bims-cytox1 2021-03-21 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2021–03–21
fourteen papers selected by
Gavin McStay, Staffordshire University

SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells.
Functional segmentation of CoQ and cyt c pools by respiratory complex superassembly.
Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation.
Clinical and molecular characterization of mitochondrial DNA disorders in a group of Argentinian pediatric patients.
Uniparental isodisomy of chromosome 2 causing MRPL44-related multisystem mitochondrial disease.
DNAJC30 biallelic mutations extend mitochondrial complex I-deficient phenotypes to include recessive Leber's hereditary optic neuropathy.
A nuclear-based quality control pathway for non-imported mitochondrial proteins.
m.3243A>G carriers develop syndromic or non-syndromic multisystem phenotypes over time.
Peroxisomal-derived ether phospholipids link nucleotides to respirasome assembly.
Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.
The mitochondrial intermembrane space: the most constricted mitochondrial sub-compartment with the largest variety of protein import pathways.
Leigh Syndrome as a Phenotype of Near-Homoplasmic m.8344 A>G Variant in Children.
Nuclear genome-wide associations with mitochondrial heteroplasmy.
Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution.

Biochim Biophys Acta Bioenerg. 2021 Mar 13. pii: S0005-2728(21)00047-5. [Epub ahead of print] 148414

SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells.

Erika Fernández-Vizarra, Sandra López-Calcerrada, Luke E Formosa, Rafael Pérez-Pérez, Shujing Ding, Ian M Fearnley, Joaquín Arenas, Miguel A Martín, Massimo Zeviani, Michael T Ryan, Cristina Ugalde.

  The study of the mitochondrial respiratory chain (MRC) function in relation with its structural organization is of great interest due to the central role of this system in eukaryotic cell metabolism. The complexome profiling technique has provided invaluable information for our understanding of the composition and assembly of the individual MRC complexes, and also of their association into larger supercomplexes (SCs) and respirasomes. The formation of the SCs has been highly debated, and their assembly and regulation mechanisms are still unclear. Previous studies demonstrated a prominent role for COX7A2L (SCAFI) as a structural protein bridging the association of individual MRC complexes III and IV in the minor SC III2 + IV, although its relevance for respirasome formation and function remains controversial. In this work, we have used SILAC-based complexome profiling to dissect the structural organization of the human MRC in HEK293T cells depleted of SCAFI (SCAFIKO) by CRISPR-Cas9 genome editing. SCAFI ablation led to a preferential loss of SC III2 + IV and of a minor subset of respirasomes without affecting OXPHOS function. Our data suggest that the loss of SCAFI-dependent respirasomes in SCAFIKO cells is mainly due to alterations on early stages of CI assembly, without impacting the biogenesis of complexes III and IV. Contrary to the idea of SCAFI being the main player in respirasome formation, SILAC-complexome profiling showed that, in wild-type cells, the majority of respirasomes (ca. 70%) contained COX7A2 and that these species were present at roughly the same levels when SCAFI was knocked-out. We thus demonstrate the co-existence of structurally distinct respirasomes defined by the preferential binding of complex IV via COX7A2, rather than SCAFI, in human cultured cells.

Keywords:  COX7A2; COX7A2L/SCAFI; Mitochondria; oxidative phosphorylation; respiratory chain; respiratory supercomplexes

DOI:  https://doi.org/10.1016/j.bbabio.2021.148414
Free Radic Biol Med. 2021 Mar 12. pii: S0891-5849(21)00162-3. [Epub ahead of print]

Functional segmentation of CoQ and cyt c pools by respiratory complex superassembly.

Pablo Hernansanz-Agustín, José Antonio Enríquez.

  Electron transfer between respiratory complexes is an essential step for the efficiency of the mitochondrial oxidative phosphorylation. Until recently, it was stablished that ubiquinone and cytochrome c formed homogenous single pools in the inner mitochondrial membrane which were not influenced by the presence of respiratory supercomplexes. However, this idea was challenged by the fact that bottlenecks in electron transfer appeared after disruption of supercomplexes into their individual complexes. The postulation of the plasticity model embraced all these observations and concluded that complexes and supercomplexes co-exist and are dedicated to a spectrum of metabolic requirements. Here, we review the involvement of superassembly in complex I stability, the role of supercomplexes in ROS production and the segmentation of the CoQ and cyt c pools, together with their involvement in signaling and disease. Taking apparently conflicting literature we have built up a comprehensive model for the segmentation of CoQ and cyt c mediated by supercomplexes, discuss the current limitations and provide a prospect of the current knowledge in the field.

Keywords:  CoQ; cyt c; pools; respirasomes; supercomplexes

DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.03.010
Hum Mutat. 2021 Mar 14.

Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation.

Alessandra Torraco, Alessia Nasca, Daniela Verrigni, Alessandra Pennisi, Maha S Zaki, Giorgia Olivieri, Zahra Assouline, Diego Martinelli, Reza Maroofian, Teresa Rizza, Michela Di Nottia, Federica Invernizzi, Eleonora Lamantea, Daniela Longo, Henry Houlden, Holger Prokisch, Agnès Rötig, Carlo Dionisi-Vici, Enrico Bertini, Daniele Ghezzi, Rosalba Carrozzo, Daria Diodato.

  Isolated biochemical deficiency of mitochondrial complex I is the most frequent signature amongst mitochondrial diseases and is associated with a wide variety of clinical symptoms. Leigh syndrome represents the most frequent neuroradiological finding in patients with complex I defect and >80 monogenic causes have been involved in the disease. In this report, we describe 7 patients from four unrelated families harbouring novel NDUFA12 variants, 6 of them presenting with Leigh syndrome. Molecular genetic characterization was performed using next generation sequencing combined with the Sanger method. Biochemical and protein studies were achieved by enzymatic activities, blue native gel electrophoresis and Western blotting. All patients displayed novel homozygous mutations in the NDUFA12 gene leading to the virtual absence of the corresponding protein. Surprisingly, despite in none of the analyzed patients NDUFA12 protein was detected, they present a different onset and clinical course of the disease. Our report expands the array of genetic alterations in NDUFA12 and underlines phenotype variability associated with NDUFA12 defect. This article is protected by copyright. All rights reserved.

Keywords:  Leigh syndrome; NADH ubiquinone oxidoreductase; NDUFA12; mitochondrial disease

DOI:  https://doi.org/10.1002/humu.24195
Mol Genet Metab Rep. 2021 Jun;27 100733

Clinical and molecular characterization of mitochondrial DNA disorders in a group of Argentinian pediatric patients.

Mariana Amina Loos, Gimena Gomez, Lía Mayorga, Roberto Horacio Caraballo, Hernán Diego Eiroa, María Gabriela Obregon, Carlos Rugilo, Fabiana Lubieniecki, Ana Lía Taratuto, María Saccoliti, Cristina Noemi Alonso, Hilda Verónica Aráoz.

   Objective: To describe the clinical and molecular features of a group of Argentinian pediatric patients with mitochondrial DNA (mtDNA) disorders, and to evaluate the results of the implementation of a classical approach for the molecular diagnosis of mitochondrial diseases.
Methods: Clinical data from 27 patients with confirmed mtDNA pathogenic variants were obtained from a database of 89 patients with suspected mitochondrial disease, registered from 2014 to 2020. Clinical data, biochemical analysis, neuroimaging findings, muscle biopsy and molecular studies were analyzed.
Results: Patients were 18 females and 9 males, with ages at onset ranging from 1 week to 14 years (median = 4 years). The clinical phenotypes were: mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome (n = 11), Leigh syndrome (n = 5), Kearns-Sayre syndrome (n = 3), Chronic Progressive External Ophthalmoplegia (n = 2), Leber hereditary optic neuropathy (n = 2), myoclonic epilepsy associated with ragged-red fibers (n = 1) and reversible infantile myopathy with cytochrome-C oxidase deficiency (n = 3). Most of the patients harbored pathogenic single nucleotide variants, mainly involving mt-tRNA genes, such as MT-TL1, MT-TE and MT-TK. Other point variants were found in complex I subunits, like MT-ND6, MT-ND4, MT-ND5; or in MT-ATP6. The m.13513G > A variant in MT-ND5 and the m.9185 T > C variant in MT-ATP6 were apparently de novo. The rest of the patients presented large scale-rearrangements, either the "common" deletion or a larger deletion.
Conclusions: This study highlights the clinical and genetic heterogeneity of pediatric mtDNA disorders. All the cases presented with classical phenotypes, being MELAS the most frequent. Applying classical molecular methods, it was possible to achieve a genetic diagnosis in 30% of the cases, suggesting that this is an effective first approach, especially for those centers from low-middle income countries, leaving NGS studies for those patients with inconclusive results.

Keywords:  Leigh syndrome; MELAS; Mitochondrial DNA; Mitochondrial diseases; Molecular diagnosis; Pediatrics

DOI:  https://doi.org/10.1016/j.ymgmr.2021.100733
Mol Biol Rep. 2021 Mar 19.

Uniparental isodisomy of chromosome 2 causing MRPL44-related multisystem mitochondrial disease.

Alejandro Horga, Andreea Manole, Alice L Mitchell, Enrico Bugiardini, Iain P Hargreaves, Walied Mowafi, Conceição Bettencourt, Emma L Blakely, Langping He, James M Polke, Catherine E Woodward, Ilaria Dalla Rosa, Sachit Shah, Alan M Pittman, Ros Quinlivan, Mary M Reilly, Robert W Taylor, Ian J Holt, Michael G Hanna, Robert D S Pitceathly, Antonella Spinazzola, Henry Houlden.

  Mutations in nuclear-encoded protein subunits of the mitochondrial ribosome are an increasingly recognised cause of oxidative phosphorylation system (OXPHOS) disorders. Among them, mutations in the MRPL44 gene, encoding a structural protein of the large subunit of the mitochondrial ribosome, have been identified in four patients with OXPHOS defects and early-onset hypertrophic cardiomyopathy with or without additional clinical features. A 23-year-old individual with cardiac and skeletal myopathy, neurological involvement, and combined deficiency of OXPHOS complexes in skeletal muscle was clinically and genetically investigated. Analysis of whole-exome sequencing data revealed a homozygous mutation in MRPL44 (c.467 T > G), which was not present in the biological father, and a region of homozygosity involving most of chromosome 2, raising the possibility of uniparental disomy. Short-tandem repeat and genome-wide SNP microarray analyses of the family trio confirmed complete maternal uniparental isodisomy of chromosome 2. Mitochondrial ribosome assembly and mitochondrial translation were assessed in patient derived-fibroblasts. These studies confirmed that c.467 T > G affects the stability or assembly of the large subunit of the mitochondrial ribosome, leading to impaired mitochondrial protein synthesis and decreased levels of multiple OXPHOS components. This study provides evidence of complete maternal uniparental isodisomy of chromosome 2 in a patient with MRPL44-related disease, and confirms that MRLP44 mutations cause a mitochondrial translation defect that may present as a multisystem disorder with neurological involvement.

Keywords:  MRPL44; Mitochondrial disease; Oxidative phosphorylation; Uniparental disomy; Whole-exome sequencing

DOI:  https://doi.org/10.1007/s11033-021-06188-1
J Clin Invest. 2021 Mar 15. pii: 147734. [Epub ahead of print]131(6):

DNAJC30 biallelic mutations extend mitochondrial complex I-deficient phenotypes to include recessive Leber's hereditary optic neuropathy.

Janey L Wiggs.

Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disease and in most cases is caused by mutations in mitochondrial DNA-encoded (mtDNA-encoded) respiratory complex I subunit ND1, ND4, or ND6. In this issue of the JCI, Stenton et al. describe biallelic mutations in a nuclear DNA-encoded gene, DNAJC30, establishing recessively inherited LHON (arLHON). Functional studies suggest that DNAJC30 is a protein chaperone required for exchange of damaged complex I subunits. Hallmark mtDNA LHON features were also found in arLHON, including incomplete penetrance, male predominance, and positive response to idebenone therapy. These results extend complex I-deficient phenotypes to include recessively inherited optic neuropathy, with important clinical implications for genetic counseling and therapeutic considerations.

DOI: https://doi.org/10.1172/JCI147734
Elife. 2021 Mar 18. pii: e61230. [Epub ahead of print]10

A nuclear-based quality control pathway for non-imported mitochondrial proteins.

Viplendra Ps Shakya, William A Barbeau, Tianyao Xiao, Christina S Knutson, Max H Schuler, Adam L Hughes.

  Mitochondrial import deficiency causes cellular toxicity due to the accumulation of non-imported mitochondrial precursor proteins, termed mitoprotein-induced stress. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we cataloged the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment in S. cerevisiae. We found that a number of non-imported mitochondrial proteins localize to the nucleus, where they are subjected to proteasome-dependent degradation through a process we term nuclear-associated mitoprotein degradation (mitoNUC). Recognition and destruction of mitochondrial precursors by the mitoNUC pathway requires the presence of an N-terminal mitochondrial targeting sequence (MTS) and is mediated by combined action of the E3 ubiquitin ligases San1, Ubr1, and Doa10. Impaired breakdown of precursors leads to alternative sequestration in nuclear-associated foci. These results identify the nucleus as an important destination for the disposal of non-imported mitochondrial precursors.

Keywords:  S. cerevisiae; cell biology

DOI:  https://doi.org/10.7554/eLife.61230
CEN Case Rep. 2021 Mar 18.

m.3243A>G carriers develop syndromic or non-syndromic multisystem phenotypes over time.

J Finsterer.



Keywords:  Heteroplasmy; MELAS; Mitochondrial disorder; Myopathy; Respiratory chain; m.3243A>G

DOI:  https://doi.org/10.1007/s13730-021-00591-0
Nat Chem Biol. 2021 Mar 15.

Peroxisomal-derived ether phospholipids link nucleotides to respirasome assembly.

Christopher F Bennett, Katherine E O'Malley, Elizabeth A Perry, Eduardo Balsa, Pedro Latorre-Muro, Christopher L Riley, Chi Luo, Mark Jedrychowski, Steven P Gygi, Pere Puigserver.

The protein complexes of the mitochondrial electron transport chain exist in isolation and in higher order assemblies termed supercomplexes (SCs) or respirasomes (SC I+III2+IV). The association of complexes I, III and IV into the respirasome is regulated by unknown mechanisms. Here, we designed a nanoluciferase complementation reporter for complex III and IV proximity to determine in vivo respirasome levels. In a chemical screen, we found that inhibitors of the de novo pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH) potently increased respirasome assembly and activity. By-passing DHODH inhibition via uridine supplementation decreases SC assembly by altering mitochondrial phospholipid composition, specifically elevated peroxisomal-derived ether phospholipids. Cell growth rates upon DHODH inhibition depend on ether lipid synthesis and SC assembly. These data reveal that nucleotide pools signal to peroxisomes to modulate synthesis and transport of ether phospholipids to mitochondria for SC assembly, which are necessary for optimal cell growth in conditions of nucleotide limitation.

DOI: https://doi.org/10.1038/s41589-021-00772-z
Neurol Genet. 2021 Apr;7(2): e566

Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.

Helene Bruhn, Kristin Samuelsson, Florian A Schober, Martin Engvall, Nicole Lesko, Rolf Wibom, Inger Nennesmo, Javier Calvo-Garrido, Rayomand Press, Henrik Stranneheim, Christoph Freyer, Anna Wedell, Anna Wredenberg.

Objective: To investigate the pathogenicity of a novel MT-ND3 mutation identified in a patient with adult-onset sensorimotor axonal polyneuropathy and report the clinical, morphologic, and biochemical findings.
Methods: Clinical assessments and morphologic and biochemical investigations of skeletal muscle and cultured myoblasts from the patient were performed. Whole-genome sequencing (WGS) of DNA from skeletal muscle and Sanger sequencing of mitochondrial DNA (mtDNA) from both skeletal muscle and cultured myoblasts were performed. Heteroplasmic levels of mutated mtDNA in different tissues were quantified by last-cycle hot PCR.
Results: Muscle showed ragged red fibers, paracrystalline inclusions, a significant reduction in complex I (CI) respiratory chain (RC) activity, and decreased adenosine triphosphate (ATP) production for all substrates used by CI. Sanger sequencing of DNA from skeletal muscle detected a unique previously unreported heteroplasmic mutation in mtDNA encoded MT-ND3, coding for a subunit in CI. WGS confirmed the mtDNA mutation but did not detect any other mutation explaining the disease. Cultured myoblasts, however, did not carry the mutation, and RC activity measurements in myoblasts were normal.
Conclusions: We report a case with adult-onset sensorimotor axonal polyneuropathy caused by a novel mtDNA mutation in MT-ND3. Loss of heteroplasmy in blood, cultured fibroblasts and myoblasts from the patient, and normal measurement of RC activity of the myoblasts support pathogenicity of the mutation. These findings highlight the importance of mitochondrial investigations in patients presenting with seemingly idiopathic polyneuropathy, especially if muscle also is affected.

DOI: https://doi.org/10.1212/NXG.0000000000000566
Open Biol. 2021 Mar;11(3): 210002

The mitochondrial intermembrane space: the most constricted mitochondrial sub-compartment with the largest variety of protein import pathways.

Ruairidh Edwards, Ross Eaglesfield, Kostas Tokatlidis.

  The mitochondrial intermembrane space (IMS) is the most constricted sub-mitochondrial compartment, housing only about 5% of the mitochondrial proteome, and yet is endowed with the largest variability of protein import mechanisms. In this review, we summarize our current knowledge of the major IMS import pathway based on the oxidative protein folding pathway and discuss the stunning variability of other IMS protein import pathways. As IMS-localized proteins only have to cross the outer mitochondrial membrane, they do not require energy sources like ATP hydrolysis in the mitochondrial matrix or the inner membrane electrochemical potential which are critical for import into the matrix or insertion into the inner membrane. We also explore several atypical IMS import pathways that are still not very well understood and are guided by poorly defined or completely unknown targeting peptides. Importantly, many of the IMS proteins are linked to several human diseases, and it is therefore crucial to understand how they reach their normal site of function in the IMS. In the final part of this review, we discuss current understanding of how such IMS protein underpin a large spectrum of human disorders.

Keywords:  intermembrane space; mitochondria; oxidative protein folding; protein import

DOI:  https://doi.org/10.1098/rsob.210002
Child Neurol Open. 2021 Jan-Dec;8:8 2329048X21991382

Leigh Syndrome as a Phenotype of Near-Homoplasmic m.8344 A>G Variant in Children.

Sam Nicholas Russo, Amy Goldstein, Amel Karaa, Mary Kay Koenig, Melissa Walker.

  In the field of mitochondrial medicine, correlation of clinical phenotype with mutation heteroplasmy remains an outstanding question with few, if any, clear thresholds corresponding to a given phenotype. The m.8344A>G mutation is most commonly associated with myoclonus epilepsy and ragged red fiber syndrome (MERRF) at varying levels of heteroplasmy. However, a handful of cases been previously reported in which individuals homoplasmic or nearly homoplasmic for this mutation in the blood have presented with multiple bulbar palsies, respiratory failure, and progressive neurologic decline almost uniformly following a respiratory illness. MRI brain in all affected individuals revealed symmetric T2 hyperintense lesions of subcortical gray matter structures, consistent with Leigh syndrome. Here, we present 3 cases with clinical, biochemical, and neuro-imaging findings with the additional reporting of spinal lesions. This new phenotype supports a heteroplasmy-dependent phenotype model for this mutation and recognition of this can help clinicians with diagnosis and anticipatory clinical guidance.

Keywords:  Leigh syndrome; MERRF; heteroplasmy; homoplasmy; mitochondria; phenotype

DOI:  https://doi.org/10.1177/2329048X21991382
Sci Adv. 2021 Mar;pii: eabe7520. [Epub ahead of print]7(12):

Nuclear genome-wide associations with mitochondrial heteroplasmy.

23andMe Research Team

The role of the nuclear genome in maintaining the stability of the mitochondrial genome (mtDNA) is incompletely known. mtDNA sequence variants can exist in a state of heteroplasmy, which denotes the coexistence of organellar genomes with different sequences. Heteroplasmic variants that impair mitochondrial capacity cause disease, and the state of heteroplasmy itself is deleterious. However, mitochondrial heteroplasmy may provide an intermediate state in the emergence of novel mitochondrial haplogroups. We used genome-wide genotyping data from 982,072 European ancestry individuals to evaluate variation in mitochondrial heteroplasmy and to identify the regions of the nuclear genome that affect it. Age, sex, and mitochondrial haplogroup were associated with the extent of heteroplasmy. GWAS identified 20 loci for heteroplasmy that exceeded genome-wide significance. This included a region overlapping mitochondrial transcription factor A (TFAM), which has multiple roles in mtDNA packaging, replication, and transcription. These results show that mitochondrial heteroplasmy has a heritable nuclear component.

DOI: https://doi.org/10.1126/sciadv.abe7520
Bioessays. 2021 Mar 17. e2100009

Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution.

Arunas Radzvilavicius.

  "Selfish" gene theories have offered invaluable insight into eukaryotic genome evolution, but they can also be misleading. The "selfish mitochondrion" hypothesis, developed in the 90s explained uniparental organelle inheritance as a mechanism of conflict resolution, improving cooperation between genetically distinct compartments of the cell. But modern population genetic models provided a more general explanation for uniparental inheritance based on mutational variance redistribution, modulating the efficiency of both purifying and adaptive selection. Nevertheless, as reviewed here, "selfish" conflict theories still dominate the literature. While these hypotheses are rich in metaphor and highly intuitive, selective focus on only one type of mitochondrial mutation limits the generality of our understanding and hinders progress in mito-nuclear evolution theory. Recognizing that uniparental inheritance may have evolved-and is maintained across the eukaryotic tree of life-because of its influence on mutational variance and improved selection will only increase the generality of our evolutionary reasoning, retaining "selfish" conflict explanations as a special case of a much broader theory.

Keywords:  evolution; selfish mitochondria; uniparental inheritance

DOI:  https://doi.org/10.1002/bies.202100009