Article
Biochemistry & Molecular Biology
Dorian M. Cheff, Chuying Huang, Karoline C. Scholzen, Radosveta Gencheva, Michael H. Ronzetti, Qing Cheng, Matthew D. Hall, Elias S. J. Arner
Summary: Ferroptosis refers to cell death triggered by iron-dependent lipid peroxidation, which can be prevented by antioxidant compounds like ferrostatin-1. Endogenous suppressors of ferroptosis include FSP-1 and the selenoprotein GPX4, while small molecules like RSL3 and ML162 can induce ferroptosis by inhibiting GPX4. However, our findings suggest that RSL3 and ML162 may not inhibit GPX4 enzymatic activity as previously believed, but instead function as inhibitors of another selenoprotein, TXNRD1. These results highlight the need for reevaluation of previous studies using RSL3 and ML162 in the context of ferroptosis.
Article
Horticulture
Juan Li, Ping Yang, Hamza Sohail, Hongbin Du, Jie Li
Summary: This study investigates the use of short-term nitrogen starvation and replenishment treatments to reduce nitrate accumulation in spinach. Results show that 8 mmol/L of nitrogen is the most effective for spinach growth. After subsequent nitrogen starvation and replenishment, the expression levels of key enzymes and genes related to nitrate metabolism decrease, indicating their potential as reference genes to reduce nitrate content in vegetables.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Yi Zhao, Yuqiang Wang, Shengnan Sun, Wentao Liu, Ling Zhu, Xuebing Yan
Summary: The forms and proportions of exogenous nitrogen have significant effects on soil enzyme activities, nutrient contents, and plant growth. Different forms and proportions of nitrogen fertilization can stimulate soil enzyme activities, accelerate nutrient transformation, and promote alfalfa growth.
Article
Biochemistry & Molecular Biology
Rodrigo Arias-Cartin, Alexandre Uzel, Farida Seduk, Guillaume Gerbaud, Fabien Pierrel, Marianne Broc, Regine Lebrun, Bruno Guigliarelli, Axel Magalon, Stephane Grimaldi, Anne Walburger
Summary: This study expands our knowledge of the FDH family by identifying a noncanonical FDH that differs in terms of architecture, amino acid conservation around the molybdenum cofactor, and reactivity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Fiona Jamieson, Zhe Ji, Eric J. Belfield, Zhong Jie Ding, Shao Jian Zheng, Nicholas P. Harberd
Summary: Genetic analysis reveals the important role of ethylene signaling in regulating nitrogen metabolism in Arabidopsis thaliana. Ethylene signaling can regulate nitrate assimilation enzyme activity to control nitrogen metabolism.
Article
Biochemistry & Molecular Biology
Karna Gowda, Derek Ping, Madhav Mani, Seppe Kuehn
Summary: The metabolic activities of microbial communities are crucial for the evolution and persistence of life on Earth. This study shows that the dynamics of metabolites in a community can be predicted based on the genes possessed by each member of the community, providing insights into how genome evolution impacts metabolism.
Article
Microbiology
Florian P. Rosenbaum, Anja Poehlein, Rolf Daniel, Volker Mueller
Summary: M. thermoacetica is capable of using dimethyl sulfoxide (DMSO) as an electron acceptor, which promotes its growth on glucose or H-2 + CO2. DMSO reductase activity was observed in the membranes of M. thermoacetica, with the enzyme exhibiting high activity at pH 5 and 60 degrees C. The study also identified potential DMSO reductase subunits and discussed their function and the proposed electron transport chain involving DMSO as the final electron acceptor.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Dimitry Y. Y. Sorokin, Tamara V. V. Tikhonova, Hanna Koch, Eveline M. M. van den Berg, Renske S. S. Hinderks, Martin Pabst, Natalia I. I. Dergousova, Anastasia Y. Y. Soloveva, Gijs J. J. Kuenen, Vladimir O. O. Popov, Mark C. M. van Loosdrecht, Sebastian Lucker
Summary: This study discovered a new copper-depleted dissimilatory nitrate-reducing organism called Trichlorobacter ammonificans. It can actively grow using acetate as the electron donor and carbon source, and nitrate as the electron acceptor, with hydrogen as an additional electron donor. The organism uses an octaheme cytochrome c protein called TaNiR to carry out the dissimilatory nitrate reduction. These findings highlight the importance of this organism in various anaerobic systems such as rice paddy soil and wastewater treatment facilities.
Article
Biochemistry & Molecular Biology
Young Eun Hwang, Seonghun Im, Ju Hyun Cho, Wonsik Lee, Byung-Kwan Cho, Bong Hyun Sung, Sun Chang Kim
Summary: Antimicrobial peptides (AMPs) have been studied as potential antimicrobial coating agents, but an efficient and economical method for AMP production is lacking. Researchers successfully synthesized an AMP coating material and demonstrated its equivalent performance to peptides obtained through solid-phase synthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yutaro Mori, Shuhei Noda, Tomokazu Shirai, Akihiko Kondo
Summary: This study successfully synthesized 1,3-butadiene from glucose through an artificial metabolic pathway. Improving enzyme efficiency through computational simulations and controlling dissolved oxygen levels and pH are crucial for high production yields. The findings suggest the potential of producing nonbiological compounds from renewable carbon sources using rational enzyme design strategies.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Gul Naaz, Naushad Alam, Amit Kumar
Summary: In this study, EDTA was used to treat Pb-polluted soil and showed remarkable efficiency. The results suggested that 5 mmol of EDTA was optimal for phytoremediation of soil polluted with up to 1000 mg Pb kg(-1). P. Vijay variety proved to be a stronger accumulator of Pb compared to PM 25.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ya-Jiao Zhu, Sheng-Chen Huang, Zhi-Gang Qian, Xiao-Xia Xia
Summary: An efficient biosynthetic strategy was developed to produce large amounts of DOPA-incorporated structural proteins for fabricating hydrogels with tunable mechanical properties. Synthetic genes encoding repetitive resilin-like proteins (RLPs) with varying proportions of tyrosine residues were constructed and DOPA was incorporated into RLPs via mis-aminoacylation. By developing a stoichiometry-guided two-phase culture strategy, high levels of DOPA-incorporated RLPs were produced with a high DOPA incorporation yield. The DOPA-containing RLPs were then successfully cross-linked into hydrogels via facile DOPA-Fe3+ complexations.
Article
Plant Sciences
Megavath Gayatri, Megavath Ravi, Harsh Chauhan, Ekta Mulani, Sachin Phogat, Karnam Venkatesh, Pranab Kumar Mandal
Summary: This study analyzed nitrate reductase in wheat and found that it responds to nitrogen stress. Among the homeologues, NR 6-1D showed the strongest response to nitrogen stress, while NR 6-1B had the least contribution. The expression of homeologues was linked to the presence of N-responsive cis-elements. Additionally, there were greater differences within a genotype than between different genotypes.
PLANT GROWTH REGULATION
(2023)
Article
Multidisciplinary Sciences
Viet Linh Dao, Sheena Chan, Jingyun Zhang, Russell Kai Jie Ngo, Chueh Loo Poh
Summary: SENAX is a highly efficient DNA assembly method based on enzymatic homology, capable of assembling multiple DNA fragments at ambient temperature with short homology overlap. It overcomes the limitation of short fragment assembly in existing technologies and enables a more modular approach to DNA assembly, reducing the cost of DNA synthesis.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Yi Wang, Yanxiang Zhao, Shanshan Wang, Junfeng Liu, Xiqing Wang, Yanlai Han, Fang Liu
Summary: Overexpressing endogenous NADPH-dependent 2-alkenal reductase (ZmAER) in maize enhanced tolerance to low nitrogen stress, reduced oxidative stress, and improved nutrient use efficiency. Up-regulated ZmAER expression increased biomass, nitrogen accumulation, NUE, and leaf photosynthesis in transgenic plants compared to wild-type plants under low nitrogen conditions.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Chemistry, Multidisciplinary
Andrei Gurinov, Benedikt Sieland, Andrey Kuzhelev, Hossam Elgabarty, Thomas D. Kuehne, Thomas Prisner, Jan Paradies, Marc Baldus, Konstantin L. Ivanov, Svetlana Pylaeva
Summary: A novel set of polarizing agents - mixed-valence compounds have been investigated through theoretical and experimental methods, showcasing their performance in high-field dynamic nuclear polarization (DNP) NMR experiments in the solid state. These compounds, with molecular mobility persisting even in solids, can be used to conduct Overhauser-DNP experiments in the solid state, providing favorable conditions for dynamic nuclear polarization formation at ultra-high magnetic fields.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biophysics
Burkhard Endeward, Yanping Hu, Guangcan Bai, Guoquan Liu, Thomas F. Prisner, Xianyang Fang
Summary: Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is a powerful method for studying the structure and dynamics of biological macromolecules, providing distance distribution information from 1.8 to 6 nm when the biomolecules are labeled with paramagnetic tags. This study demonstrates the measurement of long-range distances up to 14 nm on a large RNA molecule using a combination of site-directed spin labeling and RNA perdeuteration. The perdeuteration technique extends the observation time windows of PELDOR and allows for the determination of long distances and conformational flexibility in large RNAs.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Rodrigo Arias-Cartin, Alexandre Uzel, Farida Seduk, Guillaume Gerbaud, Fabien Pierrel, Marianne Broc, Regine Lebrun, Bruno Guigliarelli, Axel Magalon, Stephane Grimaldi, Anne Walburger
Summary: This study expands our knowledge of the FDH family by identifying a noncanonical FDH that differs in terms of architecture, amino acid conservation around the molybdenum cofactor, and reactivity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Andrei A. Kuzhelev, Danhua Dai, Vasyl Denysenkov, Igor A. Kirilyuk, Elena G. Bagryanskaya, Thomas F. Prisner
Summary: A series of nitroxide radicals with different substituents and overall sizes were systematically studied to quantify the contribution of radical rotational dynamics to inner-sphere dynamics at high magnetic fields. The experiments, conducted at 9.4 T, demonstrated that considering the rotational motion of the radical can quantitatively predict the observed enhancements.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Andrei A. Kuzhelev, Danhua Dai, Vasyl Denysenkov, Thomas F. Prisner
Summary: Dynamic nuclear polarization (DNP) is a powerful method to enhance NMR sensitivity. Recent research has found that similar to the solid effect and thermal mixing, DNP enhancements can be observed in the fluid phase. This discovery opens up new possibilities for DNP applications in macromolecular systems at ambient temperatures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Cameron D. Fyfe, Noelia Bernardo-Garcia, Laura Fradale, Stephane Grimaldi, Alain Guillot, Clemence Brewee, Leonard M. G. Chavas, Pierre Legrand, Alhosna Benjdia, Olivier Berteau
Summary: Methyl-coenzyme M reductase plays a central role in regulating global methane levels. The study of Methanosarcina acetivorans' Mmp10 provides insights into its unique enzyme structure and catalytic control mechanism, as well as the structural changes prior to catalysis. This research is important for understanding the catalytic mechanism of the emerging superfamily of B-12-dependent radical SAM enzymes.
Article
Chemistry, Physical
Sinan Al-Attar, Julia Rendon, Marlon Sidore, Jean-Pierre Duneau, Farida Seduk, Frederic Biaso, Stephane Grimaldi, Bruno Guigliarelli, Axel Magalon
Summary: This study reports the mechanistic importance of a set of conserved residues lining the substrate entry tunnel in Escherichia coli nitrate reductase A (Nar), a paradigmatic enzyme of the Mo/W-bisPGD superfamily, and reveals their pivotal role in substrate affinity and proton transfer to the Mo active site. The research suggests that motion of Glu-581 side chain and surrounding polar residues control hydration inside the protein core, proton transfer, and substrate selectivity towards the active site, providing an additional determinant for tuning reactivity and selectivity in Nar. It is proposed that a gating mechanism is at play in several other members of the superfamily.
Article
Chemistry, Multidisciplinary
Frank Kaiser, Burkhard Endeward, Alberto Collauto, Ute Scheffer, Thomas F. Prisner, Michael W. Gobel
Summary: This article introduces a synthetic method for phosphoramidite that reduces the complexity and special equipment requirement of previous methods by using a photocaged benzyl group to attach the TPA spin label. A doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized using this method and studied by PELDOR. The results showed that while TPA does not significantly affect the overall thermal stability of the fold, changes in local mobility were detected by in-line probing.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Pierre Dorlet, Guillaume Gerbaud, Emilien Etienne, Stephane Grimaldi, Bruno Guigliarelli, Valerie Belle
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Review
Chemistry, Multidisciplinary
James Eills, Dmitry Budker, Silvia Cavagnero, Eduard Y. Chekmenev, Stuart J. Elliott, Sami Jannin, Anne Lesage, Joerg Matysik, Thomas Meersmann, Thomas Prisner, Jeffrey A. Reimer, Hanming Yang, Igor V. Koptyug
Summary: Magnetic resonance techniques, especially medical magnetic resonance imaging, are widely used in various scientific disciplines and practical applications. The development of spin hyperpolarization has greatly boosted both fundamental and applied magnetic resonance. Hyperpolarization techniques significantly enhance the signal intensity of magnetic resonance, overcoming its low sensitivity and opening up new possibilities for applications.
Article
Chemistry, Multidisciplinary
Markus Kurth, Uladzimir Barayeu, Hassan Gharibi, Andrei Kuzhelev, Kai Riedmiller, Jennifer Zilke, Kasimir Noack, Vasyl Denysenkov, Reinhard Kappl, Thomas F. Prisner, Roman A. Zubarev, Tobias P. Dick, Frauke Graeter
Summary: We discovered that collagen, the main structural protein of connective tissues, possesses redox activity. Dihydroxyphenylalanine (DOPA) residues, oxidation products of tyrosine residues, were found to be common in collagen derived from different connective tissues. These DOPA residues were found to have significant radical scavenging capacity, functioning as a redox relay by converting to quinone and generating hydrogen peroxide. Our findings establish DOPA residues as redox-active side chains of collagen, possibly protecting connective tissues from radicals formed under mechanical stress and/or inflammation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Andrei A. Kuzhelev, Vasyl Denysenkov, Iram M. Ahmad, Olga Yu. Rogozhnikova, Dmitry Trukhin, Elena G. Bagryanskaya, Victor M. Tormyshev, Snorri Th. Sigurdsson, Thomas F. Prisner
Summary: Dynamic nuclear polarization (DNP) is an effective method for enhancing the sensitivity of nuclear magnetic resonance (NMR) experiments. This study demonstrates that DNP can achieve over 50 times enhancement in viscous liquids using narrow-line polarizing agents and a microwave/RF double-resonance probehead. The results show potential applications of this new DNP approach for chemistry and biology, as demonstrated by the hyperpolarized 1H NMR spectra of tripeptides, triglycine, and glypromate in glycerol-d8.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Danhua Dai, Vasyl Denysenkov, Elena G. Bagryanskaya, Victor M. Tormyshev, Thomas F. Prisner, Andrei A. Kuzhelev
Summary: Dynamic nuclear polarization (DNP) is used to increase sensitivity in nuclear magnetic resonance (NMR), with recent advancements in high-field solid-effect DNP on H-1 nuclei in viscous liquids. This study expands the application of DNP in viscous media to C-13 nuclei. By combining solid-effect H-1 DNP with INEPT transfer, C-13 nuclei were successfully hyperpolarized using a triarylmethyl radical as a polarizing agent and glycerol-C-13(3) as an analyte, achieving enhancement factors of up to 45 at 9.4 T and room temperature.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Chemistry, Physical
Burkhard Endeward, Matthias Bretschneider, Paul Trenkler, Thomas F. Prisner
Summary: In this paper, the application of shaped pulses in EPR spectroscopy is described. Fast arbitrary waveform generators are used to generate pulses for broadband excitation of paramagnetic species. The implementation and optimization of these broadband pulses in existing EPR spectrometers are discussed in detail. Shaped pulses are also reviewed for their applications in broadband inversion of longitudinal magnetization and creation/manipulation of transverse magnetization in dipolar and hyperfine EPR spectroscopy, demonstrating their potential to improve the performance of pulsed EPR experiments.
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
(2023)