bims-cytox1 2021-10-24 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2021–10–24
eleven papers selected by
Gavin McStay, Staffordshire University

Mitochondrial Translation Occurs Preferentially in the Peri-Nuclear Mitochondrial Network of Cultured Human Cells.
Identification of a Novel m.3955G>A Variant in MT-ND1 Associated with Leigh Syndrome.
An in vitro system to silence mitochondrial gene expression.
Interrogating Mitochondrial Biology and Disease Using CRISPR/Cas9 Gene Editing.
Research progress on the physiological function of mtDNA and its specific detection and therapy.
Adult-Onset Leigh Syndrome due to an m.13513G>A Mutation.
Human Mitochondrial DNA: Particularities and Diseases.
Creating Cell Model 2.0 Using Patient Samples Carrying a Pathogenic Mitochondrial DNA Mutation: iPSC Approach for LHON.
Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane.
Sub-Cellular Metabolomics Contributes Mitochondria-Specific Metabolic Insights to a Mouse Model of Leigh Syndrome.
On the dynamic and even reversible nature of Leigh syndrome: Lessons from human imaging and mouse models.

Biology (Basel). 2021 Oct 15. pii: 1050. [Epub ahead of print]10(10):

Mitochondrial Translation Occurs Preferentially in the Peri-Nuclear Mitochondrial Network of Cultured Human Cells.

Christin A Albus, Rolando Berlinguer-Palmini, Caroline Hewison, Fiona McFarlane, Elisabeta-Ana Savu, Robert N Lightowlers, Zofia M Chrzanowska-Lightowlers, Matthew Zorkau.

  Human mitochondria are highly dynamic organelles, fusing and budding to maintain reticular networks throughout many cell types. Although extending to the extremities of the cell, the majority of the network is concentrated around the nucleus in most of the commonly cultured cell lines. This organelle harbours its own genome, mtDNA, with a different gene content to the nucleus, but the expression of which is critical for maintaining oxidative phosphorylation. Recent advances in click chemistry have allowed us to visualise sites of mitochondrial protein synthesis in intact cultured cells. We show that the majority of translation occurs in the peri-nuclear region of the network. Further analysis reveals that whilst there is a slight peri-nuclear enrichment in the levels of mitoribosomal protein and mitochondrial rRNA, it is not sufficient to explain this substantial heterogeneity in the distribution of translation. Finally, we also show that in contrast, a mitochondrial mRNA does not show such a distinct gradient in distribution. These data suggest that the relative lack of translation in the peripheral mitochondrial network is not due to an absence of mitoribosomes or an insufficient supply of the mt-mRNA transcripts.

Keywords:  co-localisation; heterogeneity; mammalian; mitochondria; peri-nuclear; peripheral; protein synthesis

DOI:  https://doi.org/10.3390/biology10101050
Mitochondrion. 2021 Oct 14. pii: S1567-7249(21)00142-2. [Epub ahead of print]

Identification of a Novel m.3955G>A Variant in MT-ND1 Associated with Leigh Syndrome.

Manting Xu, Robert Kopajtich, Matthias Elstner, Hua Li, Zhimei Liu, Junling Wang, Holger Prokisch, Fang Fang.

  Leigh syndrome (LS) is one of the most common mitochondrial diseases in children, for which at least 90 causative genes have been identified. However, many LS patients have no genetic diagnosis, indicating that more disease-related genes remain to be identified. In this study, we identified a novel variant, m.3955G>A, in mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) in two unrelated LS patients, manifesting as infancy-onset frequent seizures, neurodegeneration, elevated lactate levels, and bilateral symmetrical lesions in the brainstem, basal ganglia, and thalamus. Transfer of the mutant mtDNA with m.3955G>A into cybrids disturbed the MT-ND1 expression and CI assembly, followed by remarkable mitochondrial dysfunction, reactive oxygen species production, and mitochondrial membrane potential reduction. Our findings demonstrated the pathogenicity of the novel m.3955G>A variant, and extend the spectrum of pathogenic mtDNA variants.

Keywords:  Leigh syndrome; MT-ND1; Novel mitochondrial DNA variant; cybrid cells

DOI:  https://doi.org/10.1016/j.mito.2021.10.002
Cell. 2021 Oct 11. pii: S0092-8674(21)01116-8. [Epub ahead of print]

An in vitro system to silence mitochondrial gene expression.

Luis Daniel Cruz-Zaragoza, Sven Dennerlein, Andreas Linden, Roya Yousefi, Elena Lavdovskaia, Abhishek Aich, Rebecca R Falk, Ridhima Gomkale, Thomas Schöndorf, Markus T Bohnsack, Ricarda Richter-Dennerlein, Henning Urlaub, Peter Rehling.

  The human mitochondrial genome encodes thirteen core subunits of the oxidative phosphorylation system, and defects in mitochondrial gene expression lead to severe neuromuscular disorders. However, the mechanisms of mitochondrial gene expression remain poorly understood due to a lack of experimental approaches to analyze these processes. Here, we present an in vitro system to silence translation in purified mitochondria. In vitro import of chemically synthesized precursor-morpholino hybrids allows us to target translation of individual mitochondrial mRNAs. By applying this approach, we conclude that the bicistronic, overlapping ATP8/ATP6 transcript is translated through a single ribosome/mRNA engagement. We show that recruitment of COX1 assembly factors to translating ribosomes depends on nascent chain formation. By defining mRNA-specific interactomes for COX1 and COX2, we reveal an unexpected function of the cytosolic oncofetal IGF2BP1, an RNA-binding protein, in mitochondrial translation. Our data provide insight into mitochondrial translation and innovative strategies to investigate mitochondrial gene expression.

Keywords:  IGF2BP1; antisense; mitochondria; mitochondrial ribosome; morpholino; oxidative phosphorylation; translation

DOI:  https://doi.org/10.1016/j.cell.2021.09.033
Genes (Basel). 2021 Oct 12. pii: 1604. [Epub ahead of print]12(10):

Interrogating Mitochondrial Biology and Disease Using CRISPR/Cas9 Gene Editing.

Jia-Xin Tang, Angela Pyle, Robert W Taylor, Monika Oláhová.

  Mitochondrial disease originates from genetic changes that impact human bodily functions by disrupting the mitochondrial oxidative phosphorylation system. MitoCarta is a curated and published inventory that sheds light on the mitochondrial proteome, but the function of some mitochondrially-localised proteins remains poorly characterised. Consequently, various gene editing systems have been employed to uncover the involvement of these proteins in mitochondrial biology and disease. CRISPR/Cas9 is an efficient, versatile, and highly accurate genome editing tool that was first introduced over a decade ago and has since become an indispensable tool for targeted genetic manipulation in biological research. The broad spectrum of CRISPR/Cas9 applications serves as an attractive and tractable system to study genes and pathways that are essential for the regulation and maintenance of mitochondrial health. It has opened possibilities of generating reliable cell and animal models of human disease, and with further exploitation of the technology, large-scale genomic screenings have uncovered a wealth of fundamental mechanistic insights. In this review, we describe the applications of CRISPR/Cas9 system as a genome editing tool to uncover new insights into pathomechanisms of mitochondrial diseases and/or biological processes involved in mitochondrial function.

Keywords:  CRISPR/Cas9; cell and animal models; genome editing; genome-wide CRISPR libraries screening; mitochondrial biology; mitochondrial disease

DOI:  https://doi.org/10.3390/genes12101604
Chembiochem. 2021 Oct 18.

Research progress on the physiological function of mtDNA and its specific detection and therapy.

Congcong Zhang, Yufei Xue, Lan Wang, Qiong Wu, Bin Fang, Yu Shen, Hua Bai, Bo Peng, Naidi Yang, Lin Li.

  Mitochondrial DNA (mtDNA) is a mitochondrial genetic material, which is a circular double-stranded deoxyribonucleotide found in the mitochondria of cells. Despite the diminutive size of mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases that are characterized by defects in oxidative phosphorylation. Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is further complicated since mtDNA mutations can cause various clinical symptoms. To obtain more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on mtDNA are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, detection and their applications in mechanisms exploration and treatment of mtDNA mutation-related disorders. Noting that we specifically discuss how these probes and drugs for mtDNA are designed and developed. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.

Keywords:  DNA targeting; Fluorescent probes; Mitochondrial DNA; mitochondrial dysfunction; mitochondrial therapy

DOI:  https://doi.org/10.1002/cbic.202100474
Intern Med. 2021 Oct 19.

Adult-Onset Leigh Syndrome due to an m.13513G>A Mutation.

Hiroaki Hirosawa, Takamasa Nukui, Kyo Noguchi, Yuji Nakatsuji.



Keywords:  Leigh syndrome; mitochondrial disease; renal failure

DOI:  https://doi.org/10.2169/internalmedicine.8445-21
Biomedicines. 2021 Oct 01. pii: 1364. [Epub ahead of print]9(10):

Human Mitochondrial DNA: Particularities and Diseases.

Mouna Habbane, Julio Montoya, Taha Rhouda, Yousra Sbaoui, Driss Radallah, Sonia Emperador.

  Mitochondria are the cell's power site, transforming energy into a form that the cell can employ for necessary metabolic reactions. These organelles present their own DNA. Although it codes for a small number of genes, mutations in mtDNA are common. Molecular genetics diagnosis allows the analysis of DNA in several areas such as infectiology, oncology, human genetics and personalized medicine. Knowing that the mitochondrial DNA is subject to several mutations which have a direct impact on the metabolism of the mitochondrion leading to many diseases, it is therefore necessary to detect these mutations in the patients involved. To date numerous mitochondrial mutations have been described in humans, permitting confirmation of clinical diagnosis, in addition to a better management of the patients. Therefore, different techniques are employed to study the presence or absence of mitochondrial mutations. However, new mutations are discovered, and to determine if they are the cause of disease, different functional mitochondrial studies are undertaken using transmitochondrial cybrid cells that are constructed by fusion of platelets of the patient that presents the mutation, with rho osteosarcoma cell line. Moreover, the contribution of next generation sequencing allows sequencing of the entire human genome within a single day and should be considered in the diagnosis of mitochondrial mutations.

Keywords:  mitochondrial diseases; molecular diagnosis; mtDNA; mutation

DOI:  https://doi.org/10.3390/biomedicines9101364
Methods Mol Biol. 2021 Oct 21.

Creating Cell Model 2.0 Using Patient Samples Carrying a Pathogenic Mitochondrial DNA Mutation: iPSC Approach for LHON.

Pragya Singh, Tyler Bahr, Xiaoxu Zhao, Peiqing Hu, Marcel Daadi, TaoSheng Huang, Yidong Bai.

  Leber's Hereditary Optic Neuropathy is the most prevalent mitochondrial neurological disease caused by mutations in mitochondrial DNA encoded respiratory complex I subunits. Although the genetic origin for Leber's hereditary optic neuropathy was identified about 30 years ago, the underlying pathogenesis is still unclear primarily due to the lack of a relevant system or cell model. Current models are limited to lymphoblasts, fibroblasts, or cybrid cell lines. As the disease phenotype is limited to retinal ganglion cells, induced pluripotent stem cells will serve as an excellent model for studying this tissue-specific disease, elucidating its underlying molecular mechanisms, and identifying novel therapeutic targets. Here, we describe a detailed protocol for the generation of retinal ganglion cells, and also cardiomyocytes for proof of iPSC pluripotency.

Keywords:  Induced pluripotent stem cell; LHON; Retinal ganglion cells; mtDNA

DOI:  https://doi.org/10.1007/7651_2021_384
EMBO J. 2021 Oct 18. e108428

Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane.

Yang Xu, Hediye Erdjument-Bromage, Colin K L Phoon, Thomas A Neubert, Mindong Ren, Michael Schlame.

  Mitochondrial cristae are extraordinarily crowded with proteins, which puts stress on the bilayer organization of lipids. We tested the hypothesis that the high concentration of proteins drives the tafazzin-catalyzed remodeling of fatty acids in cardiolipin, thereby reducing bilayer stress in the membrane. Specifically, we tested whether protein crowding induces cardiolipin remodeling and whether the lack of cardiolipin remodeling prevents the membrane from accumulating proteins. In vitro, the incorporation of large amounts of proteins into liposomes altered the outcome of the remodeling reaction. In yeast, the concentration of proteins involved in oxidative phosphorylation (OXPHOS) correlated with the cardiolipin composition. Genetic ablation of either remodeling or biosynthesis of cardiolipin caused a substantial drop in the surface density of OXPHOS proteins in the inner membrane of the mouse heart and Drosophila flight muscle mitochondria. Our data suggest that OXPHOS protein crowding induces cardiolipin remodelling and that remodeled cardiolipin supports the high concentration of these proteins in the inner mitochondrial membrane.

Keywords:  Barth syndrome; lipid-protein interaction; macromolecular crowding; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.15252/embj.2021108428
Metabolites. 2021 Sep 28. pii: 658. [Epub ahead of print]11(10):

Sub-Cellular Metabolomics Contributes Mitochondria-Specific Metabolic Insights to a Mouse Model of Leigh Syndrome.

Gunter van der Walt, Jeremie Z Lindeque, Shayne Mason, Roan Louw.

  Direct injury of mitochondrial respiratory chain (RC) complex I by Ndufs4 subunit mutations results in complex I deficiency (CID) and a progressive encephalomyopathy, known as Leigh syndrome. While mitochondrial, cytosolic and multi-organelle pathways are known to be involved in the neuromuscular LS pathogenesis, compartment-specific metabolomics has, to date, not been applied to murine models of CID. We thus hypothesized that sub-cellular metabolomics would be able to contribute organelle-specific insights to known Ndufs4 metabolic perturbations. To that end, whole brains and skeletal muscle from late-stage Ndufs4 mice and age/sex-matched controls were harvested for mitochondrial and cytosolic isolation. Untargeted 1H-NMR and semi-targeted LC-MS/MS metabolomics was applied to the resulting cell fractions, whereafter important variables (VIPs) were selected by univariate statistics. A predominant increase in multiple targeted amino acids was observed in whole-brain samples, with a more prominent effect at the mitochondrial level. Similar pathways were implicated in the muscle tissue, showing a greater depletion of core metabolites with a compartment-specific distribution, however. The altered metabolites expectedly implicate altered redox homeostasis, alternate RC fueling, one-carbon metabolism, urea cycling and dysregulated proteostasis to different degrees in the analyzed tissues. A first application of EDTA-chelated magnesium and calcium measurement by NMR also revealed tissue- and compartment-specific alterations, implicating stress response-related calcium redistribution between neural cell compartments, as well as whole-cell muscle magnesium depletion. Altogether, these results confirm the ability of compartment-specific metabolomics to capture known alterations related to Ndufs4 KO and CID while proving its worth in elucidating metabolic compartmentalization in said pathways that went undetected in the diluted whole-cell samples previously studied.

Keywords:  1H-NMR; LC-MS/MS; Ndufs4; complex I deficiency; cytosol; metabolomics; mitochondria; mitochondrial disease; sub-cellular metabolomics

DOI:  https://doi.org/10.3390/metabo11100658
Curr Opin Neurobiol. 2021 Oct 13. pii: S0959-4388(21)00107-0. [Epub ahead of print]72 80-90

On the dynamic and even reversible nature of Leigh syndrome: Lessons from human imaging and mouse models.

Melissa A Walker, Maria Miranda, Amanda Allred, Vamsi K Mootha.

Leigh syndrome (LS) is a neurodegenerative disease characterized by bilaterally symmetric brainstem or basal ganglia lesions. More than 80 genes, largely impacting mitochondrial energy metabolism, can underlie LS, and no approved medicines exist. Described 70 years ago, LS was initially diagnosed by the characteristic, necrotic lesions on autopsy. It has been broadly assumed that antemortem neuroimaging abnormalities in these regions correspond to end-stage histopathology. However, clinical observations and animal studies suggest that neuroimaging findings may represent an intermediate state, that is more dynamic than previously appreciated, and even reversible. We review this literature, discuss related conditions that are treatable, and present two new LS cases with radiographic improvement. We review studies in which hypoxia reverses advanced LS in a mouse model. The fluctuating and potentially reversible nature of radiographic LS lesions will be important in clinical trial design. Better understanding of this plasticity could lead to new therapies.

DOI: https://doi.org/10.1016/j.conb.2021.09.006