bims-mikwok 2022-12-04 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2022–12–04
eleven papers selected by
Avinash N. Mukkala, University of Toronto

A20 binding and inhibitor of nuclear factor kappa B (NF-κB)-1 (ABIN-1) - a novel modulator of mitochondrial autophagy.
Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.
Inhibition of cellular senescence hallmarks by mitochondrial transplantation in senescence-induced ARPE-19 cells.
Engineering Extracellular Vesicles to Modulate Their Innate Mitochondrial Load.
RAB7A GTPase Is Involved in Mitophagosome Formation and Autophagosome-Lysosome Fusion in N2a Cells Treated with the Prion Protein Fragment 106-126.
Expression of Synj2bp in mouse liver regulates the extent of wrappER-mitochondria contact to maintain hepatic lipid homeostasis.
Prohibitin1 maintains mitochondrial quality in Isoproterenol-Induced Cardiac Hypertrophy in H9C2 cells.
Mitochondria and cell death-associated inflammation.
Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
Mitochondrial citrate accumulation drives alveolar epithelial cell necroptosis in lipopolysaccharide-induced acute lung injury.
An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.

Am J Physiol Cell Physiol. 2022 Nov 28.

A20 binding and inhibitor of nuclear factor kappa B (NF-κB)-1 (ABIN-1) - a novel modulator of mitochondrial autophagy.

Rosetta Merline, Heiko Rödig, Jinyang Zeng-Brouwers, Chiara Poluzzi, Georg Tascher, Jonas Michaelis, Jaime Lopez-Mosqueda, Andrew Rhiner, Lisa Sophie Huber, Valentina Diehl, Ivan Dikic, Donat Kögel, Christian Münch, Malgorzata Wygrecka, Liliana Schaefer.

  A20 binding inhibitor of nuclear factor kappa B (NF-κB)-1 (ABIN-1), a polyubiquitin-binding protein, is a signal-induced autophagy receptor that attenuates NF-κB-mediated inflammation and cell death. The present study aimed to elucidate the potential role of ABIN-1 in mitophagy, a biological process whose outcome is decisive in diverse physiological and pathological settings. Microtubule-associated proteins 1A/1B light chain 3B-II (LC3B-II) was found to be in complex with ectopically expressed hemagglutinin (HA)-tagged-full length (FL)-ABIN-1. Bacterial expression of ABIN-1 and LC3A and LC3B showed direct binding of ABIN-1 to LC3 proteins, while mutations in the LC3-interacting region (LIR) 1 and 2 motifs of ABIN-1 abrogated ABIN-1/LC3B-II complex formation. Importantly, induction of autophagy in HeLa cells resulted in co-localization of ABIN-1 with LC3B-II in autophagosomes and with lysosomal associated membrane protein 1 (LAMP-1) in autophagolysosomes, leading to co-degradation of ABIN-1 with p62. Interestingly, ABIN-1 was found to translocate to damaged mitochondria in HeLa-mCherry-Parkin cells. In line with this observation, CRISPR/Cas9-mediated deletion of ABIN-1 significantly inhibited the degradation of the mitochondrial outer membrane proteins voltage-dependent anion-selective channel 1 (VDAC-1), mitofusin-2 (MFN2), and translocase of outer mitochondrial membrane (TOM)20. Additionally, siRNA-mediated knockdown of ABIN-1 significantly decreased lysosomal uptake of mitochondria in HeLa cells expressing mCherry-Parkin and the fluorescence reporter mt-mKEIMA. Collectively, our results identify ABIN-1 as a novel and selective mitochondrial autophagy regulator that promotes mitophagy, thereby adding a new player to the complex cellular machinery regulating mitochondrial homeostasis.

Keywords:  LC3-interacting region; Mitophagy; Selective autophagy receptor; mitochondrial outer membrane proteins

DOI:  https://doi.org/10.1152/ajpcell.00493.2022
iScience. 2022 Dec 22. 25(12): 105502

Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.

Shao-Ting Chiu, Wen-Wei Tseng, An-Chi Wei.

  Mitochondria, semi-autonomous eukaryotic organelles, participate in energy production and metabolism, making mitochondrial quality control crucial. As most mitochondrial proteins are encoded by nuclear genes, maintaining mitochondrial function and quality depends on proper mitochondria-nucleus communication and designated mitochondrial retrograde signaling. Early studies focused on retrograde signaling participants and specific gene knockouts. However, mitochondrial signal modulation remains elusive. A mathematical model based on ordinary differential equations was proposed to simulate signal propagation to nucleus following mitochondrial damage in yeast. Mitochondrial retrograde signaling decisions were described using a Boolean model. Dynamics of retrograde signaling were analyzed and extended to evaluate the model response to noisy damage signals. Simulation revealed localized protein concentration dynamics, including waveforms, frequency response, and robustness under noise. Retrograde signaling is bistable with localized steady states, and increased damage compromises robustness. We elucidated mitochondrial retrograde signaling, thus providing a basis for drug design against yeast and fungi.

Keywords:  Biological sciences; Cell biology; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2022.105502
Neurobiol Aging. 2022 Nov 06. pii: S0197-4580(22)00231-7. [Epub ahead of print]121 157-165

Inhibition of cellular senescence hallmarks by mitochondrial transplantation in senescence-induced ARPE-19 cells.

Sung-Eun Noh, Seok Jae Lee, Tae Geol Lee, Kyu-Sang Park, Jeong Hun Kim.

  Retinal pigment epithelium (RPE) damage is a major factor in age-related macular degeneration (AMD). The RPE in AMD shows mitochondrial dysfunction suggesting an association of AMD with mitochondrial function. Therefore, exogenous mitochondrial transplantation for restoring and replacing dysfunctional mitochondria may be an effective therapeutic strategy for AMD. Here, we investigated the effects of extrinsic mitochondrial transplantation on senescence-induced ARPE-19 cells. We demonstrated mitochondrial dysfunction in replicative senescence-induced ARPE-19 cells after repeated passage. Imbalanced mitophagy and mitochondrial dynamics resulted in increased mitochondrial numbers and elevated levels of mitochondrial and intracellular reactive oxygen species. Exogenous mitochondrial transplantation improved mitochondrial dysfunction and alleviated cellular senescence hallmarks, such as increased cell size, increased senescence-associated β-galactosidase activity, augmented NF-κB activity, increased inflammatory cytokines, and upregulated the cyclin-dependent kinase inhibitors p21 and p16. Further, cellular senescence properties were improved by exogenous mitochondrial transplantation in oxidative stress-induced senescent ARPE-19 cells. These results indicate that exogenous mitochondrial transplantation modulates cellular senescence and may be considered a novel therapeutic strategy for AMD.

Keywords:  Age-related macular degeneration; Exogenous mitochondrial transplantation; Oxidative stress; Retinal pigment epithelium; Senescence

DOI:  https://doi.org/10.1016/j.neurobiolaging.2022.11.003
Cell Mol Bioeng. 2022 Oct;15(5): 367-389

Engineering Extracellular Vesicles to Modulate Their Innate Mitochondrial Load.

Kandarp M Dave, Duncan X Dobbins, Maura N Farinelli, Abigail Sullivan, Jadranka Milosevic, Donna B Stolz, Jeongyun Kim, Siyang Zheng, Devika S Manickam.

   Introduction: Extracellular vesicles (EVs) are promising carriers for the delivery of biotherapeutic cargo such as RNA and proteins. We have previously demonstrated that the innate EV mitochondria in microvesicles (MVs), but not exosomes (EXOs) can be transferred to recipient BECs and mouse brain slice neurons. Here, we sought to determine if the innate EV mitochondrial load can be further increased via increasing mitochondrial biogenesis in the donor cells. We hypothesized that mitochondria-enriched EVs ("mito-EVs") may increase the recipient BEC ATP levels to a greater extent than naïve MVs.
Methods: We treated NIH/3T3, a fibroblast cell line and hCMEC/D3, a human brain endothelial cell (BEC) line using resveratrol to activate peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α), the central mediator of mitochondrial biogenesis. Naïve EVs and mito-EVs isolated from the non-activated and activated donor cells were characterized using transmission electron microscopy, dynamic light scattering and nanoparticle tracking analysis. The effect of mito-EVs on resulting ATP levels in the recipient BECs were determined using Cell Titer Glo ATP assay. The uptake of Mitotracker Red-stained EVs into recipient BECs and their colocalization with recipient BEC mitochondria were studied using flow cytometry and fluorescence microscopy.
Results: Resveratrol treatment increased PGC-1α expression in the donor cells. Mito-MVs but not mito-EXOs showed increased expression of mitochondrial markers ATP5A and TOMM20 compared to naïve MVs. TEM images showed that a greater number of mito-MVs contained mitochondria compared to naïve MVs. Mito-MVs but not mito-EXOs showed a larger particle diameter compared to their naïve EV counterparts from the non-activated cells suggesting increased mitochondria incorporation. Mito-EVs were generated at higher particle concentrations compared to naïve EVs from non-activated cells. Mito-EVs increased the cellular ATP levels and transferred their mitochondrial load into the recipient BECs. Mito-MV mitochondria also colocalized with recipient BEC mitochondria.
Conclusions: Our results suggest that the pharmacological modulation of mitochondrial biogenesis in the donor cells can change the mitochondrial load in the secreted MVs. Outcomes of physicochemical characterization studies and biological assays confirmed the superior effects of mito-MVs compared to naïve MVs-suggesting their potential to improve mitochondrial function in neurovascular and neurodegenerative diseases.
Supplementary Information: The online version contains supplementary material available at 10.1007/s12195-022-00738-8.

Keywords:  ATP; Brain endothelial cells; EVs; Exosomes; Metabolic function; Microvesicles; Mitochondria; PGC-1α

DOI:  https://doi.org/10.1007/s12195-022-00738-8
Mol Neurobiol. 2022 Nov 30.

RAB7A GTPase Is Involved in Mitophagosome Formation and Autophagosome-Lysosome Fusion in N2a Cells Treated with the Prion Protein Fragment 106-126.

Zhiping Li, Mengyu Lai, Jie Li, Dongming Yang, Mengyang Zhao, Dongdong Wang, Zhixin Sun, Pei Wen, Fengting Gou, Yuexin Dai, Yilan Ji, Deming Zhao, Jian Qiao, Lifeng Yang.

  Failed communication between mitochondria and lysosomes causes dysfunctional mitochondria, which may induce mitochondria-related neurodegenerative diseases. Here, we show that RAB7A, a small GTPase of the Rab family, mediates the crosstalk between these two important organelles to maintain homeostasis in N2a cells treated with PrP106-126. Specifically, we demonstrate that mitophagy deficiency in N2a cells caused by PrP106-126 is associated with dysregulated RAB7A localization in mitochondria. Cells lacking RAB7A display decreased mitochondrial colocalization with lysosomes and significantly increased mitochondrial protein expression, resulting in inhibited mitophagy. In contrast, overexpression of GTP-bound RAB7A directly induces lysosome colocalization with mitochondria. Further study revealed that GTP-bound RAB7A protects mitochondrial homeostasis by supporting autophagosome biogenesis. Moreover, we suggest that depletion of RAB7A leads to gross morphological changes in lysosomes, which prevents autophagosome-lysosome fusion and interferes with the breakdown of autophagic cargo within lysosomes. Overexpression of GTP-bound RAB7A can also alleviate PrP106-126-induced morphological damage and dysfunction of mitochondria, reducing neuronal apoptosis. Collectively, our data demonstrate that RAB7A successfully drives mitochondria to the autophagosomal lumen for degradation, suggesting that the communication of proteotoxic stress from mitochondria to lysosomes requires RAB7A, as a signaling molecule, to establish a link between the disturbed mitochondrial network and its remodeling. These findings indicate that small molecules regulating mitophagy have the potential to modulate cellular homeostasis and the clinical course of neurodegenerative diseases. Proposed model of mitophagy regulated by RAB7A. (1) Accumulating PrP106-126 induced mitophagy. (2) RAB7A is recruited to mitochondria. (3) ATG5-12 and ATG9A (5) vesicles are recruited to the autophagosome formation sites in a RAB7A-dependent manner. The ATG5-12 complex recruits and anchors LC3-I to form active LC3-II (4), accelerating mitophagosomal formation. The ATG9A vesicles are thought to be a source of membranes for autophagosome assembly. The recruitment of proteins and lipids induces membrane expansion and subsequent closure to form the mitophagosome. (6) Maintenance of the normal low lysosomal PH depends on active (GTP-bound) RAB7A. (7) RAB7A recruits effector molecules responsible for tight membrane interactions, and directly or indirectly, the subsequent autophagosome merges with the lysosome, and the cargo is completely degraded.

Keywords:  Mitochondria; Mitophagy; N2a; Neurodegenerative diseases; PrP106–126; RAB7A

DOI:  https://doi.org/10.1007/s12035-022-03118-5
Biol Direct. 2022 Dec 01. 17(1): 37

Expression of Synj2bp in mouse liver regulates the extent of wrappER-mitochondria contact to maintain hepatic lipid homeostasis.

Nicolò Ilacqua, Irene Anastasia, Danylo Aloshyn, Rana Ghandehari-Alavijeh, Emily Ann Peluso, Madelaine C Brearley-Sholto, Leonardo V Pellegrini, Andrea Raimondi, Thomas Q de Aguiar Vallim, Luca Pellegrini.

   BACKGROUND: In mouse liver hepatocytes, nearly half of the surface area of every mitochondrion is covered by wrappER, a wrapping-type of ER that is rich in fatty acids and synthesizes lipoproteins (VLDL) (Anastasia et al. in Cell Rep 34:108873, 2021; Hurtley in Science (80- ) 372:142-143, 2021; Ilacqua et al. in J Cell Sci 135:1-11, 2021). A disruption of the ultrastructure of the wrappER-mitochondria contact results in altered fatty acid flux, leading to hepatic dyslipidemia (Anastasia et al. 2021). The molecular mechanism that regulates the extent of wrappER-mitochondria contacts is unknown.
METHODS: We evaluated the expression level of the mitochondrial protein Synj2bp in the liver of normal and obese (ob/ob) mice. In addition, we silenced its expression in the liver using an AAV8 vector. We coupled quantitative EM morphometric analysis to proteomics and lipid analyses on these livers.
RESULTS: The expression level of Synj2bp in the liver positively correlates with the extent of wrappER-mitochondria contacts. A 50% reduction in wrappER-mitochondria contacts causes hepatic dyslipidemia, characterized by a gross accumulation of lipid droplets in the liver, an increased hepatic secretion of VLDL and triglycerides, a curtailed ApoE expression, and an increased capacity of mitochondrial fatty acid respiration.
CONCLUSION: Synj2bp regulates the extent of wrappER-mitochondria contacts in the liver, thus contributing to the control of hepatic lipid flux.

Keywords:  ApoE; Electron microscopy; Fatty acid; Inter-organelle contact; Lipoparticles; MAM; MERC; Mitochondria; NAFLD; Rrbp1; Synj2bp; VLDL; WrappER

DOI:  https://doi.org/10.1186/s13062-022-00344-8
Biol Cell. 2022 Dec 01.

Prohibitin1 maintains mitochondrial quality in Isoproterenol-Induced Cardiac Hypertrophy in H9C2 cells.

Moumita Chakrabarti, Ganesh Kumar Raut, Nishant Jain, Manika Pal Bhadra.

  Various types of stress initially induce a state of 'Cardiac Hypertrophy (CH) in the heart. But, persistent escalation of cardiac stress leads to progression from an adaptive physiological to a maladaptive pathological state. So, elucidating molecular mechanisms that can attenuate CH is imperative in developing cardiac therapies. Previously, we showed that Prohibitin1 (PHB1) has a protective role in CH-induced oxidative stress. Nevertheless, it is unclear how PHB1, a mitochondrial protein, has a protective role in CH. Therefore, we hypothesized that PHB1 maintains mitochondrial quality in CH. To test this hypothesis, we used Isoproterenol (ISO) to induce CH in H9C2 cells overexpressing PHB1 and elucidated mitochondrial quality control pathways. We found that overexpressing PHB1 attenuates ISO-induced CH and restores mitochondrial morphology in H9C2 cells. In addition, PHB1 blocks the pro-hypertrophic IGF1R/AKT pathway and restores the mitochondrial membrane polarization in ISO-treated cells. We observed that overexpressing PHB1 promotes mitochondrial biogenesis, improves mitochondrial respiratory capacity, and triggers mitophagy. We conclude that PHB1 maintains mitochondrial quality in ISO-induced CH in H9C2 cells. Based on our results, we suggest that small molecules that induce PHB1 in cardiac cells may prove beneficial in developing cardiac therapies. This article is protected by copyright. All rights reserved.

Keywords:  Cardiac hypertrophy; H9C2; OCR; PHB1; mitochondrial quality; mitophagy

DOI:  https://doi.org/10.1111/boc.202200094
Cell Death Differ. 2022 Nov 29.

Mitochondria and cell death-associated inflammation.

Esmee Vringer, Stephen W G Tait.

Mitochondria have recently emerged as key drivers of inflammation associated with cell death. Many of the pro-inflammatory pathways activated during cell death occur upon mitochondrial outer membrane permeabilization (MOMP), the pivotal commitment point to cell death during mitochondrial apoptosis. Permeabilised mitochondria trigger inflammation, in part, through the release of mitochondrial-derived damage-associated molecular patterns (DAMPs). Caspases, while dispensable for cell death during mitochondrial apoptosis, inhibit activation of pro-inflammatory pathways after MOMP. Some of these mitochondrial-activated inflammatory pathways can be traced back to the bacterial ancestry of mitochondria. For instance, mtDNA and bacterial DNA are highly similar thereby activating similar cell autonomous immune signalling pathways. The bacterial origin of mitochondria suggests that inflammatory pathways found in cytosol-invading bacteria may be relevant to mitochondrial-driven inflammation after MOMP. In this review, we discuss how mitochondria can initiate inflammation during cell death highlighting parallels with bacterial activation of inflammation. Moreover, we discuss the roles of mitochondrial inflammation during cell death and how these processes may potentially be harnessed therapeutically, for instance to improve cancer treatment.

DOI: https://doi.org/10.1038/s41418-022-01094-w
Nat Commun. 2022 Nov 28. 13(1): 7338

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.

Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M Bernard, Nourdine Bah, Mariana Silva Dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore, James I MacRae, Maria Greco, Thomas Reinheckel, Matthias Trost, Maximiliano G Gutierrez.

Transient lysosomal damage after infection with cytosolic pathogens or silica crystals uptake results in protease leakage. Whether limited leakage of lysosomal contents into the cytosol affects the function of cytoplasmic organelles is unknown. Here, we show that sterile and non-sterile lysosomal damage triggers a cell death independent proteolytic remodelling of the mitochondrial proteome in macrophages. Mitochondrial metabolic reprogramming required leakage of lysosomal cathepsins and was independent of mitophagy, mitoproteases and proteasome degradation. In an in vivo mouse model of endomembrane damage, live lung macrophages that internalised crystals displayed impaired mitochondrial function. Single-cell RNA-sequencing revealed that lysosomal damage skewed metabolic and immune responses in alveolar macrophages subsets with increased lysosomal content. Functionally, drug modulation of macrophage metabolism impacted host responses to Mycobacterium tuberculosis infection in an endomembrane damage dependent way. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprograming after endomembrane damage.

DOI: https://doi.org/10.1038/s41467-022-34632-8
Exp Mol Med. 2022 Nov 28.

Mitochondrial citrate accumulation drives alveolar epithelial cell necroptosis in lipopolysaccharide-induced acute lung injury.

Hui-Hui Yang, Hui-Ling Jiang, Jia-Hao Tao, Chen-Yu Zhang, Jian-Bing Xiong, Jin-Tong Yang, Yu-Biao Liu, Wen-Jing Zhong, Xin-Xin Guan, Jia-Xi Duan, Yan-Feng Zhang, Shao-Kun Liu, Jian-Xin Jiang, Yong Zhou, Cha-Xiang Guan.

Necroptosis is the major cause of death in alveolar epithelial cells (AECs) during acute lung injury (ALI). Here, we report a previously unrecognized mechanism for necroptosis. We found an accumulation of mitochondrial citrate (citratemt) in lipopolysaccharide (LPS)-treated AECs because of the downregulation of Idh3α and citrate carrier (CIC, also known as Slc25a1). shRNA- or inhibitor-mediated inhibition of Idh3α and Slc25a1 induced citratemt accumulation and necroptosis in vitro. Mice with AEC-specific Idh3α and Slc25a1 deficiency exhibited exacerbated lung injury and AEC necroptosis. Interestingly, the overexpression of Idh3α and Slc25a1 decreased citratemt levels and rescued AECs from necroptosis. Mechanistically, citratemt accumulation induced mitochondrial fission and excessive mitophagy in AECs. Furthermore, citratemt directly interacted with FUN14 domain-containing protein 1 (FUNDC1) and promoted the interaction of FUNDC1 with dynamin-related protein 1 (DRP1), leading to excessive mitophagy-mediated necroptosis and thereby initiating and promoting ALI. Importantly, necroptosis induced by citratemt accumulation was inhibited in FUNDC1-knockout AECs. We show that citratemt accumulation is a novel target for protection against ALI involving necroptosis.

DOI: https://doi.org/10.1038/s12276-022-00889-8
Elife. 2022 Nov 30. pii: e84279. [Epub ahead of print]11

An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.

Tricia T Nguyen, Gia K Voeltz.

  Mitochondria are dynamic organelles that undergo cycles of fission and fusion at a unified platform defined by endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCSs). These MCSs or nodes co-localize fission and fusion machinery. We set out to identify how ER-associated mitochondrial nodes can regulate both fission and fusion machinery assembly. We have used a promiscuous biotin ligase linked to the fusion machinery, Mfn1, and proteomics to identify an ER membrane protein, ABHD16A, as a major regulator of node formation. In the absence of ABHD16A, fission and fusion machineries fail to recruit to ER-associated mitochondrial nodes and fission and fusion rates are significantly reduced. ABHD16A contains an acyltransferase motif and an α/β hydrolase domain and point mutations in critical residues of these regions fail to rescue the formation of ER-associated mitochondrial hot spots. These data suggest a mechanism whereby ABHD16A functions by altering phospholipid composition at ER-mitochondria MCSs. Our data present the first example of an ER membrane protein that regulates the recruitment of both fission and fusion machineries to mitochondria.

Keywords:  cell biology; human

DOI:  https://doi.org/10.7554/eLife.84279