bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2020–09–13
thirteen papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. SLC25A51 is a mammalian mitochondrial NAD+ transporter.
  2. Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis.
  3. Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
  4. ER-mitochondria contacts promote mtDNA nucleoids active transportation via mitochondrial dynamic tubulation.
  5. The E3 Ubiquitin Ligase SYVN1 Ubiquitinates Atlastins to Remodel the Endoplasmic Reticulum Network.
  6. Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast.
  7. FIT2 is an acyl-coenzyme A diphosphatase crucial for endoplasmic reticulum homeostasis.
  8. Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts.
  9. Dichotomous role of the human mitochondrial Na+/Ca2+/Li+ exchanger NCLX in colorectal cancer growth and metastasis.
  10. Loss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology.
  11. Metabolic Characterization and Consequences of Mitochondrial Pyruvate Carrier Deficiency in Drosophila melanogaster.
  12. A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts.
  13. GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission.
  1. Nature. 2020 Sep 09.
    SLC25A51 is a mammalian mitochondrial NAD+ transporter.
    Timothy S Luongo, Jared M Eller, Mu-Jie Lu, Marc Niere, Fabio Raith, Caroline Perry, Marc R Bornstein, Paul Oliphint, Lin Wang, Melanie R McReynolds, Marie E Migaud, Joshua D Rabinowitz, F Brad Johnson, Kai Johnsson, Mathias Ziegler, Xiaolu A Cambronne, Joseph A Baur.
      Mitochondria require nicotinamide adenine dinucleotide (NAD+) in order to carry out the fundamental processes that fuel respiration and mediate cellular energy transduction. Mitochondrial NAD+ transporters have been identified in yeast and plants1,2 but their very existence is controversial in mammals3-5. Here we demonstrate that mammalian mitochondria are capable of taking up intact NAD+ and identify SLC25A51 (an essential6,7 mitochondrial protein of previously unknown function, also known as MCART1) as a mammalian mitochondrial NAD+ transporter. Loss of SLC25A51 decreases mitochondrial but not whole-cell NAD+ content, impairs mitochondrial respiration, and blocks the uptake of NAD+ into isolated mitochondria. Conversely, overexpression of SLC25A51 or a nearly identical paralog, SLC25A52, increases mitochondrial NAD+ levels and restores NAD+ uptake into yeast mitochondria lacking endogenous NAD+ transporters. Together, these findings identify SLC25A51 as the first transporter capable of importing NAD+ into mammalian mitochondria.
    DOI:  https://doi.org/10.1038/s41586-020-2741-7
  2. Cell. 2020 Aug 30. pii: S0092-8674(20)30947-8. [Epub ahead of print]
    Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis.
    François Bonnay, Ana Veloso, Victoria Steinmann, Thomas Köcher, Merve Deniz Abdusselamoglu, Sunanjay Bajaj, Elisa Rivelles, Lisa Landskron, Harald Esterbauer, Robert P Zinzen, Juergen A Knoblich.
      Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here we demonstrate that metabolic reprogramming induced by mitochondrial fusion can be rate-limiting for immortalization of tumor-initiating cells (TICs) and trigger their irreversible dedication to tumorigenesis. Using single-cell transcriptomics, we find that Drosophila brain tumors contain a rapidly dividing stem cell population defined by upregulation of oxidative phosphorylation (OxPhos). We combine targeted metabolomics and in vivo genetic screening to demonstrate that OxPhos is required for tumor cell immortalization but dispensable in neural stem cells (NSCs) giving rise to tumors. Employing an in vivo NADH/NAD+ sensor, we show that NSCs precisely increase OxPhos during immortalization. Blocking OxPhos or mitochondrial fusion stalls TICs in quiescence and prevents tumorigenesis through impaired NAD+ regeneration. Our work establishes a unique connection between cellular metabolism and immortalization of tumor-initiating cells.
    Keywords:  bioenergetics; cell immortalization; mitochondrial dynamics; neural stem cells; tumor heterogeneity; tumorigenesis
    DOI:  https://doi.org/10.1016/j.cell.2020.07.039
  3. Cell Rep. 2020 Sep 08. pii: S2211-1247(20)31114-1. [Epub ahead of print]32(10): 108125
    Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
    Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A Kelley, Michael Steinbaugh, Erin J Cram, William B Mair.
      Individually, dysfunction of both the endoplasmic reticulum (ER) and mitochondria has been linked to aging, but how communication between these organelles might be targeted to promote longevity is unclear. Here, we provide evidence that, in Caenorhabditis elegans, inhibition of the conserved unfolded protein response (UPRER) mediator, activating transcription factor (atf)-6, increases lifespan by modulating calcium homeostasis and signaling to mitochondria. Atf-6 loss confers longevity via downregulation of the ER calcium buffer, calreticulin. ER calcium release via the inositol triphosphate receptor (IP3R/itr-1) is required for longevity, while IP3R/itr-1 gain of function is sufficient to extend lifespan. Highlighting coordination between organelles, the mitochondrial calcium import channel mcu-1 is also required for atf-6 longevity. IP3R inhibition leads to impaired mitochondrial bioenergetics and hyperfusion, which is sufficient to suppress long life in atf-6 mutants. This study reveals the importance of organellar calcium handling as a critical output for the UPRER in determining the quality of aging.
    Keywords:  InsP3R; UPR; aging; calreticulin; interorganelle communication; longevity
    DOI:  https://doi.org/10.1016/j.celrep.2020.108125
  4. Nat Commun. 2020 09 08. 11(1): 4471
    ER-mitochondria contacts promote mtDNA nucleoids active transportation via mitochondrial dynamic tubulation.
    Jinshan Qin, Yuting Guo, Boxin Xue, Peng Shi, Yang Chen, Qian Peter Su, Huiwen Hao, Shujuan Zhao, Congying Wu, Li Yu, Dong Li, Yujie Sun.
      A human cell contains hundreds to thousands of mitochondrial DNA (mtDNA) packaged into nucleoids. Currently, the segregation and allocation of nucleoids are thought to be passively determined by mitochondrial fusion and division. Here we provide evidence, using live-cell super-resolution imaging, that nucleoids can be actively transported via KIF5B-driven mitochondrial dynamic tubulation (MDT) activities that predominantly occur at the ER-mitochondria contact sites (EMCS). We further demonstrate that a mitochondrial inner membrane protein complex MICOS links nucleoids to Miro1, a KIF5B receptor on mitochondria, at the EMCS. We show that such active transportation is a mechanism essential for the proper distribution of nucleoids in the peripheral zone of the cell. Together, our work identifies an active transportation mechanism of nucleoids, with EMCS serving as a key platform for the interplay of nucleoids, MICOS, Miro1, and KIF5B to coordinate nucleoids segregation and transportation.
    DOI:  https://doi.org/10.1038/s41467-020-18202-4
  5. iScience. 2020 Aug 24. pii: S2589-0042(20)30686-6. [Epub ahead of print]23(9): 101494
    The E3 Ubiquitin Ligase SYVN1 Ubiquitinates Atlastins to Remodel the Endoplasmic Reticulum Network.
    Yupeng Zhao, Zhigang Feng, Yan Zou, Yanfen Liu.
      Atlastin (ATL) is a class of dynamin-like GTPases shaping endoplasmic reticulum (ER) by mediating homotypic membrane fusion. Defect of ATLs leads to abnormal ER structure and hereditary spastic paraplegia (HSP), a neurodegenerative disease with progressive spasticity. How ATLs are regulated to maintain the ER dynamics is not clear. Here, we found that SYVN1, an E3 ubiquitin ligase on the ER membrane, regulates ER shape and COPII exporting by mediating ubiquitination on ATLs, especially ATL1. ATL1 is ubiquitinated by SYVN1 strongly on K285 and mildly on K287. Ubiquitination on ATL1 does not result in protein degradation but inhibits ATL1 GTPase activity. SYVN1 overexpression compensates the excessive ER network fusion caused by ATL1 overexpression. Accordingly, the role of SYVN1 and ATL1 in regulating ER morphology is also recapitulated in Caenorhabditis elegans. Taken together, our study reveals a different role of SYVN1 in ER remodeling through mediating ubiquitination on ATLs.
    Keywords:  Biological Sciences; Cell Biology; Molecular Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101494
  6. EMBO Rep. 2020 Sep 07. e50845
    Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast.
    Michal Malecki, Stephan Kamrad, Markus Ralser, Jürg Bähler.
      When glucose is available, many organisms repress mitochondrial respiration in favour of aerobic glycolysis, or fermentation in yeast, that suffices for ATP production. Fission yeast cells, however, rely partially on respiration for rapid proliferation under fermentative conditions. Here, we determined the limiting factors that require respiratory function during fermentation. When inhibiting the electron transport chain, supplementation with arginine was necessary and sufficient to restore rapid proliferation. Accordingly, a systematic screen for mutants growing poorly without arginine identified mutants defective in mitochondrial oxidative metabolism. Genetic or pharmacological inhibition of respiration triggered a drop in intracellular levels of arginine and amino acids derived from the Krebs cycle metabolite alpha-ketoglutarate: glutamine, lysine and glutamic acid. Conversion of arginine into these amino acids was required for rapid proliferation when blocking the respiratory chain. The respiratory block triggered an immediate gene expression response diagnostic of TOR inhibition, which was muted by arginine supplementation or without the AMPK-activating kinase Ssp1. The TOR-controlled proteins featured biased composition of amino acids reflecting their shortage after respiratory inhibition. We conclude that respiration supports rapid proliferation in fermenting fission yeast cells by boosting the supply of Krebs cycle-derived amino acids.
    Keywords:   S. pombe ; arginine; cellular metabolism; fermentation; respiration
    DOI:  https://doi.org/10.15252/embr.202050845
  7. J Cell Biol. 2020 Oct 05. pii: e202006111. [Epub ahead of print]219(10):
    FIT2 is an acyl-coenzyme A diphosphatase crucial for endoplasmic reticulum homeostasis.
    Michel Becuwe, Laura M Bond, Antonio F M Pinto, Sebastian Boland, Niklas Mejhert, Shane D Elliott, Marcelo Cicconet, Morven M Graham, Xinran N Liu, Olga Ilkayeva, Alan Saghatelian, Tobias C Walther, Robert V Farese.
      The endoplasmic reticulum is a cellular hub of lipid metabolism, coordinating lipid synthesis with continuous changes in metabolic flux. Maintaining ER lipid homeostasis despite these fluctuations is crucial to cell function and viability. Here, we identify a novel mechanism that is crucial for normal ER lipid metabolism and protects the ER from dysfunction. We identify the molecular function of the evolutionarily conserved ER protein FIT2 as a fatty acyl-coenzyme A (CoA) diphosphatase that hydrolyzes fatty acyl-CoA to yield acyl 4'-phosphopantetheine. This activity of FIT2, which is predicted to be active in the ER lumen, is required in yeast and mammalian cells for maintaining ER structure, protecting against ER stress, and enabling normal lipid storage in lipid droplets. Our findings thus solve the long-standing mystery of the molecular function of FIT2 and highlight the maintenance of optimal fatty acyl-CoA levels as key to ER homeostasis.
    DOI:  https://doi.org/10.1083/jcb.202006111
  8. Cell Rep. 2020 Sep 08. pii: S2211-1247(20)31097-4. [Epub ahead of print]32(10): 108108
    Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts.
    Wen-Chih Lee, Xing Ji, Itzhak Nissim, Fanxin Long.
      The metabolic program of osteoblasts, the chief bone-making cells, remains incompletely understood. Here in murine calvarial cells, we establish that osteoblast differentiation under aerobic conditions is coupled with a marked increase in glucose consumption and lactate production but reduced oxygen consumption. As a result, aerobic glycolysis accounts for approximately 80% of the ATP production in mature osteoblasts. In vivo tracing with 13C-labeled glucose in the mouse shows that glucose in bone is readily metabolized to lactate but not organic acids in the TCA cycle. Glucose tracing in osteoblast cultures reveals that pyruvate is carboxylated to form malate integral to the malate-aspartate shuttle. RNA sequencing (RNA-seq) identifies Me2, encoding the mitochondrial NAD-dependent isoform of malic enzyme, as being specifically upregulated during osteoblast differentiation. Knockdown of Me2 markedly reduces the glycolytic flux and impairs osteoblast proliferation and differentiation. Thus, the mitochondrial malic enzyme functionally couples the mitochondria with aerobic glycolysis in osteoblasts.
    Keywords:  TCA cycle; aerobic glycolysis; bone; differentiation; malate-aspartate shuttle; malic enzyme; metabolic tracing; metabolism; mitochondria; osteoblast
    DOI:  https://doi.org/10.1016/j.celrep.2020.108108
  9. Elife. 2020 Sep 11. pii: e59686. [Epub ahead of print]9
    Dichotomous role of the human mitochondrial Na+/Ca2+/Li+ exchanger NCLX in colorectal cancer growth and metastasis.
    Trayambak Pathak, Maxime Gueguinou, Vonn Walter, Celine Delierneux, Martin T Johnson, Xuexin Zhang, Ping Xin, Ryan E Yoast, Scott M Emrich, Gregory R Yochum, Israel Sekler, Walter A Koltun, Donald L Gill, Nadine Hempel, Mohamed Trebak.
      Despite the established role of mitochondria in cancer, the mechanisms by which mitochondrial Ca2+ (mtCa2+) regulates tumorigenesis remain incompletely understood. The crucial role of mtCa2+ in tumorigenesis is highlighted by altered expression of proteins mediating mtCa2+ uptake and extrusion in cancer. Here, we demonstrate decreased expression of the mitochondrial Na+/Ca2+/Li+ exchanger NCLX (SLC8B1) in human colorectal tumors and its association with advanced-stage disease in patients. Downregulation of NCLX causes mtCa2+ overload, mitochondrial depolarization, decreased expression of cell-cycle genes and reduced tumor size in xenograft and spontaneous colorectal cancer mouse models. Concomitantly, NCLX downregulation drives metastatic spread, chemoresistance, and expression of epithelial-to-mesenchymal, hypoxia, and stem cell pathways. Mechanistically, mtCa2+ overload leads to increased mitochondrial reactive oxygen species, which activate HIF1α signaling supporting metastasis of NCLX-null tumor cells. Thus, loss of NCLX is a novel driver of metastasis, indicating that regulation of mtCa2+ is a novel therapeutic approach in metastatic colorectal cancer.
    Keywords:  human; molecular biophysics; mouse; structural biology
    DOI:  https://doi.org/10.7554/eLife.59686
  10. Nat Commun. 2020 Sep 11. 11(1): 4589
    Loss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology.
    Sahar Elouej, Karim Harhouri, Morgane Le Mao, Genevieve Baujat, Sheela Nampoothiri, Hϋlya Kayserili, Nihal Al Menabawy, Laila Selim, Arianne Llamos Paneque, Christian Kubisch, Davor Lessel, Robert Rubinsztajn, Chayki Charar, Catherine Bartoli, Coraline Airault, Jean-François Deleuze, Agnes Rötig, Peter Bauer, Catarina Pereira, Abigail Loh, Nathalie Escande-Beillard, Antoine Muchir, Lisa Martino, Yosef Gruenbaum, Song-Hua Lee, Philippe Manivet, Guy Lenaers, Bruno Reversade, Nicolas Lévy, Annachiara De Sandre-Giovannoli.
      Mandibuloacral dysplasia syndromes are mainly due to recessive LMNA or ZMPSTE24 mutations, with cardinal nuclear morphological abnormalities and dysfunction. We report five homozygous null mutations in MTX2, encoding Metaxin-2 (MTX2), an outer mitochondrial membrane protein, in patients presenting with a severe laminopathy-like mandibuloacral dysplasia characterized by growth retardation, bone resorption, arterial calcification, renal glomerulosclerosis and severe hypertension. Loss of MTX2 in patients' primary fibroblasts leads to loss of Metaxin-1 (MTX1) and mitochondrial dysfunction, including network fragmentation and oxidative phosphorylation impairment. Furthermore, patients' fibroblasts are resistant to induced apoptosis, leading to increased cell senescence and mitophagy and reduced proliferation. Interestingly, secondary nuclear morphological defects are observed in both MTX2-mutant fibroblasts and mtx-2-depleted C. elegans. We thus report the identification of a severe premature aging syndrome revealing an unsuspected link between mitochondrial composition and function and nuclear morphology, establishing a pathophysiological link with premature aging laminopathies and likely explaining common clinical features.
    DOI:  https://doi.org/10.1038/s41467-020-18146-9
  11. Metabolites. 2020 Sep 06. pii: E363. [Epub ahead of print]10(9):
    Metabolic Characterization and Consequences of Mitochondrial Pyruvate Carrier Deficiency in Drosophila melanogaster.
    Chloé Simard, Andréa Lebel, Eric Pierre Allain, Mohamed Touaibia, Etienne Hebert-Chatelain, Nicolas Pichaud.
      In insect, pyruvate is generally the predominant oxidative substrate for mitochondria. This metabolite is transported inside mitochondria via the mitochondrial pyruvate carrier (MPC), but whether and how this transporter controls mitochondrial oxidative capacities in insects is still relatively unknown. Here, we characterize the importance of pyruvate transport as a metabolic control point for mitochondrial substrate oxidation in two genotypes of an insect model, Drosophila melanogaster, differently expressing MPC1, an essential protein for the MPC function. We evaluated the kinetics of pyruvate oxidation, mitochondrial oxygen consumption, metabolic profile, activities of metabolic enzymes, and climbing abilities of wild-type (WT) flies and flies harboring a deficiency in MPC1 (MPC1def). We hypothesized that MPC1 deficiency would cause a metabolic reprogramming that would favor the oxidation of alternative substrates. Our results show that the MPC1def flies display significantly reduced climbing capacity, pyruvate-induced oxygen consumption, and enzymatic activities of pyruvate kinase, alanine aminotransferase, and citrate synthase. Moreover, increased proline oxidation capacity was detected in MPC1def flies, which was associated with generally lower levels of several metabolites, and particularly those involved in amino acid catabolism such as ornithine, citrulline, and arginosuccinate. This study therefore reveals the flexibility of mitochondrial substrate oxidation allowing Drosophila to maintain cellular homeostasis.
    Keywords:  drosophila; kinetics; metabolomics; mitochondrial pyruvate carrier; mitochondrial respiration
    DOI:  https://doi.org/10.3390/metabo10090363
  12. Nat Commun. 2020 Sep 09. 11(1): 4509
    A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts.
    Youjun Zhang, Arun Sampathkumar, Sandra Mae-Lin Kerber, Corné Swart, Carsten Hille, Kumar Seerangan, Alexander Graf, Lee Sweetlove, Alisdair R Fernie.
      Glycolysis is one of the primordial pathways of metabolism, playing a pivotal role in energy metabolism and biosynthesis. Glycolytic enzymes are known to form transient multi-enzyme assemblies. Here we examine the wider protein-protein interactions of plant glycolytic enzymes and reveal a moonlighting role for specific glycolytic enzymes in mediating the co-localization of mitochondria and chloroplasts. Knockout mutation of phosphoglycerate mutase or enolase resulted in a significantly reduced association of the two organelles. We provide evidence that phosphoglycerate mutase and enolase form a substrate-channelling metabolon which is part of a larger complex of proteins including pyruvate kinase. These results alongside a range of genetic complementation experiments are discussed in the context of our current understanding of chloroplast-mitochondrial interactions within photosynthetic eukaryotes.
    DOI:  https://doi.org/10.1038/s41467-020-18234-w
  13. Sci Rep. 2020 Sep 08. 10(1): 14777
    GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission.
    Felipe Montecinos-Franjola, Brianna L Bauer, Jason A Mears, Rajesh Ramachandran.
      Green fluorescent protein (GFP)-tagging is the prevalent strategy to monitor protein dynamics in living cells. However, the consequences of appending the bulky GFP moiety to the protein of interest are rarely investigated. Here, using a powerful combination of quantitative fluorescence spectroscopic and imaging techniques, we have examined the oligomerization dynamics of the GFP-tagged mitochondrial fission GTPase dynamin-related protein 1 (Drp1) both in vitro and in vivo. We find that GFP-tagged Drp1 exhibits impaired oligomerization equilibria in solution that corresponds to a greatly diminished cooperative GTPase activity in comparison to native Drp1. Consequently, GFP-tagged Drp1 constitutes aberrantly stable, GTP-resistant supramolecular assemblies both in vitro and in vivo, neither of which reflects a more dynamic native Drp1 oligomerization state. Indeed, GFP-tagged Drp1 is detected more frequently per unit length over mitochondria in Drp1-null mouse embryonic fibroblasts (MEFs) compared to wild-type (wt) MEFs, indicating that the drastically reduced GTP turnover restricts oligomer disassembly from the mitochondrial surface relative to mixed oligomers comprising native and GFP-tagged Drp1. Yet, GFP-tagged Drp1 retains the capacity to mediate membrane constriction in vitro and mitochondrial division in vivo. These findings suggest that instead of robust assembly-disassembly dynamics, persistent Drp1 higher-order oligomerization over membranes is sufficient for mitochondrial fission.
    DOI:  https://doi.org/10.1038/s41598-020-71655-x
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