Article
Engineering, Environmental
Jianxian Sun, Holly Barrett, David Ross Hall, Steven Kutarna, Xiaoqin Wu, Yan Wang, Hui Peng
Summary: This study demonstrated that natural OH-BDEs exhibit strong antibacterial activities against Escherichia coli, while marine gamma-proteobacteria showed resistance to 6OH-BDE47 mainly through the action of FabV. Field studies revealed that sponges containing high concentrations of 6OH-BDE47 had a distinct microbiome community structure and selectively enriched FabV.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Review
Microbiology
Fernanda S. M. Hopf, Candida D. Roth, Eduardo V. de Souza, Luiza Galina, Alexia M. Czeczot, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro
Summary: This article reviews the diversity, structure, and catalytic properties of enoyl-ACP reductases (ENRs) and their potential as drug development targets. It also discusses the complex evolutionary history of bacterial ENRs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Cesar Gago-Cordoba, Jorge Val-Calvo, David Abia, Alberto Diaz-Talavera, Andres Miguel-Arribas, Rocio Aguilar Suarez, Jan Maarten van Dijl, Ling Juan Wu, Wilfried J. J. Meijer
Summary: Conjugation, the process of DNA transfer between bacterial cells through a connecting channel, plays a significant role in the spread of antibiotic resistance genes. Adhesin proteins encoded by conjugative elements, such as pLS20 in Bacillus subtilis, are essential for effective conjugation in Gram-positive bacteria. These adhesins, containing a class II type thioester domain (TED), are widely conserved in Gram-positive bacteria and may provide new insights into combating antibiotic resistance by targeting the first step of cell recognition and attachment in conjugation.
Article
Microbiology
Patricia L. Walker, Himadri B. Pakrasia
Summary: We identified a protein called HltA that plays a key role in the high light tolerance of Synechococcus elongatus UTEX 2973. HltA contains a functional PP2C-type protein phosphatase domain and a regulatory N-terminal GAF domain. It is widely found in cyanobacteria and is important for the photosynthetic lifestyle of these organisms.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
William Gao, Thomas A. Jones, Elena Rivas
Summary: The article introduces a bioinformatics method that combines iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. By studying five fungal genomes, 17 novel candidate functional non-coding RNAs that display structurally conservation were identified.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Polymer Science
Shafer M. Soars, Bruce E. Kirkpatrick, Benjamin D. Fairbanks, Joshua T. Kamps, Kristi S. Anseth, Christopher N. Bowman
Summary: This study describes the synthesis of a self-immolative polymer derived from amino acids and the subsequent functionalization of the polymer backbone through post-polymerization modification. The resulting polymer can be crosslinked to form mechanically robust hydrogels using a photoreactive thiol-ene reaction, and the hydrogels can undergo self-immolation under specific conditions.
POLYMER INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
A. M. U. B. Mahfuz, Felipe Stambuk Opazo, Luis F. Aguilar, Muhammad Nasir Iqbal
Summary: Carfilzomib has been identified as a potential inhibitor of the ENRs of K. pneumoniae and M. tuberculosis, and it has been shown to exhibit bactericidal activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Organic
Sabry H. H. Younes, F. Hollmann
Summary: A simple and solvent-free method for synthesizing (thio)esters from acid chlorides at room temperature is presented. The use of FeCl3 (5 mol%) allows for easy and highly selective conversion of equimolar starting materials. Additionally, the recycling of the catalyst has been successfully demonstrated.
TETRAHEDRON LETTERS
(2023)
Article
Immunology
Anna Adler, Vivek Anand Manivel, Karin Fromell, Yuji Teramura, Kristina N. Ekdahl, Bo Nilsson
Summary: The aim of this study was to define the conditions for storing native C3 without generating C3(H2O) and to introduce a robust method. The results showed that freezing native C3 in the precipitated form was the best method to avoid loss of function and generation of C3(H2O), while incubating native C3 in a buffer at pH 11.0 consistently generated C3(H2O).
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Chemistry, Organic
Xi Wang, Zhi-Bing Dong
Summary: Thiocarboxylates, as a common feature of natural products, play a crucial role in biology and pharmaceuticals, inspiring the development of new therapeutic drugs. In the past two decades, research and developments in thioester-based medicinal chemistry have been rapidly growing. This review summarizes the main methods for synthesizing thiocarboxylates, providing general insights for accessing more effective thioester-based drugs.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Review
Chemistry, Inorganic & Nuclear
Stephane Besson, M. Gabriela Almeida, Celia M. Silveira
Summary: In recent years, there has been a growing social and political awareness of the importance of studying, monitoring, and controlling anthropological activities that have a significant impact on the environment and human health. The nitrogen cycle is of particular concern, and understanding the biological, chemical, and physical processes associated with it has attracted attention from various scientific disciplines. Bioinorganic chemists have made remarkable contributions to understanding the enzymology of the dissimilatory and assimilatory pathways in the nitrogen cycle. The constant development of tools and techniques has kept this field active and highly relevant in current research. This paper reviews the latest advancements in the understanding of the structural characteristics of nitrite reducing enzymes involved in both dissimilatory and assimilatory pathways.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Pharmacology & Pharmacy
Svenja Zonneveld, Adina Gawi, Erik B. Wilms, Peter van Vliet, Elsbeth M. Westerman
Summary: Intoxications with sulpiride are rare, and treatment is mainly symptomatic with supportive care. In this case, the patient was successfully treated with activated charcoal, laxatives, and sodium bicarbonate in the Intensive Care Unit (ICU), leading to stabilized hemodynamics and normalized ECG the following day. It is important to avoid antiarrhythmic drugs, except for lidocaine, epinephrine, and dopamine, as they may worsen arrhythmia and hypotension.
BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY
(2021)
Article
Multidisciplinary Sciences
Inokentijs Josts, Katharina Veith, Vincent Normant, Isabelle J. Schalk, Henning Tidow
Summary: The study reported the crystal structure of the inner membrane protein FoxB, revealing its mechanism in Fe-siderophore uptake. Through in vitro assays and in vivo studies, the results establish FoxB as an inner membrane reductase involved in releasing iron from ferrioxamine during Fesiderophore uptake.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Environmental Sciences
Agnieszka Chlopas-Konowalek, Kaja Tusiewicz, Olga Wachelko, Pawel Szpot, Marcin Zawadzki
Summary: This study presents the first reported case of a simultaneous amphetamine and methamphetamine intoxication of a cat. The toxicological study analyzed the concentrations of these substances in various biological materials. Intentional or accidental poisoning of pets with psychoactive substances is a serious problem that poses a risk to the health and life of animals. Thus, it is important to increase awareness of the high risk of poisoning in domestic animals and to research the pharmacokinetic mechanisms of drugs in animals.
Review
Environmental Sciences
Kaja Tusiewicz, Patryk Kuropka, Elzbieta Workiewicz, Olga Wachelko, Pawel Szpot, Marcin Zawadzki
Summary: In recent times, the global use of sodium nitrite for suicide has increased, and the recreational use of nitrites, known as poppers, has also been observed. This research paper presents an epidemiological analysis and evaluation of analytical methods based on available papers and reports on nitrates, nitrites, and poppers intoxications. A total of 128 papers documenting 492 intoxication cases were analyzed, and six additional cases were briefly examined. The review of nitrite poisoning cases over the past 100 years highlights the ongoing use and significant risk it poses to society.
Article
Cell Biology
Andrew C. Hunt, James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien-Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien-Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. Matochko, Christy A. Thomson, Bastian Vogeli, Antje Kruger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetic, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary-Jane Navarro, Nuttada Panpradist, Michael Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P. J. Whelan, Lance Stewart, Michael S. Diamond, David Veesler, Michael C. Jewett, David Baker
Summary: Researchers used a cell-free expression workflow to screen and optimize constructs containing computationally designed miniprotein inhibitors of SARS-CoV-2. They found that a homotrimeric version of the ACE2 mimic AHB2 (TRI2-2) achieved the broadest efficacy. The TRI2-2 miniprotein neutralized Omicron, Delta, and other variants with greater potency than clinically used monoclonal antibodies. It also provided prophylactic and therapeutic protection against SARS-CoV-2 in mice when administered intranasally. The designed miniprotein receptor mimics offer a widely applicable antiviral therapeutic strategy with advantages over antibodies and native receptor traps.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Bastian Vogeli, Luca Schulz, Shivani Garg, Katia Tarasava, James M. Clomburg, Seung Hwan Lee, Aislinn Gonnot, Elamar Hakim Moully, Blaise R. Kimmel, Loan Tran, Hunter Zeleznik, Steven D. Brown, Sean D. Simpson, Milan Mrksich, Ashty S. Karim, Ramon Gonzalez, Michael Kopke, Michael C. Jewett
Summary: The study demonstrates the use of a high-throughput in vitro prototyping workflow to screen unique pathway combinations and identify enzyme sets for enhanced product selectivity. The combination of reverse beta-oxidation (r-BOX) pathway and Wood-Ljungdahl pathway allows for selective synthesis of C4-C6 acids and alcohols in Escherichia coli and Clostridium autoethanogenum.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Marta Rodriguez-Martinez, Jens Nielsen, Sam Dupont, Jessica Vamathevan, Beverley J. Glover, Lindsey C. Crosswell, Brendan Rouse, Ben F. Luisi, Chris Bowler, Susan M. Gasser, Detlev Arendt, Tobias J. Erb, Victor de Lorenzo, Edith Heard, Kiran Raosaheb Patil
Summary: Molecular biology has great potential in addressing climate change and biodiversity loss, but it is currently not well incorporated into strategies. We call for a community-wide action to bring molecular biology to the forefront of climate change solutions.
Article
Chemistry, Multidisciplinary
Hasan DeMirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vogeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmueller, Tobias J. Erb, Esteban Vohringer-Martinez, Soichi Wakatsuki
Summary: This study used various experimental methods to investigate the structural organization of ECR in Kitasatospora setae, and found that its catalytic activity is carried out by a pair of dimers. The results reveal the dynamic organization and synchronized inter- and intrasubunit communications of this enzyme during catalysis.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Pascal Pfister, Jan Zarzycki, Tobias J. Erb
Summary: Mesaconyl-CoA transferase is a key enzyme in the 3-hydroxypropionate bi-cycle, and its unique ability to catalyze intramolecular CoA transfer has been elucidated through crystal structure analysis.
Review
Chemistry, Multidisciplinary
Sarah Bierbaumer, Maren Nattermann, Luca Schulz, Reinhard Zschoche, Tobias J. Erb, Christoph K. Winkler, Matthias Tinzl, Silvia M. Glueck
Summary: Enzymatic carbon dioxide fixation is important for converting inorganic carbon from the atmosphere into organic biomass. However, the thermodynamics and utilization of CO2 make it challenging for biotechnological applications. This review provides an overview of natural CO2-fixing enzymes, discusses their applications, and suggests strategies for improving efficiency. It also explores the potential of using reduced CO2 derivates and offers a techno-economic perspective on reducing CO2 emissions.
Article
Biochemistry & Molecular Biology
Christoph Diehl, Patrick D. Gerlinger, Nicole Paczia, Tobias J. Erb
Summary: Anaplerosis, a feature of metabolism, has been applied to synthetic in vitro metabolic networks to achieve carbon-positive synthesis of compounds. In this research, anaplerotic strategies were used to access a new-to-nature CO2-fixation pathway and successfully produce 6-deoxyerythronolide B. This work demonstrates the design and customization of anaplerotic modules to enhance and expand synthetic capabilities in complex in vitro reaction networks.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pascal Pfister, Christoph Diehl, Eric Hammarlund, Martina Carrillo, Tobias J. Erb
Summary: SucD is an enzyme involved in the CETCH cycle, and this study found that it has relatively small side reactions except for mesaconyl-C1-CoA. By mutating the SucD enzyme, a highly specific variant was obtained, which has potential applications in biocatalysis and synthetic biology.
Article
Biotechnology & Applied Microbiology
Lennart Schada von Borzyskowski, Helena Schulz-Mirbach, Mauricio Troncoso Castellanos, Francesca Severi, Paul A. Gomez-Coronado, Nicole Paczia, Timo Glatter, Arren Bar-Even, Steffen N. Lindner, Tobias J. Erb
Summary: Ethylene glycol (EG) is a promising feedstock for bioprocesses and can be used to produce PET and other polyester fibers and plastics. Currently, most bacteria assimilate EG via the glycerate pathway, which is energy-inefficient and produces CO2. However, the recently discovered BHAC offers a more efficient and carbon-conserving route for EG assimilation.
METABOLIC ENGINEERING
(2023)
Article
Chemistry, Physical
Rodrigo Recabarren, Matthias Tinzl, David Adrian Saez, Aharon Gomez, Tobias J. Erb, Esteban Vohringer-Martinez
Summary: Researchers used computer simulations and high-level ab initio calculations to trace the free energy changes along two possible reaction paths, revealing the microscopic mechanism of nature's most efficient CO2-fixing enzyme in storing reactive enolate species as a strategy.
Article
Multidisciplinary Sciences
Richard McLean, Thomas Schwander, Christoph Diehl, Nina Socorro Cortina, Nicole Paczia, Jan Zarzycki, Tobias J. Erb
Summary: Nature has developed eight different pathways to capture and convert CO2, but these pathways have limitations and only represent a fraction of the potential solutions. To overcome these limitations, scientists have designed a new CO2-fixation pathway called the HydrOxyPropionyl-CoA/Acrylyl-CoA (HOPAC) cycle. Through step-wise implementation and optimization using engineering approaches and machine learning, the HOPAC cycle can convert approximately 3.0 mM of CO2 into glycolate within 2 hours. This research provides a foundation for potential applications of the HOPAC cycle.
Article
Biochemistry & Molecular Biology
Pascal Pfister, Jan Zarzycki, Tobias J. Erb
Summary: Mct is a key enzyme in the 3-hydroxypropionate bi-cycle that catalyzes intra-molecular CoA transfer with high efficiency. The enzyme maintains a sealed central cavity, allowing for successful transfer of CoA between the C1 and C4 positions of mesaconate.
Article
Biochemical Research Methods
Daniel G. Marchal, Luca Schulz, Ingmar Schuster, Jelena Ivanovska, Nicole Paczia, Simone Prinz, Jan Zarzycki, Tobias J. Erb
Summary: In this study, a machine learning-supported workflow was developed to improve the efficiency of GCC enzyme, resulting in increased reaction rate and reduced energy demand. This optimization addresses the limitations of the photorespiration bypass pathway.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Frederik V. Schmidt, Luca Schulz, Jan Zarzycki, Simone Prinz, Niels N. Oehlmann, Tobias J. Erb, Johannes G. Rebelein
Summary: Nitrogenases are enzymes that can catalyze the reduction of dinitrogen to ammonia. Recent research has shown that nitrogenases can also reduce carbon dioxide and carbon monoxide to hydrocarbon compounds. In this study, the structure of the iron nitrogenase complex from Rhodobacter capsulatus was determined using cryogenic electron microscopy, revealing the presence of an [Fe8S9C-(R)-homocitrate] cluster in the active site. The study also highlighted differences in the interface between the two catalytic halves of the iron and molybdenum nitrogenases, which may influence the nitrogenase mechanism.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Luca Schulz, Zhijun Guo, Jan Zarzycki, Wieland Steinchen, Jan M. Schuller, Thomas Heimerl, Simone Prinz, Oliver Mueller-Cajar, Tobias J. Erb, Georg K. A. Hochberg
Summary: This study uses ancestral sequence reconstruction to reveal an important event in the adaptation of photosynthetic organisms to an oxygenated environment, concerning the evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that have strong discrimination between carbon dioxide and oxygen. Through gaining an accessory subunit before atmospheric oxygen was present, Rubisco increased its specificity and carboxylation efficiency. The research provides insights into the adaptation to rising ambient oxygen levels, opens up possibilities for studying essential interactions, and sheds light on the determinants of specificity in Rubisco.
