bims-cytox1 2019-01-06 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2019‒01‒06
eight papers selected by
Gavin McStay
Staffordshire University

ROMO1 is a constituent of the human presequence translocase required for YME1L protease import.
Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome.
Cryo-EM structure of the yeast respiratory supercomplex.
Wild-type and mutant (G2019S) leucine-rich repeat kinase 2 (LRRK2) associate with subunits of the translocase of outer mitochondrial membrane (TOM) complex.
Overexpression of branched-chain amino acid aminotransferases rescues the growth defects of cells lacking the Barth syndrome-related gene TAZ1.
Mitochondria, OxPhos, and neurodegeneration: cells are not just running out of gas.
Mitochondrial Sco proteins are involved in oxidative stress defense.
Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.

J Cell Biol. 2018 Dec 31. pii: jcb.201806093. [Epub ahead of print]

ROMO1 is a constituent of the human presequence translocase required for YME1L protease import.

Frank Richter, Sven Dennerlein, Miroslav Nikolov, Daniel C Jans, Nataliia Naumenko, Abhishek Aich, Thomas MacVicar, Andreas Linden, Stefan Jakobs, Henning Urlaub, Thomas Langer, Peter Rehling.

The mitochondrial presequence translocation machinery (TIM23 complex) is conserved between the yeast Saccharomyces cerevisiae and humans; however, functional characterization has been mainly performed in yeast. Here, we define the constituents of the human TIM23 complex using mass spectrometry and identified ROMO1 as a new translocase constituent with an exceptionally short half-life. Analyses of a ROMO1 knockout cell line revealed aberrant inner membrane structure and altered processing of the GTPase OPA1. We show that in the absence of ROMO1, mitochondria lose the inner membrane YME1L protease, which participates in OPA1 processing and ROMO1 turnover. While ROMO1 is dispensable for general protein import along the presequence pathway, we show that it participates in the dynamics of TIM21 during respiratory chain biogenesis and is specifically required for import of YME1L. This selective import defect can be linked to charge distribution in the unusually long targeting sequence of YME1L. Our analyses establish an unexpected link between mitochondrial protein import and inner membrane protein quality control.

DOI: https://doi.org/10.1083/jcb.201806093
Neurogenetics. 2019 Jan 03.

Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome.

Nurun Nahar Borna, Yoshihito Kishita, Masakazu Kohda, Sze Chern Lim, Masaru Shimura, Yibo Wu, Kaoru Mogushi, Yukiko Yatsuka, Hiroko Harashima, Yuichiro Hisatomi, Takuya Fushimi, Keiko Ichimoto, Kei Murayama, Akira Ohtake, Yasushi Okazaki.

  Pentatricopeptide repeat domain proteins are a large family of RNA-binding proteins involved in mitochondrial RNA editing, stability, and translation. Mitochondrial translation machinery defects are an expanding group of genetic diseases in humans. We describe a patient who presented with low birth weight, mental retardation, and optic atrophy. Brain MRI showed abnormal bilateral signals at the basal ganglia and brainstem, and the patient was diagnosed as Leigh syndrome. Exome sequencing revealed two potentially loss-of-function variants [c.415-2A>G, and c.1747_1748insCT (p.Phe583Serfs*3)] in PTCD3 (also known as MRPS39). PTCD3, a member of the pentatricopeptide repeat domain protein family, is a component of the small mitoribosomal subunit. The patient had marked decreases in mitochondrial complex I and IV levels and activities, oxygen consumption and ATP biosynthesis, and generalized mitochondrial translation defects in fibroblasts. Quantitative proteomic analysis revealed decreased levels of the small mitoribosomal subunits. Complementation experiments rescued oxidative phosphorylation complex I and IV levels and activities, ATP biosynthesis, and MT-RNR1 rRNA transcript level, providing functional validation of the pathogenicity of identified variants. This is the first report of an association of PTCD3 mutations with Leigh syndrome along with combined oxidative phosphorylation deficiencies caused by defects in the mitochondrial translation machinery.

Keywords:  Leigh syndrome; Mitochondrial translation; Oxidative phosphorylation; PTCD3; Small mitoribosomal subunit

DOI:  https://doi.org/10.1007/s10048-018-0561-9
Nat Struct Mol Biol. 2019 Jan;26(1): 50-57

Cryo-EM structure of the yeast respiratory supercomplex.

Sorbhi Rathore, Jens Berndtsson, Lorena Marin-Buera, Julian Conrad, Marta Carroni, Peter Brzezinski, Martin Ott.

Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.

DOI: https://doi.org/10.1038/s41594-018-0169-7
Exp Cell Res. 2018 Dec 28. pii: S0014-4827(18)31186-8. [Epub ahead of print]

Wild-type and mutant (G2019S) leucine-rich repeat kinase 2 (LRRK2) associate with subunits of the translocase of outer mitochondrial membrane (TOM) complex.

Annika Neethling, Lize Engelbrecht, Ben Loos, Craig Kinnear, Rensu Theart, Shameemah Abrahams, Thomas Niesler, George D Mellick, Monique Williams, Soraya Bardien.

  Leucine-rich repeat kinase 2 (LRRK2) is important in various cellular processes including mitochondrial homeostasis and mutations in this gene lead to Parkinson's disease (PD). However, the full spectrum of LRRK2's functions remain to be elucidated. The translocase of outer mitochondrial membrane (TOM) complex is essential for the import of almost all nuclear-encoded mitochondrial proteins and is fundamental for cellular survival. Using co-immunoprecipitation, super-resolution structured illumination microscopy (SR-SIM), and 3D virtual reality (VR) assisted co-localization analysis techniques we show that wild-type and mutant (G2019S) LRRK2 associate and co-localize with subunits of the TOM complex, either under basal (dimethyl sulfoxide, DMSO) or stress-induced (carbonyl cyanide m-chlorophenyl hydrazine, CCCP) conditions. Interestingly, LRRK2 interacted with TOM40 under both DMSO and CCCP conditions, and when the PD causing mutation, G2019S was introduced, the association was not altered. Moreover, overexpression of G2019S LRRK2 resulted in the formation of large, perinuclear aggregates that co-localized with the TOM complex. Taken together, this is the first study to show that both WT and mutant LRRK2 associate with the TOM complex subunits. These findings provide additional evidence for LRRK2's role in mitochondrial function which has important implications for its role in PD pathogenesis.

Keywords:  LRRK2; Parkinson's disease; TOM complex; TOM40; co-immunoprecipitation; co-localization

DOI:  https://doi.org/10.1016/j.yexcr.2018.12.022
J Mol Med (Berl). 2019 Jan 03.

Overexpression of branched-chain amino acid aminotransferases rescues the growth defects of cells lacking the Barth syndrome-related gene TAZ1.

Diana Antunes, Arpita Chowdhury, Abhishek Aich, Sreedivya Saladi, Nofar Harpaz, Mark Stahl, Maya Schuldiner, Johannes M Herrmann, Peter Rehling, Doron Rapaport.

  The yeast protein Taz1 is the orthologue of human Tafazzin, a phospholipid acyltransferase involved in cardiolipin (CL) remodeling via a monolyso CL (MLCL) intermediate. Mutations in Tafazzin lead to Barth syndrome (BTHS), a metabolic and neuromuscular disorder that primarily affects the heart, muscles, and immune system. Similar to observations in fibroblasts and platelets from patients with BTHS or from animal models, abolishing yeast Taz1 results in decreased total CL amounts, increased levels of MLCL, and mitochondrial dysfunction. However, the biochemical mechanisms underlying the mitochondrial dysfunction in BTHS remain unclear. To better understand the pathomechanism of BTHS, we searched for multi-copy suppressors of the taz1Δ growth defect in yeast cells. We identified the branched-chain amino acid transaminases (BCATs) Bat1 and Bat2 as such suppressors. Similarly, overexpression of the mitochondrial isoform BCAT2 in mammalian cells lacking TAZ improves their growth. Elevated levels of Bat1 or Bat2 did not restore the reduced membrane potential, altered stability of respiratory complexes, or the defective accumulation of MLCL species in yeast taz1Δ cells. Importantly, supplying yeast or mammalian cells lacking TAZ1 with certain amino acids restored their growth behavior. Hence, our findings suggest that the metabolism of amino acids has an important and disease-relevant role in cells lacking Taz1 function. KEY MESSAGES: Bat1 and Bat2 are multi-copy suppressors of retarded growth of taz1Δ yeast cells. Overexpression of Bat1/2 in taz1Δ cells does not rescue known mitochondrial defects. Supplementation of amino acids enhances growth of cells lacking Taz1 or Tafazzin. Altered metabolism of amino acids might be involved in the pathomechanism of BTSH.

Keywords:  Barth syndrome; Cardiolipin; Mitochondria; Tafazzin/TAZ1

DOI:  https://doi.org/10.1007/s00109-018-1728-4
J Clin Invest. 2019 Jan 02. pii: 120848. [Epub ahead of print]129(1): 34-45

Mitochondria, OxPhos, and neurodegeneration: cells are not just running out of gas.

Estela Area-Gomez, Cristina Guardia-Laguarta, Eric A Schon, Serge Przedborski.

Mitochondrial respiratory deficiencies have been observed in numerous neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. For decades, these reductions in oxidative phosphorylation (OxPhos) have been presumed to trigger an overall bioenergetic crisis in the neuron, resulting in cell death. While the connection between respiratory defects and neuronal death has never been proven, this hypothesis has been supported by the detection of nonspecific mitochondrial DNA mutations in these disorders. These findings led to the notion that mitochondrial respiratory defects could be initiators of these common neurodegenerative disorders, instead of being consequences of a prior insult, a theory we believe to be misconstrued. Herein, we review the roots of this mitochondrial hypothesis and offer a new perspective wherein mitochondria are analyzed not only from the OxPhos point of view, but also as a complex organelle residing at the epicenter of many metabolic pathways.

DOI: https://doi.org/10.1172/JCI120848
Redox Biol. 2018 Dec 12. pii: S2213-2317(18)30990-X. [Epub ahead of print]21 101079

Mitochondrial Sco proteins are involved in oxidative stress defense.

Aslihan Ekim Kocabey, Luise Kost, Maria Gehlhar, Gerhard Rödel, Uta Gey.

  Members of the evolutionary conserved Sco protein family have been intensively studied regarding their role in the assembly of the mitochondrial cytochrome c oxidase. However, experimental and structural data, specifically the presence of a thioredoxin-like fold, suggest that Sco proteins may also play a role in redox homeostasis. In our study, we addressed this putative function of Sco proteins using Saccharomyces cerevisiae as a model system. Like many eukaryotes, this yeast possesses two SCO homologs (SCO1 and SCO2). Mutants bearing a deletion of either of the two genes are not affected in their growth under oxidative stress. However, the concomitant deletion of the SOD1 gene encoding the superoxide dismutase 1 resulted in a distinct phenotype: double deletion strains lacking SCO1 or SCO2 and SOD1 are highly sensitive to oxidative stress and show dramatically increased ROS levels. The respiratory competent double deletion strain Δsco2Δsod1 paved the way to investigate the putative antioxidant function of SCO homologs apart from their role in respiration by complementation analysis. Sco homologs from Drosophila, Arabidopsis, human and two other yeast species were integrated into the genome of the double deletion mutant and the transformants were analyzed for their growth under oxidative stress. Interestingly, all homologs except for Kluyveromyces lactis K07152 and Arabidopsis thaliana HCC1 were able to complement the phenotype, indicating their role in oxidative stress defense. We further applied this complementation-based system to investigate whether pathogenic point mutations affect the putative antioxidant role of hSco2. Surprisingly, all of the mutant alleles failed to restore the ROS-sensitivity of the Δsco2Δsod1 strain. In conclusion, our data not only provide clear evidence for the function of Sco proteins in oxidative stress defense but also offer a valuable tool to investigate this role for other homologous proteins.

Keywords:  Mitochondria; Oxidative stress response; ROS; Saccharomyces cerevisiae; Sco proteins; Sod1

DOI:  https://doi.org/10.1016/j.redox.2018.101079
Nat Struct Mol Biol. 2019 Jan;26(1): 78-83

Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.

Andrew M Hartley, Natalya Lukoyanova, Yunyi Zhang, Alfredo Cabrera-Orefice, Susanne Arnold, Brigitte Meunier, Nikos Pinotsis, Amandine Maréchal.

Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III2IV2 SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.

DOI: https://doi.org/10.1038/s41594-018-0172-z