bims-mitdyn 2023-09-10 papers

bims-mitdyn

Biomed News

on Mitochondrial dynamics: mechanisms

Issue of 2023–09–10
twelve papers selected by
Edmond Chan, Queen’s University, School of Medicine

Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation.
Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling.
A mitochondrial EglN1-AMPKα axis drives breast cancer progression by enhancing metabolic adaptation to hypoxic stress.
Ets1 facilitates EMT/invasion through Drp1-mediated mitochondrial fragmentation in ovarian cancer.
C17orf80 binds the mitochondrial genome to promote its replication.
The Orf9b protein of SARS-CoV-2 modulates mitochondrial protein biogenesis.
Lon degrades stable substrates slowly but with enhanced processivity, redefining the attributes of a successful AAA+ protease.
LINC00116-encoded microprotein mitoregulin regulates fatty acid metabolism at the mitochondrial outer membrane.
Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth.
Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations.
TRAP1 inhibits MARCH5-mediated MIC60 degradation to alleviate mitochondrial dysfunction and apoptosis of cardiomyocytes under diabetic conditions.
Secretion of mitochondrial DNA via exosomes promotes inflammation in Behçet's syndrome.

Cell Discov. 2023 Sep 07. 9(1): 92

Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation.

Terytty Yang Li, Qi Wang, Arwen W Gao, Xiaoxu Li, Yu Sun, Adrienne Mottis, Minho Shong, Johan Auwerx.

Lysosomes are central platforms for not only the degradation of macromolecules but also the integration of multiple signaling pathways. However, whether and how lysosomes mediate the mitochondrial stress response (MSR) remain largely unknown. Here, we demonstrate that lysosomal acidification via the vacuolar H+-ATPase (v-ATPase) is essential for the transcriptional activation of the mitochondrial unfolded protein response (UPRmt). Mitochondrial stress stimulates v-ATPase-mediated lysosomal activation of the mechanistic target of rapamycin complex 1 (mTORC1), which then directly phosphorylates the MSR transcription factor, activating transcription factor 4 (ATF4). Disruption of mTORC1-dependent ATF4 phosphorylation blocks the UPRmt, but not other similar stress responses, such as the UPRER. Finally, ATF4 phosphorylation downstream of the v-ATPase/mTORC1 signaling is indispensable for sustaining mitochondrial redox homeostasis and protecting cells from ROS-associated cell death upon mitochondrial stress. Thus, v-ATPase/mTORC1-mediated ATF4 phosphorylation via lysosomes links mitochondrial stress to UPRmt activation and mitochondrial function resilience.

DOI: https://doi.org/10.1038/s41421-023-00589-1
Mol Cell. 2023 Sep 07. pii: S1097-2765(23)00641-X. [Epub ahead of print]83(17): 3188-3204.e7

Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling.

Olivia Harding, Elisabeth Holzer, Julia F Riley, Sascha Martens, Erika L F Holzbaur.

  Failure to clear damaged mitochondria via mitophagy disrupts physiological function and may initiate damage signaling via inflammatory cascades, although how these pathways intersect remains unclear. We discovered that nuclear factor kappa B (NF-κB) essential regulator NF-κB effector molecule (NEMO) is recruited to damaged mitochondria in a Parkin-dependent manner in a time course similar to recruitment of the structurally related mitophagy adaptor, optineurin (OPTN). Upon recruitment, NEMO partitions into phase-separated condensates distinct from OPTN but colocalizing with p62/SQSTM1. NEMO recruitment, in turn, recruits the active catalytic inhibitor of kappa B kinase (IKK) component phospho-IKKβ, initiating NF-κB signaling and the upregulation of inflammatory cytokines. Consistent with a potential neuroinflammatory role, NEMO is recruited to mitochondria in primary astrocytes upon oxidative stress. These findings suggest that damaged, ubiquitinated mitochondria serve as an intracellular platform to initiate innate immune signaling, promoting the formation of activated IKK complexes sufficient to activate NF-κB signaling. We propose that mitophagy and NF-κB signaling are initiated as parallel pathways in response to mitochondrial stress.

Keywords:  ALS; NEMO; NF-κB; NF-κB effector molecule; Parkin; Parkinson’s disease; SQSTM1/p62; amyotrophic lateral sclerosis; cell stress; innate immunity; mitophagy; neurodegeneration; neuroinflammation; optineurin nuclear factor kappa B; phase separation; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2023.08.005
EMBO J. 2023 Sep 04. e113743

A mitochondrial EglN1-AMPKα axis drives breast cancer progression by enhancing metabolic adaptation to hypoxic stress.

Weiwei Jiang, Mengyao Zhang, Chuan Gao, Chaojun Yan, Ronghui Gao, Ziwei He, Xin Wei, Jingjing Xiong, Zilun Ruan, Qian Yang, Jinpeng Li, Qifang Li, Ziyi Zhong, Mengna Zhang, Qianqian Yuan, Hankun Hu, Shuang Wang, Ming-Ming Hu, Cheguo Cai, Gao-Song Wu, Chao Jiang, Ya-Lin Zhang, Chen-Song Zhang, Jing Zhang.

  Mitochondria play essential roles in cancer cell adaptation to hypoxia, but the underlying mechanisms remain elusive. Through mitochondrial proteomic profiling, we here find that the prolyl hydroxylase EglN1 (PHD2) accumulates on mitochondria under hypoxia. EglN1 substrate-binding region in the β2β3 loop is responsible for its mitochondrial translocation and contributes to breast tumor growth. Furthermore, we identify AMP-activated protein kinase alpha (AMPKα) as an EglN1 substrate on mitochondria. The EglN1-AMPKα interaction is essential for their mutual mitochondrial translocation. After EglN1 prolyl-hydroxylates AMPKα under normoxia, they rapidly dissociate following prolyl-hydroxylation, leading to their immediate release from mitochondria. In contrast, hypoxia results in constant EglN1-AMPKα interaction and their accumulation on mitochondria, leading to the formation of a Ca2+ /calmodulin-dependent protein kinase 2 (CaMKK2)-EglN1-AMPKα complex to activate AMPKα phosphorylation, ensuring metabolic homeostasis and breast tumor growth. Our findings identify EglN1 as an oxygen-sensitive metabolic checkpoint signaling hypoxic stress to mitochondria through its β2β3 loop region, suggesting a potential therapeutic target for breast cancer.

Keywords:  AMPKα; EglN1; hypoxia; metabolic homeostasis; mitochondrial translocation

DOI:  https://doi.org/10.15252/embj.2023113743
iScience. 2023 Sep 15. 26(9): 107537

Ets1 facilitates EMT/invasion through Drp1-mediated mitochondrial fragmentation in ovarian cancer.

Deepshikha Ghosh, Suman Pakhira, Damayanti Das Ghosh, Susanta Roychoudhury, Sib Sankar Roy.

  Ovarian cancer has sustained as a major cause of cancer-related female mortality owing to its aggressive nature and a dearth of early detection markers. Ets1 oncoprotein, a transcription factor belonging to the Ets family, is a well-established promoter of epithelial to mesenchymal transition (EMT) and a prospective malignancy marker in ovarian cancer. Our study establishes Ets1 as a regulator of mitochondrial fission-fusion dynamics through Drp1 augmentation via direct binding at DNM1L (DRP1) promoter. Ets1 overexpression-mediated Drp1 increment resulted in mitochondrial load reduction and compromised OXPHOS Complex 5 (ATP synthase) expression, facilitating a greater reliance on glycolysis over OXPHOS. Furthermore, our work demonstrates that inhibition of mitochondrial fission through molecular or pharmacological inhibition of Drp1 successfully mitigates Ets1-associated EMT in both in vitro and in vivo syngeneic mice model. Collectively, our data highlight the role of Drp1-mediated mitochondrial fragmentation in driving Ets1-mediated bioenergetic alterations and EMT/invasion in ovarian cancer.

Keywords:  Cancer; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.107537
J Cell Biol. 2023 Oct 02. pii: e202302037. [Epub ahead of print]222(10):

C17orf80 binds the mitochondrial genome to promote its replication.

Hao Wu, Wenshuo Zhang, Fengli Xu, Kun Peng, Xiaoyu Liu, Wanqiu Ding, Qi Ma, Heping Cheng, Xianhua Wang.

Serving as the power plant and signaling hub of a cell, mitochondria contain their own genome which encodes proteins essential for energy metabolism and forms DNA-protein assemblies called nucleoids. Mitochondrial DNA (mtDNA) exists in multiple copies within each cell ranging from hundreds to tens of thousands. Maintaining mtDNA homeostasis is vital for healthy cells, and its dysregulation causes multiple human diseases. However, the players involved in regulating mtDNA maintenance are largely unknown though the core components of its replication machinery have been characterized. Here, we identify C17orf80, a functionally uncharacterized protein, as a critical player in maintaining mtDNA homeostasis. C17orf80 primarily localizes to mitochondrial nucleoid foci and exhibits robust double-stranded DNA binding activity throughout the mitochondrial genome, thus constituting a bona fide new mitochondrial nucleoid protein. It controls mtDNA levels by promoting mtDNA replication and plays important roles in mitochondrial metabolism and cell proliferation. Our findings provide a potential target for therapeutics of human diseases associated with defective mtDNA control.

DOI: https://doi.org/10.1083/jcb.202302037
J Cell Biol. 2023 Oct 02. pii: e202303002. [Epub ahead of print]222(10):

The Orf9b protein of SARS-CoV-2 modulates mitochondrial protein biogenesis.

Svenja Lenhard, Sarah Gerlich, Azkia Khan, Saskia Rödl, Jan-Eric Bökenkamp, Esra Peker, Christine Zarges, Janina Faust, Zuzana Storchova, Markus Räschle, Jan Riemer, Johannes M Herrmann.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses high amounts of the protein Orf9b to target the mitochondrial outer membrane protein Tom70. Tom70 serves as an import receptor for mitochondrial precursors and, independently of this function, is critical for the cellular antiviral response. Previous studies suggested that Orf9b interferes with Tom70-mediated antiviral signaling, but its implication for mitochondrial biogenesis is unknown. In this study, we expressed Orf9b in human HEK293 cells and observed an Orf9b-mediated depletion of mitochondrial proteins, particularly in respiring cells. To exclude that the observed depletion was caused by the antiviral response, we generated a yeast system in which the function of human Tom70 could be recapitulated. Upon expression of Orf9b in these cells, we again observed a specific decline of a subset of mitochondrial proteins and a general reduction of mitochondrial volume. Thus, the SARS-CoV-2 virus is able to modulate the mitochondrial proteome by a direct effect of Orf9b on mitochondrial Tom70-dependent protein import.

DOI: https://doi.org/10.1083/jcb.202303002
Cell Rep. 2023 Sep 01. pii: S2211-1247(23)01072-0. [Epub ahead of print]42(9): 113061

Lon degrades stable substrates slowly but with enhanced processivity, redefining the attributes of a successful AAA+ protease.

Meghann R Kasal, Hema Chandra Kotamarthi, Madeline M Johnson, Hannah M Stephens, Matthew J Lang, Robert T Sauer, Tania A Baker.

  Lon is a widely distributed AAA+ (ATPases associated with diverse cellular activities) protease known for degrading poorly folded and damaged proteins and is often classified as a weak protein unfoldase. Here, using a Lon-degron pair from Mesoplasma florum (MfLon and MfssrA, respectively), we perform ensemble and single-molecule experiments to elucidate the molecular mechanisms underpinning MfLon function. Notably, we find that MfLon unfolds and degrades stably folded substrates and that translocation of these unfolded polypeptides occurs with a ∼6-amino-acid step size. Moreover, the time required to hydrolyze one ATP corresponds to the dwell time between steps, indicating that one step occurs per ATP-hydrolysis-fueled "power stroke." Comparison of MfLon to related AAA+ enzymes now provides strong evidence that HCLR-clade enzymes function using a shared power-stroke mechanism and, surprisingly, that MfLon is more processive than ClpXP and ClpAP. We propose that ample unfoldase strength and substantial processivity are features that contribute to the Lon family's evolutionary success.

Keywords:  AAA+ enzyme processivity; AAA+ motors; AAA+ unfoldase translocation step size; CP: Molecular biology; protein degradation; single-molecule optical trapping

DOI:  https://doi.org/10.1016/j.celrep.2023.113061
iScience. 2023 Sep 15. 26(9): 107558

LINC00116-encoded microprotein mitoregulin regulates fatty acid metabolism at the mitochondrial outer membrane.

Shan Zhang, Yabo Guo, Gio Fidelito, David R L Robinson, Chao Liang, Radiance Lim, Zoë Bichler, Ruiyang Guo, Gaoqi Wu, He Xu, Quan D Zhou, Brijesh K Singh, Paul Yen, Dennis Kappei, David A Stroud, Lena Ho.

  LINC00116 encodes a microprotein first identified as Mitoregulin (MTLN), where it was reported to localize to the inner membrane of mitochondria to regulate fatty acid oxidation and oxidative phosphorylation. These initial discoveries were followed by reports with differing findings about its molecular functions and submitochondrial localization. To clarify the apparent discrepancies, we constructed multiple orthogonal methods of determining the localization of MTLN, including split GFP-based reporters that enable efficient and reliable topology analyses for microproteins. These methods unequivocally demonstrate MTLN primarily localizes to the outer membrane of mitochondria, where it interacts with enzymes of fatty acid metabolism including CPT1B and CYB5B. Loss of MTLN causes the accumulation of very long-chain fatty acids (VLCFAs), especially docosahexaenoic acid (DHA). Intriguingly, loss of MTLN protects mice against western diet/fructose-induced insulin-resistance, suggests a protective effect of VLCFAs in this context. MTLN thus serves as an attractive target to control the catabolism of VLCFAs.

Keywords:  Biochemistry; Biological sciences; Cell biology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.107558
Nat Struct Mol Biol. 2023 Sep 07.

Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth.

Anika Seel, Francesco Padovani, Moritz Mayer, Alissa Finster, Daniela Bureik, Felix Thoma, Christof Osman, Till Klecker, Kurt M Schmoller.

To maintain stable DNA concentrations, proliferating cells need to coordinate DNA replication with cell growth. For nuclear DNA, eukaryotic cells achieve this by coupling DNA replication to cell-cycle progression, ensuring that DNA is doubled exactly once per cell cycle. By contrast, mitochondrial DNA replication is typically not strictly coupled to the cell cycle, leaving the open question of how cells maintain the correct amount of mitochondrial DNA during cell growth. Here, we show that in budding yeast, mitochondrial DNA copy number increases with cell volume, both in asynchronously cycling populations and during G1 arrest. Our findings suggest that cell-volume-dependent mitochondrial DNA maintenance is achieved through nuclear-encoded limiting factors, including the mitochondrial DNA polymerase Mip1 and the packaging factor Abf2, whose amount increases in proportion to cell volume. By directly linking mitochondrial DNA maintenance to nuclear protein synthesis and thus cell growth, constant mitochondrial DNA concentrations can be robustly maintained without a need for cell-cycle-dependent regulation.

DOI: https://doi.org/10.1038/s41594-023-01091-8
JCI Insight. 2023 Sep 08. pii: e167656. [Epub ahead of print]8(17):

Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations.

Jingdian Zhang, Camilla Koolmeister, Jinming Han, Roberta Filograna, Leo Hanke, Monika Àdori, Daniel J Sheward, Sina Teifel, Shreekara Gopalakrishna, Qiuya Shao, Yong Liu, Keying Zhu, Robert A Harris, Gerald McInerney, Ben Murrell, Mike Aoun, Liselotte Bäckdahl, Rikard Holmdahl, Marcin Pekalski, Anna Wedell, Martin Engvall, Anna Wredenberg, Gunilla B Karlsson Hedestam, Xaquin Castro Dopico, Joanna Rorbach.

  Pathogenic mutations in mitochondrial (mt) tRNA genes that compromise oxidative phosphorylation (OXPHOS) exhibit heteroplasmy and cause a range of multisyndromic conditions. Although mitochondrial disease patients are known to suffer from abnormal immune responses, how heteroplasmic mtDNA mutations affect the immune system at the molecular level is largely unknown. Here, in mice carrying pathogenic C5024T in mt-tRNAAla and in patients with mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (MELAS) syndrome carrying A3243G in mt-tRNALeu, we found memory T and B cells to have lower pathogenic mtDNA mutation burdens than their antigen-inexperienced naive counterparts, including after vaccination. Pathogenic burden reduction was less pronounced in myeloid compared with lymphoid lineages, despite C5024T compromising macrophage OXPHOS capacity. Rapid dilution of the C5024T mutation in T and B cell cultures could be induced by antigen receptor-triggered proliferation and was accelerated by metabolic stress conditions. Furthermore, we found C5024T to dysregulate CD8+ T cell metabolic remodeling and IFN-γ production after activation. Together, our data illustrate that the generation of memory lymphocytes shapes the mtDNA landscape, wherein pathogenic variants dysregulate the immune response.

Keywords:  Adaptive immunity; Immunology; Metabolism; Mitochondria

DOI:  https://doi.org/10.1172/jci.insight.167656
Cell Death Differ. 2023 Sep 07.

TRAP1 inhibits MARCH5-mediated MIC60 degradation to alleviate mitochondrial dysfunction and apoptosis of cardiomyocytes under diabetic conditions.

Lingxiao Zhang, Yuanyuan Luo, Linyan Lv, Siyong Chen, Guihua Liu, Tongfeng Zhao.

Mitochondrial dysfunction and cell death play important roles in diabetic cardiomyopathy, but the underlying mechanisms remain unclear. Here, we report that mitochondrial dysfunction and cell apoptosis are prominent features of primary cardiomyocytes after exposure to high glucose/palmitate conditions. The protein level of MIC60, a core component of mitochondrial cristae, is decreased via ubiquitination and degradation under these conditions. Exogenous expression of MIC60 alleviates cristae disruption, mitochondrial dysfunction and apoptosis. Moreover, we identified MARCH5 as an E3 ubiquitin ligase that specifically targets MIC60 in this process. Indeed, MARCH5 mediates K48-linked ubiquitination of MIC60 at Lys285 to promote its degradation. Mutation of the ubiquitination site in MIC60 or the MIC60-interacting motifs in MARCH5 abrogates MARCH5-mediated MIC60 ubiquitination and degradation. Silencing MARCH5 significantly alleviates high glucose/palmitate-induced mitochondrial dysfunction and apoptosis in primary cardiomyocytes. In addition to E3 ubiquitin ligases, molecular chaperones also play important roles in protein stability. We previously reported that the mitochondrial chaperone TRAP1 inhibits the ubiquitination of MIC60, but the detailed mechanism is unknown. Here, we find that TRAP1 performs this function by competing with MARCH5 for binding to MIC60. Our findings provide new insights into the mechanism underlying mitochondrial dysfunction in cardiomyocytes in diabetic cardiomyopathy. MARCH5 promotes ubiquitination of MIC60 to induce MIC60 degradation, mitochondrial dysfunction and apoptosis in cardiomyocytes under diabetic conditions. TRAP1 inhibits MARCH5-mediated ubiquitination by competitively interacting with MIC60.

DOI: https://doi.org/10.1038/s41418-023-01218-w
EMBO J. 2023 Sep 04. e112573

Secretion of mitochondrial DNA via exosomes promotes inflammation in Behçet's syndrome.

Hachiro Konaka, Yasuhiro Kato, Toru Hirano, Kohei Tsujimoto, JeongHoon Park, Taro Koba, Wataru Aoki, Yusei Matsuzaki, Masayasu Taki, Shohei Koyama, Eri Itotagawa, Tatsunori Jo, Takehiro Hirayama, Taro Kawai, Ken J Ishii, Mitsuyoshi Ueda, Shigehiro Yamaguchi, Shizuo Akira, Takayoshi Morita, Yuichi Maeda, Masayuki Nishide, Sumiyuki Nishida, Yoshihito Shima, Masashi Narazaki, Hyota Takamatsu, Atsushi Kumanogoh.

  Mitochondrial DNA (mtDNA) leakage into the cytoplasm can occur when cells are exposed to noxious stimuli. Specific sensors recognize cytoplasmic mtDNA to promote cytokine production. Cytoplasmic mtDNA can also be secreted extracellularly, leading to sterile inflammation. However, the mode of secretion of mtDNA out of cells upon noxious stimuli and its relevance to human disease remain unclear. Here, we show that pyroptotic cells secrete mtDNA encapsulated within exosomes. Activation of caspase-1 leads to mtDNA leakage from the mitochondria into the cytoplasm via gasdermin-D. Caspase-1 also induces intraluminal membrane vesicle formation, allowing for cellular mtDNA to be taken up and secreted as exosomes. Encapsulation of mtDNA within exosomes promotes a strong inflammatory response that is ameliorated upon exosome biosynthesis inhibition in vivo. We further show that monocytes derived from patients with Behçet's syndrome (BS), a chronic systemic inflammatory disorder, show enhanced caspase-1 activation, leading to exosome-mediated mtDNA secretion and similar inflammation pathology as seen in BS patients. Collectively, our findings support that mtDNA-containing exosomes promote inflammation, providing new insights into the propagation and exacerbation of inflammation in human inflammatory diseases.

Keywords:  Behçet's syndrome; caspase-1; exosome; mitochondrial DNA; pyroptosis

DOI:  https://doi.org/10.15252/embj.2022112573