bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2022‒10‒16
twelve papers selected by
Edmond Chan
Queen’s University, School of Medicine
  1. Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.
  2. BNIP3L/NIX regulates both mitophagy and pexophagy.
  3. Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.
  4. Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.
  5. Manganese-driven CoQ deficiency.
  6. Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.
  7. Two type I topoisomerases maintain DNA topology in human mitochondria.
  8. A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tethering.
  9. Evaluation of Mitochondrial Turnover Using Fluorescence Microscopy in Drosophila.
  10. Mitoregulin controls mitochondrial function and stress-adaptation response during early phase of endoplasmic reticulum stress in breast cancer cells.
  11. Knockdown of TMEM160 leads to an increase in reactive oxygen species generation and the induction of the mitochondrial unfolded protein response.
  12. Mitochondrial fitness and cancer risk.
  1. N Engl J Med. 2022 Oct 13. 387(15): 1395-1403
    Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.
    Rebecca D Ganetzky, Andrew L Markhard, Irene Yee, Sheila Clever, Alan Cahill, Hardik Shah, Zenon Grabarek, Tsz-Leung To, Vamsi K Mootha.
      We describe the case of identical twin boys who presented with low body weight despite excessive caloric intake. An evaluation of their fibroblasts showed elevated oxygen consumption and decreased mitochondrial membrane potential. Exome analysis revealed a de novo heterozygous variant in ATP5F1B, which encodes the β subunit of mitochondrial ATP synthase (also called complex V). In yeast, mutations affecting the same region loosen coupling between the proton motive force and ATP synthesis, resulting in high rates of mitochondrial respiration. Expression of the mutant allele in human cell lines recapitulates this phenotype. These data support an autosomal dominant mitochondrial uncoupling syndrome with hypermetabolism. (Funded by the National Institutes of Health.).
    DOI:  https://doi.org/10.1056/NEJMoa2202949
  2. EMBO J. 2022 Oct 10. e111115
    BNIP3L/NIX regulates both mitophagy and pexophagy.
    Léa P Wilhelm, Juan Zapata-Muñoz, Beatriz Villarejo-Zori, Stephanie Pellegrin, Catarina Martins Freire, Ashley M Toye, Patricia Boya, Ian G Ganley.
      Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.
    Keywords:  autophagy; mitochondria; mitophagy; peroxisomes; pexophagy
    DOI:  https://doi.org/10.15252/embj.2022111115
  3. Nat Aging. 2022 Jun;2(6): 494-507
    Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.
    Edward T Schmid, Jung-Hoon Pyo, David W Walker.
      The effects of aging on the brain are widespread and can have dramatic implications on the overall health of an organism. Mitochondrial dysfunction is a hallmark of brain aging, but, the interplay between mitochondrial quality control, neuronal aging, and organismal health is not well understood. Here, we show that aging leads to a decline in mitochondrial autophagy (mitophagy) in the Drosophila brain with a concomitant increase in mitochondrial content. We find that induction of BCL2-interacting protein 3 (BNIP3), a mitochondrial outer membrane protein, in the adult nervous system induces mitophagy and prevents the accumulation of dysfunctional mitochondria in the aged brain. Importantly, neuronal induction of BNIP3-mediated mitophagy increases organismal longevity and healthspan. Furthermore, BNIP3-mediated mitophagy in the nervous system improves muscle and intestinal homeostasis in aged flies, indicating cell non-autonomous effects. Our findings identify BNIP3 as a therapeutic target to counteract brain aging and prolong overall organismal health with age.
    Keywords:  Autophagy; Intestinal barrier dysfunction; Intestinal stem cell; Mito-QC; Mitophagy; Muscle aging; Neuronal aging
    DOI:  https://doi.org/10.1038/s43587-022-00214-y
  4. Nat Commun. 2022 Oct 13. 13(1): 6058
    Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.
    Prasanna Katti, Alexander S Hall, Hailey A Parry, Peter T Ajayi, Yuho Kim, T Bradley Willingham, Christopher K E Bleck, Han Wen, Brian Glancy.
      Sustained muscle contraction occurs through interactions between actin and myosin filaments within sarcomeres and requires a constant supply of adenosine triphosphate (ATP) from nearby mitochondria. However, it remains unclear how different physical configurations between sarcomeres and mitochondria alter the energetic support for contractile function. Here, we show that sarcomere cross-sectional area (CSA) varies along its length in a cell type-dependent manner where the reduction in Z-disk CSA relative to the sarcomere center is closely coordinated with mitochondrial network configuration in flies, mice, and humans. Further, we find myosin filaments near the sarcomere periphery are curved relative to interior filaments with greater curvature for filaments near mitochondria compared to sarcoplasmic reticulum. Finally, we demonstrate variable myosin filament lattice spacing between filament ends and filament centers in a cell type-dependent manner. These data suggest both sarcomere structure and myofilament interactions are influenced by the location and orientation of mitochondria within muscle cells.
    DOI:  https://doi.org/10.1038/s41467-022-33678-y
  5. Nat Commun. 2022 Oct 13. 13(1): 6061
    Manganese-driven CoQ deficiency.
    Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F-Nora Vögtle, Fabien Pierrel, Martin Ott, Sabrina Büttner.
      Overexposure to manganese disrupts cellular energy metabolism across species, but the molecular mechanism underlying manganese toxicity remains enigmatic. Here, we report that excess cellular manganese selectively disrupts coenzyme Q (CoQ) biosynthesis, resulting in failure of mitochondrial bioenergetics. While respiratory chain complexes remain intact, the lack of CoQ as lipophilic electron carrier precludes oxidative phosphorylation and leads to premature cell and organismal death. At a molecular level, manganese overload causes mismetallation and proteolytic degradation of Coq7, a diiron hydroxylase that catalyzes the penultimate step in CoQ biosynthesis. Coq7 overexpression or supplementation with a CoQ headgroup analog that bypasses Coq7 function fully corrects electron transport, thus restoring respiration and viability. We uncover a unique sensitivity of a diiron enzyme to mismetallation and define the molecular mechanism for manganese-induced bioenergetic failure that is conserved across species.
    DOI:  https://doi.org/10.1038/s41467-022-33641-x
  6. FEBS Lett. 2022 Oct 11.
    Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.
    Fay M Allen, Ana S H Costa, Anja V Gruszczyk, Georgina R Bates, Hiran A Prag, Efterpi Nikitopoulou, Carlo Viscomi, Christian Frezza, Andrew M James, Michael P Murphy.
      The compartmentation and distribution of metabolites between mitochondria and the rest of the cell is a key parameter of cell signalling and pathology. Here, we have developed a rapid fractionation procedure that enables us to take mouse heart and liver from in vivo and within ~ 30 seconds stabilise the distribution of metabolites between mitochondria and the cytosol by rapid cooling, homogenisation and dilution. This is followed by centrifugation of mitochondria through an oil layer to separate mitochondrial and cytosolic fractions for subsequent metabolic analysis. Using this procedure revealed the in vivo compartmentation of mitochondrial metabolites and will enable assessment of the distribution of metabolites between the cytosol and mitochondria during a range of situations in vivo.
    Keywords:  compartmentation; in vivo; ischemia; metabolites; mitochondria; rapid fractionation
    DOI:  https://doi.org/10.1002/1873-3468.14511
  7. Nucleic Acids Res. 2022 Oct 10. pii: gkac857. [Epub ahead of print]
    Two type I topoisomerases maintain DNA topology in human mitochondria.
    Katja E Menger, James Chapman, Héctor Díaz-Maldonado, Mushtaq M Khazeem, Dasha Deen, Direnis Erdinc, John W Casement, Valeria Di Leo, Angela Pyle, Alejandro Rodríguez-Luis, Ian G Cowell, Maria Falkenberg, Caroline A Austin, Thomas J Nicholls.
      Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.
    DOI:  https://doi.org/10.1093/nar/gkac857
  8. Life Sci Alliance. 2023 Jan;pii: e202101305. [Epub ahead of print]6(1):
    A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tethering.
    Stephanie R Sloat, Suzanne Hoppins.
      In vertebrates, mitochondrial outer membrane fusion is mediated by two mitofusin paralogs, Mfn1 and Mfn2, conserved dynamin superfamily proteins. Here, we characterize a variant of mitofusin reported in patients with CMT2A where a serine is replaced with a proline (Mfn2-S350P and the equivalent in Mfn1, S329P). This serine is in a hinge domain (Hinge 2) that connects the globular GTPase domain to the adjacent extended helical bundle. We find that expression of this variant results in prolific and stable mitochondrial tethering that also blocks mitochondrial fusion by endogenous wild-type mitofusin. The formation of mitochondrial perinuclear clusters by this CMT2A variant requires normal GTPase domain function and formation of a mitofusin complex across two membranes. We propose that conformational dynamics mediated by Hinge 2 and regulated by GTP hydrolysis are disrupted by the substitution of proline at S329/S350 and this prevents progression from tethering to membrane fusion. Thus, our data are consistent with a model for mitofusin-mediated membrane fusion where Hinge 2 supports a power stroke to progress from the tethering complex to membrane fusion.
    DOI:  https://doi.org/10.26508/lsa.202101305
  9. Bio Protoc. 2022 Sep 05. pii: e4498. [Epub ahead of print]12(17):
    Evaluation of Mitochondrial Turnover Using Fluorescence Microscopy in Drosophila.
    Felipe Martelli.
      Mitochondrial dysfunction is associated with perturbations in the cellular oxidative status, changes in energy production and metabolic rate, and the onset of pathological processes. Classic methods of assessing mitochondrial dysfunction rely on indirect measures, such as evaluating mitochondrial DNA copy numbers, or direct but more costly and skilled techniques, such as electron microscopy. The protocol presented here was recently implemented to evaluate mitochondrial dysfunction in response to insecticide exposure in Drosophila melanogaster larvae, and it relies on the use of a previously established MitoTimer mutant strain. MitoTimer is a genetically engineered mitochondrial protein that shows green fluorescence when newly synthetized, irreversibly turning into red as mitochondria age. The protocol described here allows for the easy and direct assessment of shifts in mitochondrial turnover, with tissue-specific accuracy. This protocol can be adapted to assess changes in mitochondrial turnover in response to drugs, rearing conditions, and/or mutations in larva, pupa, or adult fruit flies.
    Keywords:   Dissection ; Drosophila ; Fluorescence microscopy ; Insecticide ; Mitochondria ; Mitochondrial turnover ; Oxidative stress ; Tissue imaging
    DOI:  https://doi.org/10.21769/BioProtoc.4498
  10. Biochim Biophys Acta Mol Basis Dis. 2022 Oct 11. pii: S0925-4439(22)00241-1. [Epub ahead of print] 166570
    Mitoregulin controls mitochondrial function and stress-adaptation response during early phase of endoplasmic reticulum stress in breast cancer cells.
    Munkyung Choi, Keon Wook Kang.
      The proper regulation of mitochondrial function is important for cellular homeostasis. Especially, in cancer cells, dysregulation of mitochondria is associated with diverse cellular events such as metabolism, redox status, and stress responses. Mitoregulin (MTLN), a micro protein encoded by LINC00116, recently has been reported to control mitochondrial functions in skeletal muscle cells and adipocytes. However, the role of MTLN in cancer cells remains unclear. In the present study, we found that MTLN regulates membrane potential and reactive oxygen species (ROS) generation of mitochondria in breast cancer cells. Moreover, MTLN deficiency resulted in abnormal mitochondria-associated ER membranes (MAMs) formation, which is crucial for stress adaptation. Indeed, the MTLN-deficient breast cancer cells failed to successfully resolve ER (endoplasmic reticulum) stress, and cell vulnerability to ER-stress inducers was significantly enhanced by the downregulation of MTLN. In conclusion, MTLN controls stress-adaptation responses in breast cancer cells as a key regulator of mitochondria-ER harmonization, and thereby its expression level may serve as an indicator of the responsiveness of cancer cells to proteasome inhibitors.
    Keywords:  ER stress; Mitochondria-associated ER membrane; Mitochondrial quality control; Mitoregulin
    DOI:  https://doi.org/10.1016/j.bbadis.2022.166570
  11. FEBS Open Bio. 2022 Oct 10.
    Knockdown of TMEM160 leads to an increase in reactive oxygen species generation and the induction of the mitochondrial unfolded protein response.
    Kosei Yamashita, Misa Haraguchi, Masato Yano.
      Transmembrane protein 160 (TMEM160) was recently reported to be localized to the mitochondrial inner membrane, but mitochondrial function was noted to be unaffected by loss of TMEM160. In contrast to these previously published findings, we report here that the absence of TMEM160 influences intracellular responses. After confirming that TMEM160 is localized in the inner mitochondrial membrane, we knocked down TMEM160 in human cultured cells and analyzed the changes in cellular responses. TMEM160 depletion led to an upregulation of the mitochondrial chaperone HSPD1, suggesting that depletion induced the mitochondrial unfolded protein response (UPRmt ). Indeed, the expression of key transcription factors that induce the UPRmt (ATF4, ATF5, and DDIT3) was increased following TMEM160 depletion. Expression of the mitochondrial protein import-receptors TOMM22 and TOMM20 was also enhanced. In addition, we observed a significant increase in reactive oxygen species (ROS) generation following TMEM160 depletion. Glutathione S-transferases, which detoxify the products of oxidative stress, were also upregulated in TMEM160-depleted cells. Immunoblot analysis was performed to detect proteins modified by 4-hydroxynonenal (which is released after the peroxidation of lipids by ROS): the expression patterns of 4-hydroxynonenal-modified proteins were altered after TMEM160 depletion, suggesting that depletion enhanced degadation of these proteins. HSPD1, TOMM22, ATF4, ATF5, and DDIT3 remained upregulated after ROS was scavenged by N-acetylcysteine, suggesting that once the UPRmt is induced by TMEM160 depletion, it is not suppresed by the subsequent detoxification of ROS. These findings suggest that TMEM160 may suppress ROS generation and stabilize mitochondrial protein(s).
    Keywords:  TMEM160; mitochondria; mitochondrial unfolded protein response; oxidative stress; reactive oxygen species
    DOI:  https://doi.org/10.1002/2211-5463.13496
  12. PLoS One. 2022 ;17(10): e0273520
    Mitochondrial fitness and cancer risk.
    Andrew V Kossenkov, Andrew Milcarek, Faiyaz Notta, Gun-Ho Jang, Julie M Wilson, Steven Gallinger, Daniel Cui Zhou, Li Ding, Jagadish C Ghosh, Michela Perego, Annamaria Morotti, Marco Locatelli, Marie E Robert, Valentina Vaira, Dario C Altieri.
      Changes in metabolism are a hallmark of cancer, but molecular signatures of altered bioenergetics to aid in clinical decision-making do not currently exist. We recently identified a group of human tumors with constitutively reduced expression of the mitochondrial structural protein, Mic60, also called mitofilin or inner membrane mitochondrial protein (IMMT). These Mic60-low tumors exhibit severe loss of mitochondrial fitness, paradoxically accompanied by increased metastatic propensity and upregulation of a unique transcriptome of Interferon (IFN) signaling and Senescence-Associated Secretory Phenotype (SASP). Here, we show that an optimized, 11-gene signature of Mic60-low tumors is differentially expressed in multiple malignancies, compared to normal tissues, and correlates with poor patient outcome. When analyzed in three independent patient cohorts of pancreatic ductal adenocarcinoma (PDAC), the Mic60-low gene signature was associated with aggressive disease variants, local inflammation, FOLFIRINOX failure and shortened survival, independently of age, gender, or stage. Therefore, the 11-gene Mic60-low signature may provide an easily accessible molecular tool to stratify patient risk in PDAC and potentially other malignancies.
    DOI:  https://doi.org/10.1371/journal.pone.0273520
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