bims-cytox1 2018-11-18 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2018–11–18
twelve papers selected by
Gavin McStay, Staffordshire University

Depletion of thiol reducing capacity impairs cytosolic but not mitochondrial Fe/S protein assembly machineries.
Functional investigation of an universally conserved leucine residue in subunit a of ATP synthase targeted by the pathogenic m.9176 T > G mutation.
Diverse phenotype in patients with complex I deficiency due to mutations in NDUFB11.
Human COX7A2L Regulates Complex III Biogenesis and Promotes Supercomplex Organization Remodeling without Affecting Mitochondrial Bioenergetics.
Rescue from galactose-induced death of Leigh Syndrome patient cells by pyruvate and NAD.
Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.
A novel heteroplasmic mutation in mitochondrial tRNAArg gene associated with non-dystrophic myotonias.
MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells.
Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease.
Atomistic insights into cardiolipin binding sites of cytochrome c oxidase.
Fear of disease progression in carriers of the m.3243A > G mutation.
Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases.

Biochim Biophys Acta Mol Cell Res. 2018 Nov 09. pii: S0167-4889(18)30335-5. [Epub ahead of print]

Depletion of thiol reducing capacity impairs cytosolic but not mitochondrial Fe/S protein assembly machineries.

Joseph J Braymer, Martin Stümpfig, Stefanie Thelen, Ulrich Mühlenhoff, Roland Lill.

  Iron‑sulfur (Fe/S) clusters are versatile inorganic cofactors that play central roles in essential cellular functions, from respiration to genome stability. >30 proteins involved in Fe/S protein biogenesis in eukaryotes are known, many of which bind clusters via cysteine residues. This opens up the possibility that the thiol-reducing glutaredoxin and thioredoxin systems are required at both the Fe/S biogenesis and target protein level to counteract thiol oxidation. To address the possible interplay of thiol redox chemistry and Fe/S protein biogenesis, we have characterized the status of the mitochondrial (ISC) and cytosolic (CIA) Fe/S protein assembly machineries in Saccharomyces cerevisiae mutants in which the three partially redundant glutathione (Glr1) and thioredoxin (Trr1 and Trr2) oxidoreductases have been inactivated in either mitochondria, cytosol, or both compartments. Cells devoid of mitochondrial oxidoreductases maintained a functional mitochondrial ISC machinery and showed no altered iron homeostasis despite a non-functional complex II of the respiratory chain due to redox-specific defects. In cells that lack either cytosolic or total cellular thiol reducing capacity, both the ISC system and iron homeostasis were normal, yet cytosolic and nuclear Fe/S target proteins were not matured. This dysfunction could be attributed to a failure in the assembly of [4Fe‑4S] clusters in the CIA factor Nar1, even though Nar1 maintained robust protein levels and stable interactions with later-acting CIA components. Overall, our analysis has uncovered a hitherto unknown thiol-dependence of the CIA machinery and has demonstrated the surprisingly varying sensitivity of Fe/S proteins to thiol oxidation.

Keywords:  Glutathione oxidoreductase; Iron homeostasis; Iron‑sulfur clusters; Saccharomyces cerevisiae; Thiol redox chemistry; Thioredoxin oxidoreductase

DOI:  https://doi.org/10.1016/j.bbamcr.2018.11.003
Biochim Biophys Acta Bioenerg. 2018 Nov 07. pii: S0005-2728(18)30167-1. [Epub ahead of print]

Functional investigation of an universally conserved leucine residue in subunit a of ATP synthase targeted by the pathogenic m.9176 T > G mutation.

Roza Kucharczyk, Alain Dautant, François Godard, Déborah Tribouillard-Tanvier, Jean-Paul di Rago.

Protons are transported from the mitochondrial matrix to the intermembrane space of mitochondria during the transfer of electrons to oxygen and shuttled back to the matrix by the a subunit and a ring of identical c subunits across the membrane domain (FO) of ATP synthase, which is coupled to ATP synthesis. A mutation (m.9176 T > G) of the mitochondrial ATP6 gene that replaces an universally conserved leucine residue into arginine at amino acid position 217 of human subunit a (aL217R) has been associated to NARP (Neuropathy, Ataxia and Retinitis Pigmentosa) and MILS (Maternally Inherited Leigh's Syndrome) diseases. We previously showed that an equivalent thereof in Saccharomyces cerevisiae (aL237R) severely impairs subunit a assembly/stability and decreases by >90% the rate of mitochondrial ATP synthesis. Herein we identified three spontaneous first-site intragenic suppressors (aR237M, aR237T and aR237S) that fully restore ATP synthase assembly. However, mitochondrial ATP synthesis rate was only partially recovered (40-50% vs wild type yeast). In light of recently described high-resolution yeast ATP synthase structures, the detrimental consequences of the aL237R change can be explained by steric and electrostatic hindrance with the universally conserved subunit a arginine residue (aR176) that is essential to FO activity. aL237 together with three other nearby hydrophobic residues have been proposed to prevent ion shortage between two physically separated hydrophilic pockets within the FO. Our results suggest that aL237 favors subunit c-ring rotation by optimizing electrostatic interaction between aR176 and an acidic residue in subunit c (cE59) known to be essential also to the activity of FO.

DOI: https://doi.org/10.1016/j.bbabio.2018.11.005
Eur J Med Genet. 2018 Nov 10. pii: S1769-7212(18)30265-9. [Epub ahead of print]

Diverse phenotype in patients with complex I deficiency due to mutations in NDUFB11.

Karit Reinson, Reka Kovacs-Nagy, Eve Õiglane-Shlik, Sander Pajusalu, Margit Nõukas, Liesbeth T Wintjes, Frans C A van den Brandt, Maaike Brink, Till Acker, Uwe Ahting, Andreas Hahn, Anne Schänzer, Tobias B Haack, Richard J Rodenburg, Katrin Õunap.

  Mitochondrial complex I deficiency is the most frequent mitochondrial disorder presenting in childhood and the mutational spectrum is highly heterogeneous. The NDUFB11 gene is one of the recently identified gene, which is located in the short arm of the X-chromosome. Here we report clinical, biochemical, functional and genetic findings of two male patients with lactic acidosis, hypertrophic cardiomyopathy and isolated complex I deficiency due to de novo hemizygous mutations (c.286C > T and c.328C > T) in the NDUFB11 gene. Neither of them had any skin manifestation The NDUFB11 gene encodes a relatively small integral membrane protein NDUFB11, which is essential for the assembly of an active complex I. The expression levels of this protein was decreased in both patient cells and a lentiviral complementation experiment also supported the notion that the complex I deficiency in those two patients is caused by NDUFB11 genetic defects. Our findings together with a review of the thirteen previously described patients demonstrate a wide spectrum of clinical features associated with NDUFB11-related complex I deficiency. However, histiocytoid cardiomyopathy and/or congenital sideroblastic anemia could be indicative for mutation in the NDUFB11 gene, while the clinical manifestation of the same mutation can be highly variable.

Keywords:  Congenital sideroblastic anemia; Histiocytoid cardiomyopathy; Mitochondrial complex I deficiency; NDUFB11

DOI:  https://doi.org/10.1016/j.ejmg.2018.11.006
Cell Rep. 2018 Nov 13. pii: S2211-1247(18)31647-4. [Epub ahead of print]25(7): 1786-1799.e4

Human COX7A2L Regulates Complex III Biogenesis and Promotes Supercomplex Organization Remodeling without Affecting Mitochondrial Bioenergetics.

Teresa Lobo-Jarne, Eva Nývltová, Rafael Pérez-Pérez, Alba Timón-Gómez, Thibaut Molinié, Austin Choi, Arnaud Mourier, Flavia Fontanesi, Cristina Ugalde, Antoni Barrientos.

  The mitochondrial respiratory chain is organized in a dynamic set of supercomplexes (SCs). The COX7A2L protein is essential for mammalian SC III2+IV assembly. However, its function in respirasome (SCs I+III2+IVn) biogenesis remains controversial. To unambiguously determine the COX7A2L role, we generated COX7A2L-knockout (COX7A2L-KO) HEK293T and U87 cells. COX7A2L-KO cells lack SC III2+IV but have enhanced complex III steady-state levels, activity, and assembly rate, normal de novo complex IV biogenesis, and delayed respirasome formation. Nonetheless, the KOs have normal respirasome steady-state levels, and only larger structures (SCs I1-2+III2+IV2-n or megacomplexes) were undetected. Functional substrate-driven competition assays showed normal mitochondrial respiration in COX7A2L-KO cells in standard and nutritional-, environmental-, and oxidative-stress-challenging conditions. We conclude that COX7A2L establishes a regulatory checkpoint for the biogenesis of CIII2 and specific SCs, but the COX7A2L-dependent MRC remodeling is essential neither to maintain mitochondrial bioenergetics nor to cope with acute cellular stresses.

Keywords:  COX7A2L; COX7RP; SCAFI; complex III; mitochondrial respiratory chain; respirasomes; supercomplexes

DOI:  https://doi.org/10.1016/j.celrep.2018.10.058
Cell Death Dis. 2018 Nov 14. 9(11): 1135

Rescue from galactose-induced death of Leigh Syndrome patient cells by pyruvate and NAD.

Eligio F Iannetti, Jan A M Smeitink, Peter H G M Willems, Julien Beyrath, Werner J H Koopman.

Cell models of mitochondrial complex I (CI) deficiency display activation of glycolysis to compensate for the loss in mitochondrial ATP production. This adaptation can mask other relevant deficiency-induced aberrations in cell physiology. Here we investigated the viability, mitochondrial morphofunction, ROS levels and ATP homeostasis of primary skin fibroblasts from Leigh Syndrome (LS) patients with isolated CI deficiency. These cell lines harbored mutations in nuclear DNA (nDNA)-encoded CI genes (NDUFS7, NDUFS8, NDUFV1) and, to prevent glycolysis upregulation, were cultured in a pyruvate-free medium in which glucose was replaced by galactose. Following optimization of the cell culture protocol, LS fibroblasts died in the galactose medium, whereas control cells did not. LS cell death was dose-dependently inhibited by pyruvate, malate, oxaloacetate, α-ketoglutarate, aspartate, and exogenous NAD+ (eNAD), but not by lactate, succinate, α-ketobutyrate, and uridine. Pyruvate and eNAD increased the cellular NAD+ content in galactose-treated LS cells to a different extent and co-incubation studies revealed that pyruvate-induced rescue was not primarily mediated by NAD+. Functionally, in LS cells glucose-by-galactose replacement increased mitochondrial fragmentation and mass, depolarized the mitochondrial membrane potential (Δψ), increased H2DCFDA-oxidizing ROS levels, increased mitochondrial ATP generation, and reduced the total cellular ATP content. These aberrations were differentially rescued by pyruvate and eNAD, supporting the conclusion that these compounds rescue galactose-induced LS cell death via different mechanisms. These findings establish a cell-based strategy for intervention testing and enhance our understanding of CI deficiency pathophysiology.

DOI: https://doi.org/10.1038/s41419-018-1179-4
Cell. 2018 Nov 15. pii: S0092-8674(18)31395-3. [Epub ahead of print]175(5): 1365-1379.e25

Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.

Katharina Weinhäupl, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, Birgit Schönfisch, Hubert Kalbacher, Beate Bersch, Doron Rapaport, Martha Brennich, Kresten Lindorff-Larsen, Nils Wiedemann, Paul Schanda.

  The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial "transfer-chaperone" system is able to guide α-helical and β-barrel membrane proteins in a "nascent chain-like" conformation through a ribosome-free compartment.

Keywords:  NMR spectroscopy; TIM complex; binding by avidity; membrane protein; mitochondria; molecular dynamics simulation; protein import; protein translocation; small-angle X-ray scattering; transfer-chaperone

DOI:  https://doi.org/10.1016/j.cell.2018.10.039
Acta Neurol Belg. 2018 Nov 14.

A novel heteroplasmic mutation in mitochondrial tRNAArg gene associated with non-dystrophic myotonias.

Mohammad Mehdi Heidari, Abolfazl Keshmirshekan, Mozhgan Bidakhavidi, Azam Khosravi, Zeinab Bandari, Mehri Khatami, Shahriar Nafissi.

  Non-dystrophic myotonias (NDM) are rare diseases caused by defects in skeletal muscle chloride and sodium ion channels. It is well established that high-energy consuming tissues such as muscular and nervous systems are exclusively dependent on the ATP generation by mitochondria. The mitochondrial dysfunction, which is caused by mitochondrial DNA mutations, played an important role in the pathogenesis of non-dystrophic myotonias. The purpose of this study is to identify mitochondrial tRNA mutations in non-dystrophic myotonias patients. In this study, 45 Iranian patients with non-dystrophic myotonia were investigated for intracellular ATP content and the mutation screening in all the mitochondrial tRNA genes by DNA sequencing. Our findings showed that lymphocyte intracellular ATP is significantly decreased in NDM patients compared with control subjects (p = 0.001). We found nine mutations in mitochondrial tRNA genes, including m.4454 T > C (in the TψC loop of tRNAMet), m.5568 A > G (tRNATrp), m.5794 T > C (in the anticodon loop of tRNACys), novel m.10438 A > T, and m.10462 T > C (in anticodon loop and ACC stem of tRNAArg), m.12308 A > G (tRNALeu(CUN)) and m.15907 A > G, m.15924 A > G, and m.15928 G > A (in the anticodon stem of tRNAThr) in 31 NDM patients. These results suggest that novel m.10438 A > T mutation is involved in NDM patients and reinforces the significant association between this mutation in mitochondrial tRNAArg Gene and NDM patients (p = 0.008).

Keywords:  Intracellular ATP; Mitochondrial tRNA genes; Mutation; Non-dystrophic myotonia

DOI:  https://doi.org/10.1007/s13760-018-1042-5
J Cell Physiol. 2018 Nov 11.

MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells.

Dennis Dahlmans, Alexandre Houzelle, Pénélope Andreux, Xu Wang, Johanna A Jörgensen, Norman Moullan, Sabine Daemen, Sander Kersten, Johan Auwerx, Joris Hoeks.

  Proper mitochondrial function plays a central role in cellular metabolism. Various diseases as well as aging are associated with diminished mitochondrial function. Previously, we identified 19 miRNAs putatively involved in the regulation of mitochondrial metabolism in skeletal muscle, a highly metabolically active tissue. In the current study, these 19 miRNAs were individually silenced in C2C12 myotubes using antisense oligonucleotides, followed by measurement of the expression of 27 genes known to play a major role in regulating mitochondrial metabolism. Based on the outcomes, we then focused on miR-382-5p and identified pathways affected by its silencing using microarrays, investigated protein expression, and studied cellular respiration. Silencing of miRNA-382-5p significantly increased the expression of several genes involved in mitochondrial dynamics and biogenesis. Conventional microarray analysis in C2C12 myotubes silenced for miRNA-382-5p revealed a collective downregulation of mitochondrial ribosomal proteins and respiratory chain proteins. This effect was accompanied by an imbalance between mitochondrial proteins encoded by the nuclear and mitochondrial DNA (1.35-fold, p < 0.01) and an induction of HSP60 protein (1.31-fold, p < 0.05), indicating activation of the mitochondrial unfolded protein response (mtUPR). Furthermore, silencing of miR-382-5p reduced basal oxygen consumption rate by 14% ( p < 0.05) without affecting mitochondrial content, pointing towards a more efficient mitochondrial function as a result of improved mitochondrial quality control. Taken together, silencing of miR-382-5p induces a mitonuclear protein imbalance and activates the mtUPR in skeletal muscle, a phenomenon that was previously associated with improved longevity.

Keywords:  microRNA; mitochondria; protein stress; skeletal muscle

DOI:  https://doi.org/10.1002/jcp.27401
Biochim Biophys Acta Mol Basis Dis. 2018 Nov 09. pii: S0925-4439(18)30450-2. [Epub ahead of print]

Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease.

E Sandra Chocron, Erin Munkácsy, Andrew M Pickering.

  The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6 kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.

Keywords:  Aging; Lifespan; Mitochondria; mtDNA

DOI:  https://doi.org/10.1016/j.bbadis.2018.09.035
Biochim Biophys Acta Bioenerg. 2018 Nov 08. pii: S0005-2728(18)30241-X. [Epub ahead of print]

Atomistic insights into cardiolipin binding sites of cytochrome c oxidase.

Aapo Malkamäki, Vivek Sharma.

  Mitochondrial cytochrome c oxidase couples the reduction of oxygen to proton pumping. Despite an overall good understanding of its molecular mechanism, the role of cardiolipin in protein function is not understood. Here, we have studied the cardiolipin-protein interactions in a dynamic context by means of atomistic molecular dynamics simulations performed on the entire structure of monomeric and dimeric forms of the enzyme. Several microseconds of simulation data reveal that the crystallographic cardiolipin molecules that glue two monomers together bind weakly in hybrid and single-component lipid bilayers and dissociate rapidly. Atomistic simulations performed in the absence of tightly bound cardiolipin molecules strongly perturb the structural integrity of subunits III and VIIa, thereby highlighting an indispensable nature of lipid-protein interactions in enzyme function such as proton uptake and oxygen channeling. Our results demonstrate the strength of molecular simulations in providing direct atomic description of lipid-protein processes that are difficult to achieve experimentally.

Keywords:  Energy transduction; Lipid-protein interactions; Molecular dynamics simulations; Proton pumping

DOI:  https://doi.org/10.1016/j.bbabio.2018.11.004
Orphanet J Rare Dis. 2018 Nov 13. 13(1): 203

Fear of disease progression in carriers of the m.3243A > G mutation.

José A E Custers, Paul de Laat, Saskia Koene, Jan Smeitink, Mirian C H Janssen, Christianne Verhaak.

   BACKGROUND: Being diagnosed with mitochondrial disease due to the m.3243A > G mutation is frequently preceded by a long diagnostic process. The disease itself is characterized by heterogeneous course and expression, so leaving patients with considerable uncertainty regarding their prognosis and treatment possibilities. This could easily result in fear of disease progression. This study investigated the presence of this fear and its correlates with genetic characteristics and clinical disease severity in m.3243A > G carriers.
METHODS: In total 125 eligible m.3243A > G mutation carriers were invited to participate in this cross-sectional study. After informed consent, participants completed questionnaires including items on socio-demographics, fear of progression, depression, anxiety, and quality of life. Clinical disease severity was assessed by the NMDAS questionnaire. Heteroplasmy levels were assessed in leucocytes, urine epithelial cells and buccal mucosa.
RESULTS: Seventy-six carriers participated in this study. Results showed that 18% reported high fear of progression. Fear of progression was significantly related to all domains of quality of life. Furthermore, fear of progression was moderately correlated with feelings of depression (r = .37), and anxiety (r = .44). Patients with moderate or severe clinical symptoms on the NMDAS experienced more fear of progression than patients with mild clinical symptoms. Fear of progression was weakly correlated with heteroplasmy in leucocytes (r = .27) and buccal mucosa (r = .31).
CONCLUSIONS: A substantial part of m.3243A > G mutation carriers experience high levels of fear of progression which coincide with significantly lower quality of life. Only a small relation with disease characteristics was found. The impact of receiving a diagnosis without therapeutic possibilities on fear is important to consider.

Keywords:  Fear of progression; M.3243A > G mutation; Mental health; Mitochondrial disease; Quality of life

DOI:  https://doi.org/10.1186/s13023-018-0951-y
J Cell Physiol. 2018 Nov 11.

Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases.

Arif Uddin, Tarikul Huda Mazumder, Supriyo Chakraborty.

  The mitochondrial cytochrome oxidase (CO) genes are involved in complex IV of the electron transport system, and dysfunction of CO genes leads to several diseases. However, no work has been reported on the codon usage pattern of these genes. We used bioinformatic methods to analyze the compositional properties and the codon usage pattern of the COI, COII, and COIII genes in fishes, birds, and mammals to understand the similarities and dissimilarities of codon usage in these genes, which gave an insight into the molecular biology of these genes. The effective number of codons (ENC) value of genes was high in different species of fishes, birds and mammals, which indicates that the codon bias of CO genes was low and the ENC values were significantly different among fishes, birds, and mammals, as revealed from the t test. The overall guanine and cytosine (GC) content in fishes, birds, and mammals was lower than 50% in all genes, indicating that the genes were AT-rich and significantly different among fishes, birds, and mammals. The TCA codon was overrepresented in fishes, birds, and mammals for the COI gene, in birds and mammals for the COII gene, but it was not overrepresented in others. Only three codons, namely CTA, CGA, and AAA, were overrepresented in all three groups for the COI, COII, and COIII genes, repectively. From the neutrality plot in fishes, birds, and mammals, it was observed that the slopes of the regression lines (regression coefficients) in the COI, COII, and COIII genes were <0.5, suggesting that natural selection played a major role, whereas mutation pressure played a minor role.

Keywords:  codon usage bias (CUB); cytochrome oxidase (CO) gene; electron transport system (ETS); mutation pressure; natural selection

DOI:  https://doi.org/10.1002/jcp.27375