bims-cytox1 2018-05-27 papers

Issue of 2018‒05‒27
four papers selected by
Gavin McStay
New York Institute of Technology

Biochim Biophys Acta. 2018 May 17. pii: S0005-2728(18)30124-5. [Epub ahead of print]

Molecular basis of diseases caused by the mtDNA mutation m.8969G>A in the subunit a of ATP synthase.

Natalia Skoczeń, Alain Dautant, Krystyna Binko, François Godard, Marine Bouhier, Xin Su, Jean-Paul Lasserre, Marie-France Giraud, Déborah Tribouillard-Tanvier, Huimei Chen, Jean-Paul di Rago, Roza Kucharczyk.

The ATP synthase which provides aerobic eukaryotes with ATP, organizes into a membrane-extrinsic catalytic domain, where ATP is generated, and a membrane-embedded FO domain that shuttles protons across the membrane. We previously identified a mutation in the mitochondrial MT-ATP6 gene (m.8969G>A) in a 14-year-old Chinese female who developed an isolated nephropathy followed by brain and muscle problems. This mutation replaces a highly conserved serine residue into asparagine at amino acid position 148 of the membrane-embedded subunit a of ATP synthase. We showed that an equivalent of this mutation in yeast (aS175N) prevents FO-mediated proton translocation. Herein we identified four first-site intragenic suppressors (aN175D, aN175K, aN175I, and aN175T), which, in light of a recently published atomic structure of yeast FO, indicating that the detrimental consequences of the original mutation result from the establishment of hydrogen bonds between aN175 and a nearby glutamate residue (aE172) that was proposed to be critical for the exit of protons from the ATP synthase towards the mitochondrial matrix. Interestingly also, we found that the aS175N mutation can be suppressed by second-site suppressors (aP12S, aI171F, aI171N, aI239F, and aI200M), of which some are very distantly located (by 20-30 Å) from the original mutation. The possibility to compensate through long-range effects the aS175N mutation is an interesting observation that holds promise for the development of therapeutic molecules.

Keywords: ATP synthase; MT-ATP6; Metabolic disease; Oxidative phosphorylation; Subunit a; mtDNA

DOI: https://doi.org/10.1016/j.bbabio.2018.05.009

Stem Cell Res. 2018 May 16. pii: S1873-5061(18)30123-5. [Epub ahead of print]30 22-33

Metabolic plasticity during transition to naïve-like pluripotency in canine embryo-derived stem cells.

I C Tobias, R R Isaac, J G Dierolf, R Khazaee, R C Cumming, D H Betts.

Pluripotent stem cells (PSCs) have been described in naïve or primed pluripotent states. Domestic dogs are useful translational models in regenerative medicine, but their embryonic stem cells (cESCs) remain narrowly investigated. Primed-like cESCs expanded in the presence of leukemia inhibitory factor and fibroblast growth factor 2 (LIF-FGF2) acquire features of naïve pluripotency when exposed to chemical inhibitors and LIF (2iL). However, proliferation of cESCs is influenced by the pluripotent state and is comparatively slower than human or mouse PSCs. We propose that different metabolic pathway activities support ATP generation and biomass accumulation necessary for LIF-FGF2 and 2iL cESC proliferation. We found that 2iL cESCs have greater respiratory capacity, altered mitochondrial chain complex stoichiometry and elevated mitochondrial polarization state. Yet, 2iL-enriched cESCs exhibited immature ultrastructure, including previously unrecognized changes to cristae organization. Enhanced ATP level in 2iL cESCs is associated with altered retrograde signalling, whereas LIF-FGF2 cESCs exhibit a lipogenic phenotype. Inhibition of oxidative phosphorylation impaired proliferation and ATP production in 2iL cESCs but not LIF-FGF2 cESCs, which remained sensitive to glycolysis inhibition. Our study reveals distinct bioenergetic mechanisms contributing to steady-state expansion of distinct canine pluripotent states that can be exploited to improve derivation and culture of canine PSCs.

Keywords: Canine; Embryonic stem cell; Mitochondria; Naïve pluripotency; Oxidative phosphorylation; Pluripotent stem cell

DOI: https://doi.org/10.1016/j.scr.2018.05.005

Biochim Biophys Acta. 2018 May 17. pii: S0005-2728(18)30125-7. [Epub ahead of print]

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase.

Xiuhong Cai, Kamran Haider, Jianxun Lu, Slaven Radic, Chang Yun Son, Qiang Cui, M R Gunner.

Cytochrome c Oxidase (CcO) reduces O2, the terminal electron acceptor, to water in the aerobic respiration electron transport chain. The energy released by O2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PLS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the PR state with the heme a3 propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit residues include His93, Ser168, Thr100 and Asn96. The hydrogen bonds between PLS cluster and P-exit clusters are mediated by a water wire in a cavity centered near Thr100, whose hydration can be interrupted by a hydrophobic pair, Leu255B (near CuA) and Ile99. Connections between the D channel and PLS via Glu286 are controlled by a second, variably hydrated cavity.SIGNIFICANCE STATEMENT: Cytochrome C oxidase plays a crucial role in cellular respiration and energy generation. It reduces O2 to water and uses the released free energy to move protons across mitochondrial and bacterial cell membranes adding to the essential electrochemical gradient. Energy storage requires that protons are taken up from the high pH, N-side and released to the low pH, P-side of the membrane. We identify a potential proton exit from a buried cluster of polar residues (the proton loading site) to the P-side of CcO via paths made up of waters and conserved residues. Two water cavities connect the proton exit pathway to the surface only when hydrated. Changing the degree of hydration may control otherwise energetically favorable proton backflow from the P-side.

Keywords: Cytochrome c oxidase; Grand canonical Monte Carlo simulations; Grotthuss shuttling; Proton transfer

DOI: https://doi.org/10.1016/j.bbabio.2018.05.010

Clin Chest Med. 2018 Jun;pii: S0272-5231(18)30025-X. [Epub ahead of print]39(2): 401-410

Metabolic Myopathies and the Respiratory System.

Patrick Koo, Jigme M Sethi.

Metabolic myopathies are a heterogeneous group of disorders characterized by inherited defects of enzymatic pathways involved in muscle cellular energetics and adenosine triphosphate synthesis. Skeletal and respiratory muscles are most affected. There are multiple mechanisms of disease. The age of onset and prognosis vary. Metabolic myopathies cause exercise intolerance, myalgia, and increase in muscle breakdown products during exercise. Some affect smooth muscle like the diaphragm and cause respiratory failure. The pathophysiology is complex and the evidence in literature to guide diagnosis and management is sparse. Treatment is limited. This review discusses the pathophysiology and diagnostic evaluation of these disorders.

Keywords: Glycogen storage disease; Lipid; Metabolic myopathies; Metabolism; Mitochondrial disease; Myopathy; Purine

DOI: https://doi.org/10.1016/j.ccm.2018.02.001