bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2021–11–28
thirteen papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
  2. The TFAM-to-mtDNA ratio defines inner-cellular nucleoid populations with distinct activity levels.
  3. Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring towards glycolysis.
  4. The PINK1 advantage: recycling mitochondria in times of trouble?
  5. The long non-coding RNA CDK6-AS1 overexpression impacts on acute myeloid leukemia differentiation and mitochondrial dynamics.
  6. A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging.
  7. A novel role of KEAP1/PGAM5 complex: ROS sensor for inducing mitophagy.
  8. A new automated tool to quantify nucleoid distribution within mitochondrial networks.
  9. The role of protein acetylation in regulating mitochondrial fusion and fission.
  10. Monitoring checkpoints of metabolism and protein biogenesis in mitochondria by Phos-tag technology.
  11. Microtubule-Based Mitochondrial Dynamics as a Valuable Therapeutic Target in Cancer.
  12. Rewiring cell signalling pathways in pathogenic mtDNA mutations.
  13. Metabolic adaptation to the chronic loss of Ca2+ signaling induced by knockout of IP3 receptors or the mitochondrial Ca2+ uniporter.
  1. Cell Metab. 2021 Nov 12. pii: S1550-4131(21)00529-5. [Epub ahead of print]
    Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
    Marcel Morgenstern, Christian D Peikert, Philipp Lübbert, Ida Suppanz, Cinzia Klemm, Oliver Alka, Conny Steiert, Nataliia Naumenko, Alexander Schendzielorz, Laura Melchionda, Wignand W D Mühlhäuser, Bettina Knapp, Jakob D Busch, Sebastian B Stiller, Stefan Dannenmaier, Caroline Lindau, Mariya Licheva, Christopher Eickhorst, Riccardo Galbusera, Ralf M Zerbes, Michael T Ryan, Claudine Kraft, Vera Kozjak-Pavlovic, Friedel Drepper, Sven Dennerlein, Silke Oeljeklaus, Nikolaus Pfanner, Nils Wiedemann, Bettina Warscheid.
      Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality control and have been linked to various diseases. Different views exist on the composition of the human mitochondrial proteome. We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). We identified interactors of translocases, respiratory chain, and ATP synthase assembly factors. The abundance of MitoCoP proteins covers six orders of magnitude and amounts to 7% of the cellular proteome with the chaperones HSP60-HSP10 being the most abundant mitochondrial proteins. MitoCoP dynamics spans three orders of magnitudes, with half-lives from hours to months, and suggests a rapid regulation of biosynthesis and assembly processes. 460 MitoCoP genes are linked to human diseases with a strong prevalence for the central nervous system and metabolism. MitoCoP will provide a high-confidence resource for placing dynamics, functions, and dysfunctions of mitochondria into the cellular context.
    Keywords:  Mitochondria; complexome; copy numbers; disease; half-lives; high-confidence proteome; human cells; protein translocation; respiratory chain; smORFs
    DOI:  https://doi.org/10.1016/j.cmet.2021.11.001
  2. Cell Rep. 2021 Nov 23. pii: S2211-1247(21)01479-0. [Epub ahead of print]37(8): 110000
    The TFAM-to-mtDNA ratio defines inner-cellular nucleoid populations with distinct activity levels.
    Christian Brüser, Jan Keller-Findeisen, Stefan Jakobs.
      In human cells, generally a single mitochondrial DNA (mtDNA) is compacted into a nucleoprotein complex denoted the nucleoid. Each cell contains hundreds of nucleoids, which tend to cluster into small groups. It is unknown whether all nucleoids are equally involved in mtDNA replication and transcription or whether distinct nucleoid subpopulations exist. Here, we use multi-color STED super-resolution microscopy to determine the activity of individual nucleoids in primary human cells. We demonstrate that only a minority of all nucleoids are active. Active nucleoids are physically larger and tend to be involved in both replication and transcription. Inactivity correlates with a high ratio of the mitochondrial transcription factor A (TFAM) to the mtDNA of the individual nucleoid, suggesting that TFAM-induced nucleoid compaction regulates nucleoid replication and transcription activity in vivo. We propose that the stable population of highly compacted inactive nucleoids represents a storage pool of mtDNAs with a lower mutational load.
    Keywords:  DNA packaging; STED nanoscopy; mitochondrial gene expression; mtDNA mutations; mtDNA replication
    DOI:  https://doi.org/10.1016/j.celrep.2021.110000
  3. iScience. 2021 Nov 18. 103471
    Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring towards glycolysis.
    Hadar Medini, Amit Zirman, Dan Mishmar.
      Mitochondria are pivotal for bioenergetics, as well as in cellular response to viral infections. Nevertheless, their role in COVID-19 was largely overlooked. Here, we analyzed available bulk RNA-seq datasets from COVID-19 patients and corresponding healthy controls (three blood datasets, N=48 healthy, 119 patients; two respiratory tract datasets, N=157 healthy, 524 patients). We found significantly reduced mtDNA gene expression in blood, but not in respiratory tract samples from patient. Next, analysis of eight single-cells RNA-seq datasets from peripheral blood mononuclear cells, nasopharyngeal samples and Broncho alveolar lavage fluid (N=1,192,243 cells), revealed significantly reduced mtDNA gene expression especially in immune system cells from patients. This associated with elevated expression of nuclear DNA-encoded OXPHOS subunits, suggesting compromised mitochondrial-nuclear co-regulation. This, together with elevated expression of ROS-response genes and glycolysis enzymes in patients, suggest rewiring towards glycolysis, thus generating beneficial conditions for SARS-CoV-2 replication. Our findings underline the centrality of mitochondrial dysfunction in COVID-19.
    Keywords:  COVID-19; RNA-seq; SARS-CoV-2; mitochondrial gene expression; mtDNA; single cells
    DOI:  https://doi.org/10.1016/j.isci.2021.103471
  4. Autophagy. 2021 Nov 23. 1-2
    The PINK1 advantage: recycling mitochondria in times of trouble?
    Zak Doric, Huihui Li, Ken Nakamura.
      Parkinson disease remains a debilitating neurodegenerative disorder, despite the discovery of multiple causative genes that account for familial forms. Prominent among these are PRKN/Parkin and PINK1, whose protein products participate in mitochondrial turnover, or mitophagy. But our poor understanding of the basic biological mechanisms driven by those genes in neurons limits our ability to target them therapeutically. Here, we summarize our recent findings enabled by a new platform to track individual mitochondria in neurons. Our analysis delineates the steps of PINK1- and PRKN-dependent mitochondrial turnover, including the unexplored fates of mitochondria after fusion with lysosomes. These studies reveal unexpected mechanisms of mitochondrial quality control, which may contribute to the reliance of neurons on PINK1 under conditions of stress.
    Keywords:  Mitophagy; PARKIN; PINK1; Parkinson’s disease; mitochondrial turnover
    DOI:  https://doi.org/10.1080/15548627.2021.1998872
  5. iScience. 2021 Nov 19. 24(11): 103350
    The long non-coding RNA CDK6-AS1 overexpression impacts on acute myeloid leukemia differentiation and mitochondrial dynamics.
    Elena Porcù, Maddalena Benetton, Valeria Bisio, Ambra Da Ros, Claudia Tregnago, Giulia Borella, Carlo Zanon, Matteo Bordi, Giuseppe Germano, Sabrina Manni, Silvia Campello, Dinesh S Rao, Franco Locatelli, Martina Pigazzi.
      Patients with acute myeloid leukemia (AML) carrying high-risk genetic lesions or high residual disease levels after therapy are particularly exposed to the risk of relapse. Here, we identified the long non-coding RNA CDK6-AS1 able to cluster an AML subgroup with peculiar gene signatures linked to hematopoietic cell differentiation and mitochondrial dynamics. CDK6-AS1 silencing triggered hematopoietic commitment in healthy CD34+ cells, whereas in AML cells the pathological undifferentiated state was rescued. This latter phenomenon derived from RUNX1 transcriptional control, responsible for the stemness of hematopoietic precursors and for the block of differentiation in AML. By CDK6-AS1 silencing in vitro, AML mitochondrial mass decreased with augmented pharmacological sensitivity to mitochondria-targeting drugs. In vivo, the combination of tigecycline and cytarabine reduced leukemia progression in the AML-PDX model with high CDK6-AS1 levels, supporting the concept of a mitochondrial vulnerability. Together, these findings uncover CDK6-AS1 as crucial in myeloid differentiation and mitochondrial mass regulation.
    Keywords:  Cancer; Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2021.103350
  6. Elife. 2021 Nov 22. pii: e73808. [Epub ahead of print]10
    A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging.
    Xingbo Yang, Gloria Ha, Dan Needleman.
      Mitochondrial metabolism is of central importance to diverse aspects of cell and developmental biology. Defects in mitochondria are associated with many diseases, including cancer, neuropathology, and infertility. Our understanding of mitochondrial metabolism in situ and dysfunction in diseases are limited by the lack of techniques to measure mitochondrial metabolic fluxes with sufficient spatiotemporal resolution. Herein, we developed a new method to infer mitochondrial metabolic fluxes in living cells with subcellular resolution from fluorescence lifetime imaging of NADH. This result is based on the use of a generic coarse-grained NADH redox model. We tested the model in mouse oocytes and human tissue culture cells subject to a wide variety of perturbations by comparing predicted fluxes through the electron transport chain (ETC) to direct measurements of oxygen consumption rate. Interpreting the FLIM measurements of NADH using this model, we discovered a homeostasis of ETC flux in mouse oocytes: perturbations of nutrient supply and energy demand of the cell do not change ETC flux despite significantly impacting NADH metabolic state. Furthermore, we observed a subcellular spatial gradient of ETC flux in mouse oocytes and found that this gradient is primarily a result of a spatially heterogeneous mitochondrial proton leak. We concluded from these observations that ETC flux in mouse oocytes is not controlled by energy demand or supply, but by the intrinsic rates of mitochondrial respiration.
    Keywords:  biochemistry; chemical biology; human; mouse; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.73808
  7. Redox Biol. 2021 Nov 11. pii: S2213-2317(21)00346-3. [Epub ahead of print]48 102186
    A novel role of KEAP1/PGAM5 complex: ROS sensor for inducing mitophagy.
    Akbar Zeb, Vinay Choubey, Ruby Gupta, Malle Kuum, Dzhamilja Safiulina, Annika Vaarmann, Nana Gogichaishvili, Mailis Liiv, Ivar Ilves, Kaido Tämm, Vladimir Veksler, Allen Kaasik.
      When ROS production exceeds the cellular antioxidant capacity, the cell needs to eliminate the defective mitochondria responsible for excessive ROS production. It has been proposed that the removal of these defective mitochondria involves mitophagy, but the mechanism of this regulation remains unclear. Here, we demonstrate that moderate mitochondrial superoxide and hydrogen peroxide production oxidates KEAP1, thus breaking the interaction between this protein and PGAM5, leading to the inhibition of its proteasomal degradation. Accumulated PGAM5 interferes with the processing of the PINK1 in the mitochondria leading to the accumulation of PINK1 on the outer mitochondrial membrane. In turn, PINK1 promotes Parkin recruitment to mitochondria and sensitizes mitochondria for autophagic removal. We also demonstrate that inhibitors of the KEAP1-PGAM5 protein-protein interaction (including CPUY192018) mimic the effect of mitochondrial ROS and sensitize mitophagy machinery, suggesting that these inhibitors could be used as pharmacological regulators of mitophagy. Together, our results show that KEAP1/PGAM5 complex senses mitochondrially generated superoxide/hydrogen peroxide to induce mitophagy.
    Keywords:  Mitophagy; NRF2/KEAP1 pathway; Neurodegenerative diseases; Oxidative stress; PINK1/Parkin pathway
    DOI:  https://doi.org/10.1016/j.redox.2021.102186
  8. Sci Rep. 2021 Nov 23. 11(1): 22755
    A new automated tool to quantify nucleoid distribution within mitochondrial networks.
    Hema Saranya Ilamathi, Mathieu Ouellet, Rasha Sabouny, Justine Desrochers-Goyette, Matthew A Lines, Gerald Pfeffer, Timothy E Shutt, Marc Germain.
      Mitochondrial DNA (mtDNA) maintenance is essential to sustain a functionally healthy population of mitochondria within cells. Proper mtDNA replication and distribution within mitochondrial networks are essential to maintain mitochondrial homeostasis. However, the fundamental basis of mtDNA segregation and distribution within mitochondrial networks is still unclear. To address these questions, we developed an algorithm, Mitomate tracker to unravel the global distribution of nucleoids within mitochondria. Using this tool, we decipher the semi-regular spacing of nucleoids across mitochondrial networks. Furthermore, we show that mitochondrial fission actively regulates mtDNA distribution by controlling the distribution of nucleoids within mitochondrial networks. Specifically, we found that primary cells bearing disease-associated mutations in the fission proteins DRP1 and MYH14 show altered nucleoid distribution, and acute enrichment of enlarged nucleoids near the nucleus. Further analysis suggests that the altered nucleoid distribution observed in the fission mutants is the result of both changes in network structure and nucleoid density. Thus, our study provides novel insights into the role of mitochondria fission in nucleoid distribution and the understanding of diseases caused by fission defects.
    DOI:  https://doi.org/10.1038/s41598-021-01987-9
  9. Biochem Soc Trans. 2021 Nov 23. pii: BST20210798. [Epub ahead of print]
    The role of protein acetylation in regulating mitochondrial fusion and fission.
    Golam M Uddin, Rafa Abbas, Timothy E Shutt.
      The dynamic processes of mitochondrial fusion and fission determine the shape of mitochondria, which can range from individual fragments to a hyperfused network, and influence mitochondrial function. Changes in mitochondrial shape can occur rapidly, allowing mitochondria to adapt to specific cues and changing cellular demands. Here, we will review what is known about how key proteins required for mitochondrial fusion and fission are regulated by their acetylation status, with acetylation promoting fission and deacetylation enhancing fusion. In particular, we will examine the roles of NAD+ dependant sirtuin deacetylases, which mediate mitochondrial acetylation, and how this post-translational modification provides an exquisite regulatory mechanism to co-ordinate mitochondrial function with metabolic demands of the cell.
    Keywords:  acetylation/deacetylation; fission; fusion; mitochondria; sirtuins
    DOI:  https://doi.org/10.1042/BST20210798
  10. J Proteomics. 2021 Nov 20. pii: S1874-3919(21)00329-8. [Epub ahead of print] 104430
    Monitoring checkpoints of metabolism and protein biogenesis in mitochondria by Phos-tag technology.
    Corvin Walter, Adinarayana Marada, Chris Meisinger.
      A role for reversible phosphorylation in regulation of mitochondrial proteins has been neglected for a long time. Particularly, the import machineries that mediate influx of more than 1000 different precursor proteins into the organelle were considered as predominantly constitutively active entities. Only recently, a combination of advanced phosphoproteomic approaches and Phos-tag technology enabled the discovery of several phosphorylation sites at the translocase of the outer membrane TOM and the identification of cellular signalling cascades that allow dynamic adaptation of the protein influx into mitochondria upon changing cellular demands. Here, we present a protocol that allows biochemical and semi-quantitative profiling of intra-mitochondrial protein phosphorylation. We exemplify this with the pyruvate dehydrogenase complex (PDH), which serves as a central metabolic switch in energy metabolism that is based on reversible phosphorylation. Phos-tag technology allows rapid monitoring of the metabolic state via simultaneous detection of phosphorylated and non-phosphorylated species of the PDH core component Pda1. Our protocol can be applied for several further intra-organellar proteins like respiratory chain complexes or protein translocases of the inner membrane. SIGNIFICANCE: Our manuscript describes for the first time how Phos-tag technology can be applied to monitor phosphorylation of intramitochondrial proteins. We exemplify this with the regulation of the pyruvate dehydrogenase complex as central regulatory switch in energy metabolism. We show that our protocol allows a rapid monitoring of the metabolic state of the cell (phosphorylated PDH is inactive while non-phosphorylated PDH is active) and can be applied for rapid profiling of different metabolic conditions as well as for profiling phosphorylation of further intramitochondrial protein (complexes).
    Keywords:  Mitochondria; Protein import; Protein translocation; Signalling; TOM complex
    DOI:  https://doi.org/10.1016/j.jprot.2021.104430
  11. Cancers (Basel). 2021 Nov 19. pii: 5812. [Epub ahead of print]13(22):
    Microtubule-Based Mitochondrial Dynamics as a Valuable Therapeutic Target in Cancer.
    Rosa Vona, Anna Maria Mileo, Paola Matarrese.
      Mitochondria constitute an ever-reorganizing dynamic network that plays a key role in several fundamental cellular functions, including the regulation of metabolism, energy production, calcium homeostasis, production of reactive oxygen species, and programmed cell death. Each of these activities can be found to be impaired in cancer cells. It has been reported that mitochondrial dynamics are actively involved in both tumorigenesis and metabolic plasticity, allowing cancer cells to adapt to unfavorable environmental conditions and, thus, contributing to tumor progression. The mitochondrial dynamics include fusion, fragmentation, intracellular trafficking responsible for redistributing the organelle within the cell, biogenesis, and mitophagy. Although the mitochondrial dynamics are driven by the cytoskeleton-particularly by the microtubules and the microtubule-associated motor proteins dynein and kinesin-the molecular mechanisms regulating these complex processes are not yet fully understood. More recently, an exchange of mitochondria between stromal and cancer cells has also been described. The advantage of mitochondrial transfer in tumor cells results in benefits to cell survival, proliferation, and spreading. Therefore, understanding the molecular mechanisms that regulate mitochondrial trafficking can potentially be important for identifying new molecular targets in cancer therapy to interfere specifically with tumor dissemination processes.
    Keywords:  cancer bioenergetics; microtubules; mitochondria dynamics; mitophagy; tunneling nanotubes
    DOI:  https://doi.org/10.3390/cancers13225812
  12. Trends Cell Biol. 2021 Nov 23. pii: S0962-8924(21)00207-5. [Epub ahead of print]
    Rewiring cell signalling pathways in pathogenic mtDNA mutations.
    Chih-Yao Chung, Gabriel E Valdebenito, Anitta R Chacko, Michael R Duchen.
      Mitochondria generate the energy to sustain cell viability and serve as a hub for cell signalling. Their own genome (mtDNA) encodes genes critical for oxidative phosphorylation. Mutations of mtDNA cause major disease and disability with a wide range of presentations and severity. We review here an emerging body of data suggesting that changes in cell metabolism and signalling pathways in response to the presence of mtDNA mutations play a key role in shaping disease presentation and progression. Understanding the impact of mtDNA mutations on cellular energy homeostasis and signalling pathways seems fundamental to identify novel therapeutic interventions with the potential to improve the prognosis for patients with primary mitochondrial disease.
    Keywords:  cell signalling; heteroplasmy; metabolic remodelling; mitochondrial disease; mtDNA
    DOI:  https://doi.org/10.1016/j.tcb.2021.10.005
  13. J Biol Chem. 2021 Nov 18. pii: S0021-9258(21)01245-X. [Epub ahead of print] 101436
    Metabolic adaptation to the chronic loss of Ca2+ signaling induced by knockout of IP3 receptors or the mitochondrial Ca2+ uniporter.
    Michael P Young, Zachary T Schug, David M Booth, David I Yule, Katsuhiko Mikoshiba, György Hajnóczky, Suresh K Joseph.
      Calcium signaling is essential for regulating many biological processes. Endoplasmic reticulum (ER) inositol trisphosphate receptors (IP3R) and the mitochondrial Ca2+ uniporter (MCU) are key proteins that regulate intracellular Ca2+ concentration. Mitochondrial Ca2+ accumulation activates Ca2+-sensitive dehydrogenases of the tricarboxylic acid (TCA) cycle that maintain the biosynthetic and bioenergetics needs of both normal and cancer cells. However, the interplay between calcium signaling and metabolism is not well understood. In this study, we used human cancer cell lines (HEK293, HeLa) with stable knockouts of all three IP3R isoforms (TKO) or MCU to examine metabolic and bioenergetic responses to the chronic loss of cytosolic and/or mitochondrial Ca2+ signaling. Our results show that TKO cells (exhibiting total loss of Ca2+ signaling) are viable, displaying a lower proliferation and oxygen consumption rate, with no significant changes in ATP levels, even when made to rely solely on the TCA cycle for energy production. MCU KO cells also maintained normal ATP levels, but showed increased proliferation, oxygen consumption, and metabolism of both glucose and glutamine. However, MCU KO cells were unable to maintain ATP levels and died when relying solely on the TCA cycle for energy. We conclude that constitutive Ca2+ signaling is dispensable for the bioenergetic needs of both IP3R TKO and MCU KO human cancer cells, likely due to adequate basal glycolytic and TCA cycle flux. However, in MCU KO cells, the higher energy expenditure associated with increased proliferation and oxygen consumption makes these cells more prone to bioenergetic failure under conditions of metabolic stress.
    Keywords:  IP(3) receptor; TCA cycle; bioenergetics; calcium signaling; glycolysis; mitochondrial calcium uniporter; mitochondrial metabolism
    DOI:  https://doi.org/10.1016/j.jbc.2021.101436
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