bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–02–19
fifty-four papers selected by
Catalina Vasilescu, Helmholz Munich
  1. The outer mitochondrial membrane protein TMEM11 demarcates spatially restricted BNIP3/BNIP3L-mediated mitophagy.
  2. Loss of mitochondrial Chchd10 or Chchd2 in zebrafish leads to an ALS-like phenotype and Complex I deficiency independent of the mitochondrial integrated stress response.
  3. Methylglyoxal-mediated Gpd1 activation restores the mitochondrial defects in a yeast model of mitochondrial DNA depletion syndrome.
  4. Macrocytosis in Mitochondrial DNA Deletion Syndromes.
  5. Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression.
  6. Elamipretide Improves ADP Sensitivity in Aged Mitochondria by Increasing Uptake through the Adenine Nucleotide Translocator (ANT).
  7. DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing.
  8. Cryo-EM and photocrosslinking studies reveal the mechanism of mitochondrial protein import by the TIM complex.
  9. Junctophilin-2 Regulates Mitochondrial Metabolism.
  10. Cone photoreceptors transfer damaged mitochondria to Müller glia.
  11. Iron status influences mitochondrial disease progression in Complex I-deficient mice.
  12. Acetylation and phosphorylation of mitochondrial transcription factor a promote mitochondrial transcription processivity.
  13. The role of the mechanistic target of rapamycin complex 1 in the regulation of mitochondrial adaptation during skeletal muscle atrophy under denervation or calorie restriction in mice.
  14. Pathological role of high sugar in mitochondrial respiratory chain defect - augmented mitochondrial stress.
  15. Dynamics & transport in 3D mitochondrial networks.
  16. Mitochondrial permeabilization in apoptosis: Advanced microscopy approaches.
  17. Dissecting the lipidic determinants of inner mitochondrial membrane structure.
  18. Reconstitution of mitochondrial transcriptional pausing.
  19. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
  20. Mitochondrial ROS as a regulator of synaptic function.
  21. Modeling and simulating human mitochondrial RNA polymerase nucleotide addition cycle using computational microscope.
  22. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A.
  23. Physiological significance of tissue-specific MICU regulation of mitochondrial calcium uptake.
  24. A novel therapeutic strategy against mitochondrial respiratory chain dysfunction-linked diseases.
  25. Molecular and cellular mechanisms underlying tissue-specific MICU-dimer assembly in the mitochondrial calcium uniporter complex.
  26. DLK-dependent mitochondrial fission drives axon degeneration and neuronal cell death.
  27. Decreased expression of mitochondrial aminoacyl-tRNA synthetases causes downregulation of OXPHOS subunits in type 2 diabetic muscle.
  28. Dissecting the impact of the degree of lipid saturation and presence of cardiolipin on the mitochondrial inner membrane mechanics.
  29. The multi-tissue landscape of somatic mtdna mutations indicates tissue specific accumulation and removal in aging.
  30. Biogenesis of mitochondrial outer membrane proteins.
  31. CryoEM of OPA1 helical structures gives perspective to mitochondrial dysfunction.
  32. Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3' Breakpoints.
  33. Conformational and functional interrelation between mitochondrial carrier proteins: UCP4, ANT, PiT.
  34. Calcium and bicarbonate signaling control mitochondrial ATP production.
  35. Trak adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport.
  36. Mitochondrial recovery by the UPRmt: Insights from C. elegans.
  37. Disease-associated mutations in Drp1 have fundamentally different effects on the mitochondrial fission machinery.
  38. New Mitochondrial Disease Identified In Monozygotic Twin Boys.
  39. Coupling of autophagy and the mitochondrial intrinsic apoptosis pathway modulates proteostasis and ageing in Caenorhabditis elegans.
  40. FDX1 regulates cellular protein lipoylation through direct binding to LIAS.
  41. Optical modulation of mitochondrial morphology and functions.
  42. Mitochondrial cristae morphology reflecting metabolism, superoxide formation, redox homeostasis, and pathology.
  43. Translation kinetics and diffusive timescales regulate mitochondrial localization of mRNAs in yeast and mammalian cells.
  44. 4D mitochondrial biophysical parameters predict cell type in human organoid tissue.
  45. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes.
  46. Long-Read Single-Cell Sequencing Using scCOLOR-seq.
  47. Depletion of plasma thymidine results in growth retardation and mitochondrial myopathy in mice overexpressing human thymidine phosphorylase.
  48. TRAF3: A novel regulator of mitochondrial physiology and metabolic pathways in B lymphocytes.
  49. Meta-analysis of NAD(P)(H) quantification results exhibits variability across mammalian tissues.
  50. Reverse electron transfer is activated during aging and contributes to aging and age-related disease.
  51. Mitochondrial uncouplers induce proton leak by activating AAC and UCP1.
  52. Mitochondrial rupture after photodamage initiates parkin-independent mitophagy in mouse hepatocytes.
  53. A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatment.
  54. Torin1 restores proliferation rate in Charcot-Marie-Tooth disease type 2A cells harbouring MFN2 (mitofusin 2) mutation.
  1. J Cell Biol. 2023 Apr 03. pii: e202204021. [Epub ahead of print]222(4):
    The outer mitochondrial membrane protein TMEM11 demarcates spatially restricted BNIP3/BNIP3L-mediated mitophagy.
    Mehmet Oguz Gok, Olivia M Connor, Xun Wang, Cameron J Menezes, Claire B Llamas, Prashant Mishra, Jonathan R Friedman.
      Mitochondria play critical roles in cellular metabolism and to maintain their integrity, they are regulated by several quality control pathways, including mitophagy. During BNIP3/BNIP3L-dependent receptor-mediated mitophagy, mitochondria are selectively targeted for degradation by the direct recruitment of the autophagy protein LC3. BNIP3 and/or BNIP3L are upregulated situationally, for example during hypoxia and developmentally during erythrocyte maturation. However, it is not well understood how they are spatially regulated within the mitochondrial network to locally trigger mitophagy. Here, we find that the poorly characterized mitochondrial protein TMEM11 forms a complex with BNIP3 and BNIP3L and co-enriches at sites of mitophagosome formation. We find that mitophagy is hyper-active in the absence of TMEM11 during both normoxia and hypoxia-mimetic conditions due to an increase in BNIP3/BNIP3L mitophagy sites, supporting a model that TMEM11 spatially restricts mitophagosome formation.
    DOI:  https://doi.org/10.1083/jcb.202204021
  2. Dev Neurobiol. 2023 Feb 16.
    Loss of mitochondrial Chchd10 or Chchd2 in zebrafish leads to an ALS-like phenotype and Complex I deficiency independent of the mitochondrial integrated stress response.
    Virginie Petel Légaré, Christian J Rampal, Tyler J N Gurberg, Mari J Aaltonen, Alexandre Janer, Lorne Zinman, Eric A Shoubridge, Gary A B Armstrong.
      Mutations in CHCHD10 and CHCHD2, encoding two paralogous mitochondrial proteins, have been identified in cases of amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTD), and Parkinson's disease (PD). Their role in disease is unclear, though both have been linked to mitochondrial respiration and mitochondrial stress responses. Here we investigated the biological roles of these proteins during vertebrate development using knockout (KO) models in zebrafish. We demonstrate that loss of either or both proteins leads to motor impairment, reduced survival and compromised neuromuscular junction (NMJ) integrity in larval zebrafish. Compensation by Chchd10 was observed in the chchd2-/- model, but not by Chchd2 in the chchd10 -/- model. The assembly of mitochondrial respiratory chain Complex I was impaired in chchd10 -/- and chchd2 -/- zebrafish larvae, but unexpectedly not in a double chchd10 -/- & chchd2 -/- model, suggesting that reduced mitochondrial Complex I cannot be solely responsible for the observed phenotypes, which are generally more severe in the double KO. We observed transcriptional activation markers of the mitochondrial integrated stress response (mt-ISR) in the double chchd10 -/- and chchd2 -/- KO model, suggesting that this pathway is involved in the restoration of Complex I assembly in our double KO model. The data presented here, demonstrates that the Complex I assembly defect in our single KO models arises independently of the mt-ISR. Furthermore, this study provides evidence that both proteins are required for normal vertebrate development. This article is protected by copyright. All rights reserved.
    Keywords:  CHCHD10; CHCHD2; amyotrophic lateral sclerosis; mitochondria; zebrafish
    DOI:  https://doi.org/10.1002/dneu.22909
  3. Biochim Biophys Acta Gen Subj. 2023 Feb 13. pii: S0304-4165(23)00026-0. [Epub ahead of print] 130328
    Methylglyoxal-mediated Gpd1 activation restores the mitochondrial defects in a yeast model of mitochondrial DNA depletion syndrome.
    Soumyajit Mukherjee, Shubhojit Das, Minakshi Bedi, Lavanya Vadupu, Writoban Basu Ball, Alok Ghosh.
      Human MPV17, an evolutionarily conserved mitochondrial inner-membrane channel protein, accounts for the tissue-specific mitochondrial DNA depletion syndrome. However, the precise molecular function of the MPV17 protein is still elusive. Previous studies showed that the mitochondrial morphology and cristae organization are severely disrupted in the MPV17 knockout cells from yeast, zebrafish, and mammalian tissues. As mitochondrial cristae morphology is strictly regulated by the membrane phospholipids composition, we measured mitochondrial membrane phospholipids (PLs) levels in yeast Saccharomyces cerevisiae MPV17 ortholog, SYM1 (Stress-inducible Yeast MPV17) deleted cells. We found that Sym1 knockout decreases the mitochondrial membrane PLs, phosphatidyl ethanolamine (PE), and inhibits respiratory growth at 37 ̊C on rich media. Both the oxygen consumption rate and the steady state expressions of mitochondrial complex II and super-complexes are compromised. Apart from mitochondrial PE defect a significant depletion of mitochondrial phosphatidyl-choline (PC) was noticed in the sym1∆ cells grown on synthetic media at both 30 ̊C and 37 ̊C temperatures. Surprisingly, exogenous supplementation of methylglyoxal (MG), an intrinsic side product of glycolysis, rescues the respiratory growth of Sym1 deficient yeast cells. Using a combination of molecular biology and lipid biochemistry, we uncovered that MG simultaneously restores both the mitochondrial PE/PC levels and the respiration by enhancing cytosolic NAD-dependent glycerol-3-phosphate dehydrogenase 1 (Gpd1) enzymatic activity. Further, MG is incapable to restore respiratory growth of the sym1∆gpd1∆ double knockout cells. Thus, our work provides Gpd1 activation as a novel strategy for combating Sym1 deficiency and PC/PE defects.
    Keywords:  Glycerol-3-phosphate dehydrogenase 1; Methylglyoxal; Mitochondrial respiratory chain; Phospholipids; SYM1
    DOI:  https://doi.org/10.1016/j.bbagen.2023.130328
  4. Acta Haematol. 2023 Feb 10.
    Macrocytosis in Mitochondrial DNA Deletion Syndromes.
    Farida Almarzooqi, Hilary Vallance, Michelle M Mezei, Anna Lehman, Gabriella Horvath, Bojana Rakic, Leslie Zypchen, Andre Mattman.
      Large single mtDNA (mitochondrial DNA) deletion syndrome is a rare inborn error of metabolism with variable heteroplasmy levels and clinical phenotype among affected individuals. Chronic progressive external ophthalmoplegia (CPEO) is the most common phenotype in adults with this form of mitochondrial disease [1-2]. The common CPEO clinical manifestations are ptosis and ophthalmoplegia. More variable phenotypic manifestations of CPEO (CPEO plus) include involvement of the peripheral nervous system and myopathy. Here, we describe a 62-year-old female with CPEO and the major mitochondrial DNA deletion present at 40% heteroplasmy, who had a coexistent previously undescribed CPEO phenotypic feature of persistent unexplained macrocytosis without anemia. Building on this case, we reviewed other major mtDNA deletion cases seen in our Adult Metabolic Diseases Clinic (AMDC) at the University of British Columbia, Vancouver, Canada from 2016 to 2022. The major mtDNA deletion cases (n=26) were compared with mtDNA missense variants identified in the clinic over the same period who acted as the comparison group (n=16). Of these, the most frequent diagnosis was maternally inherited diabetes and deafness (MIDD) and mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS). Ten out of 26 (38%) of mtDNA deletion patients had macrocytosis with elevated MCV (mean corpuscular volume), median (IQR, interquartile range) of 108fl (102-114fl). Seven of the patients with macrocytosis had no pertinent etiology. None of the comparison group had macrocytosis. There was a significant difference (P=0.000) between the MCV & MCH in the mtDNA deletion group compared to the comparison group. This communication sheds light on the association of macrocytosis with the mtDNA deletion syndrome. It would be of great interest to determine if the association is found in other mitochondrial disease clinic populations.
    DOI:  https://doi.org/10.1159/000529311
  5. bioRxiv. 2023 Feb 11. pii: 2023.02.11.528118. [Epub ahead of print]
    Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression.
    Nicholas J Kramer, Gyan Prakash, Karine Choquet, Iliana Soto, Boryana Petrova, Hope E Merens, Naama Kanarek, L Stirling Churchman.
      Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells, in which gene expression must be coordinated across organelles using distinct pools of ribosomes. How cells produce and maintain the accurate subunit stoichiometries for these OXPHOS complexes remains largely unknown. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of cytochrome c oxidase (Complex IV). We identified novel genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6 . We found that PREPL specifically regulates Complex IV biogenesis by interacting with mitochondrial protein synthesis machinery, while NME6, an uncharacterized nucleoside diphosphate kinase (NDPK), controls OXPHOS complex biogenesis through multiple mechanisms reliant on its NDPK domain. First, NME6 maintains local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Second, through stabilizing interactions with RCC1L, NME6 modulates the activity of mitoribosome regulatory complexes, leading to disruptions in mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression. Finally, we present these screens as a resource, providing a catalog of genes involved in mitonuclear gene regulation and OXPHOS biogenesis.
    DOI:  https://doi.org/10.1101/2023.02.11.528118
  6. bioRxiv. 2023 Feb 03. pii: 2023.02.01.525989. [Epub ahead of print]
    Elamipretide Improves ADP Sensitivity in Aged Mitochondria by Increasing Uptake through the Adenine Nucleotide Translocator (ANT).
    Gavin Pharaoh, Varun Kamat, Sricharan Kannan, Rudolph S Stuppard, Jeremy Whitson, Miguel Martin-Perez, Wei-Jun Qian, Michael J MacCoss, Judit Villen, Peter Rabinovitch, Matthew D Campbell, Ian R Sweet, David J Marcinek.
      Aging muscle experiences functional decline in part mediated by impaired mitochondrial ADP sensitivity. Elamipretide (ELAM) rapidly improves physiological and mitochondrial function in aging and binds directly to the mitochondrial ADP transporter ANT. We hypothesized that ELAM improves ADP sensitivity in aging leading to rescued physiological function. We measured the response to ADP stimulation in young and old muscle mitochondria with ELAM treatment, in vivo heart and muscle function, and compared protein abundance, phosphorylation, and S-glutathionylation of ADP/ATP pathway proteins. ELAM treatment increased ADP sensitivity in old muscle mitochondria by increasing uptake of ADP through the ANT and rescued muscle force and heart systolic function. Protein abundance in the ADP/ATP transport and synthesis pathway was unchanged, but ELAM treatment decreased protein s-glutathionylation incuding of ANT. Mitochondrial ADP sensitivity is rapidly modifiable. This research supports the hypothesis that ELAM improves ANT function in aging and links mitochondrial ADP sensitivity to physiological function.
    Abstract Figure:
    DOI:  https://doi.org/10.1101/2023.02.01.525989
  7. Nat Commun. 2023 Feb 16. 14(1): 874
    DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing.
    Li Mi, Ming Shi, Yu-Xuan Li, Gang Xie, Xichen Rao, Damu Wu, Aimin Cheng, Mengxiao Niu, Fengli Xu, Ying Yu, Ning Gao, Wensheng Wei, Xianhua Wang, Yangming Wang.
      Expanding mitochondrial base editing tools with broad sequence compatibility is of high need for both research and therapeutic purposes. In this study, we identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in DC context in double-stranded DNA (dsDNA). We successfully develop Ddd_Ss-derived cytosine base editors (DdCBE_Ss) and introduce mutations at multiple mitochondrial DNA (mtDNA) loci including disease-associated mtDNA mutations in previously inaccessible GC context. Finally, by introducing a single amino acid substitution from Ddd_Ss, we successfully improve the activity and sequence compatibility of DdCBE derived from DddA of Burkholderia cenocepacia (DdCBE_Bc). Our study expands mtDNA editing tool boxes and provides resources for further screening and engineering dsDNA base editors for biological and therapeutic applications.
    DOI:  https://doi.org/10.1038/s41467-023-36600-2
  8. Biophys J. 2023 Feb 10. pii: S0006-3495(22)03348-3. [Epub ahead of print]122(3S1): 452a
    Cryo-EM and photocrosslinking studies reveal the mechanism of mitochondrial protein import by the TIM complex.
    Eunyong Park.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.2432
  9. bioRxiv. 2023 Feb 08. pii: 2023.02.07.527576. [Epub ahead of print]
    Junctophilin-2 Regulates Mitochondrial Metabolism.
    Sasha Z Prisco, Lynn M Hartweck, Felipe Kazmirczak, Jenna B Mendelson, Stephanie L Deng, Satadru K Lahiri, Xander H T Wehrens, Kurt W Prins.
      Right ventricular dysfunction (RVD) is a risk factor for mortality in multiple cardiovascular diseases, but approaches to combat RVD are lacking. Therapies used for left heart failure are largely ineffective in RVD, and thus the identification of molecules that augment RV function could improve outcomes in a wide-array of cardiac limitations. Junctophilin-2 (JPH2) is an essential protein that plays important roles in cardiomyocytes, including calcium handling/maintenance of t-tubule structure and gene transcription. Additionally, JPH2 may regulate mitochondrial function as Jph2 knockout mice exhibit cardiomyocyte mitochondrial swelling and cristae derangements. Moreover, JPH2 knockdown in embryonic stem cell-derived cardiomyocytes induces downregulation of the mitochondrial protein mitofusin-2 (MFN2), which disrupts mitochondrial cristae structure and transmembrane potential. Impaired mitochondrial metabolism drives RVD, and here we evaluated the mitochondrial role of JPH2. We showed JPH2 directly interacts with MFN2, ablation of JPH2 suppresses mitochondrial biogenesis, oxidative capacity, and impairs lipid handling in iPSC-CM. Gene therapy with AAV9-JPH2 corrects RV mitochondrial morphological defects, mitochondrial fatty acid metabolism enzyme regulation, and restores the RV lipidomic signature in the monocrotaline rat model of RVD. Finally, AAV-JPH2 improves RV function without altering PAH severity, showing JPH2 provides an inotropic effect to the dysfunction RV.
    DOI:  https://doi.org/10.1101/2023.02.07.527576
  10. Cell Rep. 2023 Feb 15. pii: S2211-1247(23)00126-2. [Epub ahead of print]42(2): 112115
    Cone photoreceptors transfer damaged mitochondria to Müller glia.
    Rachel A Hutto, Kaitlyn M Rutter, Michelle M Giarmarco, Edward D Parker, Zachary S Chambers, Susan E Brockerhoff.
      Mitochondria are vital organelles that require sophisticated homeostatic mechanisms for maintenance. Intercellular transfer of damaged mitochondria is a recently identified strategy broadly used to improve cellular health and viability. Here, we investigate mitochondrial homeostasis in the vertebrate cone photoreceptor, the specialized neuron that initiates our daytime and color vision. We find a generalizable response to mitochondrial stress that leads to loss of cristae, displacement of damaged mitochondria from their normal cellular location, initiation of degradation, and transfer to Müller glia cells, a key non-neuronal support cell in the retina. Our findings show transmitophagy from cones to Müller glia as a response to mitochondrial damage. Intercellular transfer of damaged mitochondria represents an outsourcing mechanism that photoreceptors use to support their specialized function.
    Keywords:  CP: Neuroscience; Müller glia; mitochondria; mitophagy; photoreceptor; retina; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2023.112115
  11. Elife. 2023 Feb 17. pii: e75825. [Epub ahead of print]12
    Iron status influences mitochondrial disease progression in Complex I-deficient mice.
    C J Kelly, Reid K Couch, Vivian T Ha, Camille M Bodart, Judy Wu, Sydney Huff, Nicole T Herrel, Hyunsung D Kim, Azaad O Zimmermann, Jessica Shattuck, Yu-Chen Pan, Matt Kaeberlein, Anthony S Grillo.
      Mitochondrial dysfunction caused by aberrant Complex I assembly and reduced activity of the electron transport chain is pathogenic in many genetic and age-related diseases. Mice missing the Complex I subunit NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 (NDUFS4) are a leading mammalian model of severe mitochondrial disease that exhibit many characteristic symptoms of Leigh Syndrome including oxidative stress, neuroinflammation, brain lesions, and premature death. NDUFS4 knockout mice have decreased expression of nearly every Complex I subunit. As Complex I normally contains at least 8 iron-sulfur clusters and more than 25 iron atoms, we asked whether a deficiency of Complex I may lead to iron perturbations thereby accelerating disease progression. Consistent with this, iron supplementation accelerates symptoms of brain degeneration in these mice while iron restriction delays the onset of these symptoms, reduces neuroinflammation, and increases survival. NDUFS4 knockout mice display signs of iron overload in the liver including increased expression of hepcidin, and show changes in iron responsive element-regulated proteins consistent with increased cellular iron that were prevented by iron restriction. These results suggest that perturbed iron homeostasis may contribute to pathology in Leigh Syndrome and possibly other mitochondrial disorders.
    Keywords:  biochemistry; chemical biology; medicine; mouse
    DOI:  https://doi.org/10.7554/eLife.75825
  12. Biophys J. 2023 Feb 10. pii: S0006-3495(22)03546-9. [Epub ahead of print]122(3S1): 492a
    Acetylation and phosphorylation of mitochondrial transcription factor a promote mitochondrial transcription processivity.
    Sean D Reardon, Tatiana V Mishanina.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.2630
  13. Appl Physiol Nutr Metab. 2023 Feb 14.
    The role of the mechanistic target of rapamycin complex 1 in the regulation of mitochondrial adaptation during skeletal muscle atrophy under denervation or calorie restriction in mice.
    Kazuki Uemichi, Takanaga Shirai, Ryunosuke Matsuno, Tomohiro Iwata, Riku Tanimura, Tohru Takemasa.
      Mechanistic target of rapamycin complex 1 (mTORC1) is a protein complex that regulates skeletal muscle protein synthesis and hypertrophy. mTORC1-mediated signaling activities are activated during denervation-induced skeletal muscle atrophy and suppressed during calorie restriction-induced atrophy. Mitochondria control the qualitative plasticity of skeletal muscles primarily through biogenesis, fusion, and fission. We recently showed that mTORC1 activation contributes toward mitochondrial homeostasis. In this study, we examined the role of mTORC1 in mitochondrial adaptation during denervation- or calorie restriction-induced skeletal muscle atrophy. Seven-week-old Institute of Cancer Research mice were subjected to 14 days of denervation or calorie restriction combined with the administration of the mTORC1 inhibitor-"rapamycin". Our results showed that although mTORC1 inhibition did not alter mitochondrial biogenesis, content and enzyme activity, it suppressed the activation of dynamin-related protein 1 (DRP1), a mitochondrial fission-related protein in denervated muscle, and reduced DRP1 expression in calorie-restricted muscle. Furthermore, calorie restriction-induced mitochondrial fragmentation was partially suppressed by mTORC1 inhibition. Taken together, our results indicate that mTORC1 activation upon denervation and inhibition upon calorie restriction contributes to qualitative changes in muscle plasticity by at least partially regulating the mitochondrial fission response.
    Keywords:  mTORC1; mitochondrial dynamics; skeletal muscle atrophy
    DOI:  https://doi.org/10.1139/apnm-2022-0336
  14. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01622-8. [Epub ahead of print]122(3S1): 94a-95a
    Pathological role of high sugar in mitochondrial respiratory chain defect - augmented mitochondrial stress.
    Ebrima D Cham, Mei-Jie Jou.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.706
  15. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02320-7. [Epub ahead of print]122(3S1): 240a
    Dynamics & transport in 3D mitochondrial networks.
    Keaton Holt, Elena F Koslover.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1404
  16. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01187-0. [Epub ahead of print]122(3S1): 7a
    Mitochondrial permeabilization in apoptosis: Advanced microscopy approaches.
    Ana J Garcia-Saez.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.271
  17. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01636-8. [Epub ahead of print]122(3S1): 98a
    Dissecting the lipidic determinants of inner mitochondrial membrane structure.
    Kailash Venkatraman, Christopher T Lee, Guadalupe Garcia, Arijit Mahapatra, Keunyoung Kim, Guy Perkins, Sebastien Phan, Hilda A Pasolli, Jennifer Lippincott-Schwartz, Mark Ellisman, Padmini Rangamani, Itay Budin.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.720
  18. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01503-X. [Epub ahead of print]122(3S1): 70a
    Reconstitution of mitochondrial transcriptional pausing.
    An H Hsieh.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.587
  19. Nat Protoc. 2023 Feb 15.
    Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
    Caleb A Lareau, Vincent Liu, Christoph Muus, Samantha D Praktiknjo, Lena Nitsch, Pauline Kautz, Katalin Sandor, Yajie Yin, Jacob C Gutierrez, Karin Pelka, Ansuman T Satpathy, Aviv Regev, Vijay G Sankaran, Leif S Ludwig.
      Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called 'mitochondrial single-cell assay for transposase-accessible chromatin with sequencing' (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take ~3-4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.
    DOI:  https://doi.org/10.1038/s41596-022-00795-3
  20. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01623-X. [Epub ahead of print]122(3S1): 95a
    Mitochondrial ROS as a regulator of synaptic function.
    Irina Stavrovskaya, Bethany Kristi Morin, Pablo M Peixoto.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.707
  21. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01490-4. [Epub ahead of print]122(3S1): 68a
    Modeling and simulating human mitochondrial RNA polymerase nucleotide addition cycle using computational microscope.
    Shannon J McElhenney, Moises E Romero, Jin Yu.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.574
  22. bioRxiv. 2023 Feb 07. pii: 2023.02.07.526487. [Epub ahead of print]
    Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A.
    University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN)
       Objectives: Transcript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored.
    Methods: We applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis.
    Results: We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A).
    Discussion: This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.
    DOI:  https://doi.org/10.1101/2023.02.07.526487
  23. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02307-4. [Epub ahead of print]122(3S1): 237a
    Physiological significance of tissue-specific MICU regulation of mitochondrial calcium uptake.
    Madison Rodriguez, Chen-Wei Tsai, Ming-Feng Tsai.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1391
  24. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02620-0. [Epub ahead of print]122(3S1): 302a
    A novel therapeutic strategy against mitochondrial respiratory chain dysfunction-linked diseases.
    Daniele Bonesso, Andrea Mattarei, Roberta Peruzzo, Marta Favero, Andrea Rossa, Massimo Zeviani, Carlo Viscomi, Ildikò Szabò.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1704
  25. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01321-2. [Epub ahead of print]122(3S1): 35a
    Molecular and cellular mechanisms underlying tissue-specific MICU-dimer assembly in the mitochondrial calcium uniporter complex.
    Chen-Wei Tsai, Madison Rodriguez, Ming-Feng Tsai.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.405
  26. bioRxiv. 2023 Feb 01. pii: 2023.01.30.526132. [Epub ahead of print]
    DLK-dependent mitochondrial fission drives axon degeneration and neuronal cell death.
    Jorge Gómez-Deza J, Matthew Nebiyou, Mor R Alkaslasi, Preethi Somasundaran, Anastasia L Slavutsky, Michael E Ward, Trent A Watkins, Claire E Le Pichon.
      Currently there are no effective treatments for an array of neurodegenerative disorders to a large part because cell-based models fail to recapitulate disease. Here we developed a robust human iPSCbased model where laser axotomy causes retrograde axon degeneration leading to neuronal cell death. Time-lapse confocal imaging revealed that damage triggers a wave of mitochondrial fission proceeding from the site of injury to the soma. We demonstrated that mitochondrial fission and resultant cell death is entirely dependent on phosphorylation of dynamin related protein 1 (DRP1) by dual leucine zipper kinase (DLK). Importantly, we show that CRISPR mediated Drp1 depletion protected mouse retinal ganglion neurons from mitochondrial fission and degeneration after optic nerve crush. Our results provide a powerful platform for studying degeneration of human neurons, pinpoint key early events in damage related neural death and new focus for therapeutic intervention.
    DOI:  https://doi.org/10.1101/2023.01.30.526132
  27. Redox Biol. 2023 Feb 08. pii: S2213-2317(23)00031-9. [Epub ahead of print]61 102630
    Decreased expression of mitochondrial aminoacyl-tRNA synthetases causes downregulation of OXPHOS subunits in type 2 diabetic muscle.
    Iliana López-Soldado, Adrian Gabriel Torres, Raúl Ventura, Inma Martínez-Ruiz, Angels Díaz-Ramos, Evarist Planet, Diane Cooper, Agnieszka Pazderska, Krzysztof Wanic, Declan O'Hanlon, Donal J O'Gorman, Teresa Carbonell, Lluís Ribas de Pouplana, John J Nolan, Antonio Zorzano, María Isabel Hernández-Alvarez.
      Type 2 diabetes mellitus (T2D) affects millions of people worldwide and is one of the leading causes of morbidity and mortality. The skeletal muscle (SKM) is one of the most important tissues involved in maintaining glucose homeostasis and substrate oxidation, and it undergoes insulin resistance in T2D. In this study, we identify the existence of alterations in the expression of mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in skeletal muscle from two different forms of T2D: early-onset type 2 diabetes (YT2) (onset of the disease before 30 years of age) and the classical form of the disease (OT2). GSEA analysis from microarray studies revealed the repression of mitochondrial mt-aaRSs independently of age, which was validated by real-time PCR assays. In agreement with this, a reduced expression of several encoding mt-aaRSs was also detected in skeletal muscle from diabetic (db/db) mice but not in obese ob/ob mice. In addition, the expression of the mt-aaRSs proteins most relevant in the synthesis of mitochondrial proteins, threonyl-tRNA, and leucyl-tRNA synthetases (TARS2 and LARS2) were also repressed in muscle from db/db mice. It is likely that these alterations participate in the reduced expression of proteins synthesized in the mitochondria detected in db/db mice. We also document an increased iNOS abundance in mitochondrial-enriched muscle fractions from diabetic mice that may inhibit aminoacylation of TARS2 and LARS2 by nitrosative stress. Our results indicate a reduced expression of mt-aaRSs in skeletal muscle from T2D patients, which may participate in the reduced expression of proteins synthesized in mitochondria. An enhanced mitochondrial iNOS could play a regulatory role in diabetes.
    Keywords:  Mitochondrial aminoacyl tRNA synthetases; Nitric oxide; Nitrosative stress; OXPHOS; Skeletal muscle; Type 2 diabetes
    DOI:  https://doi.org/10.1016/j.redox.2023.102630
  28. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01561-2. [Epub ahead of print]122(3S1): 81a
    Dissecting the impact of the degree of lipid saturation and presence of cardiolipin on the mitochondrial inner membrane mechanics.
    Christopher T Lee, Kailash Venkatraman, Itay Budin, Padmini Rangamani.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.645
  29. Elife. 2023 Feb 17. pii: e83395. [Epub ahead of print]12
    The multi-tissue landscape of somatic mtdna mutations indicates tissue specific accumulation and removal in aging.
    Monica Sanchez-Contreras, Mariya T Sweetwyne, Kristine A Tsantilas, Jeremy A Whitson, Matthew D Campbell, Brenden F Kohrn, Hyeon Jeong Kim, Michael J Hipp, Jeanne Fredrickson, Megan M Nguyen, James B Hurley, David J Marcinek, Peter S Rabinovitch, Scott R Kennedy.
      Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
    Keywords:  genetics; genomics; mouse
    DOI:  https://doi.org/10.7554/eLife.83395
  30. Biophys J. 2023 Feb 10. pii: S0006-3495(22)03349-5. [Epub ahead of print]122(3S1): 452a
    Biogenesis of mitochondrial outer membrane proteins.
    Rebecca Voorhees.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.2433
  31. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02623-6. [Epub ahead of print]122(3S1): 303a
    CryoEM of OPA1 helical structures gives perspective to mitochondrial dysfunction.
    Sarah B Nyenhuis, Xufeng S Wu, Abigail Stanton, Marie-Paule Strub, Yang-In Yim, Bertram J Canagarajah, Jenny E Hinshaw.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1707
  32. Complex Psychiatry. 2023 Jan;8(3-4): 90-98
    Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3' Breakpoints.
    Brooke E Hjelm, Christian Ramiro, Brandi L Rollins, Audrey A Omidsalar, Daniel S Gerke, Sujan C Das, Adolfo Sequeira, Ling Morgan, Alan F Schatzberg, Jack D Barchas, Francis S Lee, Richard M Myers, Stanley J Watson, Huda Akil, William E Bunney, Marquis P Vawter.
       Introduction: Large somatic deletions of mitochondrial DNA (mtDNA) accumulate with aging in metabolically active tissues such as the brain. We have cataloged the breakpoints and frequencies of large mtDNA deletions in the human brain.
    Methods: We quantified 112 high-frequency mtDNA somatic deletions across four human brain regions with the Splice-Break2 pipeline. In addition, we utilized PLINK/Seq to test the association of mitochondrial genotypes with the abundance of these high-frequency mtDNA deletions. A conservative p value threshold of 5E-08 was used to find the significant loci.
    Results: One mtDNA SNP (T14798C) was significantly associated with mtDNA deletions in two brain regions, the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus. Since the DLPFC showed the most robust association between T14798C and two deletion breakpoints (7816-14807 and 5462-14807), this association was tested in the DLPFC of a replication sample and validated the first results. Incorporating the C allele at 14,798 bp increased the perfect/imperfect length of the repeat at the 3' breakpoint of the two associated deletions.
    Conclusion: This is the first study to identify the association of mtDNA SNP with large mtDNA deletions in the human brain. The T14798C allele located in the MT-CYB gene is a common polymorphism that occurs in several mitochondrial haplogroups. We hypothesize that the T14798C association with two deletions occurs by extending the repeat length around the 3' deletion breakpoints. This simple mechanism suggests that mtDNA SNPs can affect the mitochondrial genome structure, especially in brain where high levels of reactive oxygen species lead to deletion accumulation with aging.
    Keywords:  Dorsolateral prefrontal cortex; Mitochondrial DNA somatic deletion; Primary visual cortex; Superior temporal gyrus
    DOI:  https://doi.org/10.1159/000528051
  33. Biophys J. 2023 Feb 10. pii: S0006-3495(22)03095-8. [Epub ahead of print]122(3S1): 399a
    Conformational and functional interrelation between mitochondrial carrier proteins: UCP4, ANT, PiT.
    Marzieh Tabefam, Matthew D Smith, Masoud Jelokhani-Niaraki.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.2179
  34. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01619-8. [Epub ahead of print]122(3S1): 94a
    Calcium and bicarbonate signaling control mitochondrial ATP production.
    Maura Greiser, Mariusz Karbowski, Aaron D Kaplan, Andrew Coleman, Carmen A Mannella, W Jonathan Lederer, Liron Boyman.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.703
  35. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01276-0. [Epub ahead of print]122(3S1): 25a-26a
    Trak adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport.
    Merve Aslan, Andrew M Hensley, John Canty, Amanda Jack, Ahmet Yildiz.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.360
  36. Semin Cell Dev Biol. 2023 Feb 13. pii: S1084-9521(23)00030-7. [Epub ahead of print]
    Mitochondrial recovery by the UPRmt: Insights from C. elegans.
    Joshua D Dodge, Nicholas J Browder, Mark W Pellegrino.
      Mitochondria are multifaceted organelles, with such functions as the production of cellular energy to the regulation of cell death. However, mitochondria incur various sources of damage from the accumulation of reactive oxygen species and DNA mutations that can impact the protein folding environment and impair their function. Since mitochondrial dysfunction is often associated with reductions in organismal fitness and possibly disease, cells must have safeguards in place to protect mitochondrial function and promote recovery during times of stress. The mitochondrial unfolded protein response (UPRmt) is a transcriptional adaptation that promotes mitochondrial repair to aid in cell survival during stress. While the earlier discoveries into the regulation of the UPRmt stemmed from studies using mammalian cell culture, much of our understanding about this stress response has been bestowed to us by the model organism Caenorhabditis elegans. Indeed, the facile but powerful genetics of this relatively simple nematode has uncovered multiple regulators of the UPRmt, as well as several physiological roles of this stress response. In this review, we will summarize these major advancements originating from studies using C. elegans.
    Keywords:  Aging; C. elegans; Host-pathogen interactions; Infection; Mitochondria; Mitochondrial UPR; Stress response
    DOI:  https://doi.org/10.1016/j.semcdb.2023.02.002
  37. Biophys J. 2023 Feb 10. pii: S0006-3495(22)03497-X. [Epub ahead of print]122(3S1): 482a
    Disease-associated mutations in Drp1 have fundamentally different effects on the mitochondrial fission machinery.
    Brianna L Bauer, Kristy Rochon, Jasmine Liu, Rajesh Ramachandran, Jason A Mears.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.2581
  38. Am J Med Genet A. 2023 Mar;191(3): 655-656
    New Mitochondrial Disease Identified In Monozygotic Twin Boys.
      
    DOI:  https://doi.org/10.1002/ajmg.a.62796
  39. Cell Death Dis. 2023 Feb 11. 14(2): 110
    Coupling of autophagy and the mitochondrial intrinsic apoptosis pathway modulates proteostasis and ageing in Caenorhabditis elegans.
    Christina Ploumi, Emmanouil Kyriakakis, Nektarios Tavernarakis.
      Mitochondria preserve metabolic homeostasis and integrate stress signals, to trigger cytoprotective, or cell death pathways. Mitochondrial homeostasis and function decline with age. The mechanisms underlying the deterioration of mitochondrial homeostasis during ageing, or in age-associated pathologies, remain unclear. Here, we show that CISD-1, a mitochondrial iron-sulfur cluster binding protein, implicated in the pathogenesis of Wolfram neurodegenerative syndrome type 2, modulates longevity in the nematode Caenorhabditis elegans by engaging autophagy and the mitochondrial intrinsic apoptosis pathway. The anti-apoptotic protein CED-9 is the downstream effector that mediates CISD-1-dependent effects on proteostasis, neuronal integrity and lifespan. Moreover, intracellular iron abundance is critical for CISD-1 function, since mild iron supplementation is sufficient to decelerate ageing and partly ameliorate the disturbed mitochondrial bioenergetics and proteostasis of CISD-1 deficient animals. Our findings reveal that CISD-1 serves as a mechanistic link between autophagy and the apoptotic pathway in mitochondria to differentially modulate organismal proteostasis and ageing, and suggest novel approaches which could facilitate the treatment of Wolfram Syndrome or related diseases.
    DOI:  https://doi.org/10.1038/s41419-023-05638-x
  40. bioRxiv. 2023 Feb 04. pii: 2023.02.03.526472. [Epub ahead of print]
    FDX1 regulates cellular protein lipoylation through direct binding to LIAS.
    Margaret B Dreishpoon, Nolan R Bick, Boryana Petrova, Douglas M Warui, Alison Cameron, Squire J Booker, Naama Kanarek, Todd R Golub, Peter Tsvetkov.
      Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 regulates protein lipoylation by directly binding to the lipoyl synthase (LIAS) enzyme and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss-of-function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling of cells growing in either normal or low glucose conditions established that FDX1 loss-of-function results in the induction of both compensatory metabolism related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-functions is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.
    DOI:  https://doi.org/10.1101/2023.02.03.526472
  41. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01635-6. [Epub ahead of print]122(3S1): 97a-98a
    Optical modulation of mitochondrial morphology and functions.
    Kangqiang Qiu, Weiwei Zou, Hongbao Fang, Minggang Hao, Kritika Mehta, Zhiqi Tian, Jun-Lin Guan, Taosheng Huang, Jiajie Diao, Kai Zhang.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.719
  42. Antioxid Redox Signal. 2023 Feb 15.
    Mitochondrial cristae morphology reflecting metabolism, superoxide formation, redox homeostasis, and pathology.
    Petr Jezek, Martin Jaburek, Blanka Holendova, Hana Engstová, Andrea Dlasková.
       SIGNIFICANCE: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated mitochondrial inner membrane (IMM). Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CM) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM SAM. Cristae dimensions, shape and CJs have characteristic patterns for different metabolic regimes, physiological, and pathological situations.
    RECENT ADVANCES: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, OPA1 isoforms and MGM1 filaments, prohibitins and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid.
    CRITICAL ISSUES: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by posttranslational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation.
    FUTURE DIRECTIONS: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases.
    DOI:  https://doi.org/10.1089/ars.2022.0173
  43. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02610-8. [Epub ahead of print]122(3S1): 300a
    Translation kinetics and diffusive timescales regulate mitochondrial localization of mRNAs in yeast and mammalian cells.
    Ximena Garcia Arceo, Elena F Koslover, Brian M Zid, Aidan Brown.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1694
  44. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02622-4. [Epub ahead of print]122(3S1): 303a
    4D mitochondrial biophysical parameters predict cell type in human organoid tissue.
    Gillian McMahon, McKenna Rude, Challana Tea, Zichen Wang, Parth Natekar, Hiroyuki Hakozaki, Johannes Schöneberg.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1706
  45. Cell Genom. 2022 Sep 14. 2(9): 100168
    Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes.
    Konrad J Karczewski, Matthew Solomonson, Katherine R Chao, Julia K Goodrich, Grace Tiao, Wenhan Lu, Bridget M Riley-Gillis, Ellen A Tsai, Hye In Kim, Xiuwen Zheng, Fedik Rahimov, Sahar Esmaeeli, A Jason Grundstad, Mark Reppell, Jeff Waring, Howard Jacob, David Sexton, Paola G Bronson, Xing Chen, Xinli Hu, Jacqueline I Goldstein, Daniel King, Christopher Vittal, Timothy Poterba, Duncan S Palmer, Claire Churchhouse, Daniel P Howrigan, Wei Zhou, Nicholas A Watts, Kevin Nguyen, Huy Nguyen, Cara Mason, Christopher Farnham, Charlotte Tolonen, Laura D Gauthier, Namrata Gupta, Daniel G MacArthur, Heidi L Rehm, Cotton Seed, Anthony A Philippakis, Mark J Daly, J Wade Davis, Heiko Runz, Melissa R Miller, Benjamin M Neale.
      Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
    Keywords:  GWAS; PheWAS; biobanks; exome sequencing; rare variant association studies; rare variants
    DOI:  https://doi.org/10.1016/j.xgen.2022.100168
  46. Methods Mol Biol. 2023 ;2632 259-267
    Long-Read Single-Cell Sequencing Using scCOLOR-seq.
    Martin Philpott, Udo Oppermann, Adam P Cribbs.
      Single-cell sequencing allows for the measurement of sequence information from individual cells with next-generation sequencing (NGS). However, its application to third-generation sequencing platforms such as Oxford Nanopore has been challenging because of its lower basecalling accuracy. Here we describe the method to perform highly accurate single-cell COrrected Long-Read sequencing (scCOLOR-seq) by droplet-based encapsulation of cells and sequencing using the Oxford Nanopore Sequencing system.
    Keywords:  Long-read; Oxford Nanopore Sequencing; Single-cell
    DOI:  https://doi.org/10.1007/978-1-0716-2996-3_18
  47. J Biol Chem. 2023 Feb 09. pii: S0021-9258(23)00134-5. [Epub ahead of print] 103002
    Depletion of plasma thymidine results in growth retardation and mitochondrial myopathy in mice overexpressing human thymidine phosphorylase.
    Naomoto Harada, Haruka Nagasaki, Hiromi Yamamoto, Kenji Matsubara, Takamasa Suzuki, Akira Gomori, Tatsushi Yokogawa, Kenichi Matsuo, Kazutaka Miyadera.
      Plasma thymidine levels in rodents are higher than in other mammals including humans, possibly due to a different pattern and lower level of thymidine phosphorylase (TP) expression. Here, we generated a novel knock-in (KI) mouse line with high systemic expression of human TP to investigate this difference in nucleotide metabolism in rodents. The KI mice showed growth retardation around weaning and died by four weeks of age with a decrease in plasma thymidine level compared to the litter-control WT mice. These phenotypes were completely or partially rescued by administration of the thymidine phosphorylase inhibitor (TPI) 5-chloro-6-(2-iminopyrrolidin-1-yl) methyl-2,4(1H,3H)-pyrimidinedione hydrochloride or thymidine, respectively. Interestingly, when TPI administration was discontinued in adult animals, KI mice showed deteriorated grip strength and locomotor activity, decreased bodyweight, and subsequent hind-limb paralysis. Upon histological analyses, we observed axonal degeneration in the spinal cord, muscular atrophy with morphologically abnormal mitochondria in quadriceps, retinal degeneration, and abnormality in the exocrine pancreas. Moreover, we detected mitochondrial DNA (mtDNA) depletion in multiple tissues of KI mice. These results indicate that the KI mouse represents a new animal model for mitochondrial diseases and should be applicable for the study of differences in nucleotide metabolism between humans and mice.
    Keywords:  Mitochondrial disease; mitochondrial DNA (mtDNA); mitochondrial neurogastrointestinal encephalopathy (MNGIE); myopathy; nucleoside/nucleotide metabolism; thymidine phosphorylase (TP); transgenic mice; uridine phosphorylase (UP)
    DOI:  https://doi.org/10.1016/j.jbc.2023.103002
  48. Front Oncol. 2023 ;13 1081253
    TRAF3: A novel regulator of mitochondrial physiology and metabolic pathways in B lymphocytes.
    Jaeyong Jung, Samantha Gokhale, Ping Xie.
      Mitochondria, the organelle critical for cell survival and metabolism, are exploited by cancer cells and provide an important therapeutic target in cancers. Mitochondria dynamically undergo fission and fusion to maintain their diverse functions. Proteins controlling mitochondrial fission and fusion have been recognized as essential regulators of mitochondrial functions, mitochondrial quality control, and cell survival. In a recent proteomic study, we identified the key mitochondrial fission factor, MFF, as a new interacting protein of TRAF3, a known tumor suppressor of multiple myeloma and other B cell malignancies. This interaction recruits the majority of cytoplasmic TRAF3 to mitochondria, allowing TRAF3 to regulate mitochondrial morphology, mitochondrial functions, and mitochondria-dependent apoptosis in resting B lymphocytes. Interestingly, recent transcriptomic, metabolic and lipidomic studies have revealed that TRAF3 also vitally regulates multiple metabolic pathways in B cells, including phospholipid metabolism, glucose metabolism, and ribonucleotide metabolism. Thus, TRAF3 emerges as a novel regulator of mitochondrial physiology and metabolic pathways in B lymphocytes and B cell malignancies. Here we review current knowledge in this area and discuss relevant clinical implications.
    Keywords:  B lymphocytes; TRAF3; lymphomas; metabolism; mitochondria
    DOI:  https://doi.org/10.3389/fonc.2023.1081253
  49. Sci Rep. 2023 Feb 11. 13(1): 2464
    Meta-analysis of NAD(P)(H) quantification results exhibits variability across mammalian tissues.
    Dassine Azouaoui, Michael René Choinière, Momtafin Khan, Shahab Sayfi, Simran Jaffer, Selvia Yousef, David A Patten, Alexander E Green, Keir J Menzies.
      Nicotinamide Adenine Dinucleotide (NAD+) plays an important role in energy metabolism and signaling pathways controlling crucial cellular functions. The increased interest in NAD+ metabolism and NAD+-boosting therapies has reinforced the necessity for accurate NAD+ quantification. To examine the published NAD(P)(H) measures across mammalian tissues, we performed a meta-analysis of the existing data. An Ovid MEDLINE database search identified articles with NAD(P)(H) quantification results obtained from mammalian tissues published between 1961 and 2021. We screened 4890 records and extracted quantitative data, as well as the quantification methods, pre-analytical conditions, and subject characteristics. The extracted physiological NAD(P)(H) concentrations in various tissues from mice, rats, and humans, revealed an important inter- and intra-method variability that extended to recent publications. This highlights the relatively poor potential for cross-experimental analyses for NAD(P)(H) quantitative data and the importance of standardization for NAD(P)(H) quantification methods and pre-analytical procedures for future preclinical and clinical studies.
    DOI:  https://doi.org/10.1038/s41598-023-29607-8
  50. EMBO Rep. 2023 Feb 16. e55548
    Reverse electron transfer is activated during aging and contributes to aging and age-related disease.
    Suman Rimal, Ishaq Tantray, Yu Li, Tejinder Pal Khaket, Yanping Li, Sunil Bhurtel, Wen Li, Cici Zeng, Bingwei Lu.
      Mechanisms underlying the depletion of NAD+ and accumulation of reactive oxygen species (ROS) in aging and age-related disorders remain poorly defined. We show that reverse electron transfer (RET) at mitochondrial complex I, which causes increased ROS production and NAD+ to NADH conversion and thus lowered NAD+ /NADH ratio, is active during aging. Genetic or pharmacological inhibition of RET decreases ROS production and increases NAD+ /NADH ratio, extending the lifespan of normal flies. The lifespan-extending effect of RET inhibition is dependent on NAD+ -dependent Sirtuin, highlighting the importance of NAD+ /NADH rebalance, and on longevity-associated Foxo and autophagy pathways. RET and RET-induced ROS and NAD+ /NADH ratio changes are prominent in human induced pluripotent stem cell (iPSC) model and fly models of Alzheimer's disease (AD). Genetic or pharmacological inhibition of RET prevents the accumulation of faulty translation products resulting from inadequate ribosome-mediated quality control, rescues relevant disease phenotypes, and extends the lifespan of Drosophila and mouse AD models. Deregulated RET is therefore a conserved feature of aging, and inhibition of RET may open new therapeutic opportunities in the context of aging and age-related diseases including AD.
    Keywords:  Alzheimer's disease; NAD+/NADH ratio; lifespan; mitochondrial complex I; reverse electron transport
    DOI:  https://doi.org/10.15252/embr.202255548
  51. Biophys J. 2023 Feb 10. pii: S0006-3495(22)02637-6. [Epub ahead of print]122(3S1): 306a
    Mitochondrial uncouplers induce proton leak by activating AAC and UCP1.
    Ambre Bertholet, Andrew Natale, Paola Bisignano, Junji Suzuki, Andriy Fedorenko, James Hamilton, Tatiana Brustovetsky, Lawrence Kazak, Edward T Chouchani, Nickolay Brustovetsky, Michael Grabe, Yuriy V Kirichok.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.1721
  52. Biophys J. 2023 Feb 10. pii: S0006-3495(22)01638-1. [Epub ahead of print]122(3S1): 98a
    Mitochondrial rupture after photodamage initiates parkin-independent mitophagy in mouse hepatocytes.
    Li Li, Jiangting Hu, Zhi Zhong, Eeva-Liisa Eskelinen, John J Lemasters.
      
    DOI:  https://doi.org/10.1016/j.bpj.2022.11.722
  53. bioRxiv. 2023 Feb 03. pii: 2023.02.02.526527. [Epub ahead of print]
    A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatment.
    Yu Leng Phua, Olivia M Dâ Annibale, Anuradha Karunanidhi, Al-Walid Mohsen, Brian Kirmse, Steven F Dobrowolski, Jerry Vockley.
      Combined D, L-2-Hydroxyglutaric Aciduria (D,L-2HGA) is a rare genetic disorder caused by recessive mutations in the SLC25A1 gene that encodes the mitochondrial citrate carrier protein (CIC). SLC25A1 deficiency leads to a secondary increase in mitochondrial 2-ketoglutarate that, in turn, is reduced to neurotoxic 2-hydroxyglutarate. Clinical symptoms of Combined D,L-2HGA include neonatal encephalopathy, respiratory insufficiency and often with death in infancy. No current therapies exist, although replenishing cytosolic stores by citrate supplementation to replenish cytosolic stores has been proposed. In this study, we demonstrated that patient derived fibroblasts exhibited impaired cellular bioenergetics that were worsened with citrate supplementation. We hypothesized treating patient cells with phenylbutyrate, an FDA approved pharmaceutical drug, would reduce mitochondrial 2-ketoglutarate, leading to improved cellular bioenergetics including oxygen consumption and fatty acid oxidation. Metabolomic and RNA-seq analyses demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of phenylbutyrate, detected levels of phenylacetylglutamine was consistent with the drug acting as 2-ketoglutarate sink in patient cells. Our pre-clinical studies suggest citrate supplementation is unlikely to be an effective treatment of the disorder. However, cellular bioenergetics suggests phenylbutyrate may have interventional utility for this rare disease.
    DOI:  https://doi.org/10.1101/2023.02.02.526527
  54. Acta Myol. 2022 ;41(4): 201-206
    Torin1 restores proliferation rate in Charcot-Marie-Tooth disease type 2A cells harbouring MFN2 (mitofusin 2) mutation.
    Paola Zanfardino, Alessandro Amati, Easter Anna Petracca, Filippo M Santorelli, Vittoria Petruzzella.
       Objective: Mitofusin 2 (MFN2) is a mitochondrial outer membrane protein that serves primarily as a mitochondrial fusion protein but has additional functions including the tethering of mitochondrial-endoplasmic reticulum membranes, movement of mitochondria along axons, and control of the quality of mitochondria. Intriguingly, MFN2 has been referred to play a role in regulating cell proliferation in several cell types such that it acts as a tumour suppressor role in some forms of cancer. Previously, we found that fibroblasts derived from a Charcot-Marie-Tooth disease type 2A (CMT2A) patient with a mutation in the GTPase domain of MFN2 exhibit increased proliferation and decreased autophagy.
    Methods: Primary fibroblasts from a young patient affected by CMT2A harbouring c.650G > T/p.Cys217Phe mutation in the MFN2 gene were evaluated versus a healthy control to measure the proliferation rate by growth curves analysis and to assess the phosphorylation of protein kinase B (AKT) at Ser473 in response to different doses of torin1, a selective catalytic ATP-competitive mammalian target of rapamycin complex (mTOR) inhibitor, by immunoblot analysis.
    Results: Herein, we demonstrated that the mammalian target of rapamycin complex 2 (mTORC2) is highly activated in the CMT2AMFN2 fibroblasts to promote cell growth via the AKT(Ser473) phosphorylation-mediated signalling. We report that torin1 restores CMT2AMFN2 fibroblasts' growth rate in a dose-dependent manner by decreasing AKT(Ser473) phosphorylation.
    Conclusions: Overall, our study provides evidence for mTORC2, as a novel molecular target that lies upstream of AKT to restore the cell proliferation rate in CMT2A fibroblasts.
    Keywords:  AKT; Charcot-Marie-Tooth type 2A2; cell proliferation; mTORC2; mitofusin2
    DOI:  https://doi.org/10.36185/2532-1900-085
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