other hand, changes in the plant epigenome and activity of epigenetic regulators can impact cellular metabolism through regulation of metabolic enzymes. This review highlights recent advances in understanding the metabolic control of plant chromatin regulators and epigenomes, which contribute to plant adaptation to environmental stresses.
Article
Biotechnology & Applied Microbiology
Eugenia Messina, Camilla Pires de Souza, Claudia Cappella, Simona Nicole Barile, Pasquale Scarcia, Isabella Pisano, Luigi Palmieri, Jean-Marc Nicaud, Gennaro Agrimi
Summary: The study identified the mitochondrial carrier YlCrc1 involved in the Carnitine/Acetyl-Carnitine shuttle in Y. lipolytica. Manipulation of YlCrc1 improved propionate utilization and its conversion into OCFAs. These genetic modifications and the use of a lipogenic medium led to enhanced accumulation of OCFAs in Y. lipolytica.
MICROBIAL CELL FACTORIES
(2023)
Review
Biochemistry & Molecular Biology
Zhicheng Huang, Qing Wang, Irshad Ali Khan, Yan Li, Jing Wang, Jiaoyu Wang, Xiaohong Liu, Fucheng Lin, Jianping Lu
Summary: The methylcitrate cycle and the glyoxylate cycle are important carbon metabolic pathways in fungi, which not only convert toxic intermediates into usable substances, but also play important roles in fungal growth, development, and pathogenic processes.
Article
Chemistry, Applied
Hong Yao, Bernadine M. Flanagan, Barbara A. Williams, Deirdre Mikkelsen, Michael J. Gidley
Summary: The concentration of dietary fibre plays a critical role in the composition and metabolism of gut microbiota. This study investigated the effects of different concentrations of fructo-oligosaccharides and pectin on microbial diversity, loads, and metabolite profiles. The results showed that high concentrations of dietary fibre increased the abundance of Methanobrevibacter genus and the production of butyrate. Understanding the underlying mechanisms allows for personalized modulation of gut microbiota by adjusting dietary fibre concentrations.
FOOD HYDROCOLLOIDS
(2023)
Article
Biochemistry & Molecular Biology
Tomohiro Suzuki, Takeo Tomita, Kenta Hirayama, Michio Suzuki, Tomohisa Kuzuyama, Makoto Nishiyama
Summary: The crystal structure of a truncated form of homocitrate synthase lacking the RAM domain has been determined, revealing the involvement of subdomain II in acetyl-CoA recognition. This provides important clues for a better understanding of the catalytic mechanism of HCS within the enzyme family.
Article
Materials Science, Multidisciplinary
Sijia Guo, Yingbo Xiao, Alexey Cherevan, Dominik Eder, Liangliang Xu, Qinghan Zeng, Yuan Ouyang, Qi Zhang, Shaoming Huang
Summary: Metal-organic frameworks (MOFs) have the potential to promote the redox reaction of sulfur species (RRS) and suppress the shuttle effect in lithium-sulfur batteries (LSBs). However, most MOFs are inert in accelerating RRS due to the lack of exposed polar catalytic sites. In this study, a universal strategy is proposed to modify MOFs and expose catalytic metal clusters, resulting in vastly improved performance of LSBs.
Article
Microbiology
Marisa R. Myers, G. M. King
Summary: This article explores the relationship between CO and perchlorate reduction, and found that Ni-COX can use CO to reduce perchlorate and support growth.
Article
Chemistry, Multidisciplinary
Vivek Narisetty, Ashish A. Prabhu, Rajesh Reddy Bommareddy, Rylan Cox, Deepti Agrawal, Ashish Misra, M. Ali Haider, Amit Bhatnagar, Ashok Pandey, Vinod Kumar
Summary: This study demonstrates that Yarrowia lipolytica can utilize acetate as a carbon source for growth and accumulate succinic acid. Through adaptive laboratory evolution, the recombinant strain showed improved tolerance and efficiency in utilizing acetate to produce succinic acid. Cofermentation of acetate and glucose further increased the production of succinic acid and lipids.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Review
Immunology
Amit Singh, Xilin Zhao, Karl Drlica
Summary: Identifying heteroresistant infections and understanding the lethal action of antibiotics can help reduce the emergence of resistance in tuberculosis treatment. Studies on antimicrobial tolerance and exploring a new direction of using small molecules to enhance lethality are potential strategies to suppress the transition of MDR-TB to XDR-TB.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dhanashree Selvan, Saumen Chakraborty
Summary: We propose a Ni-p site model of ACS, which is achieved by a self-assembled trimer peptide. Spectroscopic and kinetic studies reveal that Ni binding stabilizes the peptide assembly and forms a terminal Ni-I-CO complex. When reacted with a methyl donor, the CO-bound state generates a new species with distinct spectral features. Although the metal-bound CO is unactivated, the presence of the methyl donor activates the metal-CO complex. Steric modifications above or below the Ni site result in altered properties of the ligand-bound states.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Swapneeta S. Date, Jerry M. Parks, Katherine W. Rush, Judy D. Wall, Stephen W. Ragsdale, Alexander Johs
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Angela S. Fleischhacker, Amanda L. Gunawan, Brent A. Kochert, Liu Liu, Thomas E. Wales, Maelyn C. Borowy, John R. Engen, Stephen W. Ragsdale
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Christopher D. James, Seth Wiley, Stephen W. Ragsdale, Brian M. Hoffman
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Chemistry, Physical
Steven E. Cohen, Mehmet Can, Elizabeth C. Wittenborn, Rachel A. Hendrickson, Stephen W. Ragsdale, Catherine L. Drennan
Article
Biology
Connor J. Cooper, Kaiyuan Zheng, Katherine W. Rush, Alexander Johs, Brian C. Sanders, Georgios A. Pavlopoulos, Nikos C. Kyrpides, Mircea Podar, Sergey Ovchinnikov, Stephen W. Ragsdale, Jerry M. Parks
COMMUNICATIONS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Liu Liu, Arti B. Dumbrepatil, Angela S. Fleischhacker, E. Neil G. Marsh, Stephen W. Ragsdale
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Steven E. Cohen, Edward J. Brignole, Elizabeth C. Wittenborn, Mehmet Can, Samuel Thompson, Stephen W. Ragsdale, Catherine L. Drennan
Summary: Electron microscopy was used to capture multiple snapshots of ACS, revealing previously uncharacterized domain motion and forming extended and hyperextended structural states, where the A-cluster is accessible for methylation by CFeSP.
Article
Multidisciplinary Sciences
Anindita Sarkar, Eric L. Carter, Jill B. Harland, Amy L. Speelman, Nicolai Lehnert, Stephen W. Ragsdale
Summary: Rev-Erb beta is a nuclear receptor that plays a key role in regulating circadian rhythm, metabolism, and inflammation. Heme binding to the protein affects its function as a repressor and its ability to bind other proteins. Interestingly, Rev-Erb beta exists in the Fe3+ form within the cell, contradicting its role as a gas sensor. This study demonstrates how the Fe3+ state is congruent with heme binding and cellular gas sensing, suggesting a potential mechanism for CO/NO-mediated regulation of circadian rhythm through redox changes in Rev-Erb beta.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Anjali Patwardhan, Ritimukta Sarangi, Bojana Ginovska, Simone Raugei, Stephen W. Ragsdale
Summary: Methyl-coenzyme M reductase (MCR) plays a crucial role in catalyzing both the synthesis and anaerobic oxidation of methane. Studies have shown that the active Ni(I) state of MCR binds to substrates methyl-SCoM and CoMSSCoB through their sulfonate groups to form a hexacoordinate complex, rather than directly interacting with sulfur. This suggests that both forward and reverse MCR reactions proceed through long-range electron transfer from the Ni(I)-sulfonate complexes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Biochemistry & Molecular Biology
Angela S. Fleischhacker, Anindita Sarkar, Liu Liu, Stephen W. Ragsdale
Summary: This review explores the essential roles of heme in biological processes, focusing on how it binds to HRMs and regulates protein structure, function, and degradation through changes in redox state. Two HRM-containing proteins, human heme oxygenase-2 and the transcriptional regulator Rev-erb beta, are discussed in relation to cellular heme composition and CO sensing. The importance of understanding heme distribution, CO, and heme binding affinities in various biological processes is emphasized.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Stephen W. Ragsdale
Summary: The article highlights the integral involvement of the gut microbiome in producing beneficial metabolites and preventing the formation of disease-promoting compounds.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
David A. Hanna, Courtney M. Moore, Liu Liu, Xiaojing Yuan, Iramofu M. Dominic, Angela S. Fleischhacker, Iqbal Hamza, Stephen W. Ragsdale, Amit R. Reddi
Summary: Humans express two isoforms of heme oxygenase, HO-1 and HO-2, with distinct roles in regulating heme homeostasis. HO-2 acts as a buffering factor to control heme bioavailability, while both HO-1 and HO-2 provide protection from heme toxicity via enzymatic degradation when heme is in excess.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Christopher J. Ohmer, Medhanjali Dasgupta, Anjali Patwardhan, Isabel Bogacz, Corey Kaminsky, Margaret D. Doyle, Percival Yang-Ting Chen, Stephen M. Keable, Hiroki Makita, Philipp S. Simon, Ramzi Massad, Thomas Fransson, Ruchira Chatterjee, Asmit Bhowmick, Daniel W. Paley, Nigel W. Moriarty, Aaron S. Brewster, Leland B. Gee, Roberto Alonso-Mori, Frank Moss, Franklin D. Fuller, Alexander Batyuk, Nicholas K. Sauter, Uwe Bergmann, Catherine L. Drennan, Vittal K. Yachandra, Junko Yano, Jan F. Kern, Stephen W. Ragsdale
Summary: Methyl-Coenzyme M Reductase (MCR) is a crucial enzyme in methanogenesis that has significant implications for global energy balances. However, the structure and reaction mechanism of this enzyme are still poorly understood.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Chemistry, Physical
David W. White, Daniel Esckilsen, Seung Kyu Lee, Stephen W. Ragsdale, R. Brian Dyer
Summary: This study reports a light-driven photocatalytic system for efficient reduction of carbon dioxide to carbon monoxide using CODH II and CdSe/CdS nanocrystals. High quantum yields and turnover frequencies were achieved by incorporating a low-potential redox mediator. This provides new insights into the mechanism of the enzyme.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Yue Dai, Angela S. Fleischhacker, Liu Liu, Sara Fayad, Amanda L. Gunawan, Dennis J. Stuehr, Stephen W. Ragsdale
Summary: GAPDH is involved in heme delivery to HO2, maintaining cellular heme homeostasis.
BIOLOGICAL CHEMISTRY
(2022)