bims-cytox1 2018-12-16 papers

bims-cytox1

Biomed News

on Cytochrome oxidase subunit 1

Issue of 2018–12–16
23 papers selected by
Gavin McStay, Staffordshire University

Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease.
A coronary artery disease-associated tRNAThr mutation altered mitochondrial function, apoptosis and angiogenesis.
Mitochondrial RNA Expression and Single Nucleotide Variants in Association with Clinical Parameters in Primary Breast Cancers.
Diagnosis, management, and follow-up of mitochondrial disorders in childhood: a personalized medicine in the new era of genome sequence.
Whole sequence of the mitochondrial DNA genome of Kearns Sayre Syndrome patients: Identification of deletions and variants.
Schizophrenia-associated mt-DNA SNPs exhibit highly variable haplogroup affiliation and nuclear ancestry: Bi-genomic dependence raises major concerns for link to disease.
Heteroplasmy Detection of Mitochondrial DNA A3243G Mutation Using Quantitative Real-Time PCR Assay Based on TaqMan-MGB Probes.
Quantification of Mitochondrial Genome Transcription in Male Reproductive Cells by Real-Time PCR.
NDUFV2 pseudogene (NDUFV2P1) contributes to mitochondrial complex I deficits in schizophrenia.
MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo.
Roles of the mitochondrial genetics in cancer metastasis: not to be ignored any longer.
Targeting of the respiratory chain by toxicants: beyond the toxicities to mitochondrial morphology.
Mitochondrial polymorphisms contribute to aging phenotypes in MNX mouse models.
Reduced Levels of ATP Synthase Subunit ATP5F1A Correlate with Earlier-Onset Prostate Cancer.
Temporal profile of serum mitochondrial DNA (mtDNA) in patients with aneurysmal subarachnoid hemorrhage (aSAH).
Clinical application of plasma mitochondrial DNA content in patients with lung cancer.
The mammalian mitochondrial epitranscriptome.
Elucidating the contribution of ETC complexes I and II to the respirasome formation in cardiac mitochondria.
Loss of Mitochondrial AAA Proteases AFG3L2 and YME1L Impairs Mitochondrial Structure and Respiratory Chain Biogenesis.
APOPT1/COA8 assists COX assembly and is oppositely regulated by UPS and ROS.
Mitochondrial DNA mutation m.3243A>G is associated with altered mitochondrial function in peripheral blood mononuclear cells, with heteroplasmy levels and with clinical phenotypes.
Mitochondrial gene sequence variants in children with severe malaria anaemia with or without lactic acidosis: a case control study.
Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase.

Oxid Med Cell Longev. 2018 ;2018 1435934

Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease.

María Gómez-Serrano, Emilio Camafeita, Marta Loureiro, Belén Peral.

Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.

DOI: https://doi.org/10.1155/2018/1435934
Nucleic Acids Res. 2018 Dec 12.

A coronary artery disease-associated tRNAThr mutation altered mitochondrial function, apoptosis and angiogenesis.

Zidong Jia, Ye Zhang, Qiang Li, Zhenzhen Ye, Yuqi Liu, Changzhu Fu, Xiaohui Cang, Meng Wang, Min-Xin Guan.

The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon stem of tRNAThr. Using molecular dynamics simulations, we showed that the m.15927G>A mutation caused unstable tRNAThr structure, supported by decreased melting temperature and slower electrophoretic mobility of mutated tRNA. Using cybrids constructed by transferring mitochondria from a Chinese family carrying the m.15927G>A mutation and a control into mitochondrial DNA (mtDNA)-less human umbilical vein endothelial cells, we demonstrated that the m.15927G>A mutation caused significantly decreased efficiency in aminoacylation and steady-state levels of tRNAThr. The aberrant tRNAThr metabolism yielded variable decreases in mtDNA-encoded polypeptides, respiratory deficiency, diminished membrane potential and increased the production of reactive oxygen species. The m.15927G>A mutation promoted the apoptosis, evidenced by elevated release of cytochrome c into cytosol and increased levels of apoptosis-activated proteins: caspases 3, 7, 9 and PARP. Moreover, the lower wound healing cells and perturbed tube formation were observed in mutant cybrids, indicating altered angiogenesis. Our findings provide new insights into the pathophysiology of coronary artery disease, which is manifested by tRNAThr mutation-induced alterations.

DOI: https://doi.org/10.1093/nar/gky1241
Cancers (Basel). 2018 Dec 09. pii: E500. [Epub ahead of print]10(12):

Mitochondrial RNA Expression and Single Nucleotide Variants in Association with Clinical Parameters in Primary Breast Cancers.

Marjolein J A Weerts, Marcel Smid, John A Foekens, Stefan Sleijfer, John W M Martens.

  The human mitochondrial DNA (mtDNA) encodes 37 genes, including thirteen proteins essential for the respiratory chain, and RNAs functioning in the mitochondrial translation apparatus. The total number of mtDNA molecules per cell (mtDNA content) is variable between tissue types and also between tumors and their normal counterparts. For breast cancer, tumors tend to be depleted in their mtDNA content compared to adjacent normal mammary tissue. Various studies have shown that primary breast tumors harbor somatic mtDNA variants. A decrease in mtDNA content or the presence of somatic variants could indicate a reduced mitochondrial function within breast cancer. In this explorative study we aimed to further understand genomic changes and expression of the mitochondrial genome within breast cancer, by analyzing RNA sequencing data of primary breast tumor specimens of 344 cases. We demonstrate that somatic variants detected at the mtRNA level are representative for somatic variants in the mtDNA. Also, the number of somatic variants within the mitochondrial transcriptome is not associated with mutational processes impacting the nuclear genome, but is positively associated with age at diagnosis. Finally, we observe that mitochondrial expression is related to ER status. We conclude that there is a large heterogeneity in somatic mutations of the mitochondrial genome within primary breast tumors, and differences in mitochondrial expression among breast cancer subtypes. The exact impact on metabolic differences and clinical relevance deserves further study.

Keywords:  clinicopathological markers; mitochondrial RNA variants; mitochondrial expression; primary breast cancer

DOI:  https://doi.org/10.3390/cancers10120500
Eur J Pediatr. 2018 Dec 07.

Diagnosis, management, and follow-up of mitochondrial disorders in childhood: a personalized medicine in the new era of genome sequence.

Margarida Paiva Coelho, Esmeralda Martins, Laura Vilarinho.

  Primary mitochondrial disorders are highly variable in clinical presentation, biochemistry, and molecular etiology. Mitochondrial disorders can be caused by genetic defects in the mitochondrial, in nuclear genome, or in the interplay between the two genomes. Biochemical screening tests may be inconclusive or misleading since patients, with confirmed mitochondrial disorders specially in pediatric age, may exhibit normal routine biochemistry, muscle histology, or enzymatic analysis of the mitochondrial respiratory chain. Diagnosis is often challenging even with combination of multiple criteria (clinical, biochemical, histological, and functional), as innumerous conditions cause secondary mitochondrial dysfunction. Nowadays, a definite diagnosis is only possible by genetic confirmation since no single score system is satisfactorily accurate, being sensitive but not specific.Conclusion: Awareness between physicians is of major importance considering that clinical suspicion may not be obvious regarding the heterogenicity in presentation and biochemical features of mitochondrial disorders. In this review, we provide information on diagnosis approach to patients suspected for mitochondrial disorders as well as management on chronic and acute settings. Follow-up should provide comprehensive information on patient's status, since intervention on these diseases is mostly supportive and prognosis is variable and sometimes unpredictable. What is Known: • Mitochondrial disorders are heterogenous and may present at any age, with any symptoms and any type of inheritance. • Mitochondrial disorders may be due to pathogenic variants in mitochondrial DNA (mtDNA) or nuclear genes (nDNA). What is New: • Since no single score system is satisfactorily accurate, a definite diagnosis is only possible with genetic studies with gene panels proving to be a cost-effective approach. • Clinical and biochemical features of patients without a confirmed diagnosis must be reviewed and other diagnosis must be considered. A wider genetic approach may be applied (WES or WGS).

Keywords:  Genetic diagnosis; Mitochondria; Mitochondrial disease; Respiratory chain deficiency; mtDNA

DOI:  https://doi.org/10.1007/s00431-018-3292-x
Gene. 2018 Dec 04. pii: S0378-1119(18)31228-9. [Epub ahead of print]

Whole sequence of the mitochondrial DNA genome of Kearns Sayre Syndrome patients: Identification of deletions and variants.

Angélica Saldaña-Martínez, María de Lourdes Muñoz, Gerardo Pérez-Ramírez, José Francisco Montiel-Sosa, Julio Montoya, Sonia Emperador, Eduardo Ruiz-Pesini, Sergio Cuevas-Covarrubias, Jaime López-Valdez, Rubén García Ramírez.

  Mitochondria both produce the energy of the cell as ATP via respiration and regulate cellular metabolism. Accordingly, any deletion or mutation in the mitochondrial DNA (mtDNA) may result in a disease. One of these diseases is Kearns Sayre syndrome (KSS), described for the first time in 1958, where different large-scale deletions of different sizes and at different positions have been reported in the mitochondrial genome of patients with similar clinical symptoms. In this study, sequences of the mitochondrial genome of three patients with clinic features of KSS were analyzed. Our results revealed the position, heteroplasmy percentage, size of deletions, and their haplogroups. Two patients contained deletions reported previously and one patient showed a new deletion not reported previously. These results display for the first time a systematic analysis of mtDNA variants in the whole mtDNA genome of patients with KSS to help to understand their association with the disease.

Keywords:  Haplogroup; Heteroplasmy; Large-scale deletion; Mitochondrial disease; Phylogenetic analysis

DOI:  https://doi.org/10.1016/j.gene.2018.11.085
PLoS One. 2018 ;13(12): e0208828

Schizophrenia-associated mt-DNA SNPs exhibit highly variable haplogroup affiliation and nuclear ancestry: Bi-genomic dependence raises major concerns for link to disease.

Christian M Hagen, Vanessa F Gonçalves, Paula L Hedley, Jonas Bybjerg-Grauholm, Marie Bækvad-Hansen, Christine S Hansen, Jørgen K Kanters, Jimmi Nielsen, Ole Mors, Alfonso B Demur, Thomas D Als, Merete Nordentoft, Anders Børglum, Preben B Mortensen, James Kennedy, Thomas M Werge, David M Hougaard, Michael Christiansen.

Mitochondria play a significant role in human diseases. However, disease associations with mitochondrial DNA (mtDNA) SNPs have proven difficult to replicate. An analysis of eight schizophrenia-associated mtDNA SNPs, in 23,743 Danes without a psychiatric diagnosis and 2,538 schizophrenia patients, revealed marked inter-allelic differences in mitochondrial haplogroup affiliation and nuclear ancestry. This bi-genomic dependence could entail population stratification. Only two mitochondrial SNPs, m.15043A and m.15218G, were significantly associated with schizophrenia. However, these associations disappeared when corrected for haplogroup affiliation and nuclear ancestry. The extensive bi-genomic dependence documented here is a major concern when interpreting historic, as well as designing future, mtDNA association studies.

DOI: https://doi.org/10.1371/journal.pone.0208828
Biomed Res Int. 2018 ;2018 1286480

Heteroplasmy Detection of Mitochondrial DNA A3243G Mutation Using Quantitative Real-Time PCR Assay Based on TaqMan-MGB Probes.

Enguang Rong, Hanbo Wang, Shujing Hao, Yuhong Fu, Yanyan Ma, Tianze Wang.

A point mutation of mitochondrial DNA (mtDNA) at nucleotide position 3243 A to G (mt.3243A>G) is involved in many common diseases, including maternally inherited diabetes and deafness (MIDD) and mitochondrial encephalomyopathy, lactic acidosis with stroke-like episodes (MELAS). However, the mutant level of mt.3243A>G varies both among individuals and in different organs, tissues, and even cells of single individuals. For detection of this mutation, current methods have limited universality and sensitivity and may be not adequate for a routine clinical test. Here, we develop and evaluate a rapid TaqMan-MGB quantitative real-time PCR (qPCR) method for detecting and quantifying the heteroplasmy level of mt.3243A>G in single-tube analysis. With our method, the sensitivity of detection was as low as 0.1%, but the accuracy of quantification was reliable, down to 4%. All positives could be correctly identified, and the heteroplasmy levels determined by qPCR correlated well with the results from restriction fragment length polymorphism (RFLP) and pyrosequencing assays (r = 0.921~0.973 and 0.972~0.984). In addition, we demonstrated that the urinary sediments, leukocytes, or hair follicles might be ideal templates to detect and quantify the heteroplasmy of mt.3243A>G mutation; however, they should be optimized or retreated for further accurate quantification. Our study should allow rapid and high throughput diagnostic testing and can potentially be used to clarify the association between clinical phenotype and pathogenic mitochondrial mutations derived from various tissues.

DOI: https://doi.org/10.1155/2018/1286480
Methods Mol Biol. 2019 ;1894 171-180

Quantification of Mitochondrial Genome Transcription in Male Reproductive Cells by Real-Time PCR.

Cheng Xu, Qian Liu, Jin Xu, Aihua Gu.

  Mitochondria are organelles that play a key role in the regulation of cell energy metabolism, biosynthesis, and cell death. Mitochondria are also involved in important physiological processes, such as the three-carboxylic acid cycle, the oxidation of fatty acids and amino acids, and calcium ion homeostasis. The energy demands of male germ cells during mitosis and meiosis are higher than those of somatic cells, suggesting that mitochondria play a critical role in sperm. Mitochondria are nanotoxicity targets in male germ cells. The level of mitochondrial genome transcription is reflective of mitochondrial function and can therefore be used as a quantitative index for evaluating nanotoxicity. This study describes how to use real-time PCR to evaluate the effects of nanomaterials on mitochondrial genome transcription in male reproductive cells.

Keywords:  Germ cell; Mitochondria; Nanotoxicity; Real-time PCR; Transcription

DOI:  https://doi.org/10.1007/978-1-4939-8916-4_11
Mol Psychiatry. 2018 Dec 10.

NDUFV2 pseudogene (NDUFV2P1) contributes to mitochondrial complex I deficits in schizophrenia.

Oded Bergman, Rachel Karry, Jumana Milhem, Dorit Ben-Shachar.

Mitochondria together with other cellular components maintain a constant crosstalk, modulating transcriptional and posttranslational processes. We and others demonstrated mitochondrial multifaceted dysfunction in schizophrenia, with aberrant complex I (CoI) as a major cause. Here we show deficits in CoI activity and homeostasis in schizophrenia-derived cell lines. Focusing on a core CoI subunit, NDUFV2, one of the most severely affected subunits in schizophrenia, we observed reduced protein level and functioning, with no change in mRNA transcripts. We further show that NDUFV2 pseudogene (NDUFV2P1) expression is increased in schizophrenia-derived cells and in postmortem brain specimens. In schizophrenia and controls pooled samples, NDUFV2P1 level demonstrated a significant inverse correlation with NDUFV2 pre- and matured protein level and with CoI-driven cellular respiration. Our data suggest a role for a pseudogene in its parent-gene regulation and possibly in CoI dysfunction in schizophrenia. The abnormal expression of the pseudogene may be one element of a vicious circle in which CoI deficits lead to mitochondrial dysfunction potentially affecting genome-wide regulation of gene expression, including the expression of pseudogenes.

DOI: https://doi.org/10.1038/s41380-018-0309-9
Proc Natl Acad Sci U S A. 2018 Dec 12. pii: 201816656. [Epub ahead of print]

MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo.

Erol C Bayraktar, Lou Baudrier, Ceren Özerdem, Caroline A Lewis, Sze Ham Chan, Tenzin Kunchok, Monther Abu-Remaileh, Andrew L Cangelosi, David M Sabatini, Kıvanç Birsoy, Walter W Chen.

  Mitochondria are metabolic organelles that are essential for mammalian life, but the dynamics of mitochondrial metabolism within mammalian tissues in vivo remains incompletely understood. While whole-tissue metabolite profiling has been useful for studying metabolism in vivo, such an approach lacks resolution at the cellular and subcellular level. In vivo methods for interrogating organellar metabolites in specific cell types within mammalian tissues have been limited. To address this, we built on prior work in which we exploited a mitochondrially localized 3XHA epitope tag (MITO-Tag) for the fast isolation of mitochondria from cultured cells to generate MITO-Tag Mice. Affording spatiotemporal control over MITO-Tag expression, these transgenic animals enable the rapid, cell-type-specific immunoisolation of mitochondria from tissues, which we verified using a combination of proteomic and metabolomic approaches. Using MITO-Tag Mice and targeted and untargeted metabolite profiling, we identified changes during fasted and refed conditions in a diverse array of mitochondrial metabolites in hepatocytes and found metabolites that behaved differently at the mitochondrial versus whole-tissue level. MITO-Tag Mice should have utility for studying mitochondrial physiology, and our strategy should be generally applicable for studying other mammalian organelles in specific cell types in vivo.

Keywords:  MITO-Tag Mice; lipidomics; metabolomics; mitochondria; proteomics

DOI:  https://doi.org/10.1073/pnas.1816656115
Cancer Metastasis Rev. 2018 Dec 12.

Roles of the mitochondrial genetics in cancer metastasis: not to be ignored any longer.

Thomas C Beadnell, Adam D Scheid, Carolyn J Vivian, Danny R Welch.

  Mitochondrial DNA (mtDNA) encodes for only a fraction of the proteins that are encoded within the nucleus, and therefore has typically been regarded as a lesser player in cancer biology and metastasis. Accumulating evidence, however, supports an increased role for mtDNA impacting tumor progression and metastatic susceptibility. Unfortunately, due to this delay, there is a dearth of data defining the relative contributions of specific mtDNA polymorphisms (SNP), which leads to an inability to effectively use these polymorphisms to guide and enhance therapeutic strategies and diagnosis. In addition, evidence also suggests that differences in mtDNA impact not only the cancer cells but also the cells within the surrounding tumor microenvironment, suggesting a broad encompassing role for mtDNA polymorphisms in regulating the disease progression. mtDNA may have profound implications in the regulation of cancer biology and metastasis. However, there are still great lengths to go to understand fully its contributions. Thus, herein, we discuss the recent advances in our understanding of mtDNA in cancer and metastasis, providing a framework for future functional validation and discovery.

Keywords:  Metabolism; Metastasis; Mitochondrial genetics; Polymorphism; Tumor progression

DOI:  https://doi.org/10.1007/s10555-018-9772-7
Toxicol Res (Camb). 2018 Nov 01. 7(6): 1008-1011

Targeting of the respiratory chain by toxicants: beyond the toxicities to mitochondrial morphology.

P K Zhou, R X Huang.

The mitochondrion is an important subcellular target of environmental toxicants. With environmental stress, a series of toxic effects on mitochondria are induced, which originate from the dynamic changes of mitochondrial fusion and fission, structure/membrane damage, and respiratory chain dysfunction. The toxic effects of various toxicants on mitochondrial morphology and intact membranes, and their determination of cell fate, have already been broadly studied and reported on. However, their effects on the integrity and function of the mitochondrial respiratory chain (RC) remain incompletely understood. Recently, Fan et al. and Yu et al. approached this topic by closely examining the mitochondrial toxicities, including the effect on the respiratory chain, induced by organic arsenical chemical 2-methoxy-4-(((4-(oxoarsanyl)phenyl)imino)methyl)phenol and thiourea gold(i) complexes (AuTuCl). Obviously, toxicant-induced dysfunction of the respiratory chain can hinder ATP production, and may elevate ROS generation. The increased ROS can further damage mtDNA, and consequently leads to inactivation of some RC protein-encoding mtDNA, generating a vicious circle of amplifying mitochondrial damage. We hope that these studies focused on RC structure and activity will broaden our view of mitochondrial toxicology and draw forth more profound mechanistic studies on the respiratory chain toxicity of environmental toxicants and their application in risk assessment.

DOI: https://doi.org/10.1039/c8tx00207j
Cancer Metastasis Rev. 2018 Dec 14.

Mitochondrial polymorphisms contribute to aging phenotypes in MNX mouse models.

Carolyn J Vivian, Travis M Hagedorn, Roy A Jensen, Amanda E Brinker, Danny R Welch.

  Many inbred strains of mice develop spontaneous tumors as they age. Recent awareness of the impacts of mitochondrial DNA (mtDNA) on cancer and aging has inspired developing a mitochondrial-nuclear exchange (MNX) mouse model in which nuclear DNA is paired with mitochondrial genomes from other strains of mouse. MNX mice exhibit mtDNA influences on tumorigenicity and metastasis upon mating with transgenic mice. However, we also wanted to investigate spontaneous tumor phenotypes as MNX mice age. Utilizing FVB/NJ, C57BL/6J, C3H/HeN, and BALB/cJ wild-type inbred strains, previously documented phenotypes were observed as expected in MNX mice with the same nuclear background. However, aging nuclear matched MNX mice exhibited decreased occurrence of mammary tumors in C3H/HeN mice containing C57BL/6J mitochondria compared to wild-type C3H/HeN mice. Although aging tumor phenotypes appear to be driven by nuclear genes, evidence suggesting that some differences are modified by the mitochondrial genome is presented.

Keywords:  Aging; Cancer; Mitochondria; Mouse

DOI:  https://doi.org/10.1007/s10555-018-9773-6
Oxid Med Cell Longev. 2018 ;2018 1347174

Reduced Levels of ATP Synthase Subunit ATP5F1A Correlate with Earlier-Onset Prostate Cancer.

René G Feichtinger, Georg Schäfer, Christof Seifarth, Johannes A Mayr, Barbara Kofler, Helmut Klocker.

Switching of cellular energy production from oxidative phosphorylation (OXPHOS) to aerobic glycolysis occurs in many types of tumors. However, the significance of energy metabolism for the development of prostate carcinoma is poorly understood. We investigated the expression of OXPHOS complexes in 94 human prostate carcinomas and paired benign tissue using immunohistochemistry. Overall mitochondrial mass was upregulated in carcinomas compared to benign prostate tissue in all Gleason grades. A significant direct correlation between the expression of OXPHOS complexes I, II, and V and the Gleason score was observed. However, 17% of prostate carcinomas and 18% of benign prostate tissues showed isolated or combined deficiency of OXPHOS complexes (one deficiency in 12% of the tumors, combined deficiencies in 5%). Complex I was absent in 9% of the samples, with only parts of the tumor affected. ATP5F1A, a complex V protein, was the most frequently affected subunit, in 10% of tumors and 11% of benign prostate tissues (but not both tissues in any single patient). A possible role of complex V in prostate cancer development is suggested by the significant positive correlation of ATP5F1A levels with earlier-onset prostate cancer (age at diagnosis and at prostatectomy) and free PSA percentage. The relatively high percentage (17%) of prostate carcinomas with regional foci of partial OXPHOS complex deficiencies could have important therapeutic implications.

DOI: https://doi.org/10.1155/2018/1347174
Mitochondrion. 2018 Dec 05. pii: S1567-7249(18)30017-5. [Epub ahead of print]

Temporal profile of serum mitochondrial DNA (mtDNA) in patients with aneurysmal subarachnoid hemorrhage (aSAH).

Shafqat Rasul Chaudhry, Stilla Frede, Gerald Seifert, Thomas Mehari Kinfe, Mika Niemelä, Alf Lamprecht, Sajjad Muhammad.

  Aneurysmal subarachnoid hemorrhage (aSAH) is a highly complex disease. Majority of aSAH survivors confront post-SAH complications including cerebral vasospasm (CVS) and delayed cerebral ischemia (DCI) that mainly influence the clinical outcome. Tissue damage during early brain injury may lead to release of damage associated molecular pattern molecules (DAMPs) that may initiate and sustain inflammation during the course of aSAH through activation of pattern recognition receptors. Mitochondrial DNA (mtDNA) due to unmethylated CpG motifs acts as a DAMP via binding to toll-like receptor-9. The aim of this study was to investigate the cell free circulating mtDNA in the systemic circulation of aSAH patients and its association with post-SAH complications and clinical outcome. The DNA was extracted from the serum of 80 aSAH patients at days 1, 3, 5, 7, 9, 11, 13 and from 18 healthy controls. Three representative mitochondrial gene fragments including Cytochrome B (CytB), D-Loop and Cytochrome c oxidase subunit-1 (COX-1) were quantified using a Taqman-probes based qPCR. Levels of mtDNA were quantified from standard curves generated using mtDNA extracted from HepG2 cell mitochondria. Clinical outcome of the patients was assessed by Glasgow outcome scale (GOS) and modified Rankin scale (mRS). Clinical data and post-SAH complications were recorded from patient's record file. Serum D-Loop and COX-1 were significantly elevated early after aSAH and remained high over first 2 weeks. CytB levels were however, initially unchanged but elevated later at day 7 as compared to healthy controls. Cumulative levels measured over two weeks showed significant correlations with post-SAH complications including a negative correlation of D-Loop with pneumonia infection, hydrocephalus and occurrence of epilepsy, a positive correlation of Cyt B with occurrence of CVS and a negative correlation of COX-1 with occurrence of systemic infections and seizures. Cumulative D-Loop values negatively correlated with clinical outcome. Our data suggest that mtDNA may directly or indirectly influence post-SAH complications and clinical outcome.

Keywords:  Aneurysmal subarachnoid hemorrhage; Cytochrome B; Cytochrome c oxidase; D-Loop; DAMPs; Mitochondrial DNA

DOI:  https://doi.org/10.1016/j.mito.2018.12.001
Oncol Lett. 2018 Dec;16(6): 7074-7081

Clinical application of plasma mitochondrial DNA content in patients with lung cancer.

Jianhua Chen, Lemeng Zhang, Xun Yu, Hui Zhou, Yongzhong Luo, Wei Wang, Lijing Wang.

  Alterations of mitochondrial DNA (mtDNA) have been identified in several types of solid tumor. However, to the best of our knowledge, the clinical significance of plasma mtDNA content in lung cancer remains unknown. Thus, the current study explored the diagnostic and prognostic value of plasma mtDNA quantification in patients with lung cancer. Plasma mtDNA copy numbers of patients with lung cancer (n=128) and healthy individuals (n=107) were quantified by quantitative polymerase chain reaction. Plasma mtDNA copy numbers in patients and healthy controls were 0.89×104 and 1.37×104 copies/µl, respectively (P<0.0001). Furthermore, lower plasma mtDNA content was associated with tumor size, lymph node metastases, distant metastases and serum carcinoembryonic antigen levels (P<0.05), but was not associated with pathological type, age, sex or main driver gene mutation status (P>0.05). Plasma mtDNA facilitated the detection of lung cancer at a threshold of 1.19×104 copies/µl with a sensitivity of 71.1% and specificity of 70.1%, as determined by receiver operating characteristic curve analysis. Advanced stage (III and IV) patients with a lower mtDNA copy number (cutoff: 1.02×104 copies/µl) tended to exhibit poorer prognosis (P<0.05). These results indicated that plasma mtDNA content is a promising and complementary candidate with tissue mtDNA for diagnosis and prognostic prediction for lung cancer.

Keywords:  diagnosis; lung cancer; mitochondrial DNA; prognosis; quantitative polymerase chain reaction

DOI:  https://doi.org/10.3892/ol.2018.9515
Biochim Biophys Acta Gene Regul Mech. 2018 Dec 04. pii: S1874-9399(18)30078-6. [Epub ahead of print]

The mammalian mitochondrial epitranscriptome.

Pedro Rebelo-Guiomar, Christopher A Powell, Lindsey Van Haute, Michal Minczuk.

Correct expression of the mitochondrially-encoded genes is critical for the production of the components of the oxidative phosphorylation machinery. Post-transcriptional modifications of mitochondrial transcripts have been emerging as an important regulatory feature of mitochondrial gene expression. Here we review the current knowledge on how the mammalian mitochondrial epitranscriptome participates in regulating mitochondrial homeostasis. In particular, we focus on the latest breakthroughs made towards understanding the roles of the modified nucleotides in mitochondrially-encoded ribosomal and transfer RNAs, the enzymes responsible for introducing these modifications and on recent transcriptome-wide studies reporting modifications to mitochondrial messenger RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.

DOI: https://doi.org/10.1016/j.bbagrm.2018.11.005
Sci Rep. 2018 Dec 07. 8(1): 17732

Elucidating the contribution of ETC complexes I and II to the respirasome formation in cardiac mitochondria.

Sehwan Jang, Sabzali Javadov.

Mitochondrial electron transport chain (ETC) plays a central role in ATP synthesis, and its dysfunction is associated with human diseases. Recent studies revealed that individual ETC complexes are assembled into supercomplexes. The main supercomplex, respirasome composed of complexes I, III, and IV has been suggested to improve electron channeling and control ROS production, maintain the structural integrity of ETC complexes and prevent protein aggregation in the inner mitochondrial membrane. However, many questions related to the structural organization of the respirasome, particularly, a possible role of complexes I and II in respirasome formation remain unclear. Here, we investigated whether genetic and pharmacological inhibition of complexes I and II affect respirasome assembly in cardioblast cells and isolated cardiac mitochondria. Pharmacological inhibition of the enzymatic activity of complexes I and II stimulated disruption of the respirasome. Likewise, knockdown of the complex I subunit NDUFA11 stimulated dissociation of respirasome and reduced the activity of complexes I, III, and IV. However, silencing of the membrane-anchored SDHC subunit of complex II had no effect on the respirasome assembly but reduced the activity of complexes II and IV. Downregulation of NDUFA11 or SDHC reduced ATP production and increased mitochondrial ROS production. Overall, these studies, for the first time, provide biochemical evidence that the complex I activity, and the NDUFA11 subunit are important for assembly and stability of the respirasome. The SDHC subunit of complex II is not involved in the respirasome however the complex may play a regulatory role in respirasome formation.

DOI: https://doi.org/10.1038/s41598-018-36040-9
Int J Mol Sci. 2018 Dec 07. pii: E3930. [Epub ahead of print]19(12):

Loss of Mitochondrial AAA Proteases AFG3L2 and YME1L Impairs Mitochondrial Structure and Respiratory Chain Biogenesis.

Jana Cesnekova, Marie Rodinova, Hana Hansikova, Jiri Zeman, Lukas Stiburek.

  Mitochondrial protein quality control is crucial for the maintenance of correct mitochondrial homeostasis. It is ensured by several specific mitochondrial proteases located across the various mitochondrial subcompartments. Here, we focused on characterization of functional overlap and cooperativity of proteolytic subunits AFG3L2 (AFG3 Like Matrix AAA Peptidase Subunit 2) and YME1L (YME1 like ATPase) of mitochondrial inner membrane AAA (ATPases Associated with diverse cellular Activities) complexes in the maintenance of mitochondrial structure and respiratory chain integrity. We demonstrate that loss of AFG3L2 and YME1L, both alone and in combination, results in diminished cell proliferation, fragmentation of mitochondrial reticulum, altered cristae morphogenesis, and defective respiratory chain biogenesis. The double AFG3L2/YME1L knockdown cells showed marked upregulation of OPA1 protein forms, with the most prominent increase in short OPA1 (optic atrophy 1). Loss of either protease led to marked elevation in OMA1 (OMA1 zinc metallopeptidase) (60 kDa) and severe reduction in the SPG7 (paraplegin) subunit of the m-AAA complex. Loss of the YME1L subunit led to an increased Drp1 level in mitochondrial fractions. While loss of YME1L impaired biogenesis and function of complex I, knockdown of AFG3L2 mainly affected the assembly and function of complex IV. Our results suggest cooperative and partly redundant functions of AFG3L2 and YME1L in the maintenance of mitochondrial structure and respiratory chain biogenesis and stress the importance of correct proteostasis for mitochondrial integrity.

Keywords:  AAA complex; AFG3L2; YME1L; mitochondria; protease

DOI:  https://doi.org/10.3390/ijms19123930
EMBO Mol Med. 2018 Dec 14. pii: e9582. [Epub ahead of print]

APOPT1/COA8 assists COX assembly and is oppositely regulated by UPS and ROS.

Alba Signes, Raffaele Cerutti, Anna S Dickson, Cristiane Benincá, Elizabeth C Hinchy, Daniele Ghezzi, Rosalba Carrozzo, Enrico Bertini, Michael P Murphy, James A Nathan, Carlo Viscomi, Erika Fernandez-Vizarra, Massimo Zeviani.

  Loss-of-function mutations in APOPT1, a gene exclusively found in higher eukaryotes, cause a characteristic type of cavitating leukoencephalopathy associated with mitochondrial cytochrome c oxidase (COX) deficiency. Although the genetic association of APOPT1 pathogenic variants with isolated COX defects is now clear, the biochemical link between APOPT1 function and COX has remained elusive. We investigated the molecular role of APOPT1 using different approaches. First, we generated an Apopt1 knockout mouse model which shows impaired motor skills, e.g., decreased motor coordination and endurance, associated with reduced COX activity and levels in multiple tissues. In addition, by achieving stable expression of wild-type APOPT1 in control and patient-derived cultured cells we ruled out a role of this protein in apoptosis and established instead that this protein is necessary for proper COX assembly and function. On the other hand, APOPT1 steady-state levels were shown to be controlled by the ubiquitination-proteasome system (UPS). Conversely, in conditions of increased oxidative stress, APOPT1 is stabilized, increasing its mature intramitochondrial form and thereby protecting COX from oxidatively induced degradation.

Keywords:  APOPT1‐COA8; cytochrome c oxidase; mitochondrial encephalopathy; proteasome–ubiquitin system; reactive oxygen species

DOI:  https://doi.org/10.15252/emmm.201809582
Diabet Med. 2018 Dec 07.

Mitochondrial DNA mutation m.3243A>G is associated with altered mitochondrial function in peripheral blood mononuclear cells, with heteroplasmy levels and with clinical phenotypes.

X Geng, Y Zhang, J Yan, C Chu, F Gao, Z Jiang, X Zhang, Y Chen, X Wei, Y Feng, H Lu, C Wang, F Zeng, W Jia.

AIMS: To investigate the associations among heteroplasmy levels (i.e. the proportions of mutant and wild-type mitochondrial DNA in the same cell), mitochondrial function and clinical severity of the m.3243A>G mutation.
METHODS: A total of 17 participants carrying the m.3243A>G mutation and 17 sex- and age-matched healthy controls were included in this study. Heteroplasmy levels of the m.3243A>G mutation in leukocytes, saliva and urine sediment were determined by pyrosequencing. The clinical evaluation included endocrinological, audiological and ophthalmological examinations. Mitochondrial function was determined in peripheral blood mononuclear cells isolated from participants.
RESULTS: Heteroplasmy levels in urine sediment were higher than those in leukocytes and saliva. Reduced levels of adenosine triphosphate and mitochondrial membrane potential, and increased reactive oxygen species production were observed in mutant peripheral blood mononuclear cells (all P < 0.05). Linear regression analysis indicated that higher heteroplasmy levels in peripheral blood leukocytes were associated with increased levels of glycated albumin and HbA1c , and decreased total hip bone mineral density T-score after adjustment for age and sex (all P < 0.05). Furthermore, mitochondrial membrane potential was independently associated with bone mineral density T-score at the femoral neck (P < 0.05).
CONCLUSIONS: Heteroplasmy levels in peripheral blood leukocytes and mitochondrial membrane potential in peripheral blood mononuclear cells were closely associated with clinical manifestations and were valuable for evaluation of the clinical severity of the m.3243A>G mutation. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1111/dme.13874
Malar J. 2018 Dec 13. 17(1): 467

Mitochondrial gene sequence variants in children with severe malaria anaemia with or without lactic acidosis: a case control study.

Casey Fowler, Christine Cserti-Gazdewich, Aggrey Dhabangi, Charles Musoke, Himanshu Sharma, Sami S Amr, Walter Dzik.

   BACKGROUND: Evolutionary pressure by Plasmodium falciparum malaria is known to have favoured a large number of human gene adaptations, but there is surprisingly little investigation of the effect of malaria on human mitochondrial sequence variation. Plasmodium falciparum infection can cause severe malaria anaemia (SMA) with insufficient tissue oxygenation, lactic acidosis and death. Despite equal degrees of severe anaemia, some individuals develop lactic acidosis while others do not. A case-control study design was used to investigate whether differences in host mitochondrial gene sequences were associated with lactic acidosis in SMA. Full mitochondrial sequences were obtained from 36 subjects with SMA complicated by lactic acidosis and 37 subjects with SMA without lactic acidosis. The two groups were matched for age, sex, and degree of anaemia.
RESULTS: Compared with the reference sequence, a median of 60 nucleotide variants per individual (interquartile range 4-91) was found, with an average frequency of 3.97 variants per 1000 nucleotides. The frequency and distribution of non-synonymous DNA variants in genes associated with oxidative phosphorylation were not statistically different between the two groups. Non-synonymous variants predicted to have the most disruptive effect on proteins responsible for oxidative phosphorylation were present at a similar frequency in both groups.
CONCLUSIONS: Lactic acidosis in SMA does not appear to be consistently associated with the high prevalence of any mitochondrial gene variant.

Keywords:  Anemia; DNA sequence; Lactic acidosis; Malaria; Mitochondria; Tissue oxygenation

DOI:  https://doi.org/10.1186/s12936-018-2618-5
J Biol Chem. 2018 Dec 10. pii: jbc.RA118.005473. [Epub ahead of print]

Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase.

Jędrzej M Małecki, Hanneke L D M Willemen, Rita Pinto, Angela Y Y Ho, Anders Moen, Ingrid F Kjønstad, Boudewijn M T Burgering, Fried Zwartkruis, Niels Eijkelkamp, Pål Ø Falnes.

  Lysine methylation is an important post-translational modification that is also present on mitochondrial proteins, but the mitochondrial lysine-specific methyltransferases (KMTs) responsible for modification are in most cases unknown. Here, we set out to determine the function of human family with sequence similarity 173 member B (FAM173B), a mitochondrial methyltransferase (MTase) reported to promote chronic pain. Using bioinformatics analyses and biochemical assays, we found that FAM173B contains an atypical, non-cleavable mitochondrial targeting sequence responsible for its localization to mitochondria. Interestingly, CRISPR/Cas9-mediated knock-out (KO) of FAM173B in mammalian cells abrogated trimethylation of Lys-43 in ATP synthase c-subunit (ATPSc), a modification previously reported as ubiquitous among metazoans. ATPSc methylation was restored by complementing the KO cells with enzymatically active human FAM173B or with a putative FAM173B orthologue from the nematode Caenorhabditis elegans. Interestingly, lack of Lys-43 methylation caused aberrant incorporation of ATPSc into the ATP synthase complex, and resulted in decreased ATP-generating ability of the complex, as well as decreased mitochondrial respiration. In summary, we have identified FAM173B as the long-sought KMT responsible for methylation of ATPSc, a key protein in cellular ATP production, and have demonstrated functional significance of ATPSc methylation. We suggest renaming FAM173B to ATPSc-KMT (gene name ATPSCKMT).

Keywords:  ATP synthase; ATP synthase c-subunit; F1FO-ATPase; FAM173B; metabolic regulation; methyltransferase; mitochondria; mitochondrial respiratory chain complex; oxidative phosphorylation; post-translational modification (PTM); protein lysine methylation; protein methylation

DOI:  https://doi.org/10.1074/jbc.RA118.005473