bims-cytox1 2020-01-26 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2020–01–26
eleven papers selected by
Gavin McStay, Staffordshire University

Pulse-chase SILAC-based analyses reveal selective over-synthesis and rapid turnover of mitochondrial protein components of respiratory complexes.
The mitochondrial epilepsies.
Sirtuins and the mitochondrial unfolded protein response.
Asymmetric inheritance of mitochondria in yeast.
Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis.
Kinetic coupling of the respiratory chain with ATP synthase, but not proton gradients, drives ATP production in cristae membranes.
Detection of mitochondrial DNA variants at low level heteroplasmy in pediatric CNS and extra-CNS solid tumors with three different enrichment methods.
Blood contains circulating cell-free respiratory competent mitochondria.
MMPdb and MitoPredictor: tools for facilitating comparative analysis of animal mitochondrial proteomes.
The Regulation of Mitochondrial Replacement Techniques Around the World.
Porins as helpers in mitochondrial protein translocation.

J Biol Chem. 2020 Jan 23. pii: jbc.RA119.011791. [Epub ahead of print]

Pulse-chase SILAC-based analyses reveal selective over-synthesis and rapid turnover of mitochondrial protein components of respiratory complexes.

Daniel F Bogenhagen, John D Haley.

  Mammalian mitochondria assemble four complexes of the respiratory chain (RCI, RCIII, RCIV, and RCV) by combining 13 polypeptides synthesized within mitochondria on mitochondrial ribosomes (mitoribosomes), with over 70 polypeptides encoded in nuclear DNA, translated on cytoplasmic ribosomes, and imported into mitochondria. We have previously observed that mitoribosome assembly is inefficient because some mitoribosomal proteins are produced in excess, but whether this is the case for other mitochondrial assemblies such as the RCs is unclear. We report here that pulse-chase stable isotope labeling with amino acids in cell culture (SILAC) is a valuable technique to study RC assembly because it can reveal considerable differences in the assembly rates and efficiencies of the different complexes. The SILAC analyses of HeLa cells indicated that assembly of RCV, comprising F1/Fo ATPase, is rapid with little excess subunit synthesis, but that assembly of RCI, i.e. NADH dehydrogenase, is far less efficient, with dramatic over-synthesis of numerous proteins, particularly in the matrix-exposed N- and Q-domains. Unassembled subunits were generally degraded within 3 h. We also observed differential assembly kinetics for individual complexes that were immunoprecipitated with complex-specific antibodies. Immunoprecipitation with an antibody that recognizes the ND1 subunit of RCI co-precipitated a number of proteins implicated in FeS cluster assembly and newly synthesized ubiquinol-cytochrome C reductase Rieske iron-sulfur polypeptide 1 (UQCRFS1), the Rieske FeS protein in RCIII, reflecting some coordination between RCI and RCIII assemblies. We propose that pulse-chase SILAC labeling is a useful tool for studying rates of protein complex assembly and degradation.

Keywords:  NADH dehydrogenase; mitochondria; mitochondrial respiratory chain complex; oxidative phosphorylation system; protein assembly; protein dynamic; protein synthesis; proteomics; stable isotope labeling with amino acids in cell culture (SILAC)

DOI:  https://doi.org/10.1074/jbc.RA119.011791
Eur J Paediatr Neurol. 2020 Jan 07. pii: S1090-3798(19)30441-6. [Epub ahead of print]

The mitochondrial epilepsies.

Albert Lim, Rhys H Thomas.

Mitochondria are vital organelles within cells that undertake many important metabolic roles, the most significant of which is to generate energy to support organ function. Dysfunction of the mitochondrion can lead to a wide range of clinical features, predominantly affecting organs with a high metabolic demand such as the brain. One of the main neurological manifestations of mitochondrial disease is metabolic epilepsies. These epileptic seizures are more frequently of posterior quadrant and occipital lobe onset, more likely to present with non-convulsive status epilepticus which may last months and be more resistant to treatment from the onset. The onset of can be of any age. Childhood onset epilepsy is a major phenotypic feature in mitochondrial disorders such as Alpers-Huttenlocher syndrome, pyruvate dehydrogenase complex deficiencies, and Leigh syndrome. Meanwhile, adults with classical mitochondrial disease syndrome such as MELAS, MERFF or POLG-related disorders could present with either focal or generalised seizures. There are no specific curative treatments for mitochondrial epilepsy. Generally, the epileptic seizures should be managed by specialist neurologist with appropriate use of anticonvulsants. As a general rule, especially in disorders associated with mutation in POLG, sodium valproate is best avoided because hepato-toxicity can be fulminant and fatal.

DOI: https://doi.org/10.1016/j.ejpn.2019.12.021
Curr Neuropharmacol. 2020 Jan 23.

Sirtuins and the mitochondrial unfolded protein response.

Huidan Weng, Yihong Ma, Lina Chen, Guoen Cai, Zhiting Chen, Shaochuan Zhang, Qinyong Ye.

  Mitochondrial damage is involved in many pathophysiological processes, such as tumor development, metabolism, and neurodegenerative diseases. The mitochondrial unfolded protein response (mtUPR) is the first stress-protective response initiated by mitochondrial damage, and it repairs or clears misfolded proteins to alleviate mitochondrial damage. Studies have confirmed that the sirtuin family is essential for the mitochondrial stress response; in particular, SIRT1, SIRT3, and SIRT7 participate in the mtUPR in different axes. This article summarizes the association of sirtuin and the mtUPR as well as specific molecular targets related to the mtUPR in different disease models, which will provide new inspirations for the study of mitochondrial stress, mitochondrial function protection, and mitochondrial related diseases, such as neurodegenerative diseases.

Keywords:  Mitochondria unfolded protein response; Mitochondrial stress; SIRT

DOI:  https://doi.org/10.2174/1570159X18666200123165002
Biol Chem. 2019 Dec 01. pii: /j/bchm.just-accepted/hsz-2019-0439/hsz-2019-0439.xml. [Epub ahead of print]

Asymmetric inheritance of mitochondria in yeast.

Till Klecker, Benedikt Westermann.

  Mitochondria are essential organelles of virtually all eukaryotic organisms. As they cannot be made de novo, they have to be inherited during cell division. In this review, we provide an overview on mitochondrial inheritance in Saccharomyces cerevisiae, a powerful model organism to study asymmetric cell division. Several processes have to be coordinated during mitochondrial inheritance: Mitochondrial transport along the actin cytoskeleton into the emerging bud is powered by a myosin motor protein; cell cortex anchors retain a critical fraction of mitochondria in the mother cell and bud to ensure proper partitioning; and the quantity of mitochondria inherited to the bud is controlled during cell cycle progression. Asymmetric division of yeast cells produces rejuvenated daughter cells and aging mother cells that die after a finite number of cell divisions. We highlight the critical role of mitochondria in this process and discuss how asymmetric mitochondrial partitioning and cellular aging are connected.

Keywords:  Saccharomyces cerevisiae; cell cortex anchor; mitochondrial transport; myosin; organelle partitioning; replicative aging

DOI:  https://doi.org/10.1515/hsz-2019-0439
Cell. 2020 Jan 23. pii: S0092-8674(19)31397-2. [Epub ahead of print]180(2): 296-310.e18

Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis.

Casey E Hughes, Troy K Coody, Mi-Young Jeong, Jordan A Berg, Dennis R Winge, Adam L Hughes.

  Mitochondria and lysosomes are functionally linked, and their interdependent decline is a hallmark of aging and disease. Despite the long-standing connection between these organelles, the function(s) of lysosomes required to sustain mitochondrial health remains unclear. Here, working in yeast, we show that the lysosome-like vacuole maintains mitochondrial respiration by spatially compartmentalizing amino acids. Defects in vacuole function result in a breakdown in intracellular amino acid homeostasis, which drives age-related mitochondrial decline. Among amino acids, we find that cysteine is most toxic for mitochondria and show that elevated non-vacuolar cysteine impairs mitochondrial respiration by limiting intracellular iron availability through an oxidant-based mechanism. Cysteine depletion or iron supplementation restores mitochondrial health in vacuole-impaired cells and prevents mitochondrial decline during aging. These results demonstrate that cysteine toxicity is a major driver of age-related mitochondrial deterioration and identify vacuolar amino acid compartmentation as a cellular strategy to minimize amino acid toxicity.

Keywords:  V-ATPase; aging; amino acid; cysteine; iron; lysosome; mitochondria; vacuole; yeast

DOI:  https://doi.org/10.1016/j.cell.2019.12.035
Proc Natl Acad Sci U S A. 2020 Jan 21. pii: 201917968. [Epub ahead of print]

Kinetic coupling of the respiratory chain with ATP synthase, but not proton gradients, drives ATP production in cristae membranes.

Alexandra Toth, Axel Meyrat, Stefan Stoldt, Ricardo Santiago, Dirk Wenzel, Stefan Jakobs, Christoph von Ballmoos, Martin Ott.

  Mitochondria have a characteristic ultrastructure with invaginations of the inner membrane called cristae that contain the protein complexes of the oxidative phosphorylation system. How this particular morphology of the respiratory membrane impacts energy conversion is currently unknown. One proposed role of cristae formation is to facilitate the establishment of local proton gradients to fuel ATP synthesis. Here, we determined the local pH values at defined sublocations within mitochondria of respiring yeast cells by fusing a pH-sensitive GFP to proteins residing in different mitochondrial subcompartments. Only a small proton gradient was detected over the inner membrane in wild type or cristae-lacking cells. Conversely, the obtained pH values did barely permit ATP synthesis in a reconstituted system containing purified yeast F1F0 ATP synthase, although, thermodynamically, a sufficiently high driving force was applied. At higher driving forces, where robust ATP synthesis was observed, a P-side pH value of 6 increased the ATP synthesis rate 3-fold compared to pH 7. In contrast, when ATP synthase was coreconstituted with an active proton-translocating cytochrome oxidase, ATP synthesis readily occurred at the measured, physiological pH values. Our study thus reveals that the morphology of the inner membrane does not influence the subcompartmental pH values and is not necessary for robust oxidative phosphorylation in mitochondria. Instead, it is likely that the dense packing of the oxidative phosphorylation complexes in the cristae membranes assists kinetic coupling between proton pumping and ATP synthesis.

Keywords:  ATP synthesis; cristae; energy conversion; kinetic coupling; mitochondria

DOI:  https://doi.org/10.1073/pnas.1917968117
Mitochondrion. 2020 Jan 20. pii: S1567-7249(19)30233-8. [Epub ahead of print]

Detection of mitochondrial DNA variants at low level heteroplasmy in pediatric CNS and extra-CNS solid tumors with three different enrichment methods.

Kristiyana Kaneva, Daria Merkurjev, Dejerianne Ostrow, Alex Ryutov, Petr Triska, Kevin Stachelek, David Cobrinik, Jaclyn A Biegel, Xiaowu Gai.

  The mitochondrial genome is small, 16.5kb, and yet complex to study due to an abundance of mitochondria in any given cell or tissue. Mitochondrial DNA (mtDNA) mutations have been previously described in cancer, many of which were detected at low heteroplasmy. In this study we enriched the mitochondrial genome in primary pediatric tumors for detection of mtDNA variants. We completed mtDNA enrichment using REPLI-g, Agilent SureSelect, and long-range polymerase chain reaction (LRPCR) followed by next generation sequencing (NGS) on Illumina platforms. Primary tumor and germline genomic DNA from a variety of pediatric central nervous system (CNS) and extra-CNS solid tumors were analyzed by the three different methods. Although all three methods performed equally well for detecting variants at high heteroplasmy or homoplasmy, only LRPCR and SureSelect-based enrichment methods provided consistent results for variants that were present at less than five percent heteroplasmy. We then applied both LRPCR and SureSelect to three successive samples from a patient with multiply-recurrent gliofibroma and detected a low-level novel mutation as well as a change in heteroplasmy levels of a synonymous variant that was correlated with progression of disease. Implication: This study demonstrates that LRPCR and SureSelect enrichment, but not REPLI-g, followed by NGS are accurate methods for studying the mtDNA variations at low heteroplasmy, which may be applied to studying mtDNA mutations in cancer.

Keywords:  AT/RT; CNS tumor; brain tumor; mitochondria; pediatric cancer; retinoblastoma; rhabdoid tumor; rhabdomyosarcoma; sarcoma

DOI:  https://doi.org/10.1016/j.mito.2020.01.006
FASEB J. 2020 Jan 19.

Blood contains circulating cell-free respiratory competent mitochondria.

Zahra Al Amir Dache, Amaëlle Otandault, Rita Tanos, Brice Pastor, Romain Meddeb, Cynthia Sanchez, Giuseppe Arena, Laurence Lasorsa, Andrew Bennett, Thierry Grange, Safia El Messaoudi, Thibault Mazard, Corinne Prevostel, Alain R Thierry.

  Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases.

Keywords:  blood; circulating DNA; mitochondria; mitochondrial genome; respiratory competent

DOI:  https://doi.org/10.1096/fj.201901917RR
Mitochondrion. 2020 Jan 20. pii: S1567-7249(19)30206-5. [Epub ahead of print]

MMPdb and MitoPredictor: tools for facilitating comparative analysis of animal mitochondrial proteomes.

Viraj Muthye, Gaurav Kandoi, Dennis Lavrov.

  Comparative analysis of animal mitochondrial proteomes faces two challenges: the scattering of data on experimentally-characterized animal mitochondrial proteomes across several databases, and the lack of data on mitochondrial proteomes from the majority of metazoan lineages. In this study, we developed two resources to address these challenges: 1] the Metazoan Mitochondrial Proteome Database (MMPdb), which consolidates data on experimentally-characterized mitochondrial proteomes of vertebrate and invertebrate model organisms, and 2] MitoPredictor, a novel machine-learning tool for prediction of mitochondrial proteins in animals. MMPdb allows comparative analysis of animal mitochondrial proteomes by integrating results from orthology analysis, prediction of mitochondrial targeting signals, protein domain analysis, and Gene Ontology analysis. Additionally, for mammalian mitochondrial proteins, MMPdb includes experimental evidence of localization from MitoMiner and the Human Protein Atlas. MMPdb is publicly available at https://mmpdb.eeob.iastate.edu/. MitoPredictor is a Random Forest classifier which uses orthology, mitochondrial targeting signal prediction and protein domain content to predict mitochondrial proteins in animals.

Keywords:  Database; Machine learning; Mitochondria; Proteome; Random Forest

DOI:  https://doi.org/10.1016/j.mito.2020.01.001
Annu Rev Genomics Hum Genet. 2020 Jan 21.

The Regulation of Mitochondrial Replacement Techniques Around the World.

I Glenn Cohen, Eli Y Adashi, Sara Gerke, César Palacios-González, Vardit Ravitsky.

Mitochondrial replacement techniques (MRTs, also referred to as mitochondrial replacement therapies) have given hope to many women who wish to have genetically related children but have mitochondrial DNA mutations in their eggs. MRTs have also spurred deep ethical disagreemensts and led to different regulatory approaches worldwide. In this review, we discuss the current regulation of MRTs across several countries. After discussing the basics of the science, we describe the current law and policy directions in seven countries: the United Kingdom, the United States, Canada, Australia, Germany, Israel, and Singapore. We also discuss the emerging phenomenon of medical tourism (also called medical travel) for MRTs to places like Greece, Spain, Mexico, and Ukraine. We then pull out some key findings regarding similarities and differences in regulatory approaches around the world. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 21 is August 31, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-genom-111119-101815
Biol Chem. 2019 Dec 01. pii: /j/bchm.just-accepted/hsz-2019-0438/hsz-2019-0438.xml. [Epub ahead of print]

Porins as helpers in mitochondrial protein translocation.

Alexander Grevel, Thomas Becker.

  Mitochondria import the vast majority of their proteins via dedicated protein machineries. The translocase of the outer membrane (TOM complex) forms the main entry site for precursor proteins that are produced on cytosolic ribosomes. Subsequently, different protein sorting machineries transfer the incoming preproteins to the mitochondrial outer and inner membrane, the intermembrane space and the matrix. In this review, we highlight the recently discovered role of porin, also termed voltage-dependent anion channel (VDAC), in mitochondrial protein biogenesis. Porin forms the major channel for metabolites and ions in the outer membrane of mitochondria. Two different functions of porin in protein translocation have been reported. First, it controls the formation of the TOM complex by modulating the integration of the central receptor Tom22 into the mature translocase. Second, porin promotes the transport of carrier proteins towards the carrier translocase (TIM22 complex), which inserts these preproteins into the inner membrane. Thereby, porin acts as coupling factor to spatially coordinate outer and inner membrane transport steps. Thus, porin links metabolite transport to protein import, which are both essential for mitochondrial function and biogenesis.

Keywords:  TOM complex; VDAC; carrier import; mitochondria; protein import

DOI:  https://doi.org/10.1515/hsz-2019-0438