bims-miprim 2022-11-20 papers

on Mitochondria, proteostasis and innate immunity

Issue of 2022–11–20
twelve papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.
Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.
A BAK subdomain that binds mitochondrial lipids selectively and releases cytochrome C.
AAA+ proteases: the first line of defense against mitochondrial damage.
Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1.
Delivery of mitoceuticals or respiratory competent mitochondria to sites of neurotrauma.
Mitochondrial quality control mechanisms as therapeutic targets in doxorubicin-induced cardiotoxicity.
LUBAC and NF-κB trigger a nuclear response from mitochondria.
Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.
Selection of red fluorescent protein for genetic labeling of mitochondria and intercellular transfer of viable mitochondria.
Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.
Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.

EMBO J. 2022 Nov 18. e112006

LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.

Zhixiao Wu, Lena A Berlemann, Verian Bader, Dominik A Sehr, Eva Dawin, Alberto Covallero, Jens Meschede, Lena Angersbach, Cathrin Showkat, Jonas B Michaelis, Christian Münch, Bettina Rieger, Dmitry Namgaladze, Maria Georgina Herrera, Fabienne C Fiesel, Wolfdieter Springer, Marta Mendes, Jennifer Stepien, Katalin Barkovits, Katrin Marcus, Albert Sickmann, Gunnar Dittmar, Karin B Busch, Dietmar Riedel, Marisa Brini, Jörg Tatzelt, Tito Cali, Konstanze F Winklhofer.

  Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.

Keywords:  HOIP; NEMO; OTULIN; PINK1; ubiquitin

DOI:  https://doi.org/10.15252/embj.2022112006
Proc Natl Acad Sci U S A. 2022 Nov 22. 119(47): e2210730119

Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.

Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Naotada Ishihara.

  Mitochondria have their own DNA (mtDNA), which encodes essential respiratory subunits. Under live imaging, mitochondrial nucleoids, composed of several copies of mtDNA and DNA-binding proteins, such as mitochondrial transcription factor A (TFAM), actively move inside mitochondria and change the morphology, in concert with mitochondrial membrane fission. Here we found the mitochondrial inner membrane-anchored AAA-ATPase protein ATAD3A mediates the nucleoid dynamics. Its ATPase domain exposed to the matrix binds directly to TFAM and mediates nucleoid trafficking along mitochondria by ATP hydrolysis. Nucleoid trafficking also required ATAD3A oligomerization via an interaction between the coiled-coil domains in intermembrane space. In ATAD3A deficiency, impaired nucleoid trafficking repressed the clustered and enlarged nucleoids observed in mitochondrial fission-deficient cells resulted in dispersed distribution of small nucleoids observed throughout the mitochondrial network, and this enhanced respiratory complex formation. Thus, mitochondrial fission and nucleoid trafficking cooperatively determine the size, number, and distribution of nucleoids in mitochondrial network, which should modulate respiratory complex formation.

Keywords:  ATAD3A; Drp1; mitochondrial fission; mtDNA nucleoid; respiratory complex

DOI:  https://doi.org/10.1073/pnas.2210730119
Cell Death Differ. 2022 Nov 14.

A BAK subdomain that binds mitochondrial lipids selectively and releases cytochrome C.

Haiming Dai, Kevin L Peterson, Karen S Flatten, X Wei Meng, Annapoorna Venkatachalam, Cristina Correia, Marina Ramirez-Alvarado, Yuan-Ping Pang, Scott H Kaufmann.

How BAK and BAX induce mitochondrial outer membrane (MOM) permeabilization (MOMP) during apoptosis is incompletely understood. Here we have used molecular dynamics simulations, surface plasmon resonance, and assays for membrane permeabilization in vitro and in vivo to assess the structure and function of selected BAK subdomains and their derivatives. Results of these studies demonstrate that BAK helical regions α5 and α6 bind the MOM lipid cardiolipin. While individual peptides corresponding to these helical regions lack the full biological activity of BAK, tandem peptides corresponding to α4-α5, α5-α6, or α6-α7/8 can localize exogenous proteins to mitochondria, permeabilize liposomes composed of MOM lipids, and cause MOMP in the absence of the remainder of the BAK protein. Importantly, the ability of these tandem helices to induce MOMP under cell-free conditions is diminished by mutations that disrupt the U-shaped helix-turn-helix structure of the tandem peptides or decrease their lipid binding. Likewise, BAK-induced apoptosis in intact cells is diminished by CLS1 gene interruption, which decreases mitochondrial cardiolipin content, or by BAK mutations that disrupt the U-shaped tandem peptide structure or diminish lipid binding. Collectively, these results suggest that BAK structural rearrangements during apoptosis might mobilize helices involved in specific protein-lipid interactions that are critical for MOMP.

DOI: https://doi.org/10.1038/s41418-022-01083-z
PeerJ. 2022 ;10 e14350

AAA+ proteases: the first line of defense against mitochondrial damage.

Gautam Pareek.

  Mitochondria play essential cellular roles in Adenosine triphosphate (ATP) synthesis, calcium homeostasis, and metabolism, but these vital processes have potentially deadly side effects. The production of the reactive oxygen species (ROS) and the aggregation of misfolded mitochondrial proteins can lead to severe mitochondrial damage and even cell death. The accumulation of mitochondrial damage is strongly implicated in aging and several incurable diseases, including neurodegenerative disorders and cancer. To oppose this, metazoans utilize a variety of quality control strategies, including the degradation of the damaged mitochondrial proteins by the mitochondrial-resident proteases of the ATPase Associated with the diverse cellular Activities (AAA+) family. This mini-review focuses on the quality control mediated by the mitochondrial-resident proteases of the AAA+ family used to combat the accumulation of damaged mitochondria and on how the failure of this mitochondrial quality control contributes to diseases.

Keywords:  AAA+ Protease; Mitochondria in neurological disorders; Mitochondrial Translation; Mitochondrial Unfolded Protein Response; Mitochondrial quality control

DOI:  https://doi.org/10.7717/peerj.14350
Front Physiol. 2022 ;13 1004099

Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1.

Aditya Sen, Rachel T Cox.

  Mitochondria contain their own DNA, mitochondrial DNA, which encodes thirteen proteins. However, mitochondria require thousands of proteins encoded in the nucleus to carry out their many functions. Identifying the definitive mitochondrial proteome has been challenging as methods isolating mitochondrial proteins differ and different tissues and organisms may have specialized proteomes. Mitochondrial diseases arising from single gene mutations in nucleus encoded genes could affect the mitochondrial proteome, but deciphering which effects are due to loss of specific pathways or to accumulated general mitochondrial damage is difficult. To identify specific versus general effects, we have taken advantage of mutations in three Drosophila genes, clueless, Sod2, and Pink1, which are required for mitochondrial function through different pathways. We measured changes in each mutant's mitochondrial proteome using quantitative tandem mass tag mass spectrometry. Our analysis identified protein classes that are unique to each mutant and those shared between them, suggesting that some changes in the mitochondrial proteome are due to general mitochondrial damage whereas others are gene specific. For example, clueless mutants had the greatest number of less and more abundant mitochondrial proteins whereas loss of all three genes increased stress and metabolism proteins. This study is the first to directly compare in vivo steady state levels of mitochondrial proteins by examining loss of three pathways critical for mitochondrial function. These data could be useful to understand disease etiology, and how mutations in genes critical for mitochondrial function cause specific mitochondrial proteomic changes as opposed to changes due to generalized mitochondrial damage.

Keywords:  Clueless; PINK1; SOD2; drosophila; mitochondria; mitochondrial proteome; respiratory chain complexes

DOI:  https://doi.org/10.3389/fphys.2022.1004099
Mitochondrion. 2022 Nov 09. pii: S1567-7249(22)00090-3. [Epub ahead of print]68 10-14

Delivery of mitoceuticals or respiratory competent mitochondria to sites of neurotrauma.

Samir P Patel, Felicia M Michael, Jenna L Gollihue, W Brad Hubbard, Patrick G Sullivan, Alexander G Rabchevsky.

  Herein, we review evidence that targeting mitochondrial dysfunction with 'mitoceuticals' is an effective neuroprotective strategy following neurotrauma, and that isolated exogenous mitochondria can be effectively transplanted into host spinal cord parenchyma to increase overall cellular metabolism. We further discuss control measures to ensure greatest potential for mitochondrial transfer, notably using erodible thermogelling hydrogels to deliver respiratory competent mitochondria to the injured spinal cord.

Keywords:  Bioenergetics; Hydrogel; Metabolism; Mitochondria; Oxidative phosphorylation; Spinal cord; Transplantation

DOI:  https://doi.org/10.1016/j.mito.2022.11.001
Trends Pharmacol Sci. 2022 Nov 14. pii: S0165-6147(22)00229-2. [Epub ahead of print]

Mitochondrial quality control mechanisms as therapeutic targets in doxorubicin-induced cardiotoxicity.

Lin Wu, Litao Wang, Yuxin Du, Yingmei Zhang, Jun Ren.

  Doxorubicin (DOX) is a chemotherapeutic drug that is utilized for solid tumors and hematologic malignancies, but its clinical application is hampered by life-threatening cardiotoxicity including cardiac dilation and heart failure. Mitochondrial quality control processes, including mitochondrial proteostasis, mitophagy, and mitochondrial dynamics and biogenesis, serve to maintain mitochondrial homeostasis in the cardiovascular system. Importantly, recent advances have unveiled a major role for defective mitochondrial quality control in the etiology of DOX cardiomyopathy. Moreover, specific interventions targeting these quality control mechanisms to preserve mitochondrial function have emerged as potential therapeutic strategies to attenuate DOX cardiotoxicity. However, clinical translation is challenging because of obscure mechanisms of action and potential adverse effects. The purpose of this review is to provide new insights regarding the role of mitochondrial quality control in the pathogenesis of DOX cardiotoxicity, and to explore promising therapeutic approaches targeting these mechanisms to aid clinical management.

Keywords:  doxorubicin-induced cardiotoxicity; mitochondria; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial quality control

DOI:  https://doi.org/10.1016/j.tips.2022.10.003
EMBO J. 2022 Nov 18. e112920

LUBAC and NF-κB trigger a nuclear response from mitochondria.

Junsheng Chen, Thomas Simmen.

Mitochondria are key signaling hubs for innate immune responses. In this issue, Wu et al (2022) report that remodeling of the outer mitochondrial membrane by the linear ubiquiting chain assembly complex (LUBAC) facilitates transport of activated NF-κB to the nucleus in response to TNF signaling.

DOI: https://doi.org/10.15252/embj.2022112920
iScience. 2022 Nov 18. 25(11): 105447

Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.

M A Neginskaya, S E Morris, E V Pavlov.

  An increase in permeability of the mitochondrial inner membrane, mitochondrial permeability transition (PT), is the central event responsible for cell death and tissue damage in conditions such as stroke and heart attack. PT is caused by the cyclosporin A (CSA)-dependent calcium-induced pore, the permeability transition pore (PTP). The molecular details of PTP are incompletely understood. We utilized holographic and fluorescent microscopy to assess the contribution of ATP synthase and adenine nucleotide translocator (ANT) toward PTP. In cells lacking either ATP synthase or ANT, we observed CSA-sensitive membrane depolarization, but not high-conductance PTP. In wild-type cells, calcium-induced CSA-sensitive depolarization preceded opening of PTP, which occurred only after nearly complete mitochondrial membrane depolarization. We propose that both ATP synthase and ANT are required for high-conductance PTP but not depolarization, which presumably occurs through activation of the low-conductance PT, which has a molecular nature that is different from both complexes.

Keywords:  Cell biology; Functional aspects of cell biology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2022.105447
Sci Rep. 2022 Nov 18. 12(1): 19841

Selection of red fluorescent protein for genetic labeling of mitochondria and intercellular transfer of viable mitochondria.

Isamu Taiko, Chika Takano, Masayuki Nomoto, Shingo Hayashida, Kazunori Kanemaru, Toshio Miki.

The phenomenon of intercellular mitochondrial transfer has attracted great attention in various fields of research, including stem cell biology. Elucidating the mechanism of mitochondrial transfer from healthy stem cells to cells with mitochondrial dysfunction may lead to the development of novel stem cell therapies to treat mitochondrial diseases, among other advances. To visually evaluate and analyze the mitochondrial transfer process, dual fluorescent labeling systems are often used to distinguish the mitochondria of donor and recipient cells. Although enhanced green fluorescent protein (EGFP) has been well-characterized for labeling mitochondria, other colors of fluorescent protein have been less extensively evaluated in the context of mitochondrial transfer. Here, we generated different lentiviral vectors with mitochondria-targeted red fluorescent proteins (RFPs), including DsRed, mCherry (both from Discosoma sp.) Kusabira orange (mKOκ, from Verrillofungia concinna), and TurboRFP (from Entacmaea quadricolor). Among these proteins, mitochondria-targeted DsRed and its variant mCherry often generated bright aggregates in the lysosome while other proteins did not. We further validated that TurboRFP-labeled mitochondria were successfully transferred from amniotic epithelial cells, one of the candidates for donor stem cells, to mitochondria-damaged recipient cells without losing the membrane potential. Our study provides new insight into the genetic labeling of mitochondria with red fluorescent proteins, which may be utilized to analyze the mechanism of intercellular mitochondrial transfer.

DOI: https://doi.org/10.1038/s41598-022-24297-0
iScience. 2022 Nov 18. 25(11): 105410

Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.

Christine E Robbins, Bhumil Patel, Danielle L Sawyer, Barrie Wilkinson, Brian K Kennedy, Mark A McCormick.

  Deletion of genes encoding ribosomal proteins extends lifespan in yeast. This increases translation of the functionally conserved transcription factor Gcn4, and lifespan extension in these mutants is GCN4-dependent. Gcn4 is also translationally upregulated by uncharged tRNAs, as are its C aenorhabditis elegans and mammalian functional orthologs. Here, we show that cytosolic tRNA synthetase inhibitors upregulate Gcn4 translation and extend yeast lifespan in a Gcn4-dependent manner. This cytosolic tRNA synthetase inhibitor is also able to extend the lifespan of C. elegans in an atf-4-dependent manner. We show that mitochondrial tRNA synthetase inhibitors greatly extend the lifespan of C. elegans, and this depends on atf-4. This suggests that perturbations of both cytosolic and mitochondrial translation may act in part via the same downstream pathway. These findings establish GCN4 orthologs as conserved longevity factors and, as long-lived mice exhibit elevated ATF4, leave open the possibility that tRNA synthetase inhibitors could also extend lifespan in mammals.

Keywords:  Biochemistry; Biological sciences; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2022.105410
Sci Adv. 2022 Nov 18. 8(46): eadd3855

Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.

Jonathan Schiller, Eike Laube, Ilka Wittig, Werner Kühlbrandt, Janet Vonck, Volker Zickermann.

Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.

DOI: https://doi.org/10.1126/sciadv.add3855