bims-minimp 2022-06-19 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–06–19
twelve papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy.
Mitochondrial complex I dysfunction alters the balance of soluble and membrane-bound TNF during chronic experimental colitis.
Senescent hepatic stellate cells promote liver regeneration through IL-6 and ligands of CXCR2.
Loss of hepatic DRP1 exacerbates alcoholic hepatitis by inducing megamitochondria and mitochondrial maladaptation.
cGAS and DDX41-STING mediated intrinsic immunity spreads intercellularly to promote neuroinflammation in SOD1 ALS model.
A little less aggregation a little more replication: Viral manipulation of stress granules.
Elesclomol elevates cellular and mitochondrial iron levels by delivering copper to the iron import machinery.
Mitofusin 2 positively regulates Ca2+ signaling by tethering the sarcoplasmic reticulum and mitochondria in rat aortic smooth muscle cells.
Skin Aging in Long-Lived Naked Mole-Rats is Accompanied by Increased Expression of Longevity-Associated and Tumor Suppressor Genes.
FUNDC2 promotes liver tumorigenesis by inhibiting MFN1-mediated mitochondrial fusion.
Folding and Evolution of a Repeat Protein on the Ribosome.
Current Knowledge on the Role of Cardiolipin Remodeling in the Context of Lipid Oxidation and Barth Syndrome.

J Clin Invest. 2022 Jun 14. pii: e157504. [Epub ahead of print]

OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy.

Mario K Shammas, Xiaoping Huang, Beverly P Wu, Evelyn Fessler, Insung Song, Nicholas P Randolph, Yan Li, Christopher Ke Bleck, Danielle A Springer, Carl Fratter, Ines A Barbosa, Andrew F Powers, Pedro M Quirós, Carlos Lopez-Otin, Lucas T Jae, Joanna Poulton, Derek P Narendra.

  Mitochondrial stress triggers a response in the cell's mitochondria and nucleus, but how these stress responses are coordinated in vivo is poorly understood. Here, we characterize a family with myopathy caused by a dominant p.G58R mutation in the mitochondrial protein CHCHD10. To understand the disease etiology, we developed a knock-in mouse model and found that mutant CHCHD10 aggregates in affected tissues, applying a toxic protein stress to the inner mitochondrial membrane. Unexpectedly, survival of CHCHD10 knock-in mice depended on a protective stress response mediated by OMA1. The OMA1 stress response acted both locally within mitochondria, causing mitochondrial fragmentation, and signaled outside the mitochondria, activating the integrated stress response through cleavage of DELE1. We additionally identified an isoform switch in the terminal complex of the electron transport chain as a component of this response. Our results demonstrate that OMA1 is critical for neonatal survival conditionally in the setting of inner mitochondrial membrane stress, coordinating local and global stress responses to reshape the mitochondrial network and proteome.

Keywords:  Cell Biology; Cell stress; Genetics; Mitochondria; Proteases

DOI:  https://doi.org/10.1172/JCI157504
Sci Rep. 2022 Jun 15. 12(1): 9977

Mitochondrial complex I dysfunction alters the balance of soluble and membrane-bound TNF during chronic experimental colitis.

Ainize Peña-Cearra, Miguel Angel Pascual-Itoiz, Jose Luis Lavín, Miguel Fuertes, Itziar Martín-Ruiz, Janire Castelo, Ainhoa Palacios, Diego Barriales, Asier Fullaondo, Ana M Aransay, Hector Rodríguez, Juan Anguita, Leticia Abecia.

Inflammatory bowel disease (IBD) is a complex, chronic, relapsing and heterogeneous disease induced by environmental, genomic, microbial and immunological factors. MCJ is a mitochondrial protein that regulates the metabolic status of macrophages and their response to translocated bacteria. Previously, an acute murine model of DSS-induced colitis showed increased disease severity due to MCJ deficiency. Unexpectedly, we now show that MCJ-deficient mice have augmented tumor necrosis factor α converting enzyme (TACE) activity in the context of chronic inflammation. This adaptative change likely affects the balance between soluble and transmembrane TNF and supports the association of the soluble form and a milder phenotype. Interestingly, the general shifts in microbial composition previously observed during acute inflammation were absent in the chronic model of inflammation in MCJ-deficient mice. However, the lack of the mitochondrial protein resulted in increased alpha diversity and the reduction in critical microbial members associated with inflammation, such as Ruminococcus gnavus, which could be associated with TACE activity. These results provide evidence of the dynamic metabolic adaptation of the colon tissue to chronic inflammatory changes mediated by the control of mitochondrial function.

DOI: https://doi.org/10.1038/s41598-022-13480-y
JCI Insight. 2022 Jun 16. pii: e158207. [Epub ahead of print]

Senescent hepatic stellate cells promote liver regeneration through IL-6 and ligands of CXCR2.

Naiyuan Cheng, Ki-Hyun Kim, Lester F Lau.

  Senescent cells have long been associated with deleterious effects in aging-related pathologies, although recent studies have uncovered their beneficial roles in certain contexts such as wound healing. We have found that hepatic stellate cells (HSCs) undergo senescence within two days after 2/3 partial hepatectomy (PHx) in young (2-3 month-old) mice, and elimination of these senescent cells by the senolytic drug ABT263 or using a genetic mouse model impairs liver regeneration. Senescent HSCs secrete IL-6 and CXCR2 ligands as part of the senescence-associated secretory phenotype (SASP), which induces multiple signaling pathways to stimulate liver regeneration. IL-6 activates STAT3, induces YAP activation through SRC family kinases, and synergizes with CXCL2 to activate ERK1/2 to stimulate hepatocyte proliferation. The administration of either IL-6 or CXCL2 partially restores liver regeneration in mice with senescent cell elimination, and the combination of both fully restores liver weight recovery. Furthermore, the matricellular protein CCN1/CYR61 is rapidly elevated in response to PHx and induces HSC senescence. Knock-in mice expressing a mutant CCN1 unable to bind integrin α6β1 are deficient in senescent cells and liver regeneration after PHx. Thus, HSC senescence, largely induced by CCN1, is a programmed response to PHx and plays a critical role in liver regeneration through signaling pathways activated by IL-6 and ligands of CXCR2.

Keywords:  Cellular senescence; Cytokines; Hepatology; Integrins

DOI:  https://doi.org/10.1172/jci.insight.158207
Hepatology. 2022 Jun 13.

Loss of hepatic DRP1 exacerbates alcoholic hepatitis by inducing megamitochondria and mitochondrial maladaptation.

Xiaowen Ma, Allen Chen, Luma Melo, Ana Clemente-Sanchez, Xiaojuan Chao, Ali Reza Ahmadi, Brandon Peiffer, Zhaoli Sun, Hiromi Sesaki, Tiangang Li, Xiaokun Wang, Wanqing Liu, Ramon Bataller, Hong-Min Ni, Wen-Xing Ding.

BACKGROUND & AIMS: Increased megamitochondria formation and impaired mitophagy in hepatocytes have been linked to the pathogenesis of alcohol-associated liver disease (ALD). This study aims to determine the mechanisms by which alcohol consumption increases megamitochondria formation in the pathogenesis of ALD.
APPROACH & RESULTS: Human alcoholic hepatitis (AH) liver samples were used for electron microscopy (EM), histology, and biochemical analysis. Liver-specific dynamin-related protein 1 (DRP1, gene name DNM1L, an essential gene regulating mitochondria fission) knockout (L-DRP1 KO) mice and wild-type (WT) mice were subjected to chronic plus binge alcohol feeding. Both human AH and alcohol-fed mice had decreased hepatic DRP1 with increased accumulation of hepatic megamitochondria. Mechanistic studies revealed that alcohol feeding decreased DRP1 by impairing transcription factor EB-mediated induction of DNM1L. L-DRP1 KO mice had increased megamitochondria and decreased mitophagy with increased liver injury and inflammation, which were further exacerbated by alcohol feeding. Seahorse flux and unbiased metabolomics analysis showed alcohol intake increased mitochondria oxygen consumption and hepatic NAD+, acylcarnitine, and ketone levels, which were attenuated in L-DRP1 KO mice, suggesting that loss of hepatic DRP1 leads to maladaptation to alcohol-induced metabolic stress. RNA-seq and q-PCR analysis revealed increased gene expression of the cGAS-STING-Interferon pathway in L-DRP1 KO mice regardless of alcohol feeding. Alcohol-fed L-DRP1 KO mice had increased cytosolic mtDNA and mitochondrial dysfunction leading to increased activation of cGAS-STING-Interferon signaling pathways and liver injury.
CONCLUSION: Alcohol consumption decreases hepatic DRP1 resulting in increased megamitochondria and mitochondrial maladaptation that promotes AH by mitochondria-mediated inflammation and cell injury.

DOI: https://doi.org/10.1002/hep.32604
iScience. 2022 Jun 17. 25(6): 104404

cGAS and DDX41-STING mediated intrinsic immunity spreads intercellularly to promote neuroinflammation in SOD1 ALS model.

Hong Yien Tan, Yean Kong Yong, Yuan Chao Xue, Huitao Liu, Tomomi Furihata, Esaki Muthu Shankar, Chen Seng Ng.

  Neuroinflammation exacerbates the progression of SOD1-driven amyotrophic lateral sclerosis (ALS), although the underlying mechanisms remain largely unknown. Herein, we demonstrate that misfolded SOD1 (SOD1Mut)-causing ALS results in mitochondrial damage, thus triggering the release of mtDNA and an RNA:DNA hybrid into the cytosol in an mPTP-independent manner to activate IRF3- and IFNAR-dependent type I interferon (IFN-I) and interferon-stimulating genes. The neuronal hyper-IFN-I and pro-inflammatory responses triggered in ALS-SOD1Mut were sufficiently robust to cause a strong physiological outcome in vitro and in vivo. cGAS/DDX41-STING-signaling is amplified in bystander cells through inter-neuronal gap junctions. Our results highlight the importance of a common DNA-sensing pathway between SOD1 and TDP-43 in influencing the progression of ALS.

Keywords:  Immunology; Neuroscience; Pathophysiology

DOI:  https://doi.org/10.1016/j.isci.2022.104404
Wiley Interdiscip Rev RNA. 2022 Jun 16. e1741

A little less aggregation a little more replication: Viral manipulation of stress granules.

Matthew J Brownsword, Nicolas Locker.

  Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Keywords:  G3BP1; phase separation; stress granules; stress response; virus

DOI:  https://doi.org/10.1002/wrna.1741
J Biol Chem. 2022 Jun 14. pii: S0021-9258(22)00581-6. [Epub ahead of print] 102139

Elesclomol elevates cellular and mitochondrial iron levels by delivering copper to the iron import machinery.

Natalie M Garza, Mohammad Zulkifli, Vishal M Gohil.

  Copper (Cu) and iron (Fe) are redox-active metals that serve as cofactors for many essential cellular enzymes. Disruption in the intracellular homeostasis of these metals results in debilitating and frequently fatal human disorders, such as Menkes disease and Friedreich's ataxia. Recently, we reported that an investigational anticancer drug, elesclomol (ES), can deliver Cu to critical mitochondrial cuproenzymes and has the potential to be repurposed for treatment of Cu deficiency disorders. Here, we sought to determine the specificity of ES and the ES-Cu complex in delivering Cu to cuproenzymes in different intracellular compartments. Using a combination of yeast genetics, subcellular fractionation, and inductively coupled plasma-mass spectrometry-based metal measurements, we showed that ES and ES-Cu treatment results in an increase in cellular and mitochondrial Fe content, along with the expected increase in Cu. Utilizing yeast mutants of Cu and Fe transporters, we demonstrate that ES-based elevation in cellular Fe levels is independent of the major cellular Cu importer, but is dependent on the Fe importer Ftr1 and its partner Fet3, a multicopper-oxidase. As Fet3 is metallated in the Golgi lumen, we sought to uncover the mechanism by which Fet3 receives Cu from ES. Using yeast knockouts of genes involved in Cu delivery to Fet3, we determined that ES can bypass Atx1, a metallochaperone involved in Cu delivery to the Golgi membrane Cu pump, Ccc2, but not Ccc2 itself. Taken together, our study provides a mechanism by which ES distributes Cu in cells and impacts cellular and mitochondrial Fe homeostasis.

Keywords:  Ccc2; Copper; Fet3; Golgi; iron; mitochondria

DOI:  https://doi.org/10.1016/j.jbc.2022.102139
Am J Physiol Cell Physiol. 2022 Jun 15.

Mitofusin 2 positively regulates Ca2+ signaling by tethering the sarcoplasmic reticulum and mitochondria in rat aortic smooth muscle cells.

Sou Inagaki, Yoshiaki Suzuki, Keisuke Kawasaki, Rubii Kondo, Yuji Imaizumi, Hisao Yamamura.

  Mitochondria buffer cytosolic Ca2+increases following Ca2+ influx from extracellular spaces and Ca2+ release from intracellular Ca2+ store sites under physiological circumstances. Therefore, close contact of mitochondria with the sarcoplasmic reticulum (SR) is required for maintaining Ca2+ homeostasis. Mitofusin 2 (Mfn2) localizes in both mitochondrial and SR membranes, and is hypothesized to optimize the distance and Ca2+ transfer between these organelles. However, the physiological significance of Mfn2 in vascular smooth muscle cells (VSMCs) is poorly understood. In the present study, the role of Mfn2 in the physical and functional couplings between SR and mitochondria was examined in rat aortic smooth muscle cells (rASMCs) by confocal and electron microscope imaging. When Mfn2 was knocked-down using siRNA in rASMCs, the mean distance between these organelles was extended from 16.2 to 21.6 nm. The increase in the cytosolic Ca2+ concentration ([Ca2+]cyt) induced by 100 nM arginine vasopressin (AVP) was not affected by Mfn2 siRNA knockdown, whereas cytosolic Ca2+ removal was slower after Mfn2 knockdown. Following the AVP-induced [Ca2+]cyt increase, mitochondrial Ca2+ uptake and Ca2+ refill into the SR were attenuated by Mfn2 knockdown. In addition, Mfn2-knockdown cells exhibited a loss of mitochondrial membrane potential (ΔΨmito) and lower ATP levels in mitochondria. Moreover, Mfn2 knockdown inhibited cell proliferation. In contrast, Mfn2 overexpression increased ΔΨmito and cell growth. This study strongly suggests that Mfn2 is responsible for SR-mitochondria Ca2+ signaling by tethering mitochondria to SR, thereby regulating ATP production and proliferation of VSMCs.

Keywords:  calcium; mitochondria; mitofusin; sarcoplasmic reticulum; smooth muscle

DOI:  https://doi.org/10.1152/ajpcell.00274.2021
J Invest Dermatol. 2022 Jun 09. pii: S0022-202X(22)00402-X. [Epub ahead of print]

Skin Aging in Long-Lived Naked Mole-Rats is Accompanied by Increased Expression of Longevity-Associated and Tumor Suppressor Genes.

Iqra Fatima, Guodong Chen, Natalia V Botchkareva, Andrey A Sharov, Daniel Thornton, Holly N Wilkinson, Matthew J Hardman, Andreas Grutzkau, Joao Pedro de Magalhaes, Andrei Seluanov, Ewan St J Smith, Vera Gorbunova, Andrei N Mardaryev, Chris G Faulkes, Vladimir A Botchkarev.

Naked mole rats (NMRs, Heterocephalus glaber) are long-lived mammals that possess a natural resistance to cancer and other age-related pathologies, maintaining a healthy life span for >30 years. Here, using immunohistochemical and RNAseq analyses, we compare skin morphology, cellular composition and global transcriptome signatures between young and aged (3-4 versus 19-23-year-old) NMRs. We demonstrate that similar to human skin, aging in NMRs is accompanied by a decrease of epidermal thickness, keratinocyte proliferation, and a decline in the number of Merkel cells, T-cells, antigen-presenting cells and melanocytes. Similar to human skin aging, expression levels of dermal collagens are decreased, while Mmp-9 and Mmp-11 levels increased in aged versus young NMR skin. RNAseq analyses reveal that in contrast to human or mouse skin aging, the transcript levels of several longevity-associated (Igfbp3, Igf2bp3, Ing2) and tumor-suppressor genes (Btg2, Cdkn1a, Cdkn2c, Dnmt3a, Hic1, Socs3, Sfrp1, Sfrp5, Thbs1, Tsc1, Zfp36) are increased in aged NMR skin. Overall, these data suggest that specific features in the NMR skin aging transcriptome might contribute to the resistance of NMRs to spontaneous skin carcinogenesis and provide a platform for further investigations of NMRs as a model organism for studying the biology and disease resistance of human skin.

DOI: https://doi.org/10.1016/j.jid.2022.04.028
Nat Commun. 2022 Jun 17. 13(1): 3486

FUNDC2 promotes liver tumorigenesis by inhibiting MFN1-mediated mitochondrial fusion.

Shuaifeng Li, Shixun Han, Qi Zhang, Yibing Zhu, Haitao Zhang, Junli Wang, Yang Zhao, Jianhui Zhao, Lin Su, Li Li, Dawang Zhou, Cunqi Ye, Xin-Hua Feng, Tingbo Liang, Bin Zhao.

Mitochondria generate ATP and play regulatory roles in various cellular activities. Cancer cells often exhibit fragmented mitochondria. However, the underlying mechanism remains elusive. Here we report that a mitochondrial protein FUN14 domain containing 2 (FUNDC2) is transcriptionally upregulated in primary mouse liver tumors, and in approximately 40% of human hepatocellular carcinoma (HCC). Importantly, elevated FUNDC2 expression inversely correlates with patient survival, and its knockdown inhibits liver tumorigenesis in mice. Mechanistically, the amino-terminal region of FUNDC2 interacts with the GTPase domain of mitofusin 1 (MFN1), thus inhibits its activity in promoting fusion of outer mitochondrial membrane. As a result, loss of FUNDC2 leads to mitochondrial elongation, decreased mitochondrial respiration, and reprogrammed cellular metabolism. These results identified a mechanism of mitochondrial fragmentation in cancer through MFN1 inhibition by FUNDC2, and suggested FUNDC2 as a potential therapeutic target of HCC.

DOI: https://doi.org/10.1038/s41467-022-31187-6
Front Mol Biosci. 2022 ;9 851038

Folding and Evolution of a Repeat Protein on the Ribosome.

José Alberto León-González, Perline Flatet, María Soledad Juárez-Ramírez, José Arcadio Farías-Rico.

  Life on earth is the result of the work of proteins, the cellular nanomachines that fold into elaborated 3D structures to perform their functions. The ribosome synthesizes all the proteins of the biosphere, and many of them begin to fold during translation in a process known as cotranslational folding. In this work we discuss current advances of this field and provide computational and experimental data that highlight the role of ribosome in the evolution of protein structures. First, we used the sequence of the Ankyrin domain from the Drosophila Notch receptor to launch a deep sequence-based search. With this strategy, we found a conserved 33-residue motif shared by different protein folds. Then, to see how the vectorial addition of the motif would generate a full structure we measured the folding on the ribosome of the Ankyrin repeat protein. Not only the on-ribosome folding data is in full agreement with classical in vitro biophysical measurements but also it provides experimental evidence on how folded proteins could have evolved by duplication and fusion of smaller fragments in the RNA world. Overall, we discuss how the ribosomal exit tunnel could be conceptualized as an active site that is under evolutionary pressure to influence protein folding.

Keywords:  cotranslational; evolution; folding; protein; ribosome

DOI:  https://doi.org/10.3389/fmolb.2022.851038
Front Mol Biosci. 2022 ;9 915301

Current Knowledge on the Role of Cardiolipin Remodeling in the Context of Lipid Oxidation and Barth Syndrome.

Zhuqing Liang, Michael W Schmidtke, Miriam L Greenberg.

  Barth syndrome (BTHS, OMIM 302060) is a genetic disorder caused by variants of the TAFAZZIN gene (G 4.5, OMIM 300394). This debilitating disorder is characterized by cardio- and skeletal myopathy, exercise intolerance, and neutropenia. TAFAZZIN is a transacylase that catalyzes the second step in the cardiolipin (CL) remodeling pathway, preferentially converting saturated CL species into unsaturated CLs that are susceptible to oxidation. As a hallmark mitochondrial membrane lipid, CL has been shown to be essential in a myriad of pathways, including oxidative phosphorylation, the electron transport chain, intermediary metabolism, and intrinsic apoptosis. The pathological severity of BTHS varies substantially from one patient to another, even in individuals bearing the same TAFAZZIN variant. The physiological modifier(s) leading to this disparity, along with the exact molecular mechanism linking CL to the various pathologies, remain largely unknown. Elevated levels of reactive oxygen species (ROS) have been identified in numerous BTHS models, ranging from yeast to human cell lines, suggesting that cellular ROS accumulation may participate in the pathogenesis of BTHS. Although the exact mechanism of how oxidative stress leads to pathogenesis is unknown, it is likely that CL oxidation plays an important role. In this review, we outline what is known about CL oxidation and provide a new perspective linking the functional relevance of CL remodeling and oxidation to ROS mitigation in the context of BTHS.

Keywords:  apoptosis; barth syndrome; cardiolipin; cardiolipin remodeling; oxidation

DOI:  https://doi.org/10.3389/fmolb.2022.915301