Article
Multidisciplinary Sciences
Daniel N. Grba, Injae Chung, Hannah R. Bridges, Ahmed-Noor A. Agip, Judy Hirst
Summary: A cryo-EM structure of complex I from mouse heart mitochondria reveals the mechanism of catalysis and the pathways and mechanisms of proton translocation. The study provides key questions for future research.
Article
Biochemistry & Molecular Biology
Johannes Schimpf, Sabrina Oppermann, Tatjana Gerasimova, Ana Filipa Santos Seica, Petra Hellwig, Irina Grishkovskaya, Daniel Wohlwend, David Haselbach, Thorsten Friedrich
Summary: Respiratory complex I drives proton translocation across energy-transducing membranes by oxidizing NADH and reducing (ubi)quinone. The structure of the peripheral arm of the E coli complex I has been determined, consisting of six subunits, FMN cofactor, and nine iron-sulfur clusters, using cryo electron microscopy. The fusion of catalytically important subunits in E. coli complex I results in a specific architecture of functional importance. Mutagenesis and biochemical characterization of variants have provided insights into the features of the E. coli complex and shed light on its unknown assembly.
Article
Chemistry, Multidisciplinary
Oleksii Zdorevskyi, Amina Djurabekova, Jonathan Lasham, Vivek Sharma
Summary: Respiratory complex I is an redox-driven proton pump that contributes to mitochondrial ATP generation. The recent cryo-EM structural data revealed the positions of water molecules in the membrane domain of the complex, but the flow of protons in the membrane-bound subunits is still unclear. Computer simulations on high-resolution structural data show that protons can travel through the antiporter-like subunits, including at the subunit-subunit interface parallel to the membrane. Our simulations also demonstrate the role of conserved tyrosine residues and electrostatic effects in facilitating proton transfer. These results challenge prevailing proton pumping models of respiratory complex I.
Article
Biochemistry & Molecular Biology
Bilkis Mehrin Moni, Joanna A. Quaye, Giovanni Gadda
Summary: Enzymes require flexible regions for catalysis, and the mobile regions of enzymes include gates that regulate the passage of molecules in and out of the active site. Q80 in loop 3 of the enzyme NQO plays a mechanistically essential role in NADH binding, but does not significantly affect quinone binding and hydride transfer.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jann-Louis Hau, Susann Kaltwasser, Valentin Muras, Marco S. Casutt, Georg Vohl, Bjoern Claussen, Wojtek Steffen, Alexander Leitner, Eckhard Bill, George E. Cutsail, Serena Debeer, Janet Vonck, Julia Steuber, Guenter Fritz
Summary: This study reveals that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. This mechanism is of significant importance for NADH oxidation in the human pathogen Vibrio cholerae.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Thu-Thuy Nguyen, Trang Hoang, Kiet N. Tran, Hyeonji Kim, Sei-Heon Jang, ChangWoo Lee
Summary: This study investigated the roles of aromatic amino acids in the stability and function of Trx from a psychrophilic bacterium, revealing that aromatic residues are crucial for the structural stability and active-site conformation of SpTrx.
Article
Biochemical Research Methods
Oliver M. Stockert, Chandra M. Gravel, Katherine E. Berry
Summary: This protocol introduces a three-hybrid system and a forward genetics screen to analyze RNA-protein interactions in live bacteria. The system connects the strength of an RNA-protein interaction to the transcription of a reporter gene in Escherichia coli cells. It provides a powerful complement to traditional biochemical methods for studying RNA-protein interactions.
Article
Multidisciplinary Sciences
Lisa Strotmann, Caroline Harter, Tatjana Gerasimova, Kevin Ritter, Henning J. J. Jessen, Daniel Wohlwend, Thorsten Friedrich
Summary: NADH:ubiquinone oxidoreductase, also known as respiratory complex I, is involved in cellular energy metabolism by coupling electron transfer and proton translocation. The oxidoreductase generates reactive oxygen species (ROS) as a by-product, but this does not affect the activity of the complex significantly, as it can bypass the damage caused by ROS during electron transfer.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Blake A. Sweeney, David Hoksza, Eric P. Nawrocki, Carlos Eduardo Ribas, Fabio Madeira, Jamie J. Cannone, Robin Gutell, Aparna Maddala, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Patricia P. Chan, Todd M. Lowe, Robert D. Finn, Anton I. Petrov
Summary: The authors introduced a method for predicting and visualizing a wide range of RNA structures, enabling the linking of RNA sequence to function, which helps in better understanding non-coding RNA function.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Katherine H. Richardson, John J. Wright, Mantas Simenas, Jacqueline Thiemann, Ana M. Esteves, Gemma McGuire, William K. Myers, John J. L. Morton, Michael Hippler, Marc M. Nowaczyk, Guy T. Hanke, Maxie M. Roessler
Summary: Photosynthetic Complex I (PS-CI) links the oxidation of ferredoxin and reduction of plastoquinone to proton pumping across thylakoid membranes, generating ATP in photosynthesis. By overcoming challenges, the authors determined the reduction potentials of PS-CI's iron-sulfur clusters, providing insight into the bioenergetics of the electron transfer relay.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Qiangde Duan, Shengmei Pang, Lili Feng, Baoliang Li, Linfen Lv, Yuxuan Liang, Guoqiang Zhu
Summary: Increasing evidence suggests that both subunits of heat-labile enterotoxin (LT), A (LTA) and B (LTB), play important roles in enhancing bacterial adherence. LTA increases bacterial adhesion molecules expression, while LTB mediates the initial interaction with GM1 receptors of host cells. Our study also showed that cyclic AMP (cAMP) and cholesterol play significant roles in LT-enhanced bacterial adherence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kumari Kavita, Aixia Zhang, Chin-Hsien Tai, Nadim Majdalani, Gisela Storz, Susan Gottesman
Summary: Hfq, a bacterial RNA chaperone, plays a crucial role in stabilizing small regulatory RNAs and facilitating their interactions with target mRNAs. Deletion of the C-terminal domain in Hfq leads to defects in the accumulation and function of various sRNAs, particularly those that bind to the distal face. The region between amino acids 66-72 is essential for this defect, while the CTD region beyond amino acid 72 is important for functions associated with the Hfq rim.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Xinyi Wu, Jianqiang Wu, Yu Wang, Meiwen He, Mingming He, Weikang Liu, Sheng Shu, Jin Sun, Shirong Guo
Summary: In this study, it was found that PGR5 in cucumber plays a dominant role in cyclic electron flow, interacting with other proteins and being partially related to state transitions. PGR5 is a small, mobile protein that functions when attached to protein complexes.
HORTICULTURE RESEARCH
(2021)
Article
Multidisciplinary Sciences
Masaya Fujita, Shodai Yano, Koki Shibata, Mizuki Kondo, Shojiro Hishiyama, Naofumi Kamimura, Eiji Masai
Summary: TonB-dependent transporters play a crucial role in the outer membrane transport of nutrients in microbes, with certain genes being important for the uptake of lignin-derived aromatics. Studies have shown that the tonB1 operon genes in SYK-6 are involved in the outer membrane transport of lignin-derived aromatic compounds, while exbB2/tolQ and exbD3/tolR are suggested to constitute the Tol-Pal system maintaining outer membrane integrity.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, Research & Experimental
Yi-chun Xu, Jun Su, Jia-jing Zhou, Qing Yuan, Jun-song Han
Summary: The energy shift to glycolysis is a characteristic of cancer. MT-ND1, encoded by mitochondria, is a crucial subunit of complex I necessary for oxidative phosphorylation. This study reviews the structure, biological function, and expression patterns/mutations of MT-ND1 in various cancers, suggesting its potential as a biomarker for cancer diagnosis and prognosis, as well as a target for cancer therapy.
CURRENT MEDICAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Prem Kumar Sinha, Norma Castro-Guerrero, Gaurav Patki, Motoaki Sato, Jesus Torres-Bacete, Subhash Sinha, Hideto Miyoshi, Akemi Matsuno-Yagi, Takao Yagi
Article
Immunology
Jesus Torres-Bacete, Cristina Delgado-Martin, Carolina Gomez-Moreira, Siro Simizu, Jose Luis Rodriguez-Fernandez
JOURNAL OF IMMUNOLOGY
(2015)
Article
Biotechnology & Applied Microbiology
Jesus Torres-Bacete, Daniel Hormigo, Raquel Torres-Guzman, Miguel Arroyo, Maria Pilar Castillon, Jose Luis Garcia, Carmen Acebal, Isabel de la Mata
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2015)
Review
Biophysics
Motoaki Sato, Jesus Torres-Bacete, Prem Kumar Sinha, Akemi Matsuno-Yagi, Takao Yagi
JOURNAL OF BIOENERGETICS AND BIOMEMBRANES
(2014)
Article
Biochemistry & Molecular Biology
Pilar Lopez-Cotarelo, Cristina Escribano-Diaz, Ivan Luis Gonzalez-Bethencourt, Carolina Gomez-Moreira, Maria Laura Deguiz, Jesus Torres-Bacete, Laura Gomez-Cabanas, Jaime Fernandez-Barrera, Cristina Delgado-Martin, Mario Mellado, Jose Ramon Regueiro, Maria Eugenia Miranda-Carus, Jose Luis Rodriguez-Fernandez
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Multidisciplinary Sciences
Cansu Uluseker, Jesus Torres-Bacete, Jose L. Garcia, Martin M. Hanczyc, Juan Nogales, Ozan Kahramanogullari
SCIENTIFIC REPORTS
(2019)
Article
Biotechnology & Applied Microbiology
Jesus Torres-Bacete, Jose Luis Garcia, Juan Nogales
Summary: An automata regulatory system based on cell-stress mechanisms was engineered to overcome the limitations of existing gene expression systems. A synthetic phosphate-depletion library of promoters inspired by bacterial PHO starvation system was developed, showing interesting host-dependent performance and a wide strength spectrum. By fine-tuning the initial concentration of phosphate, growth phase-dependent expression of these promoters could be achieved.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Patricia Magadan-Corpas, Suhui Ye, Alvaro Perez-Valero, Patrick L. McAlpine, Paula Valdes-Chiara, Jesus Torres-Bacete, Juan Nogales, Claudio J. Villar, Felipe Lombo
Summary: This study presents the optimized de novo heterologous production of Eriodictyol in Streptomyces albidoflavus through genome editing, which significantly increased the production yield. This finding is of great importance for the industrial production of the medicinal compound Eriodictyol.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Darwin Carranza-Saavedra, Jesus Torres-Bacete, Blas Blazquez, Claudia Patricia Sanchez Henao, Jose Edgar Zapata Montoya, Juan Nogales
Summary: Replacing traditional substrates with non-conventional carbon sources in industrial bioprocesses is crucial for sustainable chemical production in the circular economy. This study utilized systems metabolic engineering to optimize the production of 2-ketoisovalerate (2-KIV) using Escherichia coli W as a cell factory and whey as a carbon source. Through genetic modifications and metabolic modeling, a suitable microbial chassis was constructed, resulting in high yields of 2-KIV using whey as a non-conventional substrate.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Beatriz Garcia-Jimenez, Jesus Torres-Bacete, Juan Nogales
Summary: Microbes do not live in isolation but in microbial communities. Most methods and biotechnological applications involving microorganisms have been developed in the context of isolated microbes, making in vivo microbial consortia development extremely difficult and costly. Computational approaches provide a cost-effective alternative to study microbial communities via descriptive and engineering modelling.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)