bims-minimp 2022-01-02 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–01–02
eleven papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Defining the interactome of the human mitochondrial ribosome identifies SMIM4 and TMEM223 as respiratory chain assembly factors.
MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51.
The Regulatory Network of Cyclic GMP-AMP Synthase-Stimulator of Interferon Genes Pathway in Viral Evasion.
Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity.
Glucocorticoids Coordinate Macrophage Metabolism Through Regulation of the Tricarboxylic Acid Cycle.
JMJD8 is a Novel Molecular Nexus Between Adipocyte-Intrinsic Inflammation and Insulin Resistance.
Exosomes originating from infection with the cytoplasmic single-stranded RNA virus Rift Valley fever virus (RVFV) protect recipient cells by inducing RIG-I mediated IFN-B response that leads to activation of autophagy.
Astroglial ER protein Membralin is an essential neuroinflammation regulator.
The emerging roles of the CDK/cyclin complexes in antiviral innate immunity.
Antiviral immunity triggered by infection-induced host transposable elements.
Immune regulator LGP2 targets Ubc13/UBE2N to mediate widespread interference with K63 polyubiquitination and NF-κB activation.

Elife. 2021 Dec 31. pii: e68213. [Epub ahead of print]10

Defining the interactome of the human mitochondrial ribosome identifies SMIM4 and TMEM223 as respiratory chain assembly factors.

Sven Dennerlein, Sabine Poerschke, Silke Oeljeklaus, Cong Wang, Ricarda Richter-Dennerlein, Johannes Sattmann, Diana Bauermeister, Elisa Hanitsch, Stefan Stoldt, Thomas Langer, Stefan Jakobs, Bettina Warscheid, Peter Rehling.

  Human mitochondria express a genome that encodes thirteen core subunits of the oxidative phosphorylation system (OXPHOS). These proteins insert into the inner membrane co-translationally. Therefore, mitochondrial ribosomes engage with the OXA1L-insertase and membrane-associated proteins, which support membrane insertion of translation products and early assembly steps into OXPHOS complexes. To identify ribosome-associated biogenesis factors for the OXPHOS system, we purified ribosomes and associated proteins from mitochondria. We identified TMEM223 as a ribosome-associated protein involved in complex IV biogenesis. TMEM223 stimulates the translation of COX1 mRNA and is a constituent of early COX1 assembly intermediates. Moreover, we show that SMIM4 together with C12ORF73 interacts with newly synthesized cytochrome b to support initial steps of complex III biogenesis in complex with UQCC1 and UQCC2. Our analyses define the interactome of the human mitochondrial ribosome and reveal novel assembly factors for complex III and IV biogenesis that link early assembly stages to the translation machinery.

Keywords:  assembly; biochemistry; cell biology; chemical biology; mitochondria; oxidative phosphorylation; ribosome; translation

DOI:  https://doi.org/10.7554/eLife.68213
J Biochem. 2021 Dec 29. pii: mvab153. [Epub ahead of print]

MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51.

Naoki Ito, Takara Takahashi, Isshin Shiiba, Shun Nagashima, Ryoko Inatome, Shigeru Yanagi.

  The transfer of phospholipids from the endoplasmic reticulum to mitochondria via the mitochondria-endoplasmic reticulum (ER) contact site (MERCS) is essential for maintaining mitochondrial function and integrity. Here, we identified RMDN3/PTPIP51, possessing phosphatidic acid (PA)-transfer activity, as a neighboring protein of the mitochondrial E3 ubiquitin ligase MITOL/MARCH5 by proximity-dependent biotin labeling using APEX2. We found that MITOL interacts with and ubiquitinates RMDN3. Mutational analysis identified lysine residue 89 in RMDN3 as a site of ubiquitination by MITOL. Loss of MITOL or the substitution of lysine 89 to arginine in RMDN3 significantly reduced the PA-binding activity of RMDN3, suggesting that MITOL regulates the transport of PA to mitochondria by activating RMDN3. Our findings imply that ubiquitin signaling regulates phospholipid transport at the MERCS.

Keywords:  E3 ubiquitin ligase; MITOL; RMDN3; mitochondria-ER contact site; phospholipid

DOI:  https://doi.org/10.1093/jb/mvab153
Front Microbiol. 2021 ;12 790714

The Regulatory Network of Cyclic GMP-AMP Synthase-Stimulator of Interferon Genes Pathway in Viral Evasion.

Tongyu Hu, Mingyu Pan, Yue Yin, Chen Wang, Ye Cui, Quanyi Wang.

  Virus infection has been consistently threatening public health. The cyclic GMP-AMP synthase (cGAS)-Stimulator of Interferon Genes (STING) pathway is a critical defender to sense various pathogens and trigger innate immunity of mammalian cells. cGAS recognizes the pathogenic DNA in the cytosol and then synthesizes 2'3'-cyclic GMP-AMP (2'3'cGAMP). As the second messenger, cGAMP activates STING and induces the following cascade to produce type I interferon (IFN-I) to protect against infections. However, viruses have evolved numerous strategies to hinder the cGAS-STING signal transduction, promoting their immune evasion. Here we outline the current status of the viral evasion mechanism underlying the regulation of the cGAS-STING pathway, focusing on how post-transcriptional modifications, viral proteins, and non-coding RNAs involve innate immunity during viral infection, attempting to inspire new targets discovery and uncover potential clinical antiviral treatments.

Keywords:  cGAS-STING; innate immune; post-translational modification; type I interferon; viral evasion

DOI:  https://doi.org/10.3389/fmicb.2021.790714
Proc Natl Acad Sci U S A. 2022 Jan 04. pii: e2111115119. [Epub ahead of print]119(1):

Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity.

Zhongshun Liu, Congwei Jiang, Zhangmengxue Lei, Sihan Dong, Linlin Kuang, Chenxu Huang, Ying Gao, Mu Liu, Hui Xiao, Patrick Legembre, Jae U Jung, Huaping Liang, Xiaozhen Liang.

  Type I interferons (IFNs) are the first frontline of the host innate immune response against invading pathogens. Herein, we characterized an unknown protein encoded by phospholipase A2 inhibitor and LY6/PLAUR domain-containing (PINLYP) gene that interacted with TBK1 and induced type I IFN in a TBK1- and IRF3-dependent manner. Loss of PINLYP impaired the activation of IRF3 and production of IFN-β induced by DNA virus, RNA virus, and various Toll-like receptor ligands in multiple cell types. Because PINLYP deficiency in mice engendered an early embryonic lethality in mice, we generated a conditional mouse in which PINLYP was depleted in dendritic cells. Mice lacking PINLYP in dendritic cells were defective in type I IFN induction and more susceptible to lethal virus infection. Thus, PINLYP is a positive regulator of type I IFN innate immunity and important for effective host defense against viral infection.

Keywords:  innate immunity; interferon; virus infection

DOI:  https://doi.org/10.1073/pnas.2111115119
Mol Metab. 2021 Dec 22. pii: S2212-8778(21)00282-9. [Epub ahead of print] 101424

Glucocorticoids Coordinate Macrophage Metabolism Through Regulation of the Tricarboxylic Acid Cycle.

Ulrich Stifel, Eva-Maria Wolfschmitt, Josef Vogt, Ulrich Wachter, Sabine Vettorazzi, Daniel Tews, Melanie Hogg, Fabian Zink, Nora Maria Koll, Sandra Winning, Rémi Mounier, Bénédicte Chazaud, Peter Radermacher, Pamela Fischer-Posovszky, Giorgio Caratti, Jan Tuckermann.

  Glucocorticoids (GCs) are one of the most widely prescribed anti-inflammatory drugs. By acting through their cognate receptor, the glucocorticoid receptor (GR), GCs down-regulate the expression of pro-inflammatory genes, and up-regulate anti-inflammatory genes. Metabolic pathways have recently been identified as key parts of both the inflammatory activation and anti-inflammatory polarization of macrophages, immune cells responsible for acute inflammation and tissue repair. It is currently unknown whether GCs control macrophage metabolism, and if so, to what extent metabolic regulation by GCs confers anti-inflammatory activity. Using transcriptomic and metabolomic profiling of macrophages, we identified GC controlled pathways involved in metabolism, especially in mitochondrial function. Metabolic analyses revealed that GCs repress glycolysis in inflammatory myeloid cells and promote tricarboxylic acid (TCA) cycle flux, promoting succinate metabolism and preventing intracellular accumulation of succinate. Inhibition of ATP synthase attenuated GC induced transcriptional changes, likely through stalling of TCA cycle anaplerosis. We further identified a glycolytic regulatory transcription factor, HIF1α, as regulated by GCs, and as a key regulator of GC responsiveness during inflammatory challenge, further linking metabolism to GC action in macrophages.

Keywords:  Glucocorticoids; Succinate; TCA Cycle; immunometabolism; macrophage

DOI:  https://doi.org/10.1016/j.molmet.2021.101424
Diabetes. 2021 Oct 21. pii: db210596. [Epub ahead of print]

JMJD8 is a Novel Molecular Nexus Between Adipocyte-Intrinsic Inflammation and Insulin Resistance.

Dongjoo You, Byung Chul Jung, Sneha Damal Villivalam, Hee-Woong Lim, Sona Kang.

Chronic low-grade inflammation, often referred to as metainflammation, develops in response to overnutrition and is a major player in the regulation of insulin sensitivity. While many studies have investigated adipose tissue inflammation from the perspective of the immune cell compartment, little is known about how adipocytes intrinsically contribute to metainflammation and insulin resistance at the molecular level. Here, we demonstrate a novel role for Jumonji C Domain Containing Protein 8 (JMJD8) as an adipocyte-intrinsic molecular nexus between inflammation and insulin resistance. We determined that JMJD8 was highly enriched in white adipose tissue, especially in the adipocyte fraction. Adipose JMJD8 levels were dramatically increased in obesity-associated insulin resistance models. Its levels were increased by feeding and insulin, and inhibited by fasting. A JMJD8 gain of function was sufficient to drive insulin resistance, whereas loss of function improved insulin sensitivity in mouse and human adipocytes. Consistent with this, Jmjd8-ablated mice had increased whole-body and adipose insulin sensitivity and glucose tolerance on both chow and a high-fat diet, while adipocyte-specific Jmjd8-overexpressing mice displayed worsened whole-body metabolism on a high-fat diet. We found that JMJD8 affected the transcriptional regulation of inflammatory genes. In particular, it was required for LPS-mediated inflammation and insulin resistance in adipocytes. For this, JMJD8 required Interferon Regulatory Factor (IRF3) to mediate its actions in adipocytes. Together, our results demonstrate that JMJD8 acts as a novel molecular factor that drives adipocyte inflammation in conjunction with insulin sensitivity.

DOI: https://doi.org/10.2337/db21-0596
Cell Biosci. 2021 Dec 25. 11(1): 220

Exosomes originating from infection with the cytoplasmic single-stranded RNA virus Rift Valley fever virus (RVFV) protect recipient cells by inducing RIG-I mediated IFN-B response that leads to activation of autophagy.

Farhang Alem, Adeyemi A Olanrewaju, Samson Omole, Heather E Hobbs, Noor Ahsan, Graham Matulis, Christine A Brantner, Weidong Zhou, Emanuel F Petricoin, Lance A Liotta, Massimo Caputi, Sina Bavari, Yuntao Wu, Fatah Kashanchi, Ramin M Hakami.

   BACKGROUND: Although multiple studies have demonstrated a role for exosomes during virus infections, our understanding of the mechanisms by which exosome exchange regulates immune response during viral infections and affects viral pathogenesis is still in its infancy. In particular, very little is known for cytoplasmic single-stranded RNA viruses such as SARS-CoV-2 and Rift Valley fever virus (RVFV). We have used RVFV infection as a model for cytoplasmic single-stranded RNA viruses to address this gap in knowledge. RVFV is a highly pathogenic agent that causes RVF, a zoonotic disease for which no effective therapeutic or approved human vaccine exist.
RESULTS: We show here that exosomes released from cells infected with RVFV (designated as EXi-RVFV) serve a protective role for the host and provide a mechanistic model for these effects. Our results show that treatment of both naïve immune cells (U937 monocytes) and naïve non-immune cells (HSAECs) with EXi-RVFV induces a strong RIG-I dependent activation of IFN-B. We also demonstrate that this strong anti-viral response leads to activation of autophagy in treated cells and correlates with resistance to subsequent viral infection. Since we have shown that viral RNA genome is associated with EXi-RVFV, RIG-I activation might be mediated by the presence of packaged viral RNA sequences.
CONCLUSIONS: Using RVFV infection as a model for cytoplasmic single-stranded RNA viruses, our results show a novel mechanism of host protection by exosomes released from infected cells (EXi) whereby the EXi activate RIG-I to induce IFN-dependent activation of autophagy in naïve recipient cells including monocytes. Because monocytes serve as reservoirs for RVFV replication, this EXi-RVFV-induced activation of autophagy in monocytes may work to slow down or halt viral dissemination in the infected organism. These findings offer novel mechanistic insights that may aid in future development of effective vaccines or therapeutics, and that may be applicable for a better molecular understanding of how exosome release regulates innate immune response to other cytoplasmic single-stranded RNA viruses.

Keywords:  Autophagy; Exosome; IFN-B; Innate immune response; RIG-I; Rift Valley fever virus; SARS-CoV-2; Single-stranded RNA virus; Viral RNA; Virus infection

DOI:  https://doi.org/10.1186/s13578-021-00732-z
Alzheimers Dement. 2021 Dec;17 Suppl 2 e058566

Astroglial ER protein Membralin is an essential neuroinflammation regulator.

LuLin Jiang, Xiaoguang Li, Stephanie Myers, Timothy Huang, Randal J Kaufman.

BACKGROUND: The endoplasmic reticulum (ER) is the primary organelle for synthesizing membrane proteins, secretory proteins, and lipids. Disturbance of ER homeostasis in peripheral immune cells is associated with inflammatory responses. Glial cells, including astrocytes and microglia, are the immune cells in the brains, becoming reactive/gliosis during the progression of Alzheimer's disease (AD). However, whether and how glial protein homeostasis mediate the reactive state of glial cells is yet to be investigated. We previously identified a novel ER-associated degradation component, membralin/TMEM259, as an important mediator in neurodegeneration. Loss of membralin impaired the turnover of nicastrin protein, which increased gamma-secretase complex formation and activity. Knockdown membralin in the TgCRND8-AD mice exaggerated beta-amyloid-associated neuronal damage. Moreover, selective deletion of membralin in astrocytes decreased excitatory amino acid transporter 2 (EAAT2) expression and induced excitotoxicity. Elevating membralin levels in SOD1 G93A ALS mouse model can significantly extend the lifespan of the animals.
METHOD: Transcriptomic profiles of the cortex tissues and histology were analyzed in the astrocyte-conditional membralin knockout animals. Primary astrocyte ER morphology was examined by electron microscopy analysis. We crossed the transgenic membralin animals with 5xFAD animals and assessed the AD pathology.
RESULT: Astroglial membralin knockout animals develop strong neuroinflammation phenotypes. Loss of membralin in astrocytes disrupts ER homeostasis and nuclear envelop integrity, and induces senescence-like phenotypes. In contrast, the elevation of membralin in astrocytes can alleviate the induction of C3+ astrocytes upon c1q/IL1a/TNFa treatment. Further, elevating membralin levels in 5XFAD mouse model can significantly reduce the AD pathologies.
CONCLUSION: Membralin is critical in mediating the reactive states of astrocytes. Modulation of astroglial ER homeostasis can be a promising target to regulate neuroinflammation for AD therapy.

DOI: https://doi.org/10.1002/alz.058566
J Med Virol. 2021 Dec 29.

The emerging roles of the CDK/cyclin complexes in antiviral innate immunity.

Chunfu Zheng, Yan-Dong Tang.

  More than 20 members of the human Cyclin-dependent kinases (CDKs) family share the feature of being activated by cyclins. CDKs have been involved in diverse biological processes, such as cell cycle, transcription, DNA damage response, and apoptosis. If CDKs are not properly regulated, they can cause diseases like cancer. CDKs are Ser/Thr kinases that work with cyclins to control cell cycle progression. Various CDK-cyclin complexes phosphorylate particular target proteins and drive different cell cycle stages. Accumulating evidence demonstrated that CDKs play an essential role in the cell cycle; however, their roles in antiviral innate immunity are just emerging. This minireview summarizes how CDKs play their roles in antiviral innate immunity. Our goal is to draw attention to the involvement of CDKs in antiviral innate immunity, whether as separate entities or as components of CDK/cyclin complexes that have gotten less attention in the past. This article is protected by copyright. All rights reserved.

Keywords:  CDKs; JAK-STAT; NF-κB; TLR; antiviral innate immunity

DOI:  https://doi.org/10.1002/jmv.27554
Curr Opin Virol. 2021 Dec 24. pii: S1879-6257(21)00164-4. [Epub ahead of print]52 211-216

Antiviral immunity triggered by infection-induced host transposable elements.

Benjamin G Hale.

Host silencing of transposable elements (TEs) is critical to prevent genome damage and inappropriate inflammation. However, new evidence suggests that a virus-infected host may re-activate TEs and co-opt them for antiviral defense. RNA-Seq and specialized bioinformatics have revealed the diversity of virus infections that induce TEs. Furthermore, studies with influenza virus have uncovered how infection-triggered changes to the SUMOylation of TRIM28, an epigenetic co-repressor, lead to TE de-repression. Importantly, there is a growing appreciation of how de-repressed TEs stimulate antiviral gene expression, either via cis-acting enhancer functions or via their recognition as viral mimetics by innate immune nucleic acid sensors (e.g. RIG-I, mda-5 and cGAS). Understanding how viruses trigger, and counteract, TE-based antiviral immunity should provide insights into pathogenic mechanisms.

DOI: https://doi.org/10.1016/j.coviro.2021.12.006
Cell Rep. 2021 Dec 28. pii: S2211-1247(21)01675-2. [Epub ahead of print]37(13): 110175

Immune regulator LGP2 targets Ubc13/UBE2N to mediate widespread interference with K63 polyubiquitination and NF-κB activation.

Jessica J Lenoir, Jean-Patrick Parisien, Curt M Horvath.

  Lysine 63-linked polyubiquitin (K63-Ub) chains activate a range of cellular immune and inflammatory signaling pathways, including the mammalian antiviral response. Interferon and antiviral genes are triggered by TRAF family ubiquitin ligases that form K63-Ub chains. LGP2 is a feedback inhibitor of TRAF-mediated K63-Ub that can interfere with diverse immune signaling pathways. Our results demonstrate that LGP2 inhibits K63-Ub by association with and sequestration of the K63-Ub-conjugating enzyme, Ubc13/UBE2N. The LGP2 helicase subdomain, Hel2i, mediates protein interaction that engages and inhibits Ubc13/UBE2N, affecting control over a range of K63-Ub ligase proteins, including TRAF6, TRIM25, and RNF125, all of which are inactivated by LGP2. These findings establish a unifying mechanism for LGP2-mediated negative regulation that can modulate a variety of K63-Ub signaling pathways.

Keywords:  DHX58; IFN; K63-Ub; LGP2; RNF125; TRAF6; TRIM25; UBE2N; Ubc13

DOI:  https://doi.org/10.1016/j.celrep.2021.110175