bims-midmar Biomed News
on Mitochondrial DNA maintenance and replication
Issue of 2021–12–12
fourteen papers selected by
Flavia Söllner, Ludwig-Maximilians University
  1. Mitochondria Metabolomics Reveals a Role of β-Nicotinamide Mononucleotide Metabolism in Mitochondrial DNA Replication.
  2. Somatic mitochondrial DNA mutations in different grades of glioma.
  3. Surveying the mitochondrial proteome.
  4. Mitochondrial ribosomal stress in lung diseases.
  5. 2-Deoxy-D-glucose couples mitochondrial DNA replication with mitochondrial fitness and promotes the selection of wild-type over mutant mitochondrial DNA.
  6. Role of mitochondrial DNA copy number in incident cardiovascular diseases and the association between cardiovascular disease and type 2 diabetes: A follow-up study on middle-aged women.
  7. Mitochondrial Biogenesis in Neurons: How and Where.
  8. Monitoring and Modulating mtDNA G-Quadruplex Dynamics Reveal Its Close Relationship to Cell Glycolysis.
  9. Mitochondrial DNA heteroplasmy is modulated during oocyte development propagating mutation transmission.
  10. Immunofluorescence microscopy-based detection of ssDNA foci by BrdU in mammalian cells.
  11. Reduction of ER-Mitochondria Distance: a Key Feature in Alzheimer's and Parkinson's Disease, and During Cancer Treatment.
  12. Editorial: Mitochondrial Disorders: Biochemical and Molecular Basis of Disease.
  13. Measurement of fish freshness: Flow cytometry analysis of isolated muscle mitochondria.
  14. FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism.
  1. J Biochem. 2021 Dec 04. pii: mvab136. [Epub ahead of print]
    Mitochondria Metabolomics Reveals a Role of β-Nicotinamide Mononucleotide Metabolism in Mitochondrial DNA Replication.
    Tomoko Nomiyama, Daiki Setoyama, Takehiro Yasukawa, Dongchon Kang.
      Mitochondrial DNA (mtDNA) replication is tightly regulated and necessary for cellular homeostasis; however, its relationship with mitochondrial metabolism remains unclear. Advances in metabolomics integrated with the rapid isolation of mitochondria will allow for remarkable progress in analyzing mitochondrial metabolism. Here, we propose a novel methodology for mitochondria-targeted metabolomics, which employs a quick isolation procedure using a hemolytic toxin from Streptococcus pyogenes streptolysin O (SLO). SLO-isolation of mitochondria from cultured HEK293 cells is time- and labor-saving for simultaneous multi-sample processing and has been applied to various other cell lines in this study. Furthermore, our method can detect the time-dependent reduction in mitochondrial ATP in response to a glycolytic inhibitor 2-deoxyglucose, indicating the suitability to prepare metabolite analysis-competent mitochondria. Using this methodology, we searched for specific mitochondrial metabolites associated with mtDNA replication activation, and nucleotides and NAD+ were identified to be prominently altered. Most notably, treatment of β-Nicotinamide Mononucleotide (β-NMN), a precursor of NAD+, to HEK293 cells activated and improved the rate of mtDNA replication by increasing nucleotides in mitochondria and decreasing their degradation products: nucleosides. Our results suggest that β-NMN metabolism play a role in supporting mtDNA replication by maintaining the nucleotide pool balance in the mitochondria.
    Keywords:  beta-nicotinamide mononucleotide (β-NMN); metabolomics; mitochondrial DNA; nucleotide metabolism; streptolysin O
    DOI:  https://doi.org/10.1093/jb/mvab136
  2. Per Med. 2021 Dec 07.
    Somatic mitochondrial DNA mutations in different grades of glioma.
    Bee Hong Soon, Nadiah Abu, Nor Azian Abdul Murad, Sue-Mian Then, Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Mohd Saffari Mohd Haspani, Charng Jeng Toh, Ramesh Kumar, Ainul Syahrilfazli Jaafar, Anis Nabillah Mohd Azli, Mohd Syakir Mohd Azahar, Sanmugarajah Paramasvaran, Kamalanathan Palaniandy, Azmi Mohd Tamil, Rahman Jamal.
      Aim: Mitochondrial DNA (mtDNA) alterations play an important role in the multistep processes of cancer development. Gliomas are among the most diagnosed brain cancer. The relationship between mtDNA alterations and different grades of gliomas are still elusive. This study aimed to elucidate the profile of somatic mtDNA mutations in different grades of gliomas and correlate it with clinical phenotype. Materials & methods: Forty histopathologically confirmed glioma tissue samples and their matched blood were collected and subjected for mtDNA sequencing. Results & conclusion: About 75% of the gliomas harbored at least one somatic mutation in the mtDNA gene, and 45% of these mutations were pathogenic. Mutations were scattered across the mtDNA genome, and the commonest nonsynonymous mutations were located at complex I and IV of the mitochondrial respiratory chain. These findings may have implication for future research to determine the mitochondrial energetics and its downstream metabolomics on gliomas.
    Keywords:  Malaysia; cancer; genome; glioblastoma; gliomas; microarray; mitochondria; mtDNA; mutation; somatic mutation
    DOI:  https://doi.org/10.2217/pme-2021-0033
  3. Nat Cell Biol. 2021 Dec 06.
    Surveying the mitochondrial proteome.
    Dominic Winter, Thomas Becker.
      
    DOI:  https://doi.org/10.1038/s41556-021-00801-y
  4. Am J Physiol Lung Cell Mol Physiol. 2021 Dec 07.
    Mitochondrial ribosomal stress in lung diseases.
    Loukmane Karim, Beata Kosmider, Karim Bahmed.
      Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
    Keywords:  disease; lung; mitochondria; mitoribosome
    DOI:  https://doi.org/10.1152/ajplung.00078.2021
  5. Nat Commun. 2021 Dec 06. 12(1): 6997
    2-Deoxy-D-glucose couples mitochondrial DNA replication with mitochondrial fitness and promotes the selection of wild-type over mutant mitochondrial DNA.
    Boris Pantic, Daniel Ives, Mara Mennuni, Diego Perez-Rodriguez, Uxoa Fernandez-Pelayo, Amaia Lopez de Arbina, Mikel Muñoz-Oreja, Marina Villar-Fernandez, Thanh-Mai Julie Dang, Lodovica Vergani, Iain G Johnston, Robert D S Pitceathly, Robert McFarland, Michael G Hanna, Robert W Taylor, Ian J Holt, Antonella Spinazzola.
      Pathological variants of human mitochondrial DNA (mtDNA) typically co-exist with wild-type molecules, but the factors driving the selection of each are not understood. Because mitochondrial fitness does not favour the propagation of functional mtDNAs in disease states, we sought to create conditions where it would be advantageous. Glucose and glutamine consumption are increased in mtDNA dysfunction, and so we targeted the use of both in cells carrying the pathogenic m.3243A>G variant with 2-Deoxy-D-glucose (2DG), or the related 5-thioglucose. Here, we show that both compounds selected wild-type over mutant mtDNA, restoring mtDNA expression and respiration. Mechanistically, 2DG selectively inhibits the replication of mutant mtDNA; and glutamine is the key target metabolite, as its withdrawal, too, suppresses mtDNA synthesis in mutant cells. Additionally, by restricting glucose utilization, 2DG supports functional mtDNAs, as glucose-fuelled respiration is critical for mtDNA replication in control cells, when glucose and glutamine are scarce. Hence, we demonstrate that mitochondrial fitness dictates metabolite preference for mtDNA replication; consequently, interventions that restrict metabolite availability can suppress pathological mtDNAs, by coupling mitochondrial fitness and replication.
    DOI:  https://doi.org/10.1038/s41467-021-26829-0
  6. Atherosclerosis. 2021 Dec 01. pii: S0021-9150(21)01448-9. [Epub ahead of print]
    Role of mitochondrial DNA copy number in incident cardiovascular diseases and the association between cardiovascular disease and type 2 diabetes: A follow-up study on middle-aged women.
    Kristina Sundquist, Jan Sundquist, Karolina Palmer, Ashfaque A Memon.
       BACKGROUND AND AIMS: Mitochondrial DNA copy number (mtDNA-CN) is a surrogate biomarker of mitochondrial dysfunction and is associated with type 2 diabetes (T2D) and cardiovascular disease (CVD). However, despite being associated with both CVD and T2D, it is not known what role mtDNA-CN has in the association between T2D and CVD. Our aims were to investigate whether, (1) baseline mtDNA-CN is associated with CVD incidence and (2) mtDNA-CN has a role as a mediator between T2D and CVD.
    METHOD: We quantified absolute mtDNA-CN by droplet digital PCR method in a population-based follow-up study of middle aged (52-65 years) women (n = 3062). The median follow-up period was 17 years.
    RESULTS: Our results show that low baseline levels of mtDNA-CN (<111 copies/μL) were associated with an increased risk of CVD (HR = 1.32, 95% CI = 1.08; 1.63) as well as with specific CVDs: coronary heart disease (HR = 1.28, 95% CI = 0.99; 1.66), stroke (HR = 1.26, 95% CI = 0.87; 1.84) and abdominal aortic aneurysm (HR = 2.61, 95% CI = 1.03; 6.62). The associations decreased but persisted even after adjustment for potential confounders. Furthermore, our results show that the total effect of T2D on future risk of CVD was reduced after controlling for mtDNA-CN and the proportion mediated by mtDNA-CN was estimated to be 4.9%.
    CONCLUSIONS: Lower baseline mtDNA-CN is associated with incident CVD and may have a mediating effect on the association between T2D and CVD; however, this novel observation needs to be confirmed in future studies.
    Keywords:  Biomarker; Cardiovascular diseases; Mitochondria; Mitochondrial DNA
    DOI:  https://doi.org/10.1016/j.atherosclerosis.2021.11.020
  7. Int J Mol Sci. 2021 Dec 02. pii: 13059. [Epub ahead of print]22(23):
    Mitochondrial Biogenesis in Neurons: How and Where.
    Carlos Cardanho-Ramos, Vanessa Alexandra Morais.
      Neurons rely mostly on mitochondria for the production of ATP and Ca2+ homeostasis. As sub-compartmentalized cells, they have different pools of mitochondria in each compartment that are maintained by a constant mitochondrial turnover. It is assumed that most mitochondria are generated in the cell body and then travel to the synapse to exert their functions. Once damaged, mitochondria have to travel back to the cell body for degradation. However, in long cells, like motor neurons, this constant travel back and forth is not an energetically favourable process, thus mitochondrial biogenesis must also occur at the periphery. Ca2+ and ATP levels are the main triggers for mitochondrial biogenesis in the cell body, in a mechanism dependent on the Peroxisome-proliferator-activated γ co-activator-1α-nuclear respiration factors 1 and 2-mitochondrial transcription factor A (PGC-1α-NRF-1/2-TFAM) pathway. However, even though of extreme importance, very little is known about the mechanisms promoting mitochondrial biogenesis away from the cell body. In this review, we bring forward the evoked mechanisms that are at play for mitochondrial biogenesis in the cell body and periphery. Moreover, we postulate that mitochondrial biogenesis may vary locally within the same neuron, and we build upon the hypotheses that, in the periphery, local protein synthesis is responsible for giving all the machinery required for mitochondria to replicate themselves.
    Keywords:  NRF-1/2; PGC-1α; TFAM; cell body; mitochondrial biogenesis; neurodegenerative diseases; neurons; periphery
    DOI:  https://doi.org/10.3390/ijms222313059
  8. J Am Chem Soc. 2021 Dec 06.
    Monitoring and Modulating mtDNA G-Quadruplex Dynamics Reveal Its Close Relationship to Cell Glycolysis.
    Xiu-Cai Chen, Gui-Xue Tang, Wen-Hua Luo, Wen Shao, Jing Dai, Shu-Tang Zeng, Zhi-Shu Huang, Shuo-Bin Chen, Jia-Heng Tan.
      The mitochondrial DNA G-quadruplex (mtDNA G4) is a potential regulatory element for the regulation of mitochondrial functions; however, its relevance and specific roles in diseases remain largely unknown. Here, we engineered a set of chemical probes, including MitoISCH, an mtDNA G4-specific fluorescent probe, together with MitoPDS, a mitochondria-targeted G4-stabilizing agent, to thoroughly investigate mtDNA G4s. Using MitoISCH to monitor previously intractable dynamics of mtDNA G4s, we surprisingly found that their formation was prevalent only in endothelial and cancer cells that rely on glycolysis for energy production. Consistent with this, promotion of mtDNA G4 folding by MitoPDS in turn caused glycolysis-related gene activation and glycolysis enhancement. Remarkably, this close relationship among mtDNA G4s, glycolysis, and cancer cells further allowed MitoISCH to accumulate in tumors and label them in vivo. Our work reveals an unprecedented link between mtDNA G4s and cell glycolysis, suggesting that mtDNA G4s may be a novel cancer biomarker and therapeutic target deserving further exploration.
    DOI:  https://doi.org/10.1021/jacs.1c08860
  9. Sci Adv. 2021 Dec 10. 7(50): eabi5657
    Mitochondrial DNA heteroplasmy is modulated during oocyte development propagating mutation transmission.
    Haixin Zhang, Marco Esposito, Mikael G Pezet, Juvid Aryaman, Wei Wei, Florian Klimm, Claudia Calabrese, Stephen P Burr, Carolina H Macabelli, Carlo Viscomi, Mitinori Saitou, Marcos R Chiaratti, James B Stewart, Nick Jones, Patrick F Chinnery.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abi5657
  10. STAR Protoc. 2021 Dec 17. 2(4): 100978
    Immunofluorescence microscopy-based detection of ssDNA foci by BrdU in mammalian cells.
    Susan Kilgas, Anne E Kiltie, Kristijan Ramadan.
      DNA end resection converts broken ends of double-stranded DNA (dsDNA) to 3'-single-stranded DNA (3'-ssDNA). The extent of resection regulates DNA double-strand break (DSB) repair pathway choice and thereby genomic stability. Here, we characterize an optimized immunofluorescence (IF) microscopy-based protocol for measuring ssDNA in mammalian cells by labeling genomic DNA with 5-bromo-2'-deoxyuridine (BrdU). BrdU foci can be detected under non-denaturing conditions by anti-BrdU antibody, providing an accurate and reliable readout of DNA end resection in most mammalian cell lines. For complete details on the use and execution of this protocol, please refer to Kilgas et al. (2021).
    Keywords:  Antibody; Cell Biology; Cell-based Assays; Microscopy; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2021.100978
  11. Annu Int Conf IEEE Eng Med Biol Soc. 2021 Nov;2021 4412-4415
    Reduction of ER-Mitochondria Distance: a Key Feature in Alzheimer's and Parkinson's Disease, and During Cancer Treatment.
    Carmen A Perez-Leanos, Hugo E Romero-Campos, Genevieve Dupont, Virginia Gonzalez-Velez.
      One remarkable dynamic cell structure is the region between the endoplasmic reticulum (ER) and the mitochondria, termed the mitochondria-associated membranes (MAM). MAMs carry out different cellular functions such as Ca2+ homeostasis and lipid synthesis, which depend on an adequate distance separating the ER and mitochondria. A decreased distance has been observed in Alzheimer's disease, Parkinson's disease, and during cancer treatment. It is unclear how dysregulation of the spatial characteristics of MAMs can cause abnormal Ca2+ dynamics which could end in cell death. In this work, a computational model was proposed to study the relationship between a decreased ER-mitochondria distance and mitochondria-induced cell death. Our results point towards the mitochondrial permeability transition pore (mPTP) as a key cell death signaling mechanism indirectly regulated by the spatial characteristics of MAMs.Clinical Relevance- The endoplasmic reticulum-mitochondria crosstalk plays an important role in the mPTP-induced apoptosis. This process could be behind neurodegeneration in Alzheimer's and Parkinson's diseases, as well as behind the induced cell death during cancer treatment.
    DOI:  https://doi.org/10.1109/EMBC46164.2021.9631090
  12. Front Genet. 2021 ;12 769770
    Editorial: Mitochondrial Disorders: Biochemical and Molecular Basis of Disease.
    Guilhian Leipnitz, Grant M Hatch, Al-Walid Mohsen, Ronald J A Wanders.
      
    Keywords:  case report; mitochondrial disorders; pathophysiology; reaction mechanism; treatment
    DOI:  https://doi.org/10.3389/fgene.2021.769770
  13. Food Chem. 2021 Nov 27. pii: S0308-8146(21)02696-0. [Epub ahead of print] 131690
    Measurement of fish freshness: Flow cytometry analysis of isolated muscle mitochondria.
    Méline Soret, Tiffanie Bouchendhomme, Jérôme Cleach, Nathalie Jouy, Claire Crola Da Silva, Anne Devin, Thierry Grard, Philippe Lencel.
      Mitochondria are real sensors of the physiological status of tissues. After the death of an animal, they maintain physiological activity for several days. This activity is highly dependent on the availability of nutrients in the tissue. In this study, flow cytometry was used to measure the membrane potential of mitochondria isolated from European seabass (Dicentrarchus labrax) red muscle stored in ice for seven days in order to characterize fish freshness. Two probes, TMRM and Rhodamine 123, were used to measure mitochondrial potential. During the first few days (D0 to D3), isolated mitochondria maintained high potential, and then lost their potential (from D3 to D5), but were always re-polarizable after addition of substrates (glutamate, malate and succinate). From D7, the mitochondria were more strongly depolarized and were difficult to repolarize by the substrates. Using flow cytometry, we demonstrated that mitochondria were an excellent marker to confirm seabass freshness.
    Keywords:  European seabass; Fish freshness; Flow cytometry; Membrane potential; Mitochondria
    DOI:  https://doi.org/10.1016/j.foodchem.2021.131690
  14. Nucleic Acids Res. 2021 Dec 08. pii: gkab1187. [Epub ahead of print]
    FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism.
    Wenlu Fan, Xiaoye Jin, Man Xu, Yongmei Xi, Weiguo Lu, Xiaohang Yang, Min-Xin Guan, Wanzhong Ge.
      Mutations in genes encoding mitochondrial aminoacyl-tRNA synthetases are linked to diverse diseases. However, the precise mechanisms by which these mutations affect mitochondrial function and disease development are not fully understood. Here, we develop a Drosophila model to study the function of dFARS2, the Drosophila homologue of the mitochondrial phenylalanyl-tRNA synthetase, and further characterize human disease-associated FARS2 variants. Inactivation of dFARS2 in Drosophila leads to developmental delay and seizure. Biochemical studies reveal that dFARS2 is required for mitochondrial tRNA aminoacylation, mitochondrial protein stability, and assembly and enzyme activities of OXPHOS complexes. Interestingly, by modeling FARS2 mutations associated with human disease in Drosophila, we provide evidence that expression of two human FARS2 variants, p.G309S and p.D142Y, induces seizure behaviors and locomotion defects, respectively. Together, our results not only show the relationship between dysfunction of mitochondrial aminoacylation system and pathologies, but also illustrate the application of Drosophila model for functional analysis of human disease-causing variants.
    DOI:  https://doi.org/10.1093/nar/gkab1187
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