bims-minimp 2021-10-31 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2021–10–31
33 papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain.
Cytoplasmic DNA: sources, sensing, and role in aging and disease.
A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance.
DNA Damage-Induced Inflammatory Microenvironment and Adult Stem Cell Response.
Mitoepigenetics: An intriguing regulatory layer in aging and metabolic-related diseases.
Interaction between NS1 and Cellular MAVS Contributes to NS1 Mitochondria Targeting.
The many roles mitochondria play in mammalian aging.
Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3.
SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
High confidence ATFS-1 target genes for quantifying activation of the mitochondrial unfolded protein response.
Prolonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and subsequent mitochondrial accumulation in human fibroblasts.
Mitophagy antagonism by ZIKV reveals Ajuba as a regulator of PINK1 signaling, PKR-dependent inflammation, and viral invasion of tissues.
A subpopulation of arenavirus nucleoprotein localizes to mitochondria.
Multiple variants of the human presequence translocase motor subunit Magmas govern the mitochondrial import.
Mitochondrial metabolism coordinates stage-specific repair processes in macrophages during wound healing.
Mitochondria dynamics in the aged mice eye and the role in the RPE phagocytosis.
Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels.
Mitochondrial Carrier Homolog 2 Functionally Co-operates With BH3 Interacting-Domain Death Agonist in Promoting Ca2+-Induced Neuronal Injury.
Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2.
Active mitochondrial respiration in cancer: a target for the drug.
Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures.
Glycogen metabolism links glucose homeostasis to thermogenesis in adipocytes.
A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling.
The crosstalk between viral RNA- and DNA-sensing mechanisms.
Cnm1: A bridge between mitochondria and nuclear ER.
Impact of intracellular innate immune receptors on immunometabolism.
Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice.
UMP-CMP kinase 2 gene expression in macrophages is dependent on the IRF3-IFNAR signaling axis.
The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag.
Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.
Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX.
Analysis of senescence-responsive stress fiber proteome reveals reorganization of stress fibers mediated by elongation factor eEF2 in HFF-1 cells.
Red blood cells join the ranks as immune sentinels.

Dev Cell. 2021 Oct 22. pii: S1534-5807(21)00809-1. [Epub ahead of print]

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain.

Shefali Krishna, Rafael Arrojo E Drigo, Juliana S Capitanio, Ranjan Ramachandra, Mark Ellisman, Martin W Hetzer.

  In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.

Keywords:  age mosaicism; aging; electron transport chain; heterogeneity; long-lived proteins; mitochondria; muscle; neurons; protein homeostasis; supercomplexes

DOI:  https://doi.org/10.1016/j.devcel.2021.10.008
Cell. 2021 Oct 28. pii: S0092-8674(21)01117-X. [Epub ahead of print]184(22): 5506-5526

Cytoplasmic DNA: sources, sensing, and role in aging and disease.

Karl N Miller, Stella G Victorelli, Hanna Salmonowicz, Nirmalya Dasgupta, Tianhui Liu, João F Passos, Peter D Adams.

  Endogenous cytoplasmic DNA (cytoDNA) species are emerging as key mediators of inflammation in diverse physiological and pathological contexts. Although the role of endogenous cytoDNA in innate immune activation is well established, the cytoDNA species themselves are often poorly characterized and difficult to distinguish, and their mechanisms of formation, scope of function and contribution to disease are incompletely understood. Here, we summarize current knowledge in this rapidly progressing field with emphases on similarities and differences between distinct cytoDNAs, their underlying molecular mechanisms of formation and function, interactions between cytoDNA pathways, and therapeutic opportunities in the treatment of age-associated diseases.

Keywords:  aging; cancer; cytoplasmic DNA; cytoplasmic chromatin fragment; micronucleus; mitochondrial DNA; retrotransposon; senescence

DOI:  https://doi.org/10.1016/j.cell.2021.09.034
Microbiologyopen. 2021 Oct;10(5): e1238

A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance.

Antonina Shvetsova, Ali J Masud, Laura Schneider, Ulrich Bergmann, Geoffray Monteuuis, Ilkka J Miinalainen, J Kalervo Hiltunen, Alexander J Kastaniotis.

  Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence similarities that would allow inferring its functional role are not available. In this work, we describe synthetic petite mutants of GEM1 and UGO1 that depend on the presence of OM45 for respiratory growth, as well as the identification of several multicopy suppressors of the synthetic petite phenotypes. In the analysis of our mutants, we demonstrate that Om45p and Gem1p have a collaborative role in the maintenance of mitochondrial morphology, cristae structure, and mitochondrial DNA maintenance. A group of multicopy suppressors rescuing the synthetic lethal phenotypes of the mutants on non-fermentable carbon sources additionally supports this result. Our results imply that the synthetic petite phenotypes we observed are due to the disturbance of the inner mitochondrial membrane and point to this mitochondrial sub-compartment as the main target of action of Om45p, Ugo1p, and the yeast Miro GTPase Gem1p.

Keywords:   GEM1 ; OM45 ; UGO1 ; Miro GTPase; cristae organization; mitochondria; mtDNA inheritance; outer and inner mitochondrial membranes

DOI:  https://doi.org/10.1002/mbo3.1238
Front Cell Dev Biol. 2021 ;9 729136

DNA Damage-Induced Inflammatory Microenvironment and Adult Stem Cell Response.

Davide Cinat, Robert P Coppes, Lara Barazzuol.

  Adult stem cells ensure tissue homeostasis and regeneration after injury. Due to their longevity and functional requirements, throughout their life stem cells are subject to a significant amount of DNA damage. Genotoxic stress has recently been shown to trigger a cascade of cell- and non-cell autonomous inflammatory signaling pathways, leading to the release of pro-inflammatory factors and an increase in the amount of infiltrating immune cells. In this review, we discuss recent evidence of how DNA damage by affecting the microenvironment of stem cells present in adult tissues and neoplasms can affect their maintenance and long-term function. We first focus on the importance of self-DNA sensing in immunity activation, inflammation and secretion of pro-inflammatory factors mediated by activation of the cGAS-STING pathway, the ZBP1 pathogen sensor, the AIM2 and NLRP3 inflammasomes. Alongside cytosolic DNA, the emerging roles of cytosolic double-stranded RNA and mitochondrial DNA are discussed. The DNA damage response can also initiate mechanisms to limit division of damaged stem/progenitor cells by inducing a permanent state of cell cycle arrest, known as senescence. Persistent DNA damage triggers senescent cells to secrete senescence-associated secretory phenotype (SASP) factors, which can act as strong immune modulators. Altogether these DNA damage-mediated immunomodulatory responses have been shown to affect the homeostasis of tissue-specific stem cells leading to degenerative conditions. Conversely, the release of specific cytokines can also positively impact tissue-specific stem cell plasticity and regeneration in addition to enhancing the activity of cancer stem cells thereby driving tumor progression. Further mechanistic understanding of the DNA damage-induced immunomodulatory response on the stem cell microenvironment might shed light on age-related diseases and cancer, and potentially inform novel treatment strategies.

Keywords:  DNA damage; cancer; immune response; inflammation; microenvironment; stem cells

DOI:  https://doi.org/10.3389/fcell.2021.729136
Free Radic Biol Med. 2021 Oct 26. pii: S0891-5849(21)00781-4. [Epub ahead of print]

Mitoepigenetics: An intriguing regulatory layer in aging and metabolic-related diseases.

Ke Cao, Zhihui Feng, Feng Gao, Weijin Zang, Jiankang Liu.

  As a key organelle in eukaryotic cells, mitochondria play a central role in maintaining normal cellular functions. Mitochondrial dysfunction is reported to be closely related with aging and various diseases. Epigenetic modifications in nuclear genome provide a substantial layer for the modulation of nuclear-encoded gene expression. However, whether mitochondria could also be subjected to such similar epigenetic alterations and the involved mechanisms remain largely obscure and controversial. Recently, accumulating evidence has suggested that mitochondrial epigenetics, also known as mitoepigenetics may serve as an intriguing regulatory layer in mitochondrial DNA (mtDNA)-encoded gene expression. Given the potential regulatory role of mitoepigenetics, mitochondrial dysfunction derived from mitoepigenetics-induced abnormal gene expression could also be closely associated with aging and disease development. In this review, we summarized the recent advances in mitoepigenetics, with a special focus on mtDNA methylation in aging and metabolic-related diseases as well as the new methods and technologies for the study of mitoepigenetics. Uncovering the regulatory role of mitoepigenetics will help to understand the underlying mechanisms of mitochondrial dysfunction and provide novel strategies for delaying aging and preventing metabolic-related diseases.

Keywords:  Mitochondrial DNA (mtDNA) methylation; Mitochondrial epigenetics (mitoepigenetics); Mitochondrial non-coding RNAs (ncRNAs); Post-translational modifications (PTMs); mtDNA-associated proteins

DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.10.031
Viruses. 2021 Sep 23. pii: 1909. [Epub ahead of print]13(10):

Interaction between NS1 and Cellular MAVS Contributes to NS1 Mitochondria Targeting.

Yeu-Yang Tseng, Chih-Ying Kuan, Masaki Mibayashi, Chi-Jene Chen, Peter Palese, Randy A Albrecht, Wei-Li Hsu.

  Influenza A virus nonstructural protein 1 (NS1) plays an important role in evading host innate immunity. NS1 inhibits interferon (IFN) responses via multiple mechanisms, including sequestering dsRNA and suppressing retinoic acid-inducible gene I (RIG-I) signaling by interacting with RIG-I and tripartite motif-containing protein 25 (TRIM25). In the current study, we demonstrated the mitochondrial localization of NS1 at the early stage of influenza virus infection. Since NS1 does not contain mitochondria-targeting signals, we suspected that there is an association between the NS1 and mitochondrial proteins. This hypothesis was tested by demonstrating the interaction of NS1 with mitochondrial antiviral-signaling protein (MAVS) in a RIG-I-independent manner. Importantly, the association with MAVS facilitated the mitochondrial localization of NS1 and thereby significantly impeded MAVS-mediated Type I IFN production.

Keywords:  MAVS; NS1; influenza A virus; mitochondria

DOI:  https://doi.org/10.3390/v13101909
Antioxid Redox Signal. 2021 Oct 29.

The many roles mitochondria play in mammalian aging.

Caio M P F Batalha, Anibal Eugênio Vercesi, Nadja C Souza-Pinto.

SIGNIFICANCE: Aging is a natural process that affects most living organisms, resulting in increased mortality. As the world population ages, the prevalence of age-associated diseases, and their associated healthcare costs, has increased sharply. A better understanding of the molecular mechanisms that lead to cellular dysfunction may provide important targets for interventions to prevent or treat these diseases. Recent Advances: Although the mitochondrial theory of aging has been proposed over 40 years ago, recent new data has given stronger support for a central role for mitochondrial dysfunction in several pathways that are deregulated during normal aging and age-associated disease.
CRITICAL ISSUES: Several of the experimental evidence linking mitochondrial alterations to age-associated loss of function are correlative and mechanistic insight are still elusive. Here, we review how mitochondrial dysfunction may be involved in many of the known hallmarks of aging, and how these pathways interact in an intricate net of molecular relationships.
FUTURE DIRECTIONS: As it has become clear that mitochondrial dysfunction plays causative roles in normal aging and age-associated diseases, it is necessary to better define the molecular interactions and the temporal and causal relations between these changes and the relevant phenotypes seen during the aging process.

DOI: https://doi.org/10.1089/ars.2021.0074
Front Cell Dev Biol. 2021 ;9 710247

Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3.

Matthew J Jennings, Denisa Hathazi, Chi D L Nguyen, Benjamin Munro, Ute Münchberg, Robert Ahrends, Annette Schenck, Ilse Eidhof, Erik Freier, Matthis Synofzik, Rita Horvath, Andreas Roos.

  Recessive mutations in DNAJC3, an endoplasmic reticulum (ER)-resident BiP co-chaperone, have been identified in patients with multisystemic neurodegeneration and diabetes mellitus. To further unravel these pathomechanisms, we employed a non-biased proteomic approach and identified dysregulation of several key cellular pathways, suggesting a pathophysiological interplay of perturbed lipid metabolism, mitochondrial bioenergetics, ER-Golgi function, and amyloid-beta processing. Further functional investigations in fibroblasts of patients with DNAJC3 mutations detected cellular accumulation of lipids and an increased sensitivity to cholesterol stress, which led to activation of the unfolded protein response (UPR), alterations of the ER-Golgi machinery, and a defect of amyloid precursor protein. In line with the results of previous studies, we describe here alterations in mitochondrial morphology and function, as a major contributor to the DNAJC3 pathophysiology. Hence, we propose that the loss of DNAJC3 affects lipid/cholesterol homeostasis, leading to UPR activation, β-amyloid accumulation, and impairment of mitochondrial oxidative phosphorylation.

Keywords:  DNAJC3; cholesterol-stress; mitochondria; proteomics; unfolded protein response (UPR)

DOI:  https://doi.org/10.3389/fcell.2021.710247
Nature. 2021 Oct 27.

SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.

Ying Wang, Frederick S Yen, Xiphias Ge Zhu, Rebecca C Timson, Ross Weber, Changrui Xing, Yuyang Liu, Benjamin Allwein, Hanzhi Luo, Hsi-Wen Yeh, Søren Heissel, Gokhan Unlu, Eric R Gamazon, Michael G Kharas, Richard Hite, Kıvanç Birsoy.

Glutathione (GSH) is a small-molecule thiol that is abundant in all eukaryotes and has key roles in oxidative metabolism1. Mitochondria, as the major site of oxidative reactions, must maintain sufficient levels of GSH to perform protective and biosynthetic functions2. GSH is synthesized exclusively in the cytosol, yet the molecular machinery involved in mitochondrial GSH import remains unknown. Here, using organellar proteomics and metabolomics approaches, we identify SLC25A39, a mitochondrial membrane carrier of unknown function, as a regulator of GSH transport into mitochondria. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of proteins containing iron-sulfur clusters. We find that mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. Heterologous expression of an engineered bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria enables mitochondrial GSH production and ameliorates the metabolic and proliferative defects caused by its depletion. Finally, GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import in mammalian cells. Our work identifies SLC25A39 as an essential and regulated component of the mitochondrial GSH-import machinery.

DOI: https://doi.org/10.1038/s41586-021-04025-w
MicroPubl Biol. 2021 ;2021

High confidence ATFS-1 target genes for quantifying activation of the mitochondrial unfolded protein response.

Sonja K Soo, Jeremy M Van Raamsdonk.

The mitochondrial unfolded protein response (mitoUPR) is an evolutionarily conserved pathway that restores homeostasis to the mitochondria after various disturbances. This pathway has roles in both resistance to exogenous stressors and longevity. The mitoUPR is mediated by the transcription factor ATFS-1/ATF-5, which modulates the expression of genes involved in protein folding, metabolism and stress resistance. MitoUPR activation in C. elegans is most commonly evaluated through transcriptional reporter strains for the mitochondrial chaperones HSP-6 and HSP-60. In order to obtain a more comprehensive view of transcriptional changes resulting from activation of the mitoUPR, we compared gene expression changes from three different mitoUPR-activating interventions: mutation of nuo-6, RNA interference (RNAi) knockdown of spg-7,and constitutive activation of ATFS-1. We specifically focused on gene expression changes that are dependent on ATFS-1. From this comparison, we identified 61 high confidence target genes that can be used to monitor mitoUPR activation. Notably, neither hsp-6 nor hsp-60 were significantly upregulated under all three mitoUPR activating conditions. We ranked the 61 genes according to the magnitude of upregulation and identify multiple genes that may serve as robust readouts of mitoUPR activation.

DOI: https://doi.org/10.17912/micropub.biology.000484
FEBS J. 2021 Oct 24.

Prolonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and subsequent mitochondrial accumulation in human fibroblasts.

Yasuhiro Takenaka, Ikuo Inoue, Takanari Nakano, Masaaki Ikeda, Yoshihiko Kakinuma.

  Proteolytic activity declines with age, resulting in the accumulation of aggregated proteins in aged organisms. To investigate how disturbance in proteostasis causes cellular senescence, we developed a stress-induced premature senescence (SIPS) model, in which normal human fibroblast MRC-5 cells were treated with the proteasome inhibitor MG132 or the V-ATPase inhibitor bafilomycin A1 (BAFA1) for 5 days. Time-course studies revealed a significant increase in intracellular reactive oxygen species (ROS) and mitochondrial superoxide during and after drug treatment. Mitochondrial membrane potential initially decreased, suggesting temporal mitochondrial dysfunction during drug treatment, but was restored along with mitochondrial accumulation after drug treatment. AMP-activated protein kinase alpha (AMPKα) was notably activated during treatment; thereafter, intracellular ATP levels significantly increased. SIPS induction by MG132 or BAFA1 was partially attenuated by co-treatment with vitamin E or rapamycin, in which the levels of ROS, mitochondrial accumulation, and protein aggregates were suppressed, implying the critical involvement of oxidative stress and mitochondrial function in SIPS progression. Rapamycin co-treatment also augmented the expression of HSP70 and activation of AKT, which could recover proteostasis and promote cell survival, respectively. Our study proposes a possible pathway from the disturbed proteostasis to cellular senescence via excess ROS production as well as functional and quantitative changes in mitochondria.

Keywords:  DNA damage response; aggregate; lysosome; oxidative stress; proteasome

DOI:  https://doi.org/10.1111/febs.16249
Cell Rep. 2021 Oct 26. pii: S2211-1247(21)01358-9. [Epub ahead of print]37(4): 109888

Mitophagy antagonism by ZIKV reveals Ajuba as a regulator of PINK1 signaling, PKR-dependent inflammation, and viral invasion of tissues.

Sanket S Ponia, Shelly J Robertson, Kristin L McNally, Gayatri Subramanian, Gail L Sturdevant, Matthew Lewis, Forrest Jessop, Catherine Kendall, Dylan Gallegos, Arielle Hay, Cindi Schwartz, Rebecca Rosenke, Greg Saturday, Catherine M Bosio, Craig Martens, Sonja M Best.

  Dysregulated inflammation dominated by chemokine expression is a key feature of disease following infection with the globally important human pathogens Zika virus (ZIKV) and dengue virus, but a mechanistic understanding of how pro-inflammatory responses are initiated is lacking. Mitophagy is a quality-control mechanism that regulates innate immune signaling and cytokine production through selective degradation of damaged mitochondria. Here, we demonstrate that ZIKV nonstructural protein 5 (NS5) antagonizes mitophagy by binding to the host protein Ajuba and preventing its translocation to depolarized mitochondria where it is required for PINK1 activation and downstream signaling. Consequent mitophagy suppression amplifies the production of pro-inflammatory chemokines through protein kinase R (PKR) sensing of mitochondrial RNA. In Ajuba-/- mice, ZIKV induces early expression of pro-inflammatory chemokines associated with significantly enhanced dissemination to tissues. This work identifies Ajuba as a critical regulator of mitophagy and demonstrates a role for mitophagy in limiting systemic inflammation following infection by globally important human viruses.

Keywords:  PINK1; PKR; Parkin; Zika virus; chemokines; flavivirus; mitochondria; mitophagy; mtRNA; pathogenesis

DOI:  https://doi.org/10.1016/j.celrep.2021.109888
Sci Rep. 2021 Oct 26. 11(1): 21048

A subpopulation of arenavirus nucleoprotein localizes to mitochondria.

Francesca Baggio, Udo Hetzel, Lisbeth Nufer, Anja Kipar, Jussi Hepojoki.

Viruses need cells for their replication and, therefore, ways to hijack cellular functions. Mitochondria play fundamental roles within the cell in metabolism, immunity and regulation of homeostasis due to which some viruses aim to alter mitochondrial functions. Herein we show that the nucleoprotein (NP) of arenaviruses enters the mitochondria of infected cells, affecting the mitochondrial morphology. Reptarenaviruses cause boid inclusion body disease (BIBD) that is characterized, especially in boas, by the formation of cytoplasmic inclusion bodies (IBs) comprising reptarenavirus NP within the infected cells. We initiated this study after observing electron-dense material reminiscent of IBs within the mitochondria of reptarenavirus infected boid cell cultures in an ultrastructural study. We employed immuno-electron microscopy to confirm that the mitochondrial inclusions indeed contain reptarenavirus NP. Mutations to a putative N-terminal mitochondrial targeting signal (MTS), identified via software predictions in both mamm- and reptarenavirus NPs, did not affect the mitochondrial localization of NP, suggesting that it occurs independently of MTS. In support of MTS-independent translocation, we did not detect cleavage of the putative MTSs of arenavirus NPs in reptilian or mammalian cells. Furthermore, in vitro translated NPs could not enter isolated mitochondria, suggesting that the translocation requires cellular factors or conditions. Our findings suggest that MTS-independent mitochondrial translocation of NP is a shared feature among arenaviruses. We speculate that by targeting the mitochondria arenaviruses aim to alter mitochondrial metabolism and homeostasis or affect the cellular defense.

DOI: https://doi.org/10.1038/s41598-021-99887-5
J Biol Chem. 2021 Oct 26. pii: S0021-9258(21)01155-8. [Epub ahead of print] 101349

Multiple variants of the human presequence translocase motor subunit Magmas govern the mitochondrial import.

Tejashree Pradip Waingankar, Patrick D'Silva.

  Mitochondrial protein translocation is an intricately regulated process that requires dedicated translocases at the outer and inner membranes. The presequence translocase complex, TIM23, facilitates most of the import of preproteins containing presequences into the mitochondria, and its primary structural organization is highly conserved. As part of the translocase motor, two J-proteins DnaJC15 and DnaJC19, are recruited to form two independent translocation machineries (Translocase A and Translocase B, respectively). On the other hand, the J-like protein subunit of TIM23, Magmas (orthologous to the yeast subunit Pam16), can regulate human import motor activity by forming a heterodimer with DnaJC19 and DnaJC15. However, the precise coordinated regulation of two human import motors by a single Magmas protein is poorly understood. Here we report two additional Magmas variants (Magmas-1 and Magmas-2) constitutively expressed in the mammalian system. Both Magmas variants are functional orthologs of Pam16 with an evolutionarily conserved J-like domain critical for cell survival. Moreover, Magmas variants are peripherally associated with the inner membrane as part of the human import motor for translocation. Our results demonstrate that Magmas-1 is predominantly recruited to translocase B, while Magmas-2 is majorly associated with translocase A. Strikingly, both variants exhibit differential J-protein inhibitory activity in modulating import motor, thereby regulating overall translocase function. Based on our findings, we hypothesize that additional Magmas variants are of evolutionary significance in humans to maximize protein import in familial-linked pathological conditions.

Keywords:  Magmas; Mitochondria; Mitochondrial translocase of inner membrane; Protein import; Protein translocation

DOI:  https://doi.org/10.1016/j.jbc.2021.101349
Cell Metab. 2021 Oct 25. pii: S1550-4131(21)00482-4. [Epub ahead of print]

Mitochondrial metabolism coordinates stage-specific repair processes in macrophages during wound healing.

Sebastian Willenborg, David E Sanin, Alexander Jais, Xiaolei Ding, Thomas Ulas, Julian Nüchel, Milica Popović, Thomas MacVicar, Thomas Langer, Joachim L Schultze, Alexander Gerbaulet, Axel Roers, Edward J Pearce, Jens C Brüning, Aleksandra Trifunovic, Sabine A Eming.

  Wound healing is a coordinated process that initially relies on pro-inflammatory macrophages, followed by a pro-resolution function of these cells. Changes in cellular metabolism likely dictate these distinct activities, but the nature of these changes has been unclear. Here, we profiled early- versus late-stage skin wound macrophages in mice at both the transcriptional and functional levels. We found that glycolytic metabolism in the early phase is not sufficient to ensure productive repair. Instead, by combining conditional disruption of the electron transport chain with deletion of tgcqmitochondrial aspartyl-tRNA synthetase, followed by single-cell sequencing analysis, we found that a subpopulation of early-stage wound macrophages are marked by mitochondrial ROS (mtROS) production and HIF1α stabilization, which ultimately drives a pro-angiogenic program essential for timely healing. In contrast, late-phase, pro-resolving wound macrophages are marked by IL-4Rα-mediated mitochondrial respiration and mitohormesis. Collectively, we identify changes in mitochondrial metabolism as a critical control mechanism for macrophage effector functions during wound healing.

Keywords:  metabolism; mitochondria; mitochondrial repurposing; mitohormesis; monocyte/macrophage; tissue repair; type 2 immunity; wound healing

DOI:  https://doi.org/10.1016/j.cmet.2021.10.004
Exp Eye Res. 2021 Oct 21. pii: S0014-4835(21)00366-3. [Epub ahead of print] 108800

Mitochondria dynamics in the aged mice eye and the role in the RPE phagocytosis.

Tomohiro Yako, Maho Nakamura, Wataru Otsu, Shinsuke Nakamura, Masamitsu Shimazawa, Hideaki Hara.

  Aging is a predominant risk factor for various eye diseases. Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, and its etiology remains unclear. Fragmented and dysfunctional mitochondria are associated with age-related diseases. The retinal pigment epithelium (RPE), a polarized cell layer that functions in visual pigment recycling and degeneration, is suspected as the primary region site of AMD. In the present study, we investigated the relationship between mitochondrial dysfunction and RPE aging. Compared to young mice, aged pigmented mice (C57BL/6J, 12-month-old) exhibit decreased visual function without retinal thinning. Consistently, the rhodopsin expression level decreased in the outer segment of aged mice. Moreover, the cell volume of the RPE increased in aged animals. Interestingly, the expression of mitochondria dynamics-related proteins, including Drp1, was altered in the RPE-choroid complex but not in the neural retina after aging. Electron microscopy revealed that mitochondrial size decreased and cristae width increased in aged RPE. The photoreceptor outer segment (POS) treatment of ARPE-19 cells causes Drp1 activation. Furthermore, pharmacological suppression of mitochondrial fission improved the phagocytosis of the POS. These findings indicate that mitochondrial dysfunction and fission in RPE impede phagocytosis and cause retardation of the visual cycle, which can be one of the age-related defects in the retina that may contribute to the onset of AMD.

Keywords:  Aging; Dynamin related protein 1; Mitochondria; Phagocytosis; Retinal pigment epithelium

DOI:  https://doi.org/10.1016/j.exer.2021.108800
J Cell Biol. 2021 Nov 01. pii: e202104100. [Epub ahead of print]220(11):

Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels.

Michal Eisenberg-Bord, Naama Zung, Javier Collado, Layla Drwesh, Emma J Fenech, Amir Fadel, Nili Dezorella, Yury S Bykov, Doron Rapaport, Ruben Fernandez-Busnadiego, Maya Schuldiner.

Mitochondrial functions are tightly regulated by nuclear activity, requiring extensive communication between these organelles. One way by which organelles can communicate is through contact sites, areas of close apposition held together by tethering molecules. While many contacts have been characterized in yeast, the contact between the nucleus and mitochondria was not previously identified. Using fluorescence and electron microscopy in S. cerevisiae, we demonstrate specific areas of contact between the two organelles. Using a high-throughput screen, we uncover a role for the uncharacterized protein Ybr063c, which we have named Cnm1 (contact nucleus mitochondria 1), as a molecular tether on the nuclear membrane. We show that Cnm1 mediates contact by interacting with Tom70 on mitochondria. Moreover, Cnm1 abundance is regulated by phosphatidylcholine, enabling the coupling of phospholipid homeostasis with contact extent. The discovery of a molecular mechanism that allows mitochondrial crosstalk with the nucleus sets the ground for better understanding of mitochondrial functions in health and disease.

DOI: https://doi.org/10.1083/jcb.202104100
Front Cell Dev Biol. 2021 ;9 750100

Mitochondrial Carrier Homolog 2 Functionally Co-operates With BH3 Interacting-Domain Death Agonist in Promoting Ca2+-Induced Neuronal Injury.

Beatrice D'Orsi, Natalia Niewidok, Heiko Düssmann, Jochen H M Prehn.

  The BH3 interacting-domain death agonist (BID) is a pro-apoptotic member of the Bcl-2 protein family. While proteolytic processing of BID links death receptor-induced apoptosis to the mitochondrial apoptosis pathway, we previously showed that full length BID also translocates to mitochondria during Ca2+-induced neuronal cell death. Moreover, mitochondrial carrier homolog 2 (MTCH2) was identified as a mitochondrial protein that interacts with BID during cell death. We started our studies by investigating the effect of Mtch2 silencing in a well-established model of Ca2+-induced mitochondrial permeability transition pore opening in non-neuronal HCT116 cells. We found that silencing of Mtch2 inhibited mitochondrial swelling and the associated decrease in mitochondrial energetics, suggesting a pro-death function for MTCH2 during Ca2+-induced injury. Next, we explored the role of BID and MTCH2 in mediating Ca2+-induced injury in primary cortical neurons triggered by prolonged activation of NMDA glutamate receptors. Analysis of intracellular Ca2+ transients, using time-lapse confocal microscopy, revealed that neurons lacking Bid showed markedly reduced Ca2+ levels during the NMDA excitation period. These Ca2+ transients were further decreased when Mtch2 was also silenced. Collectively, our data suggest that BID and MTCH2 functionally interact to promote Ca2+-induced neuronal injury.

Keywords:  Bcl-2 family; calcium; cortical neurons; excitotoxicity; necrosis; permeability transition pore (mPTP)

DOI:  https://doi.org/10.3389/fcell.2021.750100
Nat Metab. 2021 Oct 25.

Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2.

Karthickeyan Chella Krishnan, Laurent Vergnes, Rebeca Acín-Pérez, Linsey Stiles, Michael Shum, Lijiang Ma, Etienne Mouisel, Calvin Pan, Timothy M Moore, Miklós Péterfy, Casey E Romanoski, Karen Reue, Johan L M Björkegren, Markku Laakso, Marc Liesa, Aldons J Lusis.

We have previously suggested a central role for mitochondria in the observed sex differences in metabolic traits. However, the mechanisms by which sex differences affect adipose mitochondrial function and metabolic syndrome are unclear. Here we show that in both mice and humans, adipose mitochondrial functions are elevated in females and are strongly associated with adiposity, insulin resistance and plasma lipids. Using a panel of diverse inbred strains of mice, we identify a genetic locus on mouse chromosome 17 that controls mitochondrial mass and function in adipose tissue in a sex- and tissue-specific manner. This locus contains Ndufv2 and regulates the expression of at least 89 mitochondrial genes in females, including oxidative phosphorylation genes and those related to mitochondrial DNA content. Overexpression studies indicate that Ndufv2 mediates these effects by regulating supercomplex assembly and elevating mitochondrial reactive oxygen species production, which generates a signal that increases mitochondrial biogenesis.

DOI: https://doi.org/10.1038/s42255-021-00481-w
Mol Cell Biochem. 2021 Oct 30.

Active mitochondrial respiration in cancer: a target for the drug.

Minakshi Bedi, Manju Ray, Alok Ghosh.

  The relative contribution of mitochondrial respiration and subsequent energy production in malignant cells has remained controversial to date. Enhanced aerobic glycolysis and impaired mitochondrial respiration have gained more attention in the metabolic study of cancer. In contrast to the popular concept, mitochondria of cancer cells oxidize a diverse array of metabolic fuels to generate a majority of the cellular energy by respiration. Several mitochondrial respiratory chain (MRC) subunits' expressions are critical for the growth, metastasis, and cancer cell invasion. Also, the assembly factors, which regulate the integration of individual MRC complexes into native super-complexes, are upregulated in cancer. Moreover, a series of anti-cancer drugs function by inhibiting respiration and ATP production. In this review, we have specified the roles of mitochondrial fuels, MRC subunits, and super-complex assembly factors that promote active respiration across different cancer types and discussed the potential roles of MRC inhibitor drugs in controlling cancer.

Keywords:  Cancer; Drugs; Metabolic fuels; Mitochondria; Respiratory chain subunits; Super-complex

DOI:  https://doi.org/10.1007/s11010-021-04281-4
Elife. 2021 Oct 26. pii: e70899. [Epub ahead of print]10

Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures.

Shannon Rausser, Caroline Trumpff, Marlon A McGill, Alex Junker, Wei Wang, Siu-Hong Ho, Anika Mitchell, Kalpita R Karan, Catherine E Monk, Suzanne C Segerstrom, Rebecca G Reed, Martin Picard.

  Using a high-throughput mitochondrial phenotyping platform to quantify multiple mitochondrial features among molecularly-defined immune cell subtypes, we quantify the natural variation in citrate synthase, mitochondrial DNA copy number (mtDNAcn), and respiratory chain enzymatic activities in human neutrophils, monocytes, B cells, and naïve and memory T lymphocyte subtypes. In mixed peripheral blood mononuclear cells (PBMCs) from the same individuals, we show to what extent mitochondrial measures are confounded by both cell type distributions and contaminating platelets. Cell subtype-specific measures among women and men spanning 4 decades of life indicate potential age- and sex-related differences, including an age-related elevation in mtDNAcn, which are masked or blunted in mixed PBMCs. Finally, a proof-of-concept, repeated-measures study in a single individual validates cell type differences and also reveals week-to-week changes in mitochondrial activities. Larger studies are required to validate and mechanistically extend these findings. These mitochondrial phenotyping data build upon established immunometabolic differences among leukocyte sub-populations, and provide foundational quantitative knowledge to develop interpretable blood-based assays of mitochondrial health.

Keywords:  cell biology; human; immunology; inflammation

DOI:  https://doi.org/10.7554/eLife.70899
Nature. 2021 Oct 27.

Glycogen metabolism links glucose homeostasis to thermogenesis in adipocytes.

Omer Keinan, Joseph M Valentine, Haopeng Xiao, Sushil K Mahata, Shannon M Reilly, Mohammad Abu-Odeh, Julia H Deluca, Benyamin Dadpey, Leslie Cho, Austin Pan, Ruth T Yu, Yang Dai, Christopher Liddle, Michael Downes, Ronald M Evans, Aldons J Lusis, Markku Laakso, Edward T Chouchani, Mikael Ryde'n, Alan R Saltiel.

Adipocytes increase energy expenditure in response to prolonged sympathetic activation via persistent expression of uncoupling protein 1 (UCP1)1,2. Here we report that the regulation of glycogen metabolism by catecholamines is critical for UCP1 expression. Chronic β-adrenergic activation leads to increased glycogen accumulation in adipocytes expressing UCP1. Adipocyte-specific deletion of a scaffolding protein, protein targeting to glycogen (PTG), reduces glycogen levels in beige adipocytes, attenuating UCP1 expression and responsiveness to cold or β-adrenergic receptor-stimulated weight loss in obese mice. Unexpectedly, we observed that glycogen synthesis and degradation are increased in response to catecholamines, and that glycogen turnover is required to produce reactive oxygen species leading to the activation of p38 MAPK, which drives UCP1 expression. Thus, glycogen has a key regulatory role in adipocytes, linking glucose metabolism to thermogenesis.

DOI: https://doi.org/10.1038/s41586-021-04019-8
Nat Commun. 2021 Oct 27. 12(1): 6207

A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling.

Daipayan Banerjee, Kurt Langberg, Salar Abbas, Eric Odermatt, Praveen Yerramothu, Martin Volaric, Matthew A Reidenbach, Kathy J Krentz, C Dustin Rubinstein, David L Brautigan, Tarek Abbas, Bradley D Gelfand, Jayakrishna Ambati, Nagaraj Kerur.

Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), produced by cyclic GMP-AMP synthase (cGAS), stimulates the production of type I interferons (IFN). Here we show that cGAMP activates DNA damage response (DDR) signaling independently of its canonical IFN pathways. Loss of cGAS dampens DDR signaling induced by genotoxic insults. Mechanistically, cGAS activates DDR in a STING-TBK1-dependent manner, wherein TBK1 stimulates the autophosphorylation of the DDR kinase ATM, with the consequent activation of the CHK2-p53-p21 signal transduction pathway and the induction of G1 cell cycle arrest. Despite its stimulatory activity on ATM, cGAMP suppresses homology-directed repair (HDR) through the inhibition of polyADP-ribosylation (PARylation), in which cGAMP reduces cellular levels of NAD+; meanwhile, restoring NAD+ levels abrogates cGAMP-mediated suppression of PARylation and HDR. Finally, we show that cGAMP also activates DDR signaling in invertebrate species lacking IFN (Crassostrea virginica and Nematostella vectensis), suggesting that the genome surveillance mechanism of cGAS predates metazoan interferon-based immunity.

DOI: https://doi.org/10.1038/s41467-021-26240-9
Cell Mol Life Sci. 2021 Oct 29.

The crosstalk between viral RNA- and DNA-sensing mechanisms.

Chunmei Cai, Yan-Dong Tang, Guocai Xu, Chunfu Zheng.

  Viral infections pose a severe threat to humans by causing many infectious, even fatal, diseases, such as the current pandemic disease (COVID-19) since 2019, and understanding how the host innate immune system recognizes viruses has become more important. Endosomal and cytosolic sensors can detect viral nucleic acids to induce type I interferon and proinflammatory cytokines, subsequently inducing interferon-stimulated genes for restricting viral infection. Although viral RNA and DNA sensing generally rely on diverse receptors and adaptors, the crosstalk between DNA and RNA sensing is gradually appreciated. This minireview highlights the overlap between the RNA- and DNA-sensing mechanisms in antiviral innate immunity, which significantly amplifies the antiviral innate responses to restrict viral infection and might be a potential novel target for preventing and treating viral diseases.

Keywords:  Crosstalk; DNA sensing; RNA sensing; Type I interferon; Viral infection

DOI:  https://doi.org/10.1007/s00018-021-04001-7
J Cell Biol. 2021 Nov 01. pii: e202109021. [Epub ahead of print]220(11):

Cnm1: A bridge between mitochondria and nuclear ER.

Jason C Casler, Laura L Lackner.

Few membrane contact sites have been defined at the molecular level. By using a high-throughput, microscopy-based screen, Eisenberg-Bord, Zung et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202104100) identify Cnm1 as a novel tethering protein that mediates contact between mitochondria and the nuclear ER in response to phospholipid levels.

DOI: https://doi.org/10.1083/jcb.202109021
Cell Mol Immunol. 2021 Oct 25.

Impact of intracellular innate immune receptors on immunometabolism.

Wei-Chun Chou, Elena Rampanelli, Xin Li, Jenny P-Y Ting.

  Immunometabolism, which is the metabolic reprogramming of anaerobic glycolysis, oxidative phosphorylation, and metabolite synthesis upon immune cell activation, has gained importance as a regulator of the homeostasis, activation, proliferation, and differentiation of innate and adaptive immune cell subsets that function as key factors in immunity. Metabolic changes in epithelial and other stromal cells in response to different stimulatory signals are also crucial in infection, inflammation, cancer, autoimmune diseases, and metabolic disorders. The crosstalk between the PI3K-AKT-mTOR and LKB1-AMPK signaling pathways is critical for modulating both immune and nonimmune cell metabolism. The bidirectional interaction between immune cells and metabolism is a topic of intense study. Toll-like receptors (TLRs), cytokine receptors, and T and B cell receptors have been shown to activate multiple downstream metabolic pathways. However, how intracellular innate immune sensors/receptors intersect with metabolic pathways is less well understood. The goal of this review is to examine the link between immunometabolism and the functions of several intracellular innate immune sensors or receptors, such as nucleotide-binding and leucine-rich repeat-containing receptors (NLRs, or NOD-like receptors), absent in melanoma 2 (AIM2)-like receptors (ALRs), and the cyclic dinucleotide receptor stimulator of interferon genes (STING). We will focus on recent advances and describe the impact of these intracellular innate immune receptors on multiple metabolic pathways. Whenever appropriate, this review will provide a brief contextual connection to pathogenic infections, autoimmune diseases, cancers, metabolic disorders, and/or inflammatory bowel diseases.

Keywords:  AKT-mTOR; Immunometabolism; NLRP3/AIM2 inflammasomes; NLRs; STING; innate sensors/receptors

DOI:  https://doi.org/10.1038/s41423-021-00780-y
Autophagy. 2021 Oct 25. 1-18

Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice.

Palak Ahuja, Chun Fai Ng, Brian Pak Shing Pang, Wing Suen Chan, Margaret Chui Ling Tse, Xinyi Bi, Hiu-Lam Rachel Kwan, Daniel Brobst, Oana Herlea-Pana, Xiuying Yang, Guanhua Du, Suchaorn Saengnipanthkul, Hye Lim Noh, Baowei Jiao, Jason K Kim, Chi Wai Lee, Keqiang Ye, Chi Bun Chan.

  Mitochondrial remodeling is dysregulated in metabolic diseases but the underlying mechanism is not fully understood. We report here that BDNF (brain derived neurotrophic factor) provokes mitochondrial fission and clearance in skeletal muscle via the PRKAA/AMPK-PINK1-PRKN/Parkin and PRKAA-DNM1L/DRP1-MFF pathways. Depleting Bdnf expression in myotubes reduced fatty acid-induced mitofission and mitophagy, which was associated with mitochondrial elongation and impaired lipid handling. Muscle-specific bdnf knockout (MBKO) mice displayed defective mitofission and mitophagy, and accumulation of dysfunctional mitochondria in the muscle when they were fed with a high-fat diet (HFD). These animals also have exacerbated body weight gain, increased intramyocellular lipid deposition, reduced energy expenditure, poor metabolic flexibility, and more insulin resistance. In contrast, consuming a BDNF mimetic (7,8-dihydroxyflavone) increased mitochondrial content, and enhanced mitofission and mitophagy in the skeletal muscles. Hence, BDNF is an essential myokine to maintain mitochondrial quality and function, and its repression in obesity might contribute to impaired metabolism.Abbreviation: 7,8-DHF: 7,8-dihydroxyflavone; ACACA/ACC: acetyl Coenzyme A carboxylase alpha; ACAD: acyl-Coenzyme A dehydrogenase family; ACADVL: acyl-Coenzyme A dehydrogenase, very long chain; ACOT: acyl-CoA thioesterase; CAMKK2: calcium/calmodulin-dependent protein kinase kinase 2, beta; BDNF: brain derived neurotrophic factor; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/NIX: BCL2/adenovirus E1B interacting protein 3-like; CCL2/MCP-1: chemokine (C-C motif) ligand 2; CCL5: chemokine (C-C motif) ligand 5; CNS: central nervous system; CPT1B: carnitine palmitoyltransferase 1b, muscle; Cpt2: carnitine palmitoyltransferase 2; CREB: cAMP responsive element binding protein; DNM1L/DRP1: dynamin 1-like; E2: estrogen; EHHADH: enoyl-CoenzymeA hydratase/3-hydroxyacyl CoenzymeA dehydrogenase; ESR1/ER-alpha: estrogen receptor 1 (alpha); FA: fatty acid; FAO: fatty acid oxidation; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; FFA: free fatty acids; FGF21: fibroblast growth factor 21; FUNDC1: FUN14 domain containing 1; HADHA: hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha; HFD: high-fat diet; iWAT: inguinal white adipose tissues; MAP1LC3A/LC3A: microtubule-associated protein 1 light chain 3 alpha; MBKO; muscle-specific bdnf knockout; IL6/IL-6: interleukin 6; MCEE: methylmalonyl CoA epimerase; MFF: mitochondrial fission factor; NTRK2/TRKB: neurotrophic tyrosine kinase, receptor, type 2; OPTN: optineurin; PA: palmitic acid; PARL: presenilin associated, rhomboid-like; PDH: pyruvate dehydrogenase; PINK1: PTEN induced putative kinase 1; PPARGC1A/PGC-1α: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; PRKAA/AMPK: protein kinase, AMP-activated, alpha 2 catalytic subunit; ROS: reactive oxygen species; TBK1: TANK-binding kinase 1; TG: triacylglycerides; TNF/TNFα: tumor necrosis factor; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1.

Keywords:  BDNF; mitochondria; mitophagy; muscle; obesity

DOI:  https://doi.org/10.1080/15548627.2021.1985257
PLoS One. 2021 ;16(10): e0258989

UMP-CMP kinase 2 gene expression in macrophages is dependent on the IRF3-IFNAR signaling axis.

Hera Kim, Yashwanth Subbannayya, Fiachra Humphries, Astrid Skejsol, Sneha M Pinto, Miriam Giambelluca, Terje Espevik, Katherine A Fitzgerald, Richard K Kandasamy.

Toll-like receptors (TLRs) are highly-conserved pattern recognition receptors that mediate innate immune responses to invading pathogens and endogenous danger signals released from damaged and dying cells. Activation of TLRs trigger downstream signaling cascades, that culminate in the activation of interferon regulatory factors (IRFs), which subsequently leads to type I interferon (IFN) response. In the current study, we sought to expand the scope of gene expression changes in THP1-derived macrophages upon TLR4 activation and to identify interferon-stimulated genes. RNA-seq analysis led to the identification of several known and novel differentially expressed genes, including CMPK2, particularly in association with type I IFN signaling. We performed an in-depth characterization of CMPK2 expression, a nucleoside monophosphate kinase that supplies intracellular UTP/CTP for nucleic acid synthesis in response to type I IFN signaling in macrophages. CMPK2 was significantly induced at both RNA and protein levels upon stimulation with TLR4 ligand-LPS and TLR3 ligand-Poly (I:C). Confocal microscopy and subcellular fractionation indicated CMPK2 localization in both cytoplasm and mitochondria of THP-1 macrophages. Furthermore, neutralizing antibody-based inhibition of IFNAR receptor in THP-1 cells and BMDMs derived from IFNAR KO and IRF3 KO knockout mice further revealed that CMPK2 expression is dependent on LPS/Poly (I:C) mediated IRF3- type I interferon signaling. In summary, our findings suggest that CMPK2 is a potential interferon-stimulated gene in THP-1 macrophages and that CMPK2 may facilitate IRF3- type I IFN-dependent anti-bacterial and anti-viral roles.

DOI: https://doi.org/10.1371/journal.pone.0258989
Nat Commun. 2021 Oct 26. 12(1): 6173

The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag.

Indrajit Sahu, Sachitanand M Mali, Prasad Sulkshane, Cong Xu, Andrey Rozenberg, Roni Morag, Manisha Priyadarsini Sahoo, Sumeet K Singh, Zhanyu Ding, Yifan Wang, Sharleen Day, Yao Cong, Oded Kleifeld, Ashraf Brik, Michael H Glickman.

The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.

DOI: https://doi.org/10.1038/s41467-021-26427-0
Am J Hum Genet. 2021 Oct 25. pii: S0002-9297(21)00379-7. [Epub ahead of print]

Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.

Genomics England Research Consortium

  Human mitochondrial RNase P (mt-RNase P) is responsible for 5' end processing of mitochondrial precursor tRNAs, a vital step in mitochondrial RNA maturation, and is comprised of three protein subunits: TRMT10C, SDR5C1 (HSD10), and PRORP. Pathogenic variants in TRMT10C and SDR5C1 are associated with distinct recessive or x-linked infantile onset disorders, resulting from defects in mitochondrial RNA processing. We report four unrelated families with multisystem disease associated with bi-allelic variants in PRORP, the metallonuclease subunit of mt-RNase P. Affected individuals presented with variable phenotypes comprising sensorineural hearing loss, primary ovarian insufficiency, developmental delay, and brain white matter changes. Fibroblasts from affected individuals in two families demonstrated decreased steady state levels of PRORP, an accumulation of unprocessed mitochondrial transcripts, and decreased steady state levels of mitochondrial-encoded proteins, which were rescued by introduction of the wild-type PRORP cDNA. In mt-tRNA processing assays performed with recombinant mt-RNase P proteins, the disease-associated variants resulted in diminished mitochondrial tRNA processing. Identification of disease-causing variants in PRORP indicates that pathogenic variants in all three subunits of mt-RNase P can cause mitochondrial dysfunction, each with distinct pleiotropic clinical presentations.

Keywords:  MRPP3; PRORP; Perrault syndrome; RNase P; leukodystrophy; mitochondria; primary ovarian insufficiency; rare disease; sensorineural hearing loss

DOI:  https://doi.org/10.1016/j.ajhg.2021.10.002
FEBS Lett. 2021 Oct 26.

Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX.

Kazumi Nomura, Yu Kitagawa, Marina Aihara, Yusuke Ohki, Kazumichi Furuyama, Takatsugu Hirokawa.

  The caseinolytic mitochondrial matrix peptidase chaperone subunit (ClpX) plays an important role in the heme-dependent regulation of 5-aminolevulinate synthase (ALAS1), a key enzyme in heme biosynthesis. However, the mechanisms underlying the role of ClpX in this process remain unclear. In this in vitro study, we confirmed the direct binding between ALAS1 and ClpX in a heme-dependent manner. The substitution of C108 P109 (CP motif 3 [CP3]) with A108 A109 in ALAS1 resulted in a loss of ability to bind ClpX. Computational disorder analyses revealed that CP3 was located in a potential intrinsically disordered protein region (IDPR). Thus, we propose that conditional disorder-to-order transitions in the IDPRs of ALAS1 may represent key mechanisms underlying the heme-dependent recognition of ALAS1 by ClpX.

Keywords:  ALAS1; ClpP; ClpX; ClpXP proteolytic machinery; heme-regulated proteins; intrinsically disordered protein regions; ligand-induced protein degradation; molecular chaperone

DOI:  https://doi.org/10.1002/1873-3468.14214
Mol Biol Cell. 2021 Oct 27. mbcE21050229

Analysis of senescence-responsive stress fiber proteome reveals reorganization of stress fibers mediated by elongation factor eEF2 in HFF-1 cells.

Shiyou Liu, Tsubasa S Matsui, Na Kang, Shinji Deguchi.

Stress fibers (SFs), which are actomyosin structures, reorganize in response to various cues to maintain cellular homeostasis. Currently, the protein components of SFs are only partially identified, limiting our understanding of their responses. Here we isolate SFs from human fibroblasts HFF-1 to determine with proteomic analysis the whole protein components and how they change with replicative senescence (RS), a state where cells decline in ability to replicate after repeated divisions. We found that at least 135 proteins are associated with SFs, and 63 of them are upregulated with RS, by which SFs become larger in size. Among them, we focused on eEF2 (eukaryotic translation elongation factor 2) as it exhibited upon RS the most significant increase in abundance. We show that eEF2 is critical to the reorganization and stabilization of SFs in senescent fibroblasts. Our findings provide a novel molecular basis for SFs to be reinforced to resist cellular senescence.

DOI: https://doi.org/10.1091/mbc.E21-05-0229
Nat Rev Immunol. 2021 Oct 26.

Red blood cells join the ranks as immune sentinels.

Kirsty Minton.

DOI: https://doi.org/10.1038/s41577-021-00648-2