bims-minimp 2022-04-03 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–04–03
23 papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Mitochondrial ROS signalling requires uninterrupted electron flow and is lost during ageing in flies.
Targeted clearance of p21- but not p16-positive senescent cells prevents radiation-induced osteoporosis and increased marrow adiposity.
Starting the engine of the powerhouse: mitochondrial transcription and beyond.
Contribution of proteases to the hallmarks of aging and to age-related neurodegeneration.
BAX and BAK dynamics control mitochondrial DNA release during apoptosis.
The roles and mechanisms of senescence-associated secretory phenotype (SASP): can it be controlled by senolysis?
An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model.
ER-mitochondria communication is involved in NLRP3 inflammasome activation under stress conditions in the innate immune system.
cGAS-STING mediates cytoplasmic mitochondrial-DNA-induced inflammatory signal transduction during accelerated senescence of pancreatic β-cells induced by metabolic stress.
Mitochondrial Quality Control: the Role in Cardiac Injury.
Regulatory networks controlling mitochondrial quality control in skeletal muscle.
Partial inhibition of mitochondrial-linked pyrimidine synthesis increases tumorigenic potential and lysosome accumulation.
Transient changes to metabolic homeostasis initiate mitochondrial adaptation to endurance exercise.
Endoplasmic reticulum-mitochondria miscommunication is an early and causal trigger of hepatic insulin resistance and steatosis.
Quantitative super-resolution microscopy reveals promoting mitochondrial interconnectivity protects against AKI.
Pro-inflammatory polarization of macrophages is associated with reduced endoplasmic reticulum-mitochondria interaction.
The synthesis and properties of mitochondrial targeted iron chelators.
System-level metabolic modeling facilitates unveiling metabolic signature in exceptional longevity.
Disruption of mitochondrial complex III in cap mesenchyme but not in ureteric progenitors results in defective nephrogenesis associated with amino acid deficiency.
Time to Target Mitochondrial Reactive Oxygen Species Generation from Complex I.
Time-dependent communication between multiple amino acids during protein folding.
Docking and molecular simulations reveal a quinone binding site on the surface of respiratory complex I.
Roles of miR-124-3p/Scd1 in urolithin A-induced brown adipocyte differentiation and succinate-dependent regulation of mitochondrial complex II.

Geroscience. 2022 Mar 30.

Mitochondrial ROS signalling requires uninterrupted electron flow and is lost during ageing in flies.

Charlotte Graham, Rhoda Stefanatos, Angeline E H Yek, Ruth V Spriggs, Samantha H Y Loh, Alejandro Huerta Uribe, Tong Zhang, L Miguel Martins, Oliver D K Maddocks, Filippo Scialo, Alberto Sanz.

  Mitochondrial reactive oxygen species (mtROS) are cellular messengers essential for cellular homeostasis. In response to stress, reverse electron transport (RET) through respiratory complex I generates high levels of mtROS. Suppression of ROS production via RET (ROS-RET) reduces survival under stress, while activation of ROS-RET extends lifespan in basal conditions. Here, we demonstrate that ROS-RET signalling requires increased electron entry and uninterrupted electron flow through the electron transport chain (ETC). We find that in old fruit flies, ROS-RET is abolished when electron flux is decreased and that their mitochondria produce consistently high levels of mtROS. Finally, we demonstrate that in young flies, limiting electron exit, but not entry, from the ETC phenocopies mtROS generation observed in old individuals. Our results elucidate the mechanism by which ROS signalling is lost during ageing.

Keywords:  Ageing; Complex I; Complex IV; Drosophila; Mitochondria; Reactive oxygen species; Reverse electron transport

DOI:  https://doi.org/10.1007/s11357-022-00555-x
Aging Cell. 2022 Apr 01. e13602

Targeted clearance of p21- but not p16-positive senescent cells prevents radiation-induced osteoporosis and increased marrow adiposity.

Abhishek Chandra, Anthony B Lagnado, Joshua N Farr, Madison Doolittle, Tamara Tchkonia, James L Kirkland, Nathan K LeBrasseur, Paul D Robbins, Laura J Niedernhofer, Yuji Ikeno, João F Passos, David G Monroe, Robert J Pignolo, Sundeep Khosla.

  Cellular senescence, which is a major cause of tissue dysfunction with aging and multiple other conditions, is known to be triggered by p16Ink4a or p21Cip1 , but the relative contributions of each pathway toward inducing senescence are unclear. Here, we directly addressed this issue by first developing and validating a p21-ATTAC mouse with the p21Cip1 promoter driving a "suicide" transgene encoding an inducible caspase-8 which, upon induction, selectively kills p21Cip1 -expressing senescent cells. Next, we used the p21-ATTAC mouse and the established p16-INK-ATTAC mouse to directly compare the contributions of p21Cip1 versus p16Ink4a in driving cellular senescence in a condition where a tissue phenotype (bone loss and increased marrow adiposity) is clearly driven by cellular senescence-specifically, radiation-induced osteoporosis. Using RNA in situ hybridization, we confirmed the reduction in radiation-induced p21Cip1 - or p16Ink4a -driven transcripts following senescent cell clearance in both models. However, only clearance of p21Cip1 +, but not p16Ink4a +, senescent cells prevented both radiation-induced osteoporosis and increased marrow adiposity. Reduction in senescent cells with dysfunctional telomeres following clearance of p21Cip1 +, but not p16Ink4a +, senescent cells also reduced several of the radiation-induced pro-inflammatory senescence-associated secretory phenotype factors. Thus, by directly comparing senescent cell clearance using two parallel genetic models, we demonstrate that radiation-induced osteoporosis is driven predominantly by p21Cip1 - rather than p16Ink4a -mediated cellular senescence. Further, this approach can be used to dissect the contributions of these pathways in other senescence-associated conditions, including aging across tissues.

Keywords:  bone; radiation; senescence

DOI:  https://doi.org/10.1111/acel.13602
Biol Chem. 2022 Mar 31.

Starting the engine of the powerhouse: mitochondrial transcription and beyond.

Maria Miranda, Nina A Bonekamp, Inge Kühl.

  Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.

Keywords:   inhibitor of mitochondrial transcription; PPR proteins; mitochondria; mitochondrial disease; mitochondrial gene expression; mitochondrial transcription

DOI:  https://doi.org/10.1515/hsz-2021-0416
Aging Cell. 2022 Mar 29. e13603

Contribution of proteases to the hallmarks of aging and to age-related neurodegeneration.

Mamta Rai, Michelle Curley, Zane Coleman, Fabio Demontis.

  Protein quality control ensures the degradation of damaged and misfolded proteins. Derangement of proteostasis is a primary cause of aging and age-associated diseases. The ubiquitin-proteasome and autophagy-lysosome play key roles in proteostasis but, in addition to these systems, the human genome encodes for ~600 proteases, also known as peptidases. Here, we examine the role of proteases in aging and age-related neurodegeneration. Proteases are present across cell compartments, including the extracellular space, and their substrates encompass cellular constituents, proteins with signaling functions, and misfolded proteins. Proteolytic processing by proteases can lead to changes in the activity and localization of substrates or to their degradation. Proteases cooperate with the autophagy-lysosome and ubiquitin-proteasome systems but also have independent proteolytic roles that impact all hallmarks of cellular aging. Specifically, proteases regulate mitochondrial function, DNA damage repair, cellular senescence, nutrient sensing, stem cell properties and regeneration, protein quality control and stress responses, and intercellular signaling. The capacity of proteases to regulate cellular functions translates into important roles in preserving tissue homeostasis during aging. Consequently, proteases influence the onset and progression of age-related pathologies and are important determinants of health span. Specifically, we examine how certain proteases promote the progression of Alzheimer's, Huntington's, and/or Parkinson's disease whereas other proteases protect from neurodegeneration. Mechanistically, cleavage by proteases can lead to the degradation of a pathogenic protein and hence impede disease pathogenesis. Alternatively, proteases can generate substrate byproducts with increased toxicity, which promote disease progression. Altogether, these studies indicate the importance of proteases in aging and age-related neurodegeneration.

Keywords:  aging; extracellular proteostasis; neurodegeneration; peptidase; protease; proteolysis

DOI:  https://doi.org/10.1111/acel.13603
Cell Death Differ. 2022 Mar 26.

BAX and BAK dynamics control mitochondrial DNA release during apoptosis.

Takahiro Yamazaki, Lorenzo Galluzzi.

DOI: https://doi.org/10.1038/s41418-022-00985-2
Inflamm Regen. 2022 Apr 02. 42(1): 11

The roles and mechanisms of senescence-associated secretory phenotype (SASP): can it be controlled by senolysis?

Naoko Ohtani.

  Cellular senescence is a state of irreversible cell cycle arrest that can be induced by a variety of potentially oncogenic stimuli, including DNA damage. Hence, senescence has long been considered to suppress tumorigenesis, acting as a guardian of homeostasis. However, recent studies have revealed that senescent cells exhibit the secretion of a series of inflammatory cytokines, chemokines, growth factors, and matrix remodeling factors that alter the local tissue environment and contribute to chronic inflammation and cancer. This senescence phenotype is termed as senescence-associated secretory phenotype (SASP) and is observed not only in cultured cells in vitro but also in vivo. Recently, the physiological and pathological roles of SASP have been increasingly clarified. Notably, several studies have reported that the intrinsic mechanism of SASP factor production is predominantly mediated through the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway by aberrantly accumulated DNA fragments from the nucleus of senescent cells. In contrast, various extrinsic triggers of SASP also exist in vivo, for example, the SASP induction in hepatic stellate cells in the tumor microenvironment of obesity-associated liver cancer by the translocated gut microbial metabolites. Recently, the strategy for the elimination of senescent cells (senolysis) has attracted increasing attention. Thus, the role of SASP and the effects and outcomes of senolysis in vivo will be also discussed in this review.

Keywords:  Cellular senescence; Senescence-associated secretory phenotype; Senolysis; Toll-like receptor; Tumor microenvironment; cGAS-STING pathway

DOI:  https://doi.org/10.1186/s41232-022-00197-8
J Vis Exp. 2022 Mar 09.

An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model.

Andrea Cavaliere, Silvia Marchet, Ivano Di Meo, Valeria Tiranti.

Deficiency of the mitochondrial respiratory chain complexes that carry out oxidative phosphorylation (OXPHOS) is the biochemical marker of human mitochondrial disorders. From a genetic point of view, the OXPHOS represents a unique example because it results from the complementation of two distinct genetic systems: nuclear DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, OXPHOS defects can be due to mutations affecting nuclear and mitochondrial encoded genes. The groundbreaking work by King and Attardi, published in 1989, showed that human cell lines depleted of mtDNA (named rho0) could be repopulated by exogenous mitochondria to obtain the so-called "transmitochondrial cybrids." Thanks to these cybrids containing mitochondria derived from patients with mitochondrial disorders (MDs) and nuclei from rho0 cells, it is possible to verify whether a defect is mtDNA- or nDNA-related. These cybrids are also a powerful tool to validate the pathogenicity of a mutation and study its impact at a biochemical level. This paper presents a detailed protocol describing cybrid generation, selection, and characterization.

DOI: https://doi.org/10.3791/63452
Cell Mol Life Sci. 2022 Mar 28. 79(4): 213

ER-mitochondria communication is involved in NLRP3 inflammasome activation under stress conditions in the innate immune system.

Ana Catarina Pereira, Jessica De Pascale, Rosa Resende, Susana Cardoso, Isabel Ferreira, Bruno Miguel Neves, Mylène A Carrascal, Mónica Zuzarte, Nuno Madeira, Sofia Morais, António Macedo, Anália do Carmo, Paula I Moreira, Maria Teresa Cruz, Cláudia F Pereira.

  Endoplasmic reticulum (ER) stress and mitochondrial dysfunction, which are key events in the initiation and/or progression of several diseases, are correlated with alterations at ER-mitochondria contact sites, the so-called "Mitochondria-Associated Membranes" (MAMs). These intracellular structures are also implicated in NLRP3 inflammasome activation which is an important driver of sterile inflammation, however, the underlying molecular basis remains unclear. This work aimed to investigate the role of ER-mitochondria communication during ER stress-induced NLRP3 inflammasome activation in both peripheral and central innate immune systems, by using THP-1 human monocytes and BV2 microglia cells, respectively, as in vitro models. Markers of ER stress, mitochondrial dynamics and mass, as well as NLRP3 inflammasome activation were evaluated by Western Blot, IL-1β secretion was measured by ELISA, and ER-mitochondria contacts were quantified by transmission electron microscopy. Mitochondrial Ca2+ uptake and polarization were analyzed with fluorescent probes, and measurement of aconitase and SOD2 activities monitored mitochondrial ROS accumulation. ER stress was demonstrated to activate the NLRP3 inflammasome in both peripheral and central immune cells. Studies in monocytes indicate that ER stress-induced NLRP3 inflammasome activation occurs by a Ca2+-dependent and ROS-independent mechanism, which is coupled with upregulation of MAMs-resident chaperones, closer ER-mitochondria contacts, as well as mitochondrial depolarization and impaired dynamics. Moreover, enhanced ER stress-induced NLRP3 inflammasome activation in the immune system was found associated with pathological conditions since it was observed in monocytes derived from bipolar disorder (BD) patients, supporting a pro-inflammatory status in BD. In conclusion, by demonstrating that ER-mitochondria communication plays a key role in the response of the innate immune cells to ER stress, this work contributes to elucidate the molecular mechanisms underlying NLRP3 inflammasome activation under stress conditions, and to disclose novel potential therapeutic targets for diseases associated with sterile inflammation.

Keywords:  Bipolar disorder (BD); Calcium; Endoplasmic reticulum (ER) stress; Mitochondria; Sterile inflammation; Unfolded protein response

DOI:  https://doi.org/10.1007/s00018-022-04211-7
FASEB J. 2022 May;36(5): e22266

cGAS-STING mediates cytoplasmic mitochondrial-DNA-induced inflammatory signal transduction during accelerated senescence of pancreatic β-cells induced by metabolic stress.

Huiqing Hu, Ruxing Zhao, Qin He, Chen Cui, Jia Song, Xinghong Guo, Nan Zang, Mengmeng Yang, Ying Zou, Jingwen Yang, Jinquan Li, Liming Wang, Longqing Xia, Lingshu Wang, Falian He, Xinguo Hou, Fei Yan, Li Chen.

  Type 2 diabetes mellitus (T2DM) is an age-related disease characterized by impaired pancreatic β cell function and insulin resistance. Recent studies have shown that the accumulation of senescent β cells under metabolic stress conditions leads to the progression of T2DM, while senolysis can improve the prognosis. However, the specific mechanism of β cell senescence is still unclear. In this study, we found that the increased load of senescence pancreatic β cells in both older mice and obese mice induced by high-fat diet (HFD) (DIO mice) was accompanied by activation of the Cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway and using cGAS or STING small interfering RNA or STING inhibitor C176 to downregulate this pathway reduced the senescence-associated secretion profile (SASP) and senescence of Min6 cells treated with palmitic acid or hydrogen peroxide. C176 intervention in DIO mice also significantly reduced the inflammation and senescence of the islets, thereby protecting the function of pancreatic β cell and glucose metabolism. Our study further revealed that mitochondrial DNA (mtDNA) leakage under metabolic stress conditions was critical for the activation of the cGAS-STING pathway, which can be reversed by the mtDNA depleting agent ethidium bromide. Consistently, mtDNA leakage was more severe in older mice and was accelerated by a chronic HFD. In conclusion, we demonstrate that cytoplasmic mtDNA activates the cGAS-STING pathway to mediate SASP during the accelerated senescence of pancreatic β-cells induced by metabolic stress, and this process can be downregulated by the STING inhibitor C176.

Keywords:  SASP; cGAS-STING pathway; pancreatic β cell function; senescence; type 2 diabetes mellitus

DOI:  https://doi.org/10.1096/fj.202101988R
Front Biosci (Landmark Ed). 2022 Mar 09. 27(3): 96

Mitochondrial Quality Control: the Role in Cardiac Injury.

Grażyna Sygitowicz, Dariusz Sitkiewicz.

  The heart is a highly energy-dependent organ, and most of its energy is provided by mitochondrial oxidative phosphorylation. Therefore, maintaining a well-functioning mitochondrial population is of paramount importance for cardiac homeostasis, since damaged mitochondria produce less adenosine triphosphate (ATP) and generate higher amounts of reactive oxygen species (ROS). Mitochondrial dysfunction is associated with the development of many diseases, including cardiovascular disorders. In this article, we review the role of mitochondria as key determinants of acute myocardial ischemic/reperfusion injury (IRI) and also diabetic cardiomyopathy. The structure and function of mitochondria are regulated by the mitochondrial quality control (MQC) system. Mitochondrial quality control mechanisms involve a series of adaptive responses that preserve mitochondrial structure and function as well as ensure cardiomyocyte survival and cardiac function after injury. This review summarizes the basic mechanisms of MQC, including mitochondrial dynamics (fusion and fission), mitophagy and mitochondrial biogenesis. Mitochondrial dynamics are mainly controlled by the level of fission and fusion proteins and also by their post-translational modifications. In addition, this review aims to provide a contemporary view of the importance of miRNA molecules in the regulation of mitochondrial dynamics at the post-transcriptional level. Thus, miRNAs play an important role not only in the pathogenesis and prognosis of cardiac diseases, but can also be an important therapeutic target.

Keywords:  cardiac injury; fusion and fission; miRNAs; mitochondrial biogenesis; mitochondrial dysfunction; mitophagy

DOI:  https://doi.org/10.31083/j.fbl2703096
Am J Physiol Cell Physiol. 2022 Mar 30.

Regulatory networks controlling mitochondrial quality control in skeletal muscle.

Mikhaela B Slavin, Jonathan M Memme, Ashley N Oliveira, Neushaw Moradi, David A Hood.

The adaptive plasticity of mitochondria within skeletal muscle is regulated by signals converging on a myriad of regulatory networks that operate during conditions of increased (i.e. exercise) and decreased (inactivity, disuse) energy requirements. Notably, some of the initial signals that induce adaptive responses are common to both conditions, differing in their magnitude and temporal pattern, to produce vastly opposing mitochondrial phenotypes. In response to exercise, signaling to PGC-1α and other regulators ultimately produces an abundance of high quality mitochondria, leading to reduced mitophagy and a higher mitochondrial content. This is accompanied by the presence of an enhanced protein quality control system that consists of the protein import machinery as well chaperones and proteases termed the UPRmt. The UPRmt monitors intra-organelle proteostasis, and strives to maintain a mito-nuclear balance between nuclear- and mtDNA-derived gene products via retrograde signaling from the organelle to the nucleus. In addition, antioxidant capacity is improved, affording greater protection against oxidative stress. In contrast, chronic disuse conditions produce similar signaling but result in decrements in mitochondrial quality and content. Thus, the interactive cross-talk of the regulatory networks that control organelle turnover during wide variations in muscle use and disuse remain incompletely understood, despite our improving knowledge of the traditional regulators of organelle content and function. This brief review acknowledges existing regulatory networks and summarizes recent discoveries of novel biological pathways involved in determining organelle biogenesis, dynamics, mitophagy, protein quality control and antioxidant capacity, identifying ample protein targets for therapeutic intervention that determine muscle and mitochondrial health.

DOI: https://doi.org/10.1152/ajpcell.00065.2022
Mitochondrion. 2022 Mar 25. pii: S1567-7249(22)00025-3. [Epub ahead of print]64 73-81

Partial inhibition of mitochondrial-linked pyrimidine synthesis increases tumorigenic potential and lysosome accumulation.

Claus Desler, Jon Ambæk Durhuus, Thomas Lau-Lindestrand Hansen, Sharath Anugula, Nadia Thaulov Zelander, Sisse Bøggild, Lene Juel Rasmussen.

  The correlation between mitochondrial function and oncogenesis is complex and is not fully understood. Here we determine the importance of mitochondrial-linked pyrimidine synthesis for the aggressiveness of cancer cells. The enzyme dihydroorotate dehydrogenase (DHODH) links oxidative phosphorylation to de novo synthesis of pyrimidines. We demonstrate that an inhibition of DHODH results in a respiration-independent significant increase of anchorage-independent growth but does not affect DNA repair ability. Instead, we show an autophagy-independent increase of lysosomes. The results of this study suggest that inhibition of mitochondrial-linked pyrimidine synthesis in cancer cells results in a more aggressive tumor phenotype.

Keywords:  DNA repair; Lysosome increase; Mitochondria; Mitochondrial-linked pyrimidine synthesis; Tumorigenesis

DOI:  https://doi.org/10.1016/j.mito.2022.03.005
Semin Cell Dev Biol. 2022 Mar 26. pii: S1084-9521(22)00096-9. [Epub ahead of print]

Transient changes to metabolic homeostasis initiate mitochondrial adaptation to endurance exercise.

Jessica R Dent, Ben Stocks, Dean G Campelj, Andrew Philp.

  Endurance exercise is well established to increase mitochondrial content and function in skeletal muscle, a process termed mitochondrial biogenesis. Current understanding is that exercise initiates skeletal muscle mitochondrial remodeling via modulation of cellular nutrient, energetic and contractile stress pathways. These subtle changes in the cellular milieu are sensed by numerous transduction pathways that serve to initiate and coordinate an increase in mitochondrial gene transcription and translation. The result of these acute signaling events is the promotion of growth and assembly of mitochondria, coupled to a greater capacity for aerobic ATP provision in skeletal muscle. The aim of this review is to highlight the acute metabolic events induced by endurance exercise and the subsequent molecular pathways that sense this transient change in cellular homeostasis to drive mitochondrial adaptation and remodeling.

Keywords:  Adaptation; Exercise; Metabolism; Mitochondria

DOI:  https://doi.org/10.1016/j.semcdb.2022.03.022
J Hepatol. 2022 Mar 28. pii: S0168-8278(22)00185-4. [Epub ahead of print]

Endoplasmic reticulum-mitochondria miscommunication is an early and causal trigger of hepatic insulin resistance and steatosis.

Agathe Beaulant, Maya Dia, Bruno Pillot, Marie-Agnes Chauvin, Jingwei Ji-Cao, Christine Durand, Nadia Bendridi, Stephanie Chanon, Aurelie Vieille-Marchiset, Claire Crola Da Silva, Stéphanie Patouraux, Rodolphe Anty, Antonio Iannelli, Albert Tran, Philippe Gual, Hubert Vidal, Ludovic Gomez, Melanie Paillard, Jennifer Rieusset.

   BACKGROUND & AIMS: Hepatic insulin resistance in obesity and type 2 diabetes was recently associated with endoplasmic reticulum (ER)-mitochondria miscommunication. These contact sites (mitochondria-associated membranes: MAMs) are highly dynamic and involved in many functions. Up to now, it is not clear if MAM miscommunication could have a causal role in hepatic insulin resistance and steatosis. We therefore aimed to determine whether and how organelle miscommunication plays a role in the onset and progression of hepatic metabolic impairment.
METHODS: We analyzed hepatic ER-mitochondria interactions and calcium exchange in diet-induced obese mice in a time-dependent and reversible manner, and investigated causality in hepatic metabolic alterations by expressing a specific organelle spacer or linker in mouse liver, using adenovirus.
RESULTS: Disruption of ER-mitochondria interactions and calcium exchange is an early event preceding hepatic insulin resistance and steatosis in diet-induced obese mice. Interestingly, an 8-week reversal diet concomitantly reversed hepatic organelle miscommunication and insulin resistance in obese mice. Mechanistically, disrupting structural and functional ER-mitochondria interactions through the hepatic overexpression of the organelle spacer FATE1 was sufficient to impair hepatic insulin action and glucose homeostasis. In addition, FATE1-mediated organelle miscommunication disrupted lipid-related mitochondrial oxidative metabolism and induced hepatic steatosis. Conversely, reinforcement of ER-mitochondria interactions through hepatic expression of a synthetic linker prevented diet-induced glucose intolerance after 4 weeks' overnutrition. Importantly, ER-mitochondria miscommunication was confirmed in the liver of obese patients with type-2 diabetes, and correlated with glycemia, HbA1c and HOMA-IR index.
CONCLUSIONS: ER-mitochondria miscommunication is an early causal trigger of hepatic insulin resistance and steatosis, and can be reversed by switching to a healthy diet. Thus, targeting MAMs could contribute to restoring metabolic homeostasis.
LAY SUMMARY: The literature suggests that interactions between endoplasmic reticulum (ER) and mitochondria could play a dual role in hepatic insulin resistance and steatosis during chronic obesity. The present study reappraised time-dependent regulation of hepatic ER-mitochondria interactions and calcium exchange in diet-induced obese mice and their causal role in hepatic insulin resistance and steatosis. We show that organelle miscommunication is an early causal trigger of hepatic insulin resistance and steatosis, and can be improved by nutritional strategies.

Keywords:  calcium signaling; hepatic insulin resistance; hepatic steatosis; lipid oxidation; mitochondria oxidative metabolism; mitochondria-associated membranes

DOI:  https://doi.org/10.1016/j.jhep.2022.03.017
Kidney360. 2021 Dec;2(12): 1892-1907

Quantitative super-resolution microscopy reveals promoting mitochondrial interconnectivity protects against AKI.

Kensei Taguchi, Bertha C Elias, Evan Krystofiak, Subo Qian, Snehal Sant, Haichun Yang, Agnes B Fogo, Craig R Brooks.

Background: The root of many kidney diseases in humans can be traced to alterations or damage to subcellular organelles. Mitochondrial fragmentation, endoplasmic reticulum (ER) stress, and lysosomal inhibition, among others, ultimately contribute to kidney injury and are the target of therapeutics in development. Although recent technological advancements allow for the understanding of disease states at the cellular level, investigating changes in subcellular organelles from kidney tissue remains challenging.
Methods: Using structured illumination microscopy, we imaged mitochondria and other organelles from paraffin sections of mouse tissue and human kidney biopsy specimens. The resulting images were 3D rendered to quantify mitochondrial size, content, and morphology. Results were compared with those from transmission electron microscopy and segmentation.
Results: Super-resolution imaging reveals kidney tubular epithelial cell mitochondria in rodent and human kidney tissue form large, interconnected networks under basal conditions, which are fragmented with injury. This approach can be expanded to other organelles and cellular structures including autophagosomes, ER, brush border, and cell morphology. We find that, during unilateral ischemia, mitochondrial fragmentation occurs in most tubule cells, and they remain fragmented for >96 hours. Promoting mitochondrial fusion with the fusion promotor M1 preserves mitochondrial morphology and interconnectivity and protects against cisplatin-induced kidney injury.
Conclusions: We provide, for the first time, a nonbiased, semiautomated approach for quantification of the 3D morphology of mitochondria in kidney tissue. Maintaining mitochondrial interconnectivity and morphology protects against kidney injury. Super-resolution imaging has the potential to both drive discovery of novel pathobiologic mechanisms in kidney tissue and broaden the diagnoses that can be made on human biopsy specimens.

DOI: https://doi.org/10.34067/kid.0001602021
Biochem Biophys Res Commun. 2022 Mar 17. pii: S0006-291X(22)00419-3. [Epub ahead of print]606 61-67

Pro-inflammatory polarization of macrophages is associated with reduced endoplasmic reticulum-mitochondria interaction.

Leandro Henrique de Paula Assis, Gabriel de Gabriel Dorighello, Helena Coutinho Franco de Oliveira.

  Macrophages play a role in host defense, tissue remodeling and inflammation. Different inflammatory stimuli drive macrophage phenotypes and responses. In this study we investigated the relationship between macrophages immune phenotype and mitochondrial bioenergetics, cell redox state and endoplasmic reticulum (ER)-mitochondria interaction. Bacterial lipopolysaccharide (LPS) and interferon-γ (IFNγ) pro-inflammatory stimuli decreased oxidative metabolism (basal, phosphorylating and maximal conditions) and increased baseline glycolysis (117%) and glycolytic capacity (43%) in THP-1 macrophages. In contrast, interleukin-4 (IL4) and interleukin-13 (IL13) anti-inflammatory stimuli increased the oxygen consumption rates in baseline conditions (21%) and associated with ATP production (19%). LPS + IFNγ stimuli reduced superoxide anion levels by accelerating its conversion into hydrogen peroxide (H2O2) while IL4+IL13 decreased H2O2 release rates. The source of these oxidants was extra-mitochondrial and associated with increased NOX2 and SOD1 gene expression. LPS + IFNγ stimuli decreased ER-mitochondria contact sites as measured by IP3R1-VDAC1 interaction (34%) and markedly upregulated genes involved in mitochondrial fusion (9-10 fold, MFN1 and 2) and fission (∼7 fold, DRP1 and FIS1). Conversely, IL4+IL13 stimuli did not altered ER-mitochondria interactions nor MFN1 and 2 expression. Together, these results unveil ER-mitochondria interaction pattern as a novel feature of macrophage immunological, metabolic and redox profiles.

Keywords:  Endoplasmic reticulum-mitochondria interaction; Macrophage; Mitochondrial respiration; Oxidants production

DOI:  https://doi.org/10.1016/j.bbrc.2022.03.086
Biometals. 2022 Apr 02.

The synthesis and properties of mitochondrial targeted iron chelators.

Agostino Cilibrizzi, Charareh Pourzand, Vincenzo Abbate, Olivier Reelfs, Laura Versari, Giuseppe Floresta, Robert Hider.

  Iron levels in mitochondria are critically important for the normal functioning of the organelle. Abnormal levels of iron and the associated formation of toxic oxygen radicals have been linked to a wide range of diseases and consequently it is important to be able to both monitor and control levels of the mitochondrial labile iron pool. To this end a series of iron chelators which are targeted to mitochondria have been designed. This overview describes the synthesis of some of these molecules and their application in monitoring mitochondrial labile iron pools and in selectively removing excess iron from mitochondria.

Keywords:  Chelator synthesis; Iron chelation; Iron-probe; Mitochondria

DOI:  https://doi.org/10.1007/s10534-022-00383-8
Aging Cell. 2022 Mar 27. e13595

System-level metabolic modeling facilitates unveiling metabolic signature in exceptional longevity.

Gong-Hua Li, Feifei Han, Fu-Hui Xiao, Kang-Su-Yun Gu, Qiu Shen, Weihong Xu, Wen-Xing Li, Yan-Li Wang, Bin Liang, Jing-Fei Huang, Wenzhong Xiao, Qing-Peng Kong.

  Although it is well known that metabolic control plays a crucial role in regulating the health span and life span of various organisms, little is known for the systems metabolic profile of centenarians, the paradigm of human healthy aging and longevity. Meanwhile, how to well characterize the system-level metabolic states in an organism of interest remains to be a major challenge in systems metabolism research. To address this challenge and better understand the metabolic mechanisms of healthy aging, we developed a method of genome-wide precision metabolic modeling (GPMM) which is able to quantitatively integrate transcriptome, proteome and kinetome data in predictive modeling of metabolic networks. Benchmarking analysis showed that GPMM successfully characterized metabolic reprogramming in the NCI-60 cancer cell lines; it dramatically improved the performance of the modeling with an R2 of 0.86 between the predicted and experimental measurements over the performance of existing methods. Using this approach, we examined the metabolic networks of a Chinese centenarian cohort and identified the elevated fatty acid oxidation (FAO) as the most significant metabolic feature in these long-lived individuals. Evidence from serum metabolomics supports this observation. Given that FAO declines with normal aging and is impaired in many age-related diseases, our study suggests that the elevated FAO has potential to be a novel signature of healthy aging of humans.

Keywords:  GPMM; aging; longevity; metabolic modeling; omics integration; systems biology

DOI:  https://doi.org/10.1111/acel.13595
Kidney Int. 2022 Mar 24. pii: S0085-2538(22)00212-5. [Epub ahead of print]

Disruption of mitochondrial complex III in cap mesenchyme but not in ureteric progenitors results in defective nephrogenesis associated with amino acid deficiency.

Nan Guan, Hanako Kobayashi, Ken Ishii, Olena Davidoff, Feng Sha, Talat A Ikizler, Chuan-Ming Hao, Navdeep S Chandel, Volker H Haase.

  Oxidative metabolism in mitochondria regulates cellular differentiation and gene expression through intermediary metabolites and reactive oxygen species. Its role in kidney development and pathogenesis is not completely understood. Here we inactivated ubiquinone-binding protein QPC, a subunit of mitochondrial complex III, in two types of kidney progenitor cells to investigate the role of mitochondrial electron transport in kidney homeostasis. Inactivation of QPC in sine oculis-related homeobox 2 (SIX2)-expressing cap mesenchyme progenitors, which give rise to podocytes and all nephron segments except collecting ducts, resulted in perinatal death from severe kidney dysplasia. This was characterized by decreased proliferation of SIX2 progenitors and their failure to differentiate into kidney epithelium. QPC inactivation in cap mesenchyme progenitors induced activating transcription factor 4-mediated nutritional stress responses and was associated with a reduction in kidney tricarboxylic acid cycle metabolites and amino acid levels, which negatively impacted purine and pyrimidine synthesis. In contrast, QPC inactivation in ureteric tree epithelial cells, which give rise to the kidney collecting system, did not inhibit ureteric differentiation, and resulted in the development of functional kidneys that were smaller in size. Thus, our data demonstrate that mitochondrial oxidative metabolism is critical for the formation of cap mesenchyme-derived nephron segments but dispensable for formation of the kidney collecting system. Hence, our studies reveal compartment-specific needs for metabolic reprogramming during kidney development.

Keywords:  TCA cycle; amino acids; kidney development; mitochondria; mitochondrial complex III; mitochondrial electron transport chain

DOI:  https://doi.org/10.1016/j.kint.2022.02.030
Function (Oxf). 2022 ;3(2): zqac010

Time to Target Mitochondrial Reactive Oxygen Species Generation from Complex I.

Qun Chen, Edward J Lesnefsky.

DOI: https://doi.org/10.1093/function/zqac010
Chem Sci. 2021 Apr 28. 12(16): 5944-5951

Time-dependent communication between multiple amino acids during protein folding.

Song-Ho Chong, Sihyun Ham.

Cooperativity is considered to be a key organizing principle behind biomolecular assembly, recognition and folding. However, it has remained very challenging to quantitatively characterize how cooperative processes occur on a concerted, multiple-interaction basis. Here, we address how and when the folding process is cooperative on a molecular scale. To this end, we analyze multipoint time-correlation functions probing time-dependent communication between multiple amino acids, which were computed from long folding simulation trajectories. We find that the simultaneous multiple amino-acid contact formation, which is absent in the unfolded state, starts to develop only upon entering the folding transition path. Interestingly, the transition state, whose presence is connected to the macrostate cooperative behavior known as the two-state folding, can be identified as the state in which the amino-acid cooperativity is maximal. Thus, our work not only provides a new mechanistic view on how protein folding proceeds on a multiple-interaction basis, but also offers a conceptually novel characterization of the folding transition state and the molecular origin of the phenomenological cooperative folding behavior. Moreover, the multipoint correlation function approach adopted here is general and can be used to expand the understanding of cooperative processes in complex chemical and biomolecular systems.

DOI: https://doi.org/10.1039/d0sc07025d
FEBS Lett. 2022 Apr 01.

Docking and molecular simulations reveal a quinone binding site on the surface of respiratory complex I.

Amina Djurabekova, Etienne Galemou Yoga, Aino Nyman, Antti Pirttikoski, Volker Zickermann, Outi Haapanen, Vivek Sharma.

The first component of the mitochondrial electron transport chain is respiratory complex I. Several high-resolution structures of complex I from different species have been resolved. However, despite these significant achievements, the mechanism of redox-coupled proton pumping remains elusive. Here, we combined atomistic docking, molecular dynamics simulations and site-directed mutagenesis on respiratory complex I from Yarrowia lipolytica to identify a quinone (Q) binding site on its surface near the horizontal amphipathic helices of ND1 and NDUFS7 subunits. The surface-bound Q makes stable interactions with conserved charged and polar residues, including the highly conserved Arg72 from the NDUFS7 subunit. The binding and dynamics of a Q molecule at the surface-binding site raises interesting possibilities about the mechanism of complex I, which are discussed.

DOI: https://doi.org/10.1002/1873-3468.14346
Biochem Biophys Res Commun. 2022 Mar 24. pii: S0006-291X(22)00457-0. [Epub ahead of print]

Roles of miR-124-3p/Scd1 in urolithin A-induced brown adipocyte differentiation and succinate-dependent regulation of mitochondrial complex II.

Qian Li, Lina Wang, Huan Liu, Weiyuan Ren, Zhiying Zhang, Bo Xia.

  Brown adipocytes have been linked to managing human obesity and related metabolic diseases. A large number of natural products have emerged that can activate brown adipocytes tissue (BAT) to active thermogenesis, but the epigenetic mechanisms have not been fully resolved. In this study, we identified the induction of miR-124-3p by urolithin A (UA) as a means to increase the thermogenic activity of brown adipocytes. Overexpression of miR-124-3p enhances thermogenesis by increasing mitochondrial content in brown adipocytes. Mechanistically, to clarify that miR-124-3p affects fatty acid synthesis using bioinformatics methods, it is clear that miR-124 affects the synthesis of fatty acids through the enrichment analysis of the KEGG pathway, and using dual luci. ferase to determine the target gene as stearoyl-CoA desaturase 1 (SCD1) while controlling rates of fatty acids synthesis and de novo brown fat biogenesis. Finally, in the overexpression of miR-124-3p and UA-treated BAT, succinate accumulation was enhanced in cells and fueled mitochondrial complex II activities. This study highlights a miR-124-3p/SCD1/succinate pathway that stimulates thermogenesis of BAT via the modulatory roles of UA.

Keywords:  Mitochondrial complex II; SCD1; Succinate; Urolithin A; miR-124-3p

DOI:  https://doi.org/10.1016/j.bbrc.2022.03.112