bims-minimp 2021-08-08 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2021‒08‒08
twenty-six papers selected by
Hanna Salmonowicz
International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels.
Oxidative bursts of single mitochondria mediate retrograde signaling toward the ER.
Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse.
The human cytomegalovirus protein pUL13 targets mitochondrial cristae architecture to increase cellular respiration during infection.
Mammalian Target of Rapamycin Signaling Pathway Regulates Mitochondrial Quality Control of Brown Adipocytes in Mice.
Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase.
Human Mitochondrial RNA Processing and Modifications: Overview.
Complexome Profiling: Assembly and Remodeling of Protein Complexes.
FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply.
Mff oligomerization is required for Drp1 activation and synergy with actin filaments during mitochondrial division.
Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases.
Alterations in mitochondrial morphology as a key driver of immunity and host defence.
Molecular Insights into Mitochondrial Protein Translocation and Human Disease.
Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca2+ homeostasis with adipose tissue lipolysis.
Insulin and IGF-1 receptors regulate complex-I dependent mitochondrial bioenergetics and supercomplexes via FoxOs in muscle.
A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation.
Instability in NAD+ metabolism leads to impaired cardiac mitochondrial function and communication.
Mitochondrial UPR through generations.
The stressosome, a caspase-8-activating signalling complex assembled in response to cell stress in an ATG5-mediated manner.
Minimal mitochondrial respiration is required to prevent cell death by inhibition of mTOR signaling in CoQ-deficient cells.
BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance.
iDeepSubMito: identification of protein submitochondrial localization with deep learning.
MICU1 opens the gates to cold-induced death.
Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence.
Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissue.
The Roles of Assembly Factors in Mammalian Mitoribosome Biogenesis.

Nat Cell Biol. 2021 Aug 02.

The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels.

Qian Zhang, Zihao Wang, Wenfeng Zhang, Qingbo Wen, Xinyu Li, Jun Zhou, Xueying Wu, Yongqing Guo, Yangli Liu, Changshuo Wei, Wenfeng Qian, Ye Tian.

The memory of stresses experienced by parents can be passed on to descendants as a forecast of the challenges to come. Here, we discovered that the neuronal mitochondrial perturbation-induced systemic mitochondrial unfolded protein response (UPRmt) in Caenorhabditis elegans can be transmitted to offspring over multiple generations. The transgenerational activation of UPRmt is mediated by maternal inheritance of elevated levels of mitochondrial DNA (mtDNA), which causes the proteostasis stress within mitochondria. Furthermore, results from intercrossing studies using wild C. elegans strains further support that maternal inheritance of higher levels of mtDNA can induce the UPRmt in descendants. The mitokine Wnt signalling pathway is required for the transmission of elevated mtDNA levels across generations, thereby conferring lifespan extension and stress resistance to offspring. Collectively, our results reveal that the nervous system can transmit stress signals across generations by increasing mtDNA in the germline, enabling descendants to better cope with anticipated challenges.

DOI: https://doi.org/10.1038/s41556-021-00724-8
Mol Cell. 2021 Jul 27. pii: S1097-2765(21)00583-9. [Epub ahead of print]

Oxidative bursts of single mitochondria mediate retrograde signaling toward the ER.

David M Booth, Péter Várnai, Suresh K Joseph, György Hajnóczky.

  The emerging role of mitochondria as signaling organelles raises the question of whether individual mitochondria can initiate heterotypic communication with neighboring organelles. Using fluorescent probes targeted to the endoplasmic-reticulum-mitochondrial interface, we demonstrate that single mitochondria generate oxidative bursts, rapid redox oscillations, confined to the nanoscale environment of the interorganellar contact sites. Using probes fused to inositol 1,4,5-trisphosphate receptors (IP3Rs), we show that Ca2+ channels directly sense oxidative bursts and respond with Ca2+ transients adjacent to active mitochondria. Application of specific mitochondrial stressors or apoptotic stimuli dramatically increases the frequency and amplitude of the oxidative bursts by enhancing transient permeability transition pore openings. Conversely, blocking interface Ca2+ transport via elimination of IP3Rs or mitochondrial calcium uniporter channels suppresses ER-mitochondrial Ca2+ feedback and cell death. Thus, single mitochondria initiate local retrograde signaling by miniature oxidative bursts and, upon metabolic or apoptotic stress, may also amplify signals to the rest of the cell.

Keywords:  Ca2+ microdomain; Inositol-1,4,5-trisphosphate receptor; Mitochondrial retrograde signaling; Organelle contacts; Redox nanodomain

DOI:  https://doi.org/10.1016/j.molcel.2021.07.014
Neurogenetics. 2021 Aug 03.

Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse.

Antonia Maletzko, Jana Key, Ilka Wittig, Suzana Gispert, Gabriele Koepf, Júlia Canet-Pons, Sylvia Torres-Odio, A Phillip West, Georg Auburger.

  Mitochondrial dysfunction may activate innate immunity, e.g. upon abnormal handling of mitochondrial DNA in TFAM mutants or in altered mitophagy. Recent reports showed that also deletion of mitochondrial matrix peptidase ClpP in mice triggers transcriptional upregulation of inflammatory factors. Here, we studied ClpP-null mouse brain at two ages and mouse embryonal fibroblasts, to identify which signaling pathways are responsible, employing mass spectrometry, subcellular fractionation, immunoblots, and reverse transcriptase polymerase chain reaction. Several mitochondrial unfolded protein response factors showed accumulation and altered migration in blue-native gels, prominently the co-chaperone DNAJA3. Its mitochondrial dysregulation increased also its extra-mitochondrial abundance in the nucleus, a relevant observation given that DNAJA3 modulates innate immunity. Similar observations were made for STAT1, a putative DNAJA3 interactor. Elevated expression was observed not only for the transcription factors Stat1/2, but also for two interferon-stimulated genes (Ifi44, Gbp3). Inflammatory responses were strongest for the RLR pattern recognition receptors (Ddx58, Ifih1, Oasl2, Trim25) and several cytosolic nucleic acid sensors (Ifit1, Ifit3, Oas1b, Ifi204, Mnda). The consistent dysregulation of these factors from an early age might influence also human Perrault syndrome, where ClpP loss-of-function leads to early infertility and deafness, with subsequent widespread neurodegeneration.

Keywords:  Ataxia; Leukodystrophy; MTRNR1; Mitochondrial amino acid tRNA synthetases; POLG; PRLTS3; Release of mtDNA and mtRNA; TWINKLE; cGAS-STING

DOI:  https://doi.org/10.1007/s10048-021-00657-2
Proc Natl Acad Sci U S A. 2021 Aug 10. pii: e2101675118. [Epub ahead of print]118(32):

The human cytomegalovirus protein pUL13 targets mitochondrial cristae architecture to increase cellular respiration during infection.

Cora N Betsinger, Connor S R Jankowski, William A Hofstadter, Joel D Federspiel, Clayton J Otter, Pierre M Jean Beltran, Ileana M Cristea.

  Viruses modulate mitochondrial processes during infection to increase biosynthetic precursors and energy output, fueling virus replication. In a surprising fashion, although it triggers mitochondrial fragmentation, the prevalent pathogen human cytomegalovirus (HCMV) increases mitochondrial metabolism through a yet-unknown mechanism. Here, we integrate molecular virology, metabolic assays, quantitative proteomics, and superresolution confocal microscopy to define this mechanism. We establish that the previously uncharacterized viral protein pUL13 is required for productive HCMV replication, targets the mitochondria, and functions to increase oxidative phosphorylation during infection. We demonstrate that pUL13 forms temporally tuned interactions with the mitochondrial contact site and cristae organizing system (MICOS) complex, a critical regulator of cristae architecture and electron transport chain (ETC) function. Stimulated emission depletion superresolution microscopy shows that expression of pUL13 alters cristae architecture. Indeed, using live-cell Seahorse assays, we establish that pUL13 alone is sufficient to increase cellular respiration, not requiring the presence of other viral proteins. Our findings address the outstanding question of how HCMV targets mitochondria to increase bioenergetic output and expands the knowledge of the intricate connection between mitochondrial architecture and ETC function.

Keywords:  HCMV; metabolism; mitochondria; pUL13; proteomics

DOI:  https://doi.org/10.1073/pnas.2101675118
Front Physiol. 2021 ;12 638352

Mammalian Target of Rapamycin Signaling Pathway Regulates Mitochondrial Quality Control of Brown Adipocytes in Mice.

Bahetiyaer Huwatibieke, Wenzhen Yin, Lingchao Liu, Yuxin Jin, Xinxin Xiang, Jingyan Han, Weizhen Zhang, Yin Li.

  The mammalian target of rapamycin (mTOR) is an important protein kinase that senses changes in extracellular and intracellular energy levels and plays a key role in regulating energy metabolism. Brown adipose tissue, which can be converted to white adipose tissue, contains a large number of mitochondria and regulates energy expenditure through thermogenesis. Because obesity is a process of fat accumulation due to chronic excessive energy intake, we attempted to determine whether the mTOR signaling pathway can affect the mitochondrial quality control of brown adipocytes through sensing energy status, thereby regulating brown/white adipocyte transformation. In the present study, through activation or inhibition of mTOR signaling, we detected mitochondrial biogenesis, dynamics, and autophagy-related markers in brown adipocytes. We found that activation of mTOR signaling downregulated the expression of mitochondrial biogenesis, dynamics, and autophagy-relevant markers and inhibited the mitochondrial quality control of brown adipocytes, indicating a phenotypic transformation of brown to white adipocytes. In contrast, inhibition of mTOR signaling upregulated the expression of mitochondrial biogenesis, dynamics, and mitophagy-relevant markers and strengthened mitochondrial quality control, suggesting an inhibition of the phenotypic transformation of brown to white adipocytes. In conclusion, the mTOR signaling pathway plays an important role in modulating the transformation of adipocytes by regulating mitochondrial quality control.

Keywords:  brown adipose tissue; mammalian target of rapamycin; mitochondria; obesity; white adipose tissue

DOI:  https://doi.org/10.3389/fphys.2021.638352
Int J Mol Sci. 2021 Jul 21. pii: 7779. [Epub ahead of print]22(15):

Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase.

Minu Chaudhuri, Anuj Tripathi, Fidel Soto Gonzalez.

  Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca2+ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are integrated into the signaling network to maintain cellular homeostasis under stress. Mitochondria require hundreds of proteins to perform all these functions. Since the mitochondrial genome only encodes a handful of proteins, most mitochondrial proteins are imported from the cytosol via receptor/translocase complexes on the mitochondrial outer and inner membranes known as TOMs and TIMs. Many of the subunits of these protein complexes are essential for cell survival in model yeast and other unicellular eukaryotes. Defects in the mitochondrial import machineries are also associated with various metabolic, developmental, and neurodegenerative disorders in multicellular organisms. In addition to their canonical functions, these protein translocases also help maintain mitochondrial structure and dynamics, lipid metabolism, and stress response. This review focuses on the role of Tim50, the receptor component of one of the TIM complexes, in different cellular functions, with an emphasis on the Tim50 homologue in parasitic protozoan Trypanosoma brucei.

Keywords:  HAD-phosphatase family; TIM; TIMM50; TOM; Tim50; Trypanosoma

DOI:  https://doi.org/10.3390/ijms22157779
Int J Mol Sci. 2021 Jul 27. pii: 7999. [Epub ahead of print]22(15):

Human Mitochondrial RNA Processing and Modifications: Overview.

Marta Jedynak-Slyvka, Agata Jabczynska, Roman J Szczesny.

  Mitochondria, often referred to as the powerhouses of cells, are vital organelles that are present in almost all eukaryotic organisms, including humans. They are the key energy suppliers as the site of adenosine triphosphate production, and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune response. Abnormalities occurring in mitochondria, such as mitochondrial DNA (mtDNA) mutations and disturbances at any stage of mitochondrial RNA (mtRNA) processing and translation, usually lead to severe mitochondrial diseases. A fundamental line of investigation is to understand the processes that occur in these organelles and their physiological consequences. Despite substantial progress that has been made in the field of mtRNA processing and its regulation, many unknowns and controversies remain. The present review discusses the current state of knowledge of RNA processing in human mitochondria and sheds some light on the unresolved issues.

Keywords:  RNA decay; RNA modifications; RNA processing; mitochondria; mitochondrial genome; mitochondrial transcription

DOI:  https://doi.org/10.3390/ijms22157999
Int J Mol Sci. 2021 Jul 21. pii: 7809. [Epub ahead of print]22(15):

Complexome Profiling: Assembly and Remodeling of Protein Complexes.

Ilka Wittig, Pedro Felipe Malacarne.

  Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.

Keywords:  assembly; complexome profiling; data repositories; mass spectrometry; protein complexes; protein–protein interaction; remodeling

DOI:  https://doi.org/10.3390/ijms22157809
J Cell Biol. 2021 Oct 04. pii: e201912077. [Epub ahead of print]220(10):

FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply.

Himanish Basu, Gulcin Pekkurnaz, Jill Falk, Wei Wei, Morven Chin, Judith Steen, Thomas L Schwarz.

Mitochondrial movement and distribution are fundamental to their function. Here we report a mechanism that regulates mitochondrial movement by anchoring mitochondria to the F-actin cytoskeleton. This mechanism is activated by an increase in glucose influx and the consequent O-GlcNAcylation of TRAK (Milton), a component of the mitochondrial motor-adaptor complex. The protein four and a half LIM domains protein 2 (FHL2) serves as the anchor. FHL2 associates with O-GlcNAcylated TRAK and is both necessary and sufficient to drive the accumulation of F-actin around mitochondria and to arrest mitochondrial movement by anchoring to F-actin. Disruption of F-actin restores mitochondrial movement that had been arrested by either TRAK O-GlcNAcylation or forced direction of FHL2 to mitochondria. This pathway for mitochondrial immobilization is present in both neurons and non-neuronal cells and can thereby adapt mitochondrial dynamics to changes in glucose availability.

DOI: https://doi.org/10.1083/jcb.201912077
Mol Biol Cell. 2021 Aug 04. mbcE21040224

Mff oligomerization is required for Drp1 activation and synergy with actin filaments during mitochondrial division.

Ao Liu, Frieda Kage, Henry N Higgs.

Mitochondrial division is an important cellular process in both normal and pathological conditions. The dynamin GTPase Drp1 is a central mitochondrial division protein, driving constriction of the outer mitochondrial membrane. In mammals, the outer mitochondrial membrane protein Mff is a key receptor for recruiting Drp1 from the cytosol to the mitochondrion. Actin filaments are also important in Drp1 recruitment and activation. The manner in which Mff and actin work together in Drp1 activation is unknown. Here, we show that Mff is an oligomer (most likely a trimer) that dynamically associates and disassociates through its C-terminal coiled-coil, with a Kd in the range of 10 µM. Dynamic Mff oligomerization is required for Drp1 activation. While not binding Mff directly, actin filaments enhance Mff-mediated Drp1 activation by lowering the effective Mff concentration 10-fold. Total internal reflection microscopy assays using purified proteins show that Mff interacts with Drp1 on actin filaments in a manner dependent on Mff oligomerization. In U2OS cells, oligomerization-defective Mff does not effectively rescue three defects in Mff knock-out cells: mitochondrial division, mitochondrial Drp1 recruitment, and peroxisome division. The ability of Mff to assemble into puncta on mitochondria depends on its oligomerization, as well as on actin filaments and Drp1.

DOI: https://doi.org/10.1091/mbc.E21-04-0224
Int J Mol Sci. 2021 Jul 28. pii: 8077. [Epub ahead of print]22(15):

Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases.

Henrieta Havalová, Gabriela Ondrovičová, Barbora Keresztesová, Jacob A Bauer, Vladimír Pevala, Eva Kutejová, Nina Kunová.

  Since their discovery, heat shock proteins (HSPs) have been identified in all domains of life, which demonstrates their importance and conserved functional role in maintaining protein homeostasis. Mitochondria possess several members of the major HSP sub-families that perform essential tasks for keeping the organelle in a fully functional and healthy state. In humans, the mitochondrial HSP70 chaperone system comprises a central molecular chaperone, mtHSP70 or mortalin (HSPA9), which is actively involved in stabilizing and importing nuclear gene products and in refolding mitochondrial precursor proteins, and three co-chaperones (HSP70-escort protein 1-HEP1, tumorous imaginal disc protein 1-TID-1, and Gro-P like protein E-GRPE), which regulate and accelerate its protein folding functions. In this review, we summarize the roles of mitochondrial molecular chaperones with particular focus on the human mtHsp70 and its co-chaperones, whose deregulated expression, mutations, and post-translational modifications are often considered to be the main cause of neurological disorders, genetic diseases, and malignant growth.

Keywords:  GRPE; HEP1; TID-1; cancer; mitochondrial chaperones; mortalin; mtHSP70; neurodegenerative disorders; post-translational modification; protein quality control

DOI:  https://doi.org/10.3390/ijms22158077
EMBO Rep. 2021 Aug 02. e53086

Alterations in mitochondrial morphology as a key driver of immunity and host defence.

Mariana P Cervantes-Silva, Shannon L Cox, Annie M Curtis.

  Mitochondria are dynamic organelles whose architecture changes depending on the cell's energy requirements and other signalling events. These structural changes are collectively known as mitochondrial dynamics. Mitochondrial dynamics are crucial for cellular functions such as differentiation, energy production and cell death. Importantly, it has become clear in recent years that mitochondrial dynamics are a critical control point for immune cell function. Mitochondrial remodelling allows quiescent immune cells to rapidly change their metabolism and become activated, producing mediators, such as cytokines, chemokines and even metabolites to execute an effective immune response. The importance of mitochondrial dynamics in immunity is evident, as numerous pathogens have evolved mechanisms to manipulate host cell mitochondrial remodelling in order to promote their own survival. In this review, we comprehensively address the roles of mitochondrial dynamics in immune cell function, along with modulation of host cell mitochondrial morphology during viral and bacterial infections to facilitate either pathogen survival or host immunity. We also speculate on what the future may hold in terms of therapies targeting mitochondrial morphology for bacterial and viral control.

Keywords:  bacteria; immune response; mitochondrial dynamics; therapy; virus

DOI:  https://doi.org/10.15252/embr.202153086
Genes (Basel). 2021 Jul 01. pii: 1031. [Epub ahead of print]12(7):

Molecular Insights into Mitochondrial Protein Translocation and Human Disease.

Eduardo Ruiz-Pesini, Julio Montoya, David Pacheu-Grau.

  In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.

Keywords:  disease; mitochondria; protein import

DOI:  https://doi.org/10.3390/genes12071031
Cell Metab. 2021 Jul 27. pii: S1550-4131(21)00324-7. [Epub ahead of print]

Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca2+ homeostasis with adipose tissue lipolysis.

Alicia G Gómez-Valadés, Macarena Pozo, Luis Varela, Mehdi Boutagouga Boudjadja, Sara Ramírez, Iñigo Chivite, Elena Eyre, Roberta Haddad-Tóvolli, Arnaud Obri, Maria Milà-Guasch, Jordi Altirriba, Marc Schneeberger, Mónica Imbernón, Angela R Garcia-Rendueles, Pau Gama-Perez, Jonathan Rojo-Ruiz, Bence Rácz, Maria Teresa Alonso, Ramon Gomis, Antonio Zorzano, Giuseppe D'Agostino, Clara V Alvarez, Rubén Nogueiras, Pablo M Garcia-Roves, Tamas L Horvath, Marc Claret.

  Appropriate cristae remodeling is a determinant of mitochondrial function and bioenergetics and thus represents a crucial process for cellular metabolic adaptations. Here, we show that mitochondrial cristae architecture and expression of the master cristae-remodeling protein OPA1 in proopiomelanocortin (POMC) neurons, which are key metabolic sensors implicated in energy balance control, is affected by fluctuations in nutrient availability. Genetic inactivation of OPA1 in POMC neurons causes dramatic alterations in cristae topology, mitochondrial Ca2+ handling, reduction in alpha-melanocyte stimulating hormone (α-MSH) in target areas, hyperphagia, and attenuated white adipose tissue (WAT) lipolysis resulting in obesity. Pharmacological blockade of mitochondrial Ca2+ influx restores α-MSH and the lipolytic program, while improving the metabolic defects of mutant mice. Chemogenetic manipulation of POMC neurons confirms a role in lipolysis control. Our results unveil a novel axis that connects OPA1 in POMC neurons with mitochondrial cristae, Ca2+ homeostasis, and WAT lipolysis in the regulation of energy balance.

Keywords:  OPA-1; POMC neurons; cristae; hypothalamus; lipolysis; mitochondria; obesity

DOI:  https://doi.org/10.1016/j.cmet.2021.07.008
J Clin Invest. 2021 Aug 03. pii: 146415. [Epub ahead of print]

Insulin and IGF-1 receptors regulate complex-I dependent mitochondrial bioenergetics and supercomplexes via FoxOs in muscle.

Gourav Bhardwaj, Christie M Penniman, Jayashree Jena, Pablo A Suarez Beltran, Collin Foster, Kennedy Poro, Taylor L Junck, Antentor O Hinton, Rhonda Souvenir, Jordan D Fuqua, Pablo E Morales, Roberto Bravo-Sagua, William I Sivitz, Vitor A Lira, E Dale Abel, Brian T O'Neill.

  Decreased skeletal muscle strength and mitochondrial dysfunction are characteristic of diabetes. Action of insulin and IGF-1 through insulin receptor (IR) and IGF-1 receptor (IGF1R) maintain muscle mass via suppression of FoxOs, but whether FoxO activation coordinates atrophy in concert with mitochondrial dysfunction is unknown. We show that mitochondrial respiration and complex-I activity were decreased in streptozotocin (STZ) diabetic muscle, but these defects were reversed following muscle-specific FoxO1/3/4 triple knockout in STZ-FoxO TKO. In the absence of systemic glucose or lipid abnormalities, muscle-specific IR knockout (M-IR-/-) or combined IR/IGF1R knockout (MIGIRKO) impaired mitochondrial respiration, decreased ATP production, and increased ROS. These mitochondrial abnormalities were not present in muscle-specific IR/IGF1R and FoxO1/3/4 quintuple knockout mice (M-QKO). Acute tamoxifen-inducible deletion of IR/IGF1R also decreased muscle pyruvate respiration, complex-I activity, and supercomplex assembly. Although autophagy was increased when IR/IGF1R were deleted in muscle, mitophagy was not increased. Mechanistically, RNA-seq revealed that complex-I core subunits were decreased in STZ-diabetic and MIGIRKO muscle, and these changes were not present with FoxO knockout in STZ-FoxO TKO and M-QKO. Thus, insulin-deficient diabetes or loss of insulin/IGF-1 action in muscle decreases complex-I driven mitochondrial respiration and supercomplex assembly, in part by FoxO-mediated repression of Complex-I subunit expression.

Keywords:  Endocrinology; Insulin; Mitochondria; Muscle

DOI:  https://doi.org/10.1172/JCI146415
Sci Signal. 2021 Aug 03. pii: eabe0387. [Epub ahead of print]14(694):

A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation.

Orna Ernst, Jing Sun, Bin Lin, Balaji Banoth, Michael G Dorrington, Jonathan Liang, Benjamin Schwarz, Kaitlin A Stromberg, Samuel Katz, Sharat J Vayttaden, Clinton J Bradfield, Nadia Slepushkina, Christopher M Rice, Eugen Buehler, Jaspal S Khillan, Daniel W McVicar, Catharine M Bosio, Clare E Bryant, Fayyaz S Sutterwala, Scott E Martin, Madhu Lal-Nag, Iain D C Fraser.

Noncanonical inflammasome activation by cytosolic lipopolysaccharide (LPS) is a critical component of the host response to Gram-negative bacteria. Cytosolic LPS recognition in macrophages is preceded by a Toll-like receptor (TLR) priming signal required to induce transcription of inflammasome components and facilitate the metabolic reprograming that fuels the inflammatory response. Using a genome-scale arrayed siRNA screen to find inflammasome regulators in mouse macrophages, we identified the mitochondrial enzyme nucleoside diphosphate kinase D (NDPK-D) as a regulator of both noncanonical and canonical inflammasomes. NDPK-D was required for both mitochondrial DNA synthesis and cardiolipin exposure on the mitochondrial surface in response to inflammasome priming signals mediated by TLRs, and macrophages deficient in NDPK-D had multiple defects in LPS-induced inflammasome activation. In addition, NDPK-D was required for the recruitment of TNF receptor-associated factor 6 (TRAF6) to mitochondria, which was critical for reactive oxygen species (ROS) production and the metabolic reprogramming that supported the TLR-induced gene program. NDPK-D knockout mice were protected from LPS-induced shock, consistent with decreased ROS production and attenuated glycolytic commitment during priming. Our findings suggest that, in response to microbial challenge, NDPK-D-dependent TRAF6 mitochondrial recruitment triggers an energetic fitness checkpoint required to engage and maintain the transcriptional program necessary for inflammasome activation.

DOI: https://doi.org/10.1126/scisignal.abe0387
Elife. 2021 Aug 03. pii: e59828. [Epub ahead of print]10

Instability in NAD+ metabolism leads to impaired cardiac mitochondrial function and communication.

Knut H Lauritzen, Maria Belland Olsen, Mohammed Shakil Ahmed, Kuan Yang, Johanne Egge Rinholm, Linda H Bergersen, Qin Ying Esbensen, Lars Jansen Sverkeli, Mathias Ziegler, Håvard Attramadal, Bente Halvorsen, Pål Aukrust, Arne Yndestad.

  Poly(ADP-ribose) polymerase (PARP) enzymes initiate (mt)DNA repair mechanisms and use nicotinamide adenine dinucleotide (NAD+) as energy source. Prolonged PARP activity can drain cellular NAD+ reserves, leading to de-regulation of important molecular processes. Here, we provide evidence of a pathophysiological mechanism that connects mtDNA damage to cardiac dysfunction via reduced NAD+ levels and loss of mitochondrial function and communication. Using a transgenic model, we demonstrate that high levels of mice cardiomyocyte mtDNA damage cause a reduction in NAD+ levels due to extreme DNA repair activity, causing impaired activation of NAD+-dependent SIRT3. In addition, we show that myocardial mtDNA damage in combination with high dosages of nicotinamideriboside (NR) causes an inhibition of sirtuin activity due to accumulation of nicotinamide (NAM), in addition to irregular cardiac mitochondrial morphology. Consequently, high doses of NR should be used with caution, especially when cardiomyopathic symptoms are caused by mitochondrial dysfunction and instability of mtDNA.

Keywords:  DNA repair; NAD+; SIRT3; biochemistry; cardiovascular disease; chemical biology; human; mitochondrial dna; mouse; nicotinamide riboside

DOI:  https://doi.org/10.7554/eLife.59828
Nat Cell Biol. 2021 Aug 02.

Mitochondrial UPR through generations.

Mooncheol Park, Meng C Wang.

DOI: https://doi.org/10.1038/s41556-021-00729-3
J Cell Mol Med. 2021 Aug 07.

The stressosome, a caspase-8-activating signalling complex assembled in response to cell stress in an ATG5-mediated manner.

Katarzyna Mnich, Izabela Koryga, Karolina Pakos-Zebrucka, Melissa Thomas, Susan E Logue, Leif A Eriksson, Adrienne M Gorman, Afshin Samali.

  Stress-induced apoptosis is mediated primarily through the intrinsic pathway that involves caspase-9. We previously reported that in caspase-9-deficient cells, a protein complex containing ATG5 and Fas-associated death domain (FADD) facilitated caspase-8 activation and cell death in response to endoplasmic reticulum (ER) stress. Here, we investigated whether this complex could be activated by other forms of cell stress. We show that diverse stress stimuli, including etoposide, brefeldin A and paclitaxel, as well as heat stress and gamma-irradiation, caused formation of a complex containing ATG5-ATG12, FADD and caspase-8 leading to activation of downstream caspases in caspase-9-deficient cells. We termed this complex the 'stressosome'. However, in these cells, only ER stress and heat shock led to stressosome-dependent cell death. Using in silico molecular modelling, we propose the structure of the stressosome complex, with FADD acting as an adaptor protein, interacting with pro-caspase-8 through their respective death effector domains (DEDs) and interacting with ATG5-ATG12 through its death domain (DD). This suggests that the complex could be regulated by cellular FADD-like interleukin-1β-converting enzyme-inhibitory protein (cFLIPL ), which was confirmed experimentally. This study provides strong evidence for an alternative mechanism of caspase-8 activation involving the stressosome complex.

Keywords:  apoptosis; autophagy; caspase; cell stress; integrated stress response

DOI:  https://doi.org/10.1111/jcmm.16840
Cell Death Discov. 2021 Aug 04. 7(1): 201

Minimal mitochondrial respiration is required to prevent cell death by inhibition of mTOR signaling in CoQ-deficient cells.

Ying Wang, Siegfried Hekimi.

Coenzyme Q (CoQ) is a lipid-like mobile electron transporter of the mitochondrial respiratory chain. Patients with partial loss-of-function mutations in the CoQ biosynthesis pathway suffer from partial primary CoQ deficiency (MIM 607426). This leads to mitochondrial dysfunction, which presents like mitochondrial disease syndrome (MDS). In addition, many other conditions, including MDS itself, lead to secondary CoQ deficiency. We sought to identify drugs that can alleviate the consequences of the mitochondrial dysfunction that is associated with CoQ deficiency. Loss of the CoQ-biosynthetic enzyme COQ7 prevents CoQ synthesis but leads to the accumulation of the biosynthetic intermediate demethoxyubiquinone (DMQ). Coq7-knockout mouse embryonic fibroblasts (MEFs) die when rapid ATP generation from glycolysis is prevented. We screened for drugs that could rescue cell death under these conditions. All compounds that were identified inhibit mTOR signaling. In the CoQ-deficient cells, the beneficial action mTOR inhibition appears to be mediated by inhibition of protein translation rather than by stimulation of autophagy. We further studied the Coq7-knockout cells to better determine under which conditions mTOR inhibition could be beneficial. We established that Coq7-knockout cells remain capable of a low level of mitochondrial respiration mediated by DMQ. To obtain more profound mitochondrial dysfunction, we created double-knockout mutant MEFs lacking both Coq7, as well as Pdss2, which is required for sidechain synthesis. These cells make neither CoQ nor DMQ, and their extremely small residual respiration depends on uptake of CoQ from the culture medium. Although these cells are healthy in the presence of sufficient glucose for glycolysis and do not require uridine or pyruvate supplementation, mTOR inhibitors were unable to prevent their death in the absence of sufficient glycolysis. We conclude that, for reasons that remain to be elucidated, the energy-sparing benefits of the inhibition of mTOR signaling require a minimally functional respiratory chain.

DOI: https://doi.org/10.1038/s41420-021-00591-0
Cell Rep. 2021 Aug 03. pii: S2211-1247(21)00905-0. [Epub ahead of print]36(5): 109478

BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance.

Xavier Renaudin, Miyoung Lee, Mona Shehata, Eva-Maria Surmann, Ashok R Venkitaraman.

  Oxidative stress is a ubiquitous cellular challenge implicated in aging, neurodegeneration, and cancer. By studying pathogenic mutations in the tumor suppressor BRCA2, we identify a general mechanism by which oxidative stress restricts mitochondrial (mt)DNA replication. BRCA2 inactivation induces R-loop accumulation in the mtDNA regulatory region and diminishes mtDNA replication initiation. In BRCA2-deficient cells, intracellular reactive oxygen species (ROS) are elevated, and ROS scavengers suppress the mtDNA defects. Conversely, wild-type cells exposed to oxidative stress by pharmacologic or genetic manipulation phenocopy these defects. Mechanistically, we find that 8-oxoguanine accumulation in mtDNA caused by oxidative stress suffices to impair recruitment of the mitochondrial enzyme RNaseH1 to sites of R-loop accrual, restricting mtDNA replication initiation. Thus, oxidative stress impairs RNaseH1 function to cripple mtDNA maintenance. Our findings highlight a molecular mechanism that links oxidative stress to mitochondrial dysfunction and is elicited by the inactivation of genes implicated in neurodegeneration and cancer.

Keywords:  BRCA2; PRPF8; R-loops; RNaseH1; SETX; cancer; mitochondrial DNA replication; neurodegeneration; oxidative stress

DOI:  https://doi.org/10.1016/j.celrep.2021.109478
Brief Bioinform. 2021 Jul 30. pii: bbab288. [Epub ahead of print]

iDeepSubMito: identification of protein submitochondrial localization with deep learning.

Zilong Hou, Yuning Yang, Hui Li, Ka-Chun Wong, Xiangtao Li.

  Mitochondria are membrane-bound organelles containing over 1000 different proteins involved in mitochondrial function, gene expression and metabolic processes. Accurate localization of those proteins in the mitochondrial compartments is critical to their operation. A few computational methods have been developed for predicting submitochondrial localization from the protein sequences. Unfortunately, most of these computational methods focus on employing biological features or evolutionary information to extract sequence features, which greatly limits the performance of subsequent identification. Moreover, the efficiency of most computational models is still under explored, especially the deep learning feature, which is promising but requires improvement. To address these limitations, we propose a novel computational method called iDeepSubMito to predict the location of mitochondrial proteins to the submitochondrial compartments. First, we adopted a coding scheme using the ProteinELMo to model the probability distribution over the protein sequences and then represent the protein sequences as continuous vectors. Then, we proposed and implemented convolutional neural network architecture based on the bidirectional LSTM with self-attention mechanism, to effectively explore the contextual information and protein sequence semantic features. To demonstrate the effectiveness of our proposed iDeepSubMito, we performed cross-validation on two datasets containing 424 proteins and 570 proteins respectively, and consisting of four different mitochondrial compartments (matrix, inner membrane, outer membrane and intermembrane regions). Experimental results revealed that our method outperformed other computational methods. In addition, we tested iDeepSubMito on the M187, M983 and MitoCarta3.0 to further verify the efficiency of our method. Finally, the motif analysis and the interpretability analysis were conducted to reveal novel insights into subcellular biological functions of mitochondrial proteins. iDeepSubMito source code is available on GitHub at https://github.com/houzl3416/iDeepSubMito.

Keywords:  deep learning; protein sequences; protein submitochondrial localization

DOI:  https://doi.org/10.1093/bib/bbab288
Cell Calcium. 2021 Jul 27. pii: S0143-4160(21)00105-6. [Epub ahead of print]98 102451

MICU1 opens the gates to cold-induced death.

Felicia Dietsche, Li Zhang, John W Elrod, Axel Methner.

Nakamura et al. recently discovered that the mitochondrial calcium uniporter gatekeeper, MICU1, is required for cold-induced ferroptotic cell death by modulating mitochondrial membrane potential. This function appears to be independent of its Ca2+-sensing ability. Here, we discuss their findings and suggest next steps to define MICU1's role in ferroptotic cell death.

DOI: https://doi.org/10.1016/j.ceca.2021.102451
Life (Basel). 2021 Jul 06. pii: 663. [Epub ahead of print]11(7):

Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence.

Alessandro Formaggioni, Andrea Luchetti, Federico Plazzi.

  Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be "small", yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.

Keywords:  Eukaryota; compositional bias; mitochondrial genome; mtDNA architecture; mtDNA expansion; mtDNA structure; nucleotide composition; strand asymmetry

DOI:  https://doi.org/10.3390/life11070663
Cell Rep. 2021 Aug 03. pii: S2211-1247(21)00915-3. [Epub ahead of print]36(5): 109488

Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissue.

Althea N Waldhart, Brejnev Muhire, Ben Johnson, Dean Pettinga, Zachary B Madaj, Emily Wolfrum, Holly Dykstra, Vanessa Wegert, J Andrew Pospisilik, Xianlin Han, Ning Wu.

  Hyperglycemia affects over 400 million individuals worldwide. The detrimental health effects are well studied at the tissue level, but the in vivo effects at the organelle level are poorly understood. To establish such an in vivo model, we used mice lacking TXNIP, a negative regulator of glucose uptake. Examining mitochondrial function in brown adipose tissue, we find that TXNIP KO mice have a lower content of polyunsaturated fatty acids (PUFAs) in their membrane lipids, which affects mitochondrial integrity and electron transport chain efficiency and ultimately results in lower mitochondrial heat output. This phenotype can be rescued by a ketogenic diet, confirming the usefulness of this model and highlighting one facet of early cellular damage caused by excess glucose influx.

Keywords:  BAT; PUFA; TXNIP; cold stress; glucose; ketogenic diet; lipid; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2021.109488
Mitochondrion. 2021 Jul 30. pii: S1567-7249(21)00101-X. [Epub ahead of print]

The Roles of Assembly Factors in Mammalian Mitoribosome Biogenesis.

Taru Hilander, Christopher B Jackson, Marius Robciuc, Tanzeela Bashir, Hongxia Zhao.

  As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.

Keywords:  mitochondrial translation; mitoribosome assembly factors; mitoribosome biogenesis

DOI:  https://doi.org/10.1016/j.mito.2021.07.008