bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2023–08–20
fiveteen papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. MARCH5-dependent NLRP3 ubiquitination is required for mitochondrial NLRP3-NEK7 complex formation and NLRP3 inflammasome activation.
  2. Pyruvate anaplerosis is a targetable vulnerability in persistent leukaemic stem cells.
  3. E4 ubiquitin ligase promotes mitofusin turnover and mitochondrial stress response.
  4. Dynamics of SLC25A51 reveal preference for oxidized NAD+ and substrate led transport.
  5. NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
  6. Temporal control of contact site formation reveals a relationship between mitochondrial division and Num1-mediated mitochondrial tethering.
  7. Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
  8. FASN deficiency induces a cytosol-to-mitochondria citrate flux to mitigate detachment-induced oxidative stress.
  9. FoxM1 coordinates cell division, protein synthesis, and mitochondrial activity in a subset of β cells during acute metabolic stress.
  10. The mitochondrial succinate dehydrogenase complex controls the STAT3-IL-10 pathway in inflammatory macrophages.
  11. Optogenetic cleavage of the Miro GTPase reveals the direct consequences of real-time loss of function in Drosophila.
  12. The AAA-ATPase Yta4/ATAD1 interacts with the mitochondrial divisome to inhibit mitochondrial fission.
  13. Discovery of Potent Allosteric DRP1 Inhibitors by Disrupting Protein-Protein Interaction with MiD49.
  14. Monitoring Mitochondria Function in Ferroptosis.
  15. Brain mitochondria predict a mouse's stress level.
  1. EMBO J. 2023 Aug 14. e113481
    MARCH5-dependent NLRP3 ubiquitination is required for mitochondrial NLRP3-NEK7 complex formation and NLRP3 inflammasome activation.
    Yeon-Ji Park, Niranjan Dodantenna, Yonghyeon Kim, Tae-Hwan Kim, Ho-Soo Lee, Young-Suk Yoo, June Heo, Jae-Ho Lee, Myung-Hee Kwon, Ho Chul Kang, Jong-Soo Lee, Hyeseong Cho.
      The NLRP3 inflammasome plays a key role in responding to pathogens, and endogenous damage and mitochondria are intensively involved in inflammasome activation. The NLRP3 inflammasome forms multiprotein complexes and its sequential assembly is important for its activation. Here, we show that NLRP3 is ubiquitinated by the mitochondria-associated E3 ligase, MARCH5. Myeloid cell-specific March5 conditional knockout (March5 cKO) mice failed to secrete IL-1β and IL-18 and exhibited an attenuated mortality rate upon LPS or Pseudomonas aeruginosa challenge. Macrophages derived from March5 cKO mice also did not produce IL-1β and IL-18 after microbial infection. Mechanistically, MARCH5 interacts with the NACHT domain of NLRP3 and promotes K27-linked polyubiquitination on K324 and K430 residues of NLRP3. Ubiquitination-defective NLRP3 mutants on K324 and K430 residues are not able to bind to NEK7, nor form NLRP3 oligomers leading to abortive ASC speck formation and diminished IL-1β production. Thus, MARCH5-dependent NLRP3 ubiquitination on the mitochondria is required for NLRP3-NEK7 complex formation and NLRP3 oligomerization. We propose that the E3 ligase MARCH5 is a regulator of NLRP3 inflammasome activation on the mitochondria.
    Keywords:  MARCH5; NEK7; NLRP3 inflammasome; mitochondria; ubiquitination
    DOI:  https://doi.org/10.15252/embj.2023113481
  2. Nat Commun. 2023 Aug 17. 14(1): 4634
    Pyruvate anaplerosis is a targetable vulnerability in persistent leukaemic stem cells.
    Kevin M Rattigan, Zuzana Brabcova, Daniele Sarnello, Martha M Zarou, Kiron Roy, Ryan Kwan, Lucie de Beauchamp, Amy Dawson, Angela Ianniciello, Ahmed Khalaf, Eric R Kalkman, Mary T Scott, Karen Dunn, David Sumpton, Alison M Michie, Mhairi Copland, Saverio Tardito, Eyal Gottlieb, G Vignir Helgason.
      Deregulated oxidative metabolism is a hallmark of leukaemia. While tyrosine kinase inhibitors (TKIs) such as imatinib have increased survival of chronic myeloid leukaemia (CML) patients, they fail to eradicate disease-initiating leukemic stem cells (LSCs). Whether TKI-treated CML LSCs remain metabolically deregulated is unknown. Using clinically and physiologically relevant assays, we generate multi-omics datasets that offer unique insight into metabolic adaptation and nutrient fate in patient-derived CML LSCs. We demonstrate that LSCs have increased pyruvate anaplerosis, mediated by increased mitochondrial pyruvate carrier 1/2 (MPC1/2) levels and pyruvate carboxylase (PC) activity, in comparison to normal counterparts. While imatinib reverses BCR::ABL1-mediated LSC metabolic reprogramming, stable isotope-assisted metabolomics reveals that deregulated pyruvate anaplerosis is not affected by imatinib. Encouragingly, genetic ablation of pyruvate anaplerosis sensitises CML cells to imatinib. Finally, we demonstrate that MSDC-0160, a clinical orally-available MPC1/2 inhibitor, inhibits pyruvate anaplerosis and targets imatinib-resistant CML LSCs in robust pre-clinical CML models. Collectively these results highlight pyruvate anaplerosis as a persistent and therapeutically targetable vulnerability in imatinib-treated CML patient-derived samples.
    DOI:  https://doi.org/10.1038/s41467-023-40222-z
  3. Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00563-4. [Epub ahead of print]83(16): 2976-2990.e9
    E4 ubiquitin ligase promotes mitofusin turnover and mitochondrial stress response.
    Vincent Anton, Ira Buntenbroich, Tânia Simões, Mariana Joaquim, Leonie Müller, Reinhard Buettner, Margarete Odenthal, Thorsten Hoppe, Mafalda Escobar-Henriques.
      Ubiquitin-dependent control of mitochondrial dynamics is important for protein quality and neuronal integrity. Mitofusins, mitochondrial fusion factors, can integrate cellular stress through their ubiquitylation, which is carried out by multiple E3 enzymes in response to many different stimuli. However, the molecular mechanisms that enable coordinated responses are largely unknown. Here we show that yeast Ufd2, a conserved ubiquitin chain-elongating E4 enzyme, is required for mitochondrial shape adjustments. Under various stresses, Ufd2 translocates to mitochondria and triggers mitofusin ubiquitylation. This elongates ubiquitin chains on mitofusin and promotes its proteasomal degradation, leading to mitochondrial fragmentation. Ufd2 and its human homologue UBE4B also target mitofusin mutants associated with Charcot-Marie-Tooth disease, a hereditary sensory and motor neuropathy characterized by progressive loss of the peripheral nerves. This underscores the pathophysiological importance of E4-mediated ubiquitylation in neurodegeneration. In summary, we identify E4-dependent mitochondrial stress adaptation by linking various metabolic processes to mitochondrial fusion and fission dynamics.
    Keywords:  CMT2A; Cdc48/p97; E4; Fzo1; MFN2; UBE4B; Ufd2; fusion; mitochondria; mitofusin; stress; ubiquitin
    DOI:  https://doi.org/10.1016/j.molcel.2023.07.021
  4. EMBO Rep. 2023 Aug 14. e56596
    Dynamics of SLC25A51 reveal preference for oxidized NAD+ and substrate led transport.
    Shivansh Goyal, Akhilesh Paspureddi, Mu-Jie Lu, Hsin-Ru Chan, Scott N Lyons, Crystal N Wilson, Marc Niere, Mathias Ziegler, Xiaolu A Cambronne.
      SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that contribute to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we use Molecular Dynamics simulations to reconstitute SLC25A51 homology models into lipid bilayers and to generate hypotheses to test. We observe spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51's central pore and find that mutation of these sites impairs cardiolipin binding and transporter activity. We also observe that stable formation of the required matrix gate is controlled by a single salt bridge. We identify binding sites in SLC25A51 for NAD+ and show that its selectivity for NAD+ is guided by an electrostatic interaction between the charged nicotinamide ring in the ligand and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guides the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.
    Keywords:  MCART1; SLC25A51; mitochondrial carrier family; mitochondrial transport; nicotinamide adenine dinucleotide (NAD)
    DOI:  https://doi.org/10.15252/embr.202256596
  5. J Cell Biol. 2023 10 02. pii: e202301091. [Epub ahead of print]222(10):
    NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
    You-An Su, Hsin-Yi Chiu, Yu-Chen Chang, Chieh-Ju Sung, Chih-Wei Chen, Reika Tei, Xuang-Rong Huang, Shao-Chun Hsu, Shan-Shan Lin, Hsien-Chu Wang, Yu-Chun Lin, Jui-Cheng Hsu, Hermann Bauer, Yuxi Feng, Jeremy M Baskin, Zee-Fen Chang, Ya-Wen Liu.
      Mitochondria are dynamic organelles regulated by fission and fusion processes. The fusion of membranes requires elaborative coordination of proteins and lipids and is particularly crucial for the function and quality control of mitochondria. Phosphatidic acid (PA) on the mitochondrial outer membrane generated by PLD6 facilitates the fusion of mitochondria. However, how PA promotes mitochondrial fusion remains unclear. Here, we show that a mitochondrial outer membrane protein, NME3, is required for PLD6-induced mitochondrial tethering or clustering. NME3 is enriched at the contact interface of two closely positioned mitochondria depending on PLD6, and NME3 binds directly to PA-exposed lipid packing defects via its N-terminal amphipathic helix. The PA binding function and hexamerization confer NME3 mitochondrial tethering activity. Importantly, nutrient starvation enhances the enrichment efficiency of NME3 at the mitochondrial contact interface, and the tethering ability of NME3 contributes to fusion efficiency. Together, our findings demonstrate NME3 as a tethering protein promoting selective fusion between PLD6-remodeled mitochondria for quality control.
    DOI:  https://doi.org/10.1083/jcb.202301091
  6. Mol Biol Cell. 2023 Aug 16. mbcE23050168
    Temporal control of contact site formation reveals a relationship between mitochondrial division and Num1-mediated mitochondrial tethering.
    Clare S Harper, Jason C Casler, Laura L Lackner.
      Mitochondrial division is critical for maintenance of mitochondrial morphology and cellular homeostasis. Previous work has suggested that the mitochondria-ER-cortex anchor (MECA), a tripartite membrane contact site between mitochondria, the ER, and the plasma membrane, is involved in mitochondrial division. However, its role is poorly understood. We developed a system to control MECA formation and depletion, which allowed us to investigate the relationship between MECA-mediated contact sites and mitochondrial division. Num1 is the protein that mediates mitochondria-ER-plasma membrane tethering at MECA sites. Using both rapamycin-inducible dimerization and auxin-inducible degradation components coupled with Num1, we developed systems to temporally control the formation and depletion of the native contact site. Additionally, we designed a regulatable Num1-independant mitochondria-PM tether. We found that mitochondria-PM tethering alone is not sufficient to rescue mitochondrial division and that a specific feature of Num1-mediated tethering is required. This study demonstrates the utility of systems that regulate contact site formation and depletion in studying the biological functions of membrane contact sites. [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E23-05-0168
  7. Proc Natl Acad Sci U S A. 2023 08 22. 120(34): e2306073120
    Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
    Andy Y Z Li, Ying Di, Sumaera Rathore, Ason C-Y Chiang, Jan Jezek, Hansong Ma.
      Mitochondria are dynamic organelles that undergo frequent remodeling to accommodate developmental needs. Here, we describe a striking organization of mitochondria into a large ball-like structure adjacent to the nucleus in premeiotic Drosophila melanogaster spermatocytes, which we term "mitoball". Mitoballs are transient structures that colocalize with the endoplasmic reticulum, Golgi bodies, and the fusome. We observed similar premeiotic mitochondrial clusters in a wide range of insect species, including mosquitos and cockroaches. Through a genetic screen, we identified that Milton, an adaptor protein that links mitochondria to microtubule-based motors, mediates mitoball formation. Flies lacking a 54 amino acid region in the C terminus of Milton completely lacked mitoballs, had swollen mitochondria in their spermatocytes, and showed reduced male fertility. We suggest that the premeiotic mitochondrial clustering is a conserved feature of insect spermatogenesis that supports sperm development.
    Keywords:  Milton-mediated mitochondrial trafficking; insect spermatogenesis; male fertility; mitoballs; mitochondrial clustering
    DOI:  https://doi.org/10.1073/pnas.2306073120
  8. Cell Rep. 2023 Aug 12. pii: S2211-1247(23)00982-8. [Epub ahead of print]42(8): 112971
    FASN deficiency induces a cytosol-to-mitochondria citrate flux to mitigate detachment-induced oxidative stress.
    Wenting Dai, Zhichao Wang, Guan Wang, Qiong A Wang, Ralph DeBerardinis, Lei Jiang.
      Fatty acid synthase (FASN) maintains de novo lipogenesis (DNL) to support rapid growth in most proliferating cancer cells. Lipogenic acetyl-coenzyme A (CoA) is primarily produced from carbohydrates but can arise from glutamine-dependent reductive carboxylation. Here, we show that reductive carboxylation also occurs in the absence of DNL. In FASN-deficient cells, reductive carboxylation is mainly catalyzed by isocitrate dehydrogenase-1 (IDH1), but IDH1-generated cytosolic citrate is not utilized for supplying DNL. Metabolic flux analysis (MFA) shows that FASN deficiency induces a net cytosol-to-mitochondria citrate flux through mitochondrial citrate transport protein (CTP). Previously, a similar pathway has been shown to mitigate detachment-induced oxidative stress in anchorage-independent tumor spheroids. We further report that tumor spheroids show reduced FASN activity and that FASN-deficient cells acquire resistance to oxidative stress in a CTP- and IDH1-dependent manner. Collectively, these data indicate that by inducing a cytosol-to-mitochondria citrate flux, anchorage-independent malignant cells can gain redox capacity by trading off FASN-supported rapid growth.
    Keywords:  CP: Metabolism; CP: Molecular biology; DNL; FASN inhibitor; IDH1 inhibitor; MFA; SLC25A1; anchorage-independent growth; cytosol-to-mitochondria citrate flux; de novo lipogenesis; metabolic flux analysis; redox; reductive carboxylation
    DOI:  https://doi.org/10.1016/j.celrep.2023.112971
  9. Cell Rep. 2023 Aug 16. pii: S2211-1247(23)00997-X. [Epub ahead of print]42(8): 112986
    FoxM1 coordinates cell division, protein synthesis, and mitochondrial activity in a subset of β cells during acute metabolic stress.
    Ahmad Kobiita, Pamuditha N Silva, Marc W Schmid, Markus Stoffel.
      Pancreatic β cells display functional and transcriptional heterogeneity in health and disease. The sequence of events leading to β cell heterogeneity during metabolic stress is poorly understood. Here, we characterize β cell responses to early metabolic stress in vivo by employing RNA sequencing (RNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), single-cell RNA-seq (scRNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and real-time imaging to decipher temporal events of chromatin remodeling and gene expression regulating the unfolded protein response (UPR), protein synthesis, mitochondrial function, and cell-cycle progression. We demonstrate that a subpopulation of β cells with active UPR, decreased protein synthesis, and insulin secretary capacities is more susceptible to proliferation after insulin depletion. Alleviation of endoplasmic reticulum (ER) stress precedes the progression of the cell cycle and mitosis and ensures appropriate insulin synthesis. Furthermore, metabolic stress rapidly activates key transcription factors including FoxM1, which impacts on proliferative and quiescent β cells by regulating protein synthesis, ER stress, and mitochondrial activity via direct repression of mitochondrial-encoded genes.
    Keywords:  CP: Cell biology; CP: Metabolism; ER-stress; FoxM1; early metabolic stress; heterogeneity; mitochondrial function; proliferation; protein synthesis; β cells
    DOI:  https://doi.org/10.1016/j.celrep.2023.112986
  10. iScience. 2023 Aug 18. 26(8): 107473
    The mitochondrial succinate dehydrogenase complex controls the STAT3-IL-10 pathway in inflammatory macrophages.
    Dino Gobelli, Pablo Serrano-Lorenzo, María J Esteban-Amo, Julia Serna, M Teresa Pérez-García, Antonio Orduña, Alexis A Jourdain, Miguel Á Martín-Casanueva, Miguel Á de la Fuente, María Simarro.
      The functions of macrophages are tightly regulated by their metabolic state. However, the role of the mitochondrial electron transport chain (ETC) in macrophage functions remains understudied. Here, we provide evidence that the succinate dehydrogenase (SDH)/complex II (CII) is required for respiration and plays a role in controlling effector responses in macrophages. We find that the absence of the catalytic subunits Sdha and Sdhb in macrophages impairs their ability to effectively stabilize HIF-1α and produce the pro-inflammatory cytokine IL-1β in response to LPS stimulation. We also arrive at the novel result that both subunits are essential for the LPS-driven production of IL-10, a potent negative feedback regulator of the macrophage inflammatory response. This phenomenon is explained by the fact that the absence of Sdha and Sdhb leads to the inhibition of Stat3 tyrosine phosphorylation, caused partially by the excessive accumulation of mitochondrial reactive oxygen species (mitoROS) in the knockout cells.
    Keywords:  Biological sciences; Cell biology; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2023.107473
  11. PLoS Biol. 2023 Aug 17. 21(8): e3002273
    Optogenetic cleavage of the Miro GTPase reveals the direct consequences of real-time loss of function in Drosophila.
    Francesca Mattedi, Ethlyn Lloyd-Morris, Frank Hirth, Alessio Vagnoni.
      Miro GTPases control mitochondrial morphology, calcium homeostasis, and regulate mitochondrial distribution by mediating their attachment to the kinesin and dynein motor complex. It is not clear, however, how Miro proteins spatially and temporally integrate their function as acute disruption of protein function has not been performed. To address this issue, we have developed an optogenetic loss of function "Split-Miro" allele for precise control of Miro-dependent mitochondrial functions in Drosophila. Rapid optogenetic cleavage of Split-Miro leads to a striking rearrangement of the mitochondrial network, which is mediated by mitochondrial interaction with the microtubules. Unexpectedly, this treatment did not impact the ability of mitochondria to buffer calcium or their association with the endoplasmic reticulum. While Split-Miro overexpression is sufficient to augment mitochondrial motility, sustained photocleavage shows that Split-Miro is surprisingly dispensable to maintain elevated mitochondrial processivity. In adult fly neurons in vivo, Split-Miro photocleavage affects both mitochondrial trafficking and neuronal activity. Furthermore, functional replacement of endogenous Miro with Split-Miro identifies its essential role in the regulation of locomotor activity in adult flies, demonstrating the feasibility of tuning animal behaviour by real-time loss of protein function.
    DOI:  https://doi.org/10.1371/journal.pbio.3002273
  12. PLoS Biol. 2023 Aug 17. 21(8): e3002247
    The AAA-ATPase Yta4/ATAD1 interacts with the mitochondrial divisome to inhibit mitochondrial fission.
    Jiajia He, Ke Liu, Yifan Wu, Chenhui Zhao, Shuaijie Yan, Jia-Hui Chen, Lizhu Hu, Dongmei Wang, Fan Zheng, Wenfan Wei, Chao Xu, Chengdong Huang, Xing Liu, Xuebiao Yao, Lijun Ding, Zhiyou Fang, Ai-Hui Tang, Chuanhai Fu.
      Mitochondria are in a constant balance of fusion and fission. Excessive fission or deficient fusion leads to mitochondrial fragmentation, causing mitochondrial dysfunction and physiological disorders. How the cell prevents excessive fission of mitochondria is not well understood. Here, we report that the fission yeast AAA-ATPase Yta4, which is the homolog of budding yeast Msp1 responsible for clearing mistargeted tail-anchored (TA) proteins on mitochondria, plays a critical role in preventing excessive mitochondrial fission. The absence of Yta4 leads to mild mitochondrial fragmentation in a Dnm1-dependent manner but severe mitochondrial fragmentation upon induction of mitochondrial depolarization. Overexpression of Yta4 delocalizes the receptor proteins of Dnm1, i.e., Fis1 (a TA protein) and Mdv1 (the bridging protein between Fis1 and Dnm1), from mitochondria and reduces the localization of Dnm1 to mitochondria. The effect of Yta4 overexpression on Fis1 and Mdv1, but not Dnm1, depends on the ATPase and translocase activities of Yta4. Moreover, Yta4 interacts with Dnm1, Mdv1, and Fis1. In addition, Yta4 competes with Dnm1 for binding Mdv1 and decreases the affinity of Dnm1 for GTP and inhibits Dnm1 assembly in vitro. These findings suggest a model, in which Yta4 inhibits mitochondrial fission by inhibiting the function of the mitochondrial divisome composed of Fis1, Mdv1, and Dnm1. Therefore, the present work reveals an uncharacterized molecular mechanism underlying the inhibition of mitochondrial fission.
    DOI:  https://doi.org/10.1371/journal.pbio.3002247
  13. ACS Med Chem Lett. 2023 Aug 10. 14(8): 1095-1099
    Discovery of Potent Allosteric DRP1 Inhibitors by Disrupting Protein-Protein Interaction with MiD49.
    Takeru Furuya, Jean Lin, Arina Afanaseva, Lisa Molz, Bharat Lagu, Bin Ma.
      Mitochondrial dysfunction has been attributed to many disease indications, including metabolic, cardiovascular, neoplastic, and neurodegenerative diseases. Dynamin related protein 1 (DRP1) is crucial in regulating mitochondrial fission and maintaining mitochondrial homeostasis. MiD49 is a dynamic peripheral protein receptor on the surface of the mitochondrial membrane that recruits DRP1 protein to induce mitochondrial binary fission. By targeting the protein-protein interaction of DRP1/MiD49, we have discovered a novel and potent allosteric DRP1 inhibitor that inhibits mitochondria fragmentation in vitro. X-ray cocrystal structure revealed that it locked the closed DRP1 conformation by induced dimerization.
    DOI:  https://doi.org/10.1021/acsmedchemlett.3c00223
  14. Methods Mol Biol. 2023 ;2712 103-115
    Monitoring Mitochondria Function in Ferroptosis.
    Fangquan Chen, Jiao Liu, Daolin Tang, Rui Kang.
      Ferroptosis is a type of regulated necrosis driven by uncontrolled membrane lipid peroxidation. Mitochondria, which are membrane-bound organelles present in almost all eukaryotic cells and play a central role in energy metabolism and various types of cell death, have a complicated role in ferroptosis. On one hand, mitochondrial-derived iron metabolism and reactive oxygen species (ROS) production may promote ferroptosis. On the other hand, mitochondria also possess a dihydroorotate dehydrogenase (DHODH)-dependent antioxidant system that detoxifies lipid peroxides. This chapter summarizes several methods, such as western blotting, immunofluorescence, cell viability assays, mitochondrial fluorescent probes, adenosine 5'-triphosphate (ATP) assay kits, mitochondrial respiration, and mitophagy tests, that may enable researchers to gain a deeper understanding of the dual role of mitochondria in ferroptosis.
    Keywords:  Ferroptosis; Methods; Mitochondria
    DOI:  https://doi.org/10.1007/978-1-0716-3433-2_10
  15. Nature. 2023 Aug 16.
    Brain mitochondria predict a mouse's stress level.
      
    Keywords:  Metabolism
    DOI:  https://doi.org/10.1038/d41586-023-02575-9
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