bims-mikwok 2023-04-23 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2023–04–23
ten papers selected by
Avinash N. Mukkala, University of Toronto

Mitochondrial Membrane Potential Instability on Reperfusion After Ischemia Does Not Depend on Mitochondrial Ca2+ Uptake.
MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.
Low production of mitochondrial reactive oxygen species after anoxia and reoxygenation in turtle hearts.
Induction of lysosomal and mitochondrial biogenesis by AMPK phosphorylation of FNIP1.
The Ketogenic Diet but not Hydroxycitric Acid Keeps Brain Mitochondria Quality Control and mtDNA Integrity Under Focal Stroke.
Reduced methionine synthase expression results in uracil accumulation in mitochondrial DNA and impaired oxidative capacity.
The UbiB family member Cqd1 forms a novel membrane contact site in mitochondria.
The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation.
The Smc5/6 complex is a DNA loop-extruding motor.
Metabolic profile of mesenchymal stromal cells and macrophages in the presence of polyethylene particles in a 3D model.

J Biol Chem. 2023 Apr 13. pii: S0021-9258(23)01736-2. [Epub ahead of print] 104708

Mitochondrial Membrane Potential Instability on Reperfusion After Ischemia Does Not Depend on Mitochondrial Ca2+ Uptake.

Deepthi Ashok, Kyriakos Papanicolaou, Agnieszka Sidor, Michelle Wang, Soroosh Solhjoo, Ting Liu, Brian O'Rourke.

  Physiologic Ca2+ entry via the Mitochondrial Calcium Uniporter (MCU) participates in energetic adaption to workload but may also contribute to cell death during Ischemia/Reperfusion (I/R) injury. The MCU has been identified as the primary mode of Ca2+ import into mitochondria. Several groups have tested the hypothesis that Ca2+ import via MCU is detrimental during I/R injury using genetically-engineered mouse models, yet the results from these studies are inconclusive. Furthermore, mitochondria exhibit unstable or oscillatory membrane potentials (ΔΨm) when subjected to stress, such as during I/R, but it is unclear if the primary trigger is excess influx of mitochondrial Ca2+ (mCa2+), reactive oxygen species (ROS) accumulation, or other factors. Here, we critically examine whether MCU-mediated mitochondrial Ca2+ uptake during I/R is involved in ΔΨm instability, or sustained mitochondrial depolarization, during reperfusion by acutely knocking out MCU in neonatal mouse ventricular myocyte (NMVM) monolayers subjected to simulated I/R. Unexpectedly, we find that MCU knockout does not significantly alter mCa2+ import during I/R, nor does it affect ΔΨm recovery during reperfusion. In contrast, blocking the mitochondrial sodium-calcium exchanger (mNCE) suppressed the mCa2+ increase during Ischemia but did not affect ΔΨm recovery or the frequency of ΔΨm oscillations during reperfusion, indicating that mitochondrial ΔΨm instability on reperfusion is not triggered by mCa2+. Interestingly, inhibition of mitochondrial electron transport or supplementation with antioxidants stabilized I/R-induced ΔΨm oscillations. The findings are consistent with mCa2+ overload being mediated by reverse-mode mNCE activity and support ROS-induced ROS release as the primary trigger of ΔΨm instability during reperfusion injury.

Keywords:  image processing; ischemia; mitochondrial membrane potential; oscillation; oxidative phosphorylation; reperfusion; time-series analysis; wavelet

DOI:  https://doi.org/10.1016/j.jbc.2023.104708
PLoS Comput Biol. 2023 Apr 21. 19(4): e1011060

MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.

Zichen Wang, Parth Natekar, Challana Tea, Sharon Tamir, Hiroyuki Hakozaki, Johannes Schöneberg.

Mitochondria form a network in the cell that rapidly changes through fission, fusion, and motility. Dysregulation of this four-dimensional (4D: x,y,z,time) temporal network is implicated in numerous diseases ranging from cancer to neurodegeneration. While lattice light-sheet microscopy has recently made it possible to image mitochondria in 4D, quantitative analysis methods for the resulting datasets have been lacking. Here we present MitoTNT, the first-in-class software for Mitochondrial Temporal Network Tracking in 4D live-cell fluorescence microscopy data. MitoTNT uses spatial proximity and network topology to compute an optimal tracking assignment. To validate the accuracy of tracking, we created a reaction-diffusion simulation to model mitochondrial network motion and remodeling events. We found that our tracking is >90% accurate for the ground-truth simulations and agrees well with published motility results for experimental data. We used MitoTNT to quantify 4D mitochondrial networks from human induced pluripotent stem cells. First, we characterized sub-fragment motility and analyzed network branch motion patterns. We revealed that the skeleton node motion is correlated along branch and uncorrelated in time. Second, we identified fission and fusion events with high spatiotemporal resolution. We found that mitochondrial skeleton nodes near the fission/fusion sites move nearly twice as fast as random skeleton nodes and that microtubules play a role in mediating selective fission/fusion. Finally, we developed graph-based transport simulations that model how material would distribute on experimentally measured mitochondrial temporal networks. We showed that pharmacological perturbations increase network reachability but decrease network resilience through a combination of altered mitochondrial fission/fusion dynamics and motility. MitoTNT's easy-to-use tracking module, interactive 4D visualization capability, and powerful post-tracking analysis aim at making temporal network tracking accessible to the wider mitochondria research community.

DOI: https://doi.org/10.1371/journal.pcbi.1011060
J Exp Biol. 2023 Apr 17. pii: jeb.245516. [Epub ahead of print]

Low production of mitochondrial reactive oxygen species after anoxia and reoxygenation in turtle hearts.

Amanda Bundgaard, Anja V Gruszczyk, Hiran A Prag, Catherine Williams, Angela McIntyre, Ilan M Ruhr, Andrew M James, Gina L J Galli, Michael P Murphy, Angela Fago.

  Extremely anoxia-tolerant animals, such as freshwater turtles, survive anoxia and reoxygenation without sustaining tissue damage to their hearts. In contrast, for mammals, the ischemia-reperfusion (IR) injury that leads to tissue damage during a heart attack is initiated by a burst of superoxide (O2.-) production from the mitochondrial respiratory chain upon reperfusion of ischemic tissue. Whether turtles avoid oxidative tissue damage because of an absence of mitochondrial superoxide production upon reoxygenation, or because the turtle heart is particularly protected against this damage, is unclear. Here, we investigate whether there was an increase in mitochondrial O2.- production upon the reoxygenation of anoxic red-eared slider turtle hearts in vivo and in vitro. This was done by measuring the production of H2O2, the dismutation product of O2.-, using the mitochondria-targeted mass-spectrometric probe in vivo MitoB, while in parallel assessing changes in the metabolites driving mitochondrial O2.- production succinate, ATP and ADP levels during anoxia and H2O2 consumption and production rates of isolated heart mitochondria. We found that there was no excess production of in vivo H2O2 during 1 h of reoxygenation in turtles after 3 h anoxia at room temperature, suggesting that turtle hearts most likely do not suffer oxidative injury after anoxia because their mitochondria produce no excess O2.- upon reoxygenation. Instead, our data support the conclusion that both the low levels of succinate accumulation and the maintenance of ADP levels in the anoxic turtle heart are key factors in preventing the surge of O2.- production upon reoxygenation.

Keywords:  Anoxia; Heart; Mitochondria; Oxidative damage; Reactive oxygen species; Turtle

DOI:  https://doi.org/10.1242/jeb.245516
Science. 2023 Apr 21. 380(6642): eabj5559

Induction of lysosomal and mitochondrial biogenesis by AMPK phosphorylation of FNIP1.

Nazma Malik, Bibiana I Ferreira, Pablo E Hollstein, Stephanie D Curtis, Elijah Trefts, Sammy Weiser Novak, Jingting Yu, Rebecca Gilson, Kristina Hellberg, Lingjing Fang, Arlo Sheridan, Nasun Hah, Gerald S Shadel, Uri Manor, Reuben J Shaw.

Cells respond to mitochondrial poisons with rapid activation of the adenosine monophosphate-activated protein kinase (AMPK), causing acute metabolic changes through phosphorylation and prolonged adaptation of metabolism through transcriptional effects. Transcription factor EB (TFEB) is a major effector of AMPK that increases expression of lysosome genes in response to energetic stress, but how AMPK activates TFEB remains unresolved. We demonstrate that AMPK directly phosphorylates five conserved serine residues in folliculin-interacting protein 1 (FNIP1), suppressing the function of the folliculin (FLCN)-FNIP1 complex. FNIP1 phosphorylation is required for AMPK to induce nuclear translocation of TFEB and TFEB-dependent increases of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) and estrogen-related receptor alpha (ERRα) messenger RNAs. Thus, mitochondrial damage triggers AMPK-FNIP1-dependent nuclear translocation of TFEB, inducing sequential waves of lysosomal and mitochondrial biogenesis.

DOI: https://doi.org/10.1126/science.abj5559
Mol Neurobiol. 2023 Apr 19.

The Ketogenic Diet but not Hydroxycitric Acid Keeps Brain Mitochondria Quality Control and mtDNA Integrity Under Focal Stroke.

Artem P Gureev, Denis N Silachev, Irina S Sadovnikova, Ekaterina P Krutskikh, Ekaterina V Chernyshova, Daria E Volodina, Natalia A Samoylova, Daria V Potanina, Inna Yu Burakova, Yuliya D Smirnova, Vasily N Popov, Egor Y Plotnikov.

  Mitochondrial dysfunction in the ischemic brain is one of the hallmarks of stroke. Dietary interventions such as the ketogenic diet and hydroxycitric acid supplementation (a caloric restriction mimetic) may potentially protect neurons from mitochondrial damage induced by focal stroke in mice. We showed that in control mice, the ketogenic diet and the hydroxycitric acid did not impact significantly on the mtDNA integrity and expression of genes involved in the maintenance of mitochondrial quality control in the brain, liver, and kidney. The ketogenic diet changed the bacterial composition of the gut microbiome, which via the gut-brain axis may affect the increase in anxiety behavior and reduce mice mobility. The hydroxycitric acid causes mortality and suppresses mitochondrial biogenesis in the liver. Focal stroke modelling caused a significant decrease in the mtDNA copy number in both ipsilateral and contralateral brain cortex and increased the levels of mtDNA damage in the ipsilateral hemisphere. These alterations were accompanied by a decrease in the expression of some of the genes involved in maintaining mitochondrial quality control. The ketogenic diet consumption before stroke protects mtDNA in the ipsilateral cortex, probably via activation of the Nrf2 signaling. The hydroxycitric acid, on the contrary, increased stroke-induced injury. Thus, the ketogenic diet is the most preferred variant of dietetic intervention for stroke protection compared with the hydroxycitric acid supplementation. Our data confirm some reports about hydroxycitric acid toxicity, not only for the liver but also for the brain under stroke condition.

Keywords:  Focal stroke; Gut microbiome; Hydroxycitric acid; Ketogenic diet; Mitochondrial DNA; Nrf2/ARE signal pathway

DOI:  https://doi.org/10.1007/s12035-023-03325-8
PNAS Nexus. 2023 Apr;2(4): pgad105

Reduced methionine synthase expression results in uracil accumulation in mitochondrial DNA and impaired oxidative capacity.

Katarina E Heyden, Joanna L Fiddler, Yuwen Xiu, Olga V Malysheva, Michal K Handzlik, Whitney N Phinney, Linsey Stiles, Sally P Stabler, Christian M Metallo, Marie A Caudill, Martha S Field.

  Adequate thymidylate [deoxythymidine monophosphate (dTMP) or the "T" base in DNA] levels are essential for stability of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Folate and vitamin B12 (B12) are essential cofactors in folate-mediated one-carbon metabolism (FOCM), a metabolic network which supports synthesis of nucleotides (including dTMP) and methionine. Perturbations in FOCM impair dTMP synthesis, causing misincorporation of uracil (or a "U" base) into DNA. During B12 deficiency, cellular folate accumulates as 5-methyltetrahdryfolate (5-methyl-THF), limiting nucleotide synthesis. The purpose of this study was to determine how reduced levels of the B12-dpendent enzyme methionine synthase (MTR) and dietary folate interact to affect mtDNA integrity and mitochondrial function in mouse liver. Folate accumulation, uracil levels, mtDNA content, and oxidative phosphorylation capacity were measured in male Mtr+/+ and Mtr+/- mice weaned onto either a folate-sufficient control (C) diet (2 mg/kg folic acid) or a folate-deficient (FD) diet (lacking folic acid) for 7 weeks. Mtr heterozygosity led to increased liver 5-methyl-THF levels. Mtr+/- mice consuming the C diet also exhibited a 40-fold increase in uracil in liver mtDNA. Mtr+/- mice consuming the FD diet exhibited less uracil accumulation in liver mtDNA as compared to Mtr+/+ mice consuming the FD diet. Furthermore, Mtr+/- mice exhibited 25% lower liver mtDNA content and a 20% lower maximal oxygen consumption rates. Impairments in mitochondrial FOCM are known to lead to increased uracil in mtDNA. This study demonstrates that impaired cytosolic dTMP synthesis, induced by decreased Mtr expression, also leads to increased uracil in mtDNA.

Keywords:  DNA; folate; methionine synthase; uracil; vitamin B12

DOI:  https://doi.org/10.1093/pnasnexus/pgad105
J Cell Sci. 2023 Apr 19. pii: jcs.260578. [Epub ahead of print]

The UbiB family member Cqd1 forms a novel membrane contact site in mitochondria.

Siavash Khosravi, Xenia Chelius, Ann-Katrin Unger, Daniela Rieger, Johanna Frickel, Timo Sachsenheimer, Christian Lüchtenborg, Rico Schieweck, Britta Brügger, Benedikt Westermann, Till Klecker, Walter Neupert, Max E Harner.

  Mitochondria are essential organelles of eukaryotic cells that are characterized by their unique and complex membrane system. They are confined from the cytosol by an envelope consisting of two membranes. Signals, metabolites, proteins and lipids have to be transferred across these membranes via proteinaceous contact sites to keep mitochondria functional. In the present study we identified a novel mitochondrial contact site that is formed by the inner membrane protein Cqd1 and the outer membrane proteins Por1 and Om14. Similar to the mitochondrial porin, Por1, Cqd1 is highly conserved, suggesting that this complex is conserved in form and function from yeast to human. Cqd1 is a member of the UbiB protein kinase-like family (also called aarF domain containing kinases). It was recently shown that Cqd1 in cooperation with Cqd2 controls the cellular distribution of coenzyme Q by a yet unknown mechanism. Our data suggest that Cqd1 is additionally involved in phospholipid homeostasis. Moreover, overexpression of CQD1 and CQD2 causes tethering of mitochondria to the endoplasmic reticulum, which might explain the ability of Cqd2 to rescue ERMES deletion phenotypes.

Keywords:  Contact sites; Mitochondria; Mitochondrial biogenesis; Mitochondrial morphology; Phospholipids; UbiB protein family

DOI:  https://doi.org/10.1242/jcs.260578
Proc Natl Acad Sci U S A. 2023 Apr 25. 120(17): e2210929120

The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation.

Sethu C Nair, Justin T Munro, Alexis Mann, Manuel Llinás, Sean T Prigge.

  Coenzyme A (CoA) biosynthesis is an excellent target for antimalarial intervention. While most studies have focused on the use of CoA to produce acetyl-CoA in the apicoplast and the cytosol of malaria parasites, mitochondrial acetyl-CoA production is less well understood. In the current study, we performed metabolite-labeling experiments to measure endogenous metabolites in Plasmodium falciparum lines with genetic deletions affecting mitochondrial dehydrogenase activity. Our results show that the mitochondrion is required for cellular acetyl-CoA biosynthesis and identify a synthetic lethal relationship between the two main ketoacid dehydrogenase enzymes. The activity of these enzymes is dependent on the lipoate attachment enzyme LipL2, which is essential for parasite survival solely based on its role in supporting acetyl-CoA metabolism. We also find that acetyl-CoA produced in the mitochondrion is essential for the acetylation of histones and other proteins outside of the mitochondrion. Taken together, our results demonstrate that the mitochondrion is required for cellular acetyl-CoA metabolism and protein acetylation essential for parasite survival.

Keywords:  acetyl-CoA; acetylation; lipoic acid; malaria parasites; mitochondrion

DOI:  https://doi.org/10.1073/pnas.2210929120
Nature. 2023 Apr 19.

The Smc5/6 complex is a DNA loop-extruding motor.

Biswajit Pradhan, Takaharu Kanno, Miki Umeda Igarashi, Mun Siong Loke, Martin Dieter Baaske, Jan Siu Kei Wong, Kristian Jeppsson, Camilla Björkegren, Eugene Kim.

Structural maintenance of chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes1. Whereas cohesin and condensin organize chromosomes by extrusion of DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown2. Using single-molecule imaging, we show that Smc5/6 forms DNA loops by extrusion. Upon ATP hydrolysis, Smc5/6 reels DNA symmetrically into loops at a force-dependent rate of one kilobase pair per second. Smc5/6 extrudes loops in the form of dimers, whereas monomeric Smc5/6 unidirectionally translocates along DNA. We also find that the subunits Nse5 and Nse6 (Nse5/6) act as negative regulators of loop extrusion. Nse5/6 inhibits loop-extrusion initiation by hindering Smc5/6 dimerization but has no influence on ongoing loop extrusion. Our findings reveal functions of Smc5/6 at the molecular level and establish DNA loop extrusion as a conserved mechanism among eukaryotic SMC complexes.

DOI: https://doi.org/10.1038/s41586-023-05963-3
Stem Cell Res Ther. 2023 Apr 21. 14(1): 99

Metabolic profile of mesenchymal stromal cells and macrophages in the presence of polyethylene particles in a 3D model.

Victoria Teissier, Qi Gao, Huaishuang Shen, Jiannan Li, Xueping Li, Elijah Ejun Huang, Junichi Kushioka, Masakazu Toya, Masanori Tsubosaka, Hirohito Hirata, Hossein Vahid Alizadeh, Chima V Maduka, Christopher H Contag, Yunzhi Peter Yang, Ning Zhang, Stuart B Goodman.

   BACKGROUND: Continuous cross talk between MSCs and macrophages is integral to acute and chronic inflammation resulting from contaminated polyethylene particles (cPE); however, the effect of this inflammatory microenvironment on mitochondrial metabolism has not been fully elucidated. We hypothesized that (a) exposure to cPE leads to impaired mitochondrial metabolism and glycolytic reprogramming and (b) macrophages play a key role in this pathway.
METHODS: We cultured MSCs with/without uncommitted M0 macrophages, with/without cPE in 3-dimensional gelatin methacrylate (3D GelMA) constructs/scaffolds. We evaluated mitochondrial function (membrane potential and reactive oxygen species-ROS production), metabolic pathways for adenosine triphosphate (ATP) production (glycolysis or oxidative phosphorylation) and response to stress mechanisms. We also studied macrophage polarization toward the pro-inflammatory M1 or the anti-inflammatory M2 phenotype and the osteogenic differentiation of MSCs.
RESULTS: Exposure to cPE impaired mitochondrial metabolism of MSCs; addition of M0 macrophages restored healthy mitochondrial function. Macrophages exposed to cPE-induced glycolytic reprogramming, but also initiated a response to this stress to restore mitochondrial biogenesis and homeostatic oxidative phosphorylation. Uncommitted M0 macrophages in coculture with MSC polarized to both M1 and M2 phenotypes. Osteogenesis was comparable among groups after 21 days.
CONCLUSION: This work confirmed that cPE exposure triggers impaired mitochondrial metabolism and glycolytic reprogramming in a 3D coculture model of MSCs and macrophages and demonstrated that macrophages cocultured with MSCs undergo metabolic changes to maintain energy production and restore homeostatic metabolism.

Keywords:  MSCs; Macrophage; Metabolism; Mitochondria; Polyethylene particles; Three-dimensional model

DOI:  https://doi.org/10.1186/s13287-023-03260-4