Bioenergetics articles within Nature Communications

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  • Article
    | Open Access

    Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here, the authors present a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the synthesis of biomass building blocks.

    • Matteo Mori
    • , Chuankai Cheng
    •  & Terence Hwa

  • Article
    | Open Access

    The ATP synthase FoF1 undergoes rotation in discrete 120° steps. Using cryo-EM analysis, the authors characterise intermediate structures within these 120° steps at 81°, 83°, 91°, and 101°. This shows that FoF1 undergoes a total of 15 steps in a 360° rotation, exhibiting multiple discreet movements per full rotation as opposed to one fluid motion.

    • Atsuki Nakano
    • , Jun-ichi Kishikawa
    •  & Ken Yokoyama

  • Article
    | Open Access

    Tetrahymena thermophila possesses tubular mitochondrial cristae and a highly divergent electron transport chain. Here the authors report cryo-EM structures of its half ring-shaped ~8 MDa megacomplex IV2 + (I + III2 + II)2 and ~10.6 MDa megacomplex (IV2 + I + III2 + II)2 adapted to the cristae membrane curvature.

    • Fangzhu Han
    • , Yiqi Hu
    •  & Long Zhou

  • Article
    | Open Access

    Combining molecular dynamic simulations with in vivo functional assays, Gagelin et al. identified unique molecular features of the mitochondrial carrier uncoupling protein 1 that are crucial to its inhibition by nucleotides

    • Antoine Gagelin
    • , Corentin Largeau
    •  & Bruno Miroux

  • Article
    | Open Access

    The interconnected network of cellular metabolism is potentially prone to generating oscillatory behaviour. Here, the authors use single-cell FRET measurements of pyruvate levels to reveal large periodic fluctuations in bacterial glycolysis.

    • Shuangyu Bi
    • , Manika Kargeti
    •  & Victor Sourjik

  • Article
    | Open Access

    Rhodobacter capsulatus is a favored model organism for studying bacterial photosynthesis. Here the authors present a structure of its light-harvesting–reaction center complex, which reveals that it forms a crescent shape containing only 10 LH1 αβ-subunits.

    • Kazutoshi Tani
    • , Ryo Kanno
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    Rnf reversibly reduces NAD+ by ferredoxin coupled with Na+/H+ pumping for microbial ion gradient or reduced ferredoxin formation. Here, a cryo-EM structure provides information about the participating iron and flavin cofactors, the electron transfer route and the putative Na+ passage.

    • Stella Vitt
    • , Simone Prinz
    •  & Wolfgang Buckel

  • Article
    | Open Access

    How different physical configurations between sarcomeres and mitochondria alter energetic support for contractile function of skeletal muscle is not clear. Here the authors use advanced 3D imaging and analysis techniques to show how space is made for mitochondria within the tightly packed sarcomere networks of striated muscle cells.

    • Prasanna Katti
    • , Alexander S. Hall
    •  & Brian Glancy

  • Article
    | Open Access

    Cryo-EM reveals an asymmetric bacterial photosynthetic supercomplex built upon a homodimeric reaction center core. The structure provides mechanistic insights into light excitation transfer and a possible evolutionary transition intermediate of photosynthetic machinery.

    • Ryan Puskar
    • , Chloe Du Truong
    •  & Po-Lin Chiu

  • Article
    | Open Access

    New cryo-EM structures of the formate hydrogenlyase complex from the model bacterium E. coli clarify how electrons and protons move through the complex and are combined to make H2 gas. The complex shows important similarities and differences to related bioenergetic complexes across the tree of life.

    • Ralf Steinhilper
    • , Gabriele Höff
    •  & Bonnie J. Murphy

  • Article
    | Open Access

    Here, the authors study ion transport mechanisms by introducing mutations to convert an electroneutral proton/potassium pump into a prototypical electrogenic sodium/potassium pump, explaining their selectivity and phosphorylation mechanisms.

    • Victoria C. Young
    • , Hanayo Nakanishi
    •  & Kazuhiro Abe

  • Article
    | Open Access

    How photosynthetic oxygen evolution is originated on ancient Earth is unknown. Here, the authors find that some amino acid residues at the ligand sites of the Mn cluster can be posttranslationally converted to the original carboxylate residues, which could have contributed to the evolutionary process of photosynthetic oxygen evolution.

    • Yuichiro Shimada
    • , Takehiro Suzuki
    •  & Takumi Noguchi

  • Article
    | Open Access

    The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. Here the authors examine the systems level properties of aerobic electron transport system using adaptive laboratory evolution and multi-omics analyses.

    • Amitesh Anand
    • , Arjun Patel
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    The endoperoxides of β-carotene play a key role in signaling of photooxidative stress in plant cells and are regarded as the products of chemical deactivation of singlet oxygen. The authors show that these compounds are instead formed in a reaction between oxygen and β-carotene in their triplet states, revealing the importance of the triplet states in the photoprotection of photosynthetic apparatus.

    • Mateusz Zbyradowski
    • , Mariusz Duda
    •  & Leszek Fiedor

  • Article
    | Open Access

    CryoEM of mitochondrial ATP synthase frozen during rotary catalysis reveals dramatic conformational changes in the peripheral stalk subcomplex, which enable the enzyme’s efficient synthesis of ATP.

    • Hui Guo
    •  & John L. Rubinstein

  • Article
    | Open Access

    Rhodobacter sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present structures of its native dimeric and a protein-U-lacking monomeric light-harvesting-reaction center complexes, which reveal asymmetric features for the dimer and an altered shape for the monomer.

    • Kazutoshi Tani
    • , Ryo Kanno
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    The rotary ATPases use a rotary catalytic mechanism to drive transmembrane proton movement powered by ATP hydrolysis. Here, the authors report a collection of V/A-ATPase V1 domain structures, providing insights into rotary mechanism of the enzyme and potentially other rotary motor proteins driven by ATP hydrolysis.

    • J. Kishikawa
    • , A. Nakanishi
    •  & K. Yokoyama

  • Article
    | Open Access

    ATPases are the macromolecular machines for cellular energy production. Here the authors investigate factors that govern the assembly of the F1 complex from a bacterial F-type ATPase and relate differences in activity of complexes assembled in cells and in vitro to structural changes.

    • Khanh Vu Huu
    • , Rene Zangl
    •  & Nina Morgner

  • Article
    | Open Access

    Aerobic energy metabolism is driven by proton-pumping respiratory supercomplexes. The study reports the structural basis for energy conversion in such supercomplex. It may aid metabolic engineering and drug design against diphtheria and tuberculosis.

    • Wei-Chun Kao
    • , Claire Ortmann de Percin Northumberland
    •  & Carola Hunte

  • Article
    | Open Access

    Exercise training can be therapeutic but how mitochondria respond remains unclear. Here, the authors use multiple omics techniques to reveal a complex network of non-stoichiometric mitochondrial adaptations that are prioritized or deprioritised during different phases of exercise training.

    • Cesare Granata
    • , Nikeisha J. Caruana
    •  & David J. Bishop

  • Article
    | Open Access

    The oxygen-evolving complex in Photosystem II (PSII) catalyzes the light-driven oxidation of water to oxygen and it is still under debate how the water reaches the active site. Here, the authors analyse time-resolved XFEL-based crystal structures of PSII that were determined at room temperature and report the structures of the waters in the putative channels surrounding the active site at various time-points during the reaction cycle and conclude that the O1 channel is the likely water intake pathway and the Cl1 channel the likely proton release pathway.

    • Rana Hussein
    • , Mohamed Ibrahim
    •  & Junko Yano

  • Article
    | Open Access

    The gastric H+,K+-ATPase is a proton pump that creates the acidic environment of the stomach lumen, maintaining high proton gradient across the gastric mucosa cell membrane. Here, structural analysis of rationally designed H+,K+-ATPase mutants provides insight into this and other P-type ATPases cation binding stoichiometry and mechanisms.

    • Kazuhiro Abe
    • , Kenta Yamamoto
    •  & Atsunori Oshima

  • Article
    | Open Access

    Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes. Here the authors determine the reduction potentials of the iron-sulphur clusters of PS-CI and thus the bioenergetics of the electron transfer relay.

    • Katherine H. Richardson
    • , John J. Wright
    •  & Maxie M. Roessler

  • Article
    | Open Access

    M. tuberculosis cytochrome bd oxidase is of interest as a TB drug target. Here, the authors present the 2.5 Å cryo-EM structure of M. tuberculosis cytochrome bd oxidase and identify a disulfide bond within the canonical quinol binding and oxidation domain (Q-loop) and a menaquinone-9 binding site at heme b595.

    • Schara Safarian
    • , Helen K. Opel-Reading
    •  & Hartmut Michel

  • Article
    | Open Access

    The nature of the mitochondrial permeability transition pore (PTP) is still under debate. Here, through genetically modified F-ATP synthase, the authors show that PTP formation can be mediated by F-ATP synthase or by adenine nucleotide translocator, suggesting the existence of distinct but related permeability pathways.

    • Andrea Carrer
    • , Ludovica Tommasin
    •  & Paolo Bernardi

  • Article
    | Open Access

    Formulating metabolic networks mathematically can help researchers study metabolic diseases and optimize the production of industrially important molecules. Here, the authors propose a framework that allows to model eukaryotic metabolism considering gene expression and thermodynamic constraints.

    • Omid Oftadeh
    • , Pierre Salvy
    •  & Vassily Hatzimanikatis

  • Article
    | Open Access

    Evolution selects for the fittest but must operate within the realm of the physically possible. Here, the authors present a theoretical framework that allows them to explore how ten abiotic constraints can shape the operation, regulation, and adaptation of metabolism in E. coli.

    • Amir Akbari
    • , James T. Yurkovich
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.

    • Tomoaki Kawakami
    • , Long-Jiang Yu
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.

    • Clarisse Uwizeye
    • , Johan Decelle
    •  & Giovanni Finazzi

  • Article
    | Open Access

    Reactive oxygen species (ROS) production by reverse electron transfer (RET) through complex I is thought to cause tissue damage from heart attacks. Here, the authors combine in vivo work with biochemical and cryo-EM analyses to characterize the effects of a P25L mutation in the ND6 subunit of mitochondrial complex I. They observe that this mutation does not affect oxidative phosphorylation but renders complex I unable to generate ROS by RET: ND6-P25L mice are protected against cardiac ischaemia–reperfusion injury, thus providing evidence for the proposed role of ROS production in myocardial infarction.

    • Zhan Yin
    • , Nils Burger
    •  & Judy Hirst

  • Article
    | Open Access

    Respiratory complex I plays a key role in energy metabolism. Cryo-EM structure of a mutant accessory subunit LYRM6 from the yeast Yarrowia lipolytica and molecular dynamics simulations reveal conformational changes at the interface between LYRM6 and subunit ND3, propagated further into the complex. These findings offer insight into the mechanism of proton pumping by respiratory complex I.

    • Etienne Galemou Yoga
    • , Kristian Parey
    •  & Heike Angerer

  • Article
    | Open Access

    The respiratory complex I (NADH:ubiquinone oxidoreductase) is a large redox-driven proton pump that initiates respiration in mitochondria. Here, the authors present the 3.0 Å cryo-EM structure of complex I from mouse heart mitochondria with the ubiquinone-analogue inhibitor piericidin A bound in the active site and with kinetic measurements and MD simulations they further show that this inhibitor acts competitively against the native ubiquinone-10 substrate.

    • Hannah R. Bridges
    • , Justin G. Fedor
    •  & Judy Hirst

  • Article
    | Open Access

    Diatoms are marine algae with an important role in global photosynthetic carbon fixation. Here, the authors present the 2.38 Å cryo-EM structure of photosystem I (PSI) in complex with its 24 fucoxanthin chlorophyll a/c-binding (FCPI) antenna proteins from the diatom Chaetoceros gracilis, which provides mechanistic insights into light-energy harvesting, transfer and quenching of the PSI-FCPI supercomplex.

    • Caizhe Xu
    • , Xiong Pi
    •  & Jian-Ren Shen

  • Article
    | Open Access

    ATP drives most cellular processes, although ATP production and consumption levels during mitosis remain unreported. Here, the authors combine metabolic measurements and modeling to quantify ATP levels and synthesis dynamics, revealing that ATP synthesis and consumption are lowered during mitosis.

    • Joon Ho Kang
    • , Georgios Katsikis
    •  & Teemu P. Miettinen

  • Article
    | Open Access

    The pyruvate dehydrogenase complex (PDC) is a multienzyme complex connecting glycolysis to mitochondrial oxidation of pyruvate. Cryo-EM analysis of PDC from Neurospora crassa reveals localization of fungi-specific protein X (PX) and confirms that it functions like the mammalian E3BP, recruiting the E3 component of PDC.

    • B. O. Forsberg
    • , S. Aibara
    •  & E. Lindahl

  • Article
    | Open Access

    Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the respiratory chain in bacteria and mitochondria. Here, the authors present cryo-EM and crystal structures of T. thermophilus complex I in different conformational states and further analyse them by Normal Mode Analysis and molecular dynamics simulations and conclude that quinone redox reactions are important for the coupling mechanism of complex I.

    • Javier Gutiérrez-Fernández
    • , Karol Kaszuba
    •  & Leonid A. Sazanov

  • Article
    | Open Access

    F1Fo ATP synthase consists of two coupled rotary molecular motors: the soluble ATPase F1 and the transmembrane Fo. Here, the authors present cryo-EM structures of E. coli ATP synthase in four discrete rotational sub-states at 3.1-3.4 Å resolution and observe a rotary sub-step of the Fo motor cring that reveals the mechanism of elastic coupling between the two rotary motors, which is essential for effective ATP synthesis.

    • Meghna Sobti
    • , James L. Walshe
    •  & Alastair G. Stewart

  • Article
    | Open Access

    Acyl-acyl carrier protein reductase (AAR) and aldehyde deformylating oxygenase (ADO) are the two enzymes in a cyanobacterial alkane biosynthesis pathway that is of interest for biofuel production. Here the authors provide insights into the catalytic mechanisms of AAR and the coupling between the two enzymes by determining the crystal structures of AAR alone and three AAR–ADO complexes with various bound ligands.

    • Yu Gao
    • , Hongmei Zhang
    •  & Mei Li

  • Article
    | Open Access

    The molecular identity of the mitochondrial megachannel (MMC)/permeability transition pore (PTP), a key effector of cell death, remains controversial. Here authors demonstrate that the membrane embedded bovine F-ATP synthase elicits Ca2 + -dependent currents matching those of the MMC/PTP.

    • Andrea Urbani
    • , Valentina Giorgio
    •  & Paolo Bernardi

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