bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2020‒12‒20
eighteen papers selected by
Edmond Chan
Queen’s University, School of Medicine
  1. OMA1 reprograms metabolism under hypoxia to promote colorectal cancer development.
  2. Small-molecule inhibitors of human mitochondrial DNA transcription.
  3. Mitochondrial DNA copy number in human disease: the more the better?
  4. Association and dissociation between the mitochondrial Far complex and Atg32 regulate mitophagy.
  5. Snx14 proximity labeling reveals a role in saturated fatty acid metabolism and ER homeostasis defective in SCAR20 disease.
  6. NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C.
  7. Ceramide chain length-dependent protein sorting into selective endoplasmic reticulum exit sites.
  8. Tumor Reliance on Cytosolic versus Mitochondrial One-Carbon Flux Depends on Folate Availability.
  9. The pyruvate-lactate axis modulates cardiac hypertrophy and heart failure.
  10. MIEF2 over-expression promotes tumor growth and metastasis through reprogramming of glucose metabolism in ovarian cancer.
  11. Molecular mechanisms and clinical implications of multiple forms of mitophagy in the heart.
  12. Mitochondrial Protein Import Dysfunction: Mitochondrial disease, Neurodegenerative Disease and Cancer.
  13. ER-mitochondria contact sites in neurodegeneration: genetic screening approaches to investigate novel disease mechanisms.
  14. Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing.
  15. K63-linked ubiquitylation induces global sequestration of mitochondria.
  16. Measuring Mitochondrial Respiration in Previously Frozen Biological Samples.
  17. BCL(X)L and BCL2 increase the metabolic fitness of breast cancer cells: a single-cell imaging study.
  18. The Diseased Mitoribosome.
  1. EMBO Rep. 2020 Dec 13. e50827
    OMA1 reprograms metabolism under hypoxia to promote colorectal cancer development.
    Zhida Wu, Meiling Zuo, Ling Zeng, Kaisa Cui, Bing Liu, Chaojun Yan, Li Chen, Jun Dong, Fugen Shangguan, Wanglai Hu, He He, Bin Lu, Zhiyin Song.
      Many cancer cells maintain enhanced aerobic glycolysis due to irreversible defective mitochondrial oxidative phosphorylation (OXPHOS). This phenomenon, known as the Warburg effect, is recently challenged because most cancer cells maintain OXPHOS. However, how cancer cells coordinate glycolysis and OXPHOS remains largely unknown. Here, we demonstrate that OMA1, a stress-activated mitochondrial protease, promotes colorectal cancer development by driving metabolic reprogramming. OMA1 knockout suppresses colorectal cancer development in AOM/DSS and xenograft mice models of colorectal cancer. OMA1-OPA1 axis is activated by hypoxia, increasing mitochondrial ROS to stabilize HIF-1α, thereby promoting glycolysis in colorectal cancer cells. On the other hand, under hypoxia, OMA1 depletion promotes accumulation of NDUFB5, NDUFB6, NDUFA4, and COX4L1, supporting that OMA1 suppresses OXPHOS in colorectal cancer. Therefore, our findings support a role for OMA1 in coordination of glycolysis and OXPHOS to promote colorectal cancer development and highlight OMA1 as a potential target for colorectal cancer therapy.
    Keywords:  OMA1; colorectal cancer; glycolysis; hypoxia; oxidative phosphorylation
    DOI:  https://doi.org/10.15252/embr.202050827
  2. Nature. 2020 Dec 16.
    Small-molecule inhibitors of human mitochondrial DNA transcription.
    Nina A Bonekamp, Bradley Peter, Hauke S Hillen, Andrea Felser, Tim Bergbrede, Axel Choidas, Moritz Horn, Anke Unger, Raffaella Di Lucrezia, Ilian Atanassov, Xinping Li, Uwe Koch, Sascha Menninger, Joanna Boros, Peter Habenberger, Patrick Giavalisco, Patrick Cramer, Martin S Denzel, Peter Nussbaumer, Bert Klebl, Maria Falkenberg, Claes M Gustafsson, Nils-Göran Larsson.
      Altered expression of mitochondrial DNA (mtDNA) occurs in ageing and a range of human pathologies (for example, inborn errors of metabolism, neurodegeneration and cancer). Here we describe first-in-class specific inhibitors of mitochondrial transcription (IMTs) that target the human mitochondrial RNA polymerase (POLRMT), which is essential for biogenesis of the oxidative phosphorylation (OXPHOS) system1-6. The IMTs efficiently impair mtDNA transcription in a reconstituted recombinant system and cause a dose-dependent inhibition of mtDNA expression and OXPHOS in cell lines. To verify the cellular target, we performed exome sequencing of mutagenized cells and identified a cluster of amino acid substitutions in POLRMT that cause resistance to IMTs. We obtained a cryo-electron microscopy (cryo-EM) structure of POLRMT bound to an IMT, which further defined the allosteric binding site near the active centre cleft of POLRMT. The growth of cancer cells and the persistence of therapy-resistant cancer stem cells has previously been reported to depend on OXPHOS7-17, and we therefore investigated whether IMTs have anti-tumour effects. Four weeks of oral treatment with an IMT is well-tolerated in mice and does not cause OXPHOS dysfunction or toxicity in normal tissues, despite inducing a strong anti-tumour response in xenografts of human cancer cells. In summary, IMTs provide a potent and specific chemical biology tool to study the role of mtDNA expression in physiology and disease.
    DOI:  https://doi.org/10.1038/s41586-020-03048-z
  3. FEBS Lett. 2020 Dec 12.
    Mitochondrial DNA copy number in human disease: the more the better?
    Roberta Filograna, Mara Mennuni, David Alsina, Nils-Göran Larsson.
      Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Neverthelss, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene-dense circular mitochondrial DNA (mtDNA) of about 16.5kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders, and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
    Keywords:  Alzheimer; Parkinson; TFAM; ageing; cancer; mitochondria; mitochondrial diseases; mtDNA; mtDNA copy number; neurodegenerative disorders; s disease
    DOI:  https://doi.org/10.1002/1873-3468.14021
  4. Elife. 2020 12 15. pii: e63694. [Epub ahead of print]9
    Association and dissociation between the mitochondrial Far complex and Atg32 regulate mitophagy.
    Aleksei Innokentev, Kentaro Furukawa, Tomoyuki Fukuda, Tetsu Saigusa, Keiichi Inoue, Shun-Ichi Yamashita, Tomotake Kanki.
      Mitophagy plays an important role in mitochondrial homeostasis. In yeast, the phosphorylation of the mitophagy receptor Atg32 by casein kinase 2 is essential for mitophagy. This phosphorylation is counteracted by the yeast equivalent of the STRIPAK complex consisting of the PP2A-like protein phosphatase Ppg1 and Far3-7-8-9-10-11 (Far complex), but the underlying mechanism remains elusive. Here we show that two subpopulations of the Far complex reside in the mitochondria and endoplasmic reticulum, respectively, and play distinct roles; the former inhibits mitophagy via Atg32 dephosphorylation, and the latter regulates TORC2 signaling. Ppg1 and Far11 form a subcomplex, and Ppg1 activity is required for the assembling integrity of Ppg1-Far11-Far8. The Far complex preferentially interacts with phosphorylated Atg32, and this interaction is weakened by mitophagy induction. Furthermore, the artificial tethering of Far8 to Atg32 prevents mitophagy. Taken together, the Ppg1-mediated Far complex formation and its dissociation from Atg32 are crucial for mitophagy regulation.
    Keywords:  Atg32; Far complex; Ppg1; S. cerevisiae; STRIPAK complex; autophagy; cell biology; mitophagy
    DOI:  https://doi.org/10.7554/eLife.63694
  5. Proc Natl Acad Sci U S A. 2020 Dec 11. pii: 202011124. [Epub ahead of print]
    Snx14 proximity labeling reveals a role in saturated fatty acid metabolism and ER homeostasis defective in SCAR20 disease.
    Sanchari Datta, Jade Bowerman, Hanaa Hariri, Rupali Ugrankar, Kaitlyn M Eckert, Chase Corley, Gonçalo Vale, Jeffrey G McDonald, W Mike Henne.
      Fatty acids (FAs) are central cellular metabolites that contribute to lipid synthesis, and can be stored or harvested for metabolic energy. Dysregulation in FA processing and storage causes toxic FA accumulation or altered membrane compositions and contributes to metabolic and neurological disorders. Saturated lipids are particularly detrimental to cells, but how lipid saturation levels are maintained remains poorly understood. Here, we identify the cerebellar ataxia spinocerebellar ataxia, autosomal recessive 20 (SCAR20)-associated protein Snx14, an endoplasmic reticulum (ER)-lipid droplet (LD) tethering protein, as a factor required to maintain the lipid saturation balance of cell membranes. We show that following saturated FA (SFA) treatment, the ER integrity of SNX14 KO cells is compromised, and both SNX14 KO cells and SCAR20 disease patient-derived cells are hypersensitive to SFA-mediated lipotoxic cell death. Using APEX2-based proximity labeling, we reveal the protein composition of Snx14-associated ER-LD contacts and define a functional interaction between Snx14 and Δ-9 FA desaturase SCD1. Lipidomic profiling reveals that SNX14 KO cells increase membrane lipid saturation following exposure to palmitate, phenocopying cells with perturbed SCD1 activity. In line with this, SNX14 KO cells manifest delayed FA processing and lipotoxicity, which can be rescued by SCD1 overexpression. Altogether, these mechanistic insights reveal a role for Snx14 in FA and ER homeostasis, defects in which may underlie the neuropathology of SCAR20.
    Keywords:  SCAR20 disease; desaturase; fatty acid (FA); lipid droplet (LD); sorting nexin 14
    DOI:  https://doi.org/10.1073/pnas.2011124117
  6. Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30925-4. [Epub ahead of print]
    NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C.
    Oliver B Davis, Hijai R Shin, Chun-Yan Lim, Emma Y Wu, Matthew Kukurugya, Claire F Maher, Rushika M Perera, M Paulina Ordonez, Roberto Zoncu.
      Lysosomes promote cellular homeostasis through macromolecular hydrolysis within their lumen and metabolic signaling by the mTORC1 kinase on their limiting membranes. Both hydrolytic and signaling functions require precise regulation of lysosomal cholesterol content. In Niemann-Pick type C (NPC), loss of the cholesterol exporter, NPC1, causes cholesterol accumulation within lysosomes, leading to mTORC1 hyperactivation, disrupted mitochondrial function, and neurodegeneration. The compositional and functional alterations in NPC lysosomes and nature of aberrant cholesterol-mTORC1 signaling contribution to organelle pathogenesis are not understood. Through proteomic profiling of NPC lysosomes, we find pronounced proteolytic impairment compounded with hydrolase depletion, enhanced membrane damage, and defective mitophagy. Genetic and pharmacologic mTORC1 inhibition restores lysosomal proteolysis without correcting cholesterol storage, implicating aberrant mTORC1 as a pathogenic driver downstream of cholesterol accumulation. Consistently, mTORC1 inhibition ameliorates mitochondrial dysfunction in a neuronal model of NPC. Thus, cholesterol-mTORC1 signaling controls organelle homeostasis and is a targetable pathway in NPC.
    Keywords:  ESCRT; NPC1; autophagy; cholesterol; lysosome; mTORC1; mitochondria; proteolysis; proteomics
    DOI:  https://doi.org/10.1016/j.devcel.2020.11.016
  7. Sci Adv. 2020 Dec;pii: eaba8237. [Epub ahead of print]6(50):
    Ceramide chain length-dependent protein sorting into selective endoplasmic reticulum exit sites.
    Sofia Rodriguez-Gallardo, Kazuo Kurokawa, Susana Sabido-Bozo, Alejandro Cortes-Gomez, Atsuko Ikeda, Valeria Zoni, Auxiliadora Aguilera-Romero, Ana Maria Perez-Linero, Sergio Lopez, Miho Waga, Misako Araki, Miyako Nakano, Howard Riezman, Kouichi Funato, Stefano Vanni, Akihiko Nakano, Manuel Muñiz.
      Protein sorting in the secretory pathway is crucial to maintain cellular compartmentalization and homeostasis. In addition to coat-mediated sorting, the role of lipids in driving protein sorting during secretory transport is a longstanding fundamental question that still remains unanswered. Here, we conduct 3D simultaneous multicolor high-resolution live imaging to demonstrate in vivo that newly synthesized glycosylphosphatidylinositol-anchored proteins having a very long chain ceramide lipid moiety are clustered and sorted into specialized endoplasmic reticulum exit sites that are distinct from those used by transmembrane proteins. Furthermore, we show that the chain length of ceramide in the endoplasmic reticulum membrane is critical for this sorting selectivity. Our study provides the first direct in vivo evidence for lipid chain length-based protein cargo sorting into selective export sites of the secretory pathway.
    DOI:  https://doi.org/10.1126/sciadv.aba8237
  8. Cell Metab. 2020 Dec 10. pii: S1550-4131(20)30657-4. [Epub ahead of print]
    Tumor Reliance on Cytosolic versus Mitochondrial One-Carbon Flux Depends on Folate Availability.
    Won Dong Lee, Anna Chiara Pirona, Boris Sarvin, Alon Stern, Keren Nevo-Dinur, Elazar Besser, Nikita Sarvin, Shoval Lagziel, Dzmitry Mukha, Shachar Raz, Elina Aizenshtein, Tomer Shlomi.
      Folate metabolism supplies one-carbon (1C) units for biosynthesis and methylation and has long been a target for cancer chemotherapy. Mitochondrial serine catabolism is considered the sole contributor of folate-mediated 1C units in proliferating cancer cells. Here, we show that under physiological folate levels in the cell environment, cytosolic serine-hydroxymethyltransferase (SHMT1) is the predominant source of 1C units in a variety of cancers, while mitochondrial 1C flux is overly repressed. Tumor-specific reliance on cytosolic 1C flux is associated with poor capacity to retain intracellular folates, which is determined by the expression of SLC19A1, which encodes the reduced folate carrier (RFC). We show that silencing SHMT1 in cells with low RFC expression impairs pyrimidine biosynthesis and tumor growth in vivo. Overall, our findings reveal major diversity in cancer cell utilization of the cytosolic versus mitochondrial folate cycle across tumors and SLC19A1 expression as a marker for increased reliance on SHMT1.
    Keywords:  SHMT; cancer metabolism; folate cycle; in vivo; isotope tracing; metabolomics; mitochondria; one-carbon flux; physiologic medium; reduced folate carrier; serine hydroxymethyltransferase
    DOI:  https://doi.org/10.1016/j.cmet.2020.12.002
  9. Cell Metab. 2020 Dec 11. pii: S1550-4131(20)30658-6. [Epub ahead of print]
    The pyruvate-lactate axis modulates cardiac hypertrophy and heart failure.
    Ahmad A Cluntun, Rachit Badolia, Sandra Lettlova, K Mark Parnell, Thirupura S Shankar, Nikolaos A Diakos, Kristofor A Olson, Iosif Taleb, Sean M Tatum, Jordan A Berg, Corey N Cunningham, Tyler Van Ry, Alex J Bott, Aspasia Thodou Krokidi, Sarah Fogarty, Sophia Skedros, Wojciech I Swiatek, Xuejing Yu, Bai Luo, Shannon Merx, Sutip Navankasattusas, James E Cox, Gregory S Ducker, William L Holland, Stephen H McKellar, Jared Rutter, Stavros G Drakos.
      The metabolic rewiring of cardiomyocytes is a widely accepted hallmark of heart failure (HF). These metabolic changes include a decrease in mitochondrial pyruvate oxidation and an increased export of lactate. We identify the mitochondrial pyruvate carrier (MPC) and the cellular lactate exporter monocarboxylate transporter 4 (MCT4) as pivotal nodes in this metabolic axis. We observed that cardiac assist device-induced myocardial recovery in chronic HF patients was coincident with increased myocardial expression of the MPC. Moreover, the genetic ablation of the MPC in cultured cardiomyocytes and in adult murine hearts was sufficient to induce hypertrophy and HF. Conversely, MPC overexpression attenuated drug-induced hypertrophy in a cell-autonomous manner. We also introduced a novel, highly potent MCT4 inhibitor that mitigated hypertrophy in cultured cardiomyocytes and in mice. Together, we find that alteration of the pyruvate-lactate axis is a fundamental and early feature of cardiac hypertrophy and failure.
    Keywords:  LVAD; MCT4; MPC; VB124; cardiac metabolism; heart failure; hypertrophy; lactate; mitochondria; pyruvate
    DOI:  https://doi.org/10.1016/j.cmet.2020.12.003
  10. J Exp Clin Cancer Res. 2020 Dec 14. 39(1): 286
    MIEF2 over-expression promotes tumor growth and metastasis through reprogramming of glucose metabolism in ovarian cancer.
    Shuhua Zhao, Xiaohong Zhang, Yuan Shi, Lu Cheng, Tingting Song, Bing Wu, Jia Li, Hong Yang.
      BACKGROUND: Increasing evidence has revealed the close link between mitochondrial dynamic dysfunction and cancer. MIEF2 (mitochondrial elongation factor 2) is mitochondrial outer membrane protein that functions in the regulation of mitochondrial fission. However, the expression, clinical significance and biological functions of MIEF2 are still largely unclear in human cancers, especially in ovarian cancer (OC).METHODS: The expression and clinical significance of MIEF2 were determined by qRT-PCR, western blot and immunohistochemistry analyses in tissues and cell lines of OC. The biological functions of MIEF2 in OC were determined by in vitro and in vivo cell growth and metastasis assays. Furthermore, the effect of MIEF2 on metabolic reprogramming of OC was determined by metabolomics and glucose metabolism analyses.
    RESULTS: MIEF2 expression was significantly increased in OC mainly due to the down-regulation of miR-424-5p, which predicts poor survival for patients with OC. Knockdown of MIEF2 significantly suppressed OC cell growth and metastasis both in vitro and in vivo by inhibiting G1-S cell transition, epithelial-to-mesenchymal transition (EMT) and inducing cell apoptosis, while forced expression of MIEF2 had the opposite effects. Mechanistically, mitochondrial fragmentation-suppressed cristae formation and thus glucose metabolism switch from oxidative phosphorylation to glycolysis was found to be involved in the promotion of growth and metastasis by MIEF2 in OC cells.
    CONCLUSIONS: MIEF2 plays a critical role in the progression of OC and may serve as a valuable prognostic biomarker and therapeutic target in the treatment of this malignancy.
    Keywords:  Glycolysis; Growth; Metastasis; Mitochondrial elongation factor 2; OC
    DOI:  https://doi.org/10.1186/s13046-020-01802-9
  11. Cardiovasc Res. 2020 Dec 17. pii: cvaa340. [Epub ahead of print]
    Molecular mechanisms and clinical implications of multiple forms of mitophagy in the heart.
    Toshiro Saito, Kimikazu Hamano, Junichi Sadoshima.
      Mitochondria, the primary ATP-producing organelles, are highly abundant in cardiomyocytes. Mitochondrial function readily deteriorates in the presence of stress and, thus, maintenance of mitochondrial quality is essential for sustaining pump function in the heart. Cardiomyocytes under stress attempt to maintain mitochondrial quality primarily through dynamic changes in their morphology, namely fission and fusion, degradation, and biogenesis. Mitophagy, a mitochondria-specific form of autophagy, is a major mechanism of degradation. The level of mitophagy is altered in stress conditions, which, in turn, significantly affects mitochondrial function, cardiomyocyte survival, and death and cardiac function. Thus, mitophagy has been emerging as a promising target for treatment of cardiac conditions. To develop specific interventions, modulating the activity of mitophagy in the heart, understanding how mitochondria are degraded in a given condition is important. Increasing lines of evidence suggest that there are multiple mechanisms by which mitochondria are degraded through mitophagy in the heart. For example, in addition to the well-established mechanism commonly utilized by general autophagy, involving Atg7 and LC3, recent evidence suggests that an alternative mechanism, independent of Atg7 and LC3, also mediates mitophagy in the heart. Here, we describe molecular mechanisms through which mitochondria are degraded in the heart and discuss their functional significance. We also discuss molecular interventions to modulate the activity of mitophagy and their potential applications for cardiac conditions.
    Keywords:  Alternative mitophagy; Drp1; Parkin; Rab9;  Mitophagy
    DOI:  https://doi.org/10.1093/cvr/cvaa340
  12. FEBS Lett. 2020 Dec 14.
    Mitochondrial Protein Import Dysfunction: Mitochondrial disease, Neurodegenerative Disease and Cancer.
    Catherine S Palmer, Alexander J Anderson, Diana Stojanovski.
      The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease, Parkinson's disease.
    Keywords:  Alzheimer’s disease; Cancer; Huntington’s disease; Mitochondria; Neurodegeneration; Parkinson’s disease; Protein Import; TIM; TOM
    DOI:  https://doi.org/10.1002/1873-3468.14022
  13. Cell Death Differ. 2020 Dec 17.
    ER-mitochondria contact sites in neurodegeneration: genetic screening approaches to investigate novel disease mechanisms.
    Emma Louise Wilson, Emmanouil Metzakopian.
      Mitochondria-ER contact sites (MERCS) are known to underpin many important cellular homoeostatic functions, including mitochondrial quality control, lipid metabolism, calcium homoeostasis, the unfolded protein response and ER stress. These functions are known to be dysregulated in neurodegenerative diseases, including Parkinson's disease (PD), Alzheimer's disease (AD) and amyloid lateral sclerosis (ALS), and the number of disease-related proteins and genes being associated with MERCS is increasing. However, many details regarding MERCS and their role in neurodegenerative diseases remain unknown. In this review, we aim to summarise the current knowledge regarding the structure and function of MERCS, and to update the field on current research in PD, AD and ALS. Furthermore, we will evaluate high-throughput screening techniques, including RNAi vs CRISPR/Cas9, pooled vs arrayed formats and how these could be combined with current techniques to visualise MERCS. We will consider the advantages and disadvantages of each technique and how it can be utilised to uncover novel protein pathways involved in MERCS dysfunction in neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41418-020-00705-8
  14. PLoS Genet. 2020 Dec 14. 16(12): e1009242
    Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing.
    Swaraj Basu, Xie Xie, Jay P Uhler, Carola Hedberg-Oldfors, Dusanka Milenkovic, Olivier R Baris, Sammy Kimoloi, Stanka Matic, James B Stewart, Nils-Göran Larsson, Rudolf J Wiesner, Anders Oldfors, Claes M Gustafsson, Maria Falkenberg, Erik Larsson.
      Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we establish a computational method, MitoSAlt, for accurate identification, quantification and visualization of mtDNA deletions and duplications from genomic sequencing data. Our method was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy.
    DOI:  https://doi.org/10.1371/journal.pgen.1009242
  15. Sci Rep. 2020 Dec 18. 10(1): 22334
    K63-linked ubiquitylation induces global sequestration of mitochondria.
    Thibaud J C Richard, Laura K Herzog, Julia Vornberger, Aldwin Suryo Rahmanto, Olle Sangfelt, Florian A Salomons, Nico P Dantuma.
      Even though K63-linked polyubiquitin chains do not target proteins for proteasomal degradation, they play nevertheless a complementary protective role in maintaining protein homeostasis by directing malfunctioning proteins and organelles to inclusion bodies or autophagosomes. A paradigm for this process is the sequestration and autophagic degradation of dysfunctional mitochondria. Although studies have shown that K63-ubiquitylation of mitochondrial proteins by the ubiquitin ligase Parkin is important in this process, it is presently not clear if this modification also suffices to initiate this cascade of events. To address this question, we have engineered the ubiquitin ligase ProxE3, which in an inducible manner synthesizes K63-linked ubiquitin chains on the surface of mitochondria. We found that the presence of K63-linked ubiquitin chains on mitochondria resulted in the recruitment of the ubiquitin adaptor p62 and induced a dramatic redistribution of mitochondria, which was reminiscent to the Parkin-facilitated sequestration in response to mitochondrial uncoupler. However, ProxE3 did not induce autophagic degradation of mitochondria. Our data show that K63-linked ubiquitin chains at the mitochondrial membrane are sufficient for the induction of mitochondrial sequestration, but not mitophagy, without the need of extrinsically inflicting mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s41598-020-78845-7
  16. Curr Protoc Cell Biol. 2020 Dec;89(1): e116
    Measuring Mitochondrial Respiration in Previously Frozen Biological Samples.
    Corey Osto, Ilan Y Benador, Jennifer Ngo, Marc Liesa, Linsey Stiles, Rebeca Acin-Perez, Orian S Shirihai.
      Measuring oxygen consumption allows for the role of mitochondrial function in biological phenomena and mitochondrial diseases to be determined. Although respirometry has become a common approach in disease research, current methods are limited by the necessity to process and measure tissue samples within 1 hr of acquisition. Detailed by Acin-Perez and colleagues, a new respirometry approach designed for previously frozen tissue samples eliminates these hurdles for mitochondrial study. This technique allows for the measurement of maximal respiratory capacity in samples frozen for long-term storage before testing. This protocol article describes the optimal tissue isolation methods and the combination of substrates to define electron transport chain function at high resolution in previously frozen tissue samples. © 2020 The Authors. Basic Protocol 1: Sample collection, storage, and homogenization for previously frozen tissue respirometry Basic Protocol 2: Running a Seahorse respirometry assay using previously frozen tissue samples Basic Protocol 3: Normalization to mitochondrial content for previously frozen tissue respirometry.
    Keywords:  OCR; frozen; mitochondria; respirometry
    DOI:  https://doi.org/10.1002/cpcb.116
  17. Cell Death Differ. 2020 Dec 16.
    BCL(X)L and BCL2 increase the metabolic fitness of breast cancer cells: a single-cell imaging study.
    Federico Lucantoni, Manuela Salvucci, Heiko Düssmann, Andreas U Lindner, Diether Lambrechts, Jochen H M Prehn.
      The BCL2 family of proteins regulate apoptosis by controlling mitochondrial outer membrane permeability. However, the effects on mitochondrial structure and bioenergetics have also been reported. Here we comprehensively characterized the effects of BCL2 and BCL(X)L on cellular energetics in MCF7 breast cancer cells using time-lapse confocal single-cell imaging and mitochondrial and cytosolic FRET reporters. We found that BCL2 and BCL(X)L increase the metabolic robustness of MCF7 cells, and that this was associated with increased mitochondrial NAD(P)H and ATP levels. Experiments with the F1F0 synthase inhibitor oligomycin demonstrated that BCL2 and in particular BCL(X)L, while not affecting ATP synthase activity, more efficiently coupled the mitochondrial proton motive force with ATP production. This metabolic advantage was associated with an increased resistance to nutrient deprivation and enhanced clonogenic survival in response to metabolic stress, in the absence of profound effects on cell death. Our data suggest that a primary function of BCL(X)L and BCL2 overexpression in tumor cells is to increase their resistance to metabolic stress in the tumor microenvironment, independent of cell death signaling.
    DOI:  https://doi.org/10.1038/s41418-020-00683-x
  18. FEBS Lett. 2020 Dec 12.
    The Diseased Mitoribosome.
    Alberto Ferrari, Samuel Del'Olio, Antoni Barrientos.
      Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintain a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors, impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portrait how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
    Keywords:  Mitochondrial disease; Mitochondrial ribosome; Mitochondrial translation; Mitoribosome assembly; OXPHOS deficiency
    DOI:  https://doi.org/10.1002/1873-3468.14024
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