bims-mitdyn 2022-02-27 papers

bims-mitdyn

Biomed News

on Mitochondrial dynamics: mechanisms

Issue of 2022‒02‒27
thirteen papers selected by
Edmond Chan
Queen’s University, School of Medicine

Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly.
Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy.
Brown adipose TRX2 deficiency activates mtDNA-NLRP3 to impair thermogenesis and protect against diet-induced insulin resistance.
Broad activation of the PRKN pathway triggers synaptic failure by disrupting synaptic mitochondrial supply in early tauopathy.
PINK1-parkin-mediated neuronal mitophagy deficiency in prion disease.
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
A new role of the early endosome in restricting NLRP3 inflammasome via mitophagy.
Aberrant cyclin C nuclear release induces mitochondrial fragmentation and dysfunction in MED13L syndrome fibroblasts.
FoxO transcription factors in mitochondrial homeostasis.
Measurement of Inflammasome-Induced Mitochondrial Dysfunction by Flow Cytometry.
Frequency- and spike-timing-dependent mitochondrial Ca2+ signaling regulates the metabolic rate and synaptic efficacy in cortical.
Mitochondrial and metabolic remodeling in human skin fibroblasts in response to glucose availability.
RNA-binding protein YBX1 promotes brown adipogenesis and thermogenesis via PINK1/PRKN-mediated mitophagy.

Proc Natl Acad Sci U S A. 2022 Mar 01. pii: e2110357119. [Epub ahead of print]119(9):

Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly.

Luke E Formosa, Shadi Maghool, Alice J Sharpe, Boris Reljic, Linden Muellner-Wong, David A Stroud, Michael T Ryan, Megan J Maher.

  Cytochrome c oxidase (COX) assembly factor 7 (COA7) is a metazoan-specific assembly factor, critical for the biogenesis of mitochondrial complex IV (cytochrome c oxidase). Although mutations in COA7 have been linked to complex IV assembly defects and neurological conditions such as peripheral neuropathy, ataxia, and leukoencephalopathy, the precise role COA7 plays in the biogenesis of complex IV is not known. Here, we show that loss of COA7 blocks complex IV assembly after the initial step where the COX1 module is built, progression from which requires the incorporation of copper and addition of the COX2 and COX3 modules. The crystal structure of COA7, determined to 2.4 Å resolution, reveals a banana-shaped molecule composed of five helix-turn-helix (α/α) repeats, tethered by disulfide bonds. COA7 interacts transiently with the copper metallochaperones SCO1 and SCO2 and catalyzes the reduction of disulfide bonds within these proteins, which are crucial for copper relay to COX2. COA7 binds heme with micromolar affinity, through axial ligation to the central iron atom by histidine and methionine residues. We therefore propose that COA7 is a heme-binding disulfide reductase for regenerating the copper relay system that underpins complex IV assembly.

Keywords:  COA7; X-ray crystallography; cytochrome c oxidase; heme; mitochondria

DOI:  https://doi.org/10.1073/pnas.2110357119
Neuron. 2022 Feb 19. pii: S0896-6273(22)00105-2. [Epub ahead of print]

Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy.

Angelika B Harbauer, J Tabitha Hees, Simone Wanderoy, Inmaculada Segura, Whitney Gibbs, Yiming Cheng, Martha Ordonez, Zerong Cai, Romain Cartoni, Ghazaleh Ashrafi, Chen Wang, Fabiana Perocchi, Zhigang He, Thomas L Schwarz.

  PTEN-induced kinase 1 (PINK1) is a short-lived protein required for the removal of damaged mitochondria through Parkin translocation and mitophagy. Because the short half-life of PINK1 limits its ability to be trafficked into neurites, local translation is required for this mitophagy pathway to be active far from the soma. The Pink1 transcript is associated and cotransported with neuronal mitochondria. In concert with translation, the mitochondrial outer membrane proteins synaptojanin 2 binding protein (SYNJ2BP) and synaptojanin 2 (SYNJ2) are required for tethering Pink1 mRNA to mitochondria via an RNA-binding domain in SYNJ2. This neuron-specific adaptation for the local translation of PINK1 provides distal mitochondria with a continuous supply of PINK1 for the activation of mitophagy.

Keywords:  OMP25; PINK1; Parkinson disease; RNA transport; SYNJ2BP; hitchhiking; local translation; mitophagy; synaptojanin2

DOI:  https://doi.org/10.1016/j.neuron.2022.01.035
J Clin Invest. 2022 Feb 24. pii: e148852. [Epub ahead of print]

Brown adipose TRX2 deficiency activates mtDNA-NLRP3 to impair thermogenesis and protect against diet-induced insulin resistance.

Yanrui Huang, Jenny H Zhou, Haifeng Zhang, Alberto Canfrán-Duque, Abhishek K Singh, Rachel J Perry, Gerald Shulman, Carlos Fernandez-Hernando, Wang Min.

  Brown adipose tissue (BAT), a crucial heat-generating organ, regulate whole-body energy metabolism by mediating thermogenesis. BAT inflammation is implicated in the pathogenesis of mitochondrial dysfunction and impaired thermogenesis. However, the link between BAT inflammation and systematic metabolism remains unclear. Herein, we use mice with BAT deficiency of thioredoxin-2 (TRX2), a protein that scavenges mitochondrial reactive oxygen species (ROS), to evaluate the impact of BAT inflammation on metabolism and thermogenesis and its underlying mechanism. Our results describe that BAT-specific TRX2 ablation improves systematic metabolic performance via enhancing lipid uptake, which protects mice from diet-induced obesity, hypertriglyceridemia, and insulin resistance. TRX2 deficiency impairs adaptive thermogenesis by suppressing fatty acid oxidation. Mechanistically, loss of TRX2 induces excessive mitochondrial ROS, mitochondrial integrity disruption, and cytosolic release of mitochondrial DNA, which in turn activate aberrant innate immune responses in BAT, including the cGAS-STING and the NLRP3 inflammasome pathways. We identify NLRP3 as a key converging point, as its inhibition reverses both the thermogenesis defect and the metabolic benefits seen under nutrient overload in BAT-specific Trx2-deficient mice. In conclusion, we identify TRX2 as a critical hub integrating oxidative stress, inflammation, and lipid metabolism in BAT; uncovering an adaptive mechanism underlying the link between BAT inflammation and systematic metabolism.

Keywords:  Adipose tissue; Inflammation; Innate immunity; Metabolism; Mitochondria

DOI:  https://doi.org/10.1172/JCI148852
Autophagy. 2022 Feb 19. 1-3

Broad activation of the PRKN pathway triggers synaptic failure by disrupting synaptic mitochondrial supply in early tauopathy.

Yu Young Jeong, Nuo Jia, Dhasarathan Ganesan, Qian Cai.

  Mitochondrial defects are a hallmark of Alzheimer disease (AD), with pathologically phosphorylated MAPT/tau (phospho-MAPT/tau) reported to induce mitochondrial damage. Mitophagy constitutes a key pathway of mitochondrial quality control by which damaged mitochondria are sequestered within autophagosomes for lysosomal degradation. However, the mechanistic understanding of mitophagy and its association with pathologies under tauopathy conditions remains very limited. Here, we reveal that mitochondrial stress under phospho-MAPT/tau-mediated challenges broadly activates PRKN-mediated mitophagy which induces an unexpected effect - depletion of mitochondria from synaptic terminals, a characteristic feature in early tauopathy. PRKN activation accelerates RHOT1 turnover and consequently halts RHOT1-mediated mitochondrial anterograde movement, which disrupts mitochondrial supply to tauopathy synapses and thereby impairs synaptic function. Strikingly, increasing RHOT1 levels prevents synapse loss and reverses cognitive impairment in tauopathy mice by restoring synaptic mitochondrial populations. Thus, our study uncovers an important early mechanism underlying tauopathy-linked synaptic failure and opens a new avenue for specifically targeting early synaptic dysfunction in tauopathies, including AD.Abbreviations: AAV: adeno-associated virus; AD: Alzheimer disease; FTD: Frontotemporal dementia; LTP: long-term potentiation; Δψm: mitochondrial membrane potential; Phospho-MAPT/tau: hyperphosphorylated Microtubule Associated Protein Tau/tau; RHOT1: ras homolog family member T1; RNAi: RNA interference; Tg: transgenic.

Keywords:  Alzheimer; PRKN; RHOT1; mitochondrial anterograde transport; mitophagy; synaptic dysfunction; synaptic mitochondrial deficits; tauopathy

DOI:  https://doi.org/10.1080/15548627.2022.2039987
Cell Death Dis. 2022 Feb 18. 13(2): 162

PINK1-parkin-mediated neuronal mitophagy deficiency in prion disease.

Jie Li, Mengyu Lai, Xixi Zhang, Zhiping Li, Dongming Yang, Mengyang Zhao, Dongdong Wang, Zhixin Sun, Sharjeel Ehsan, Wen Li, Hongli Gao, Deming Zhao, Lifeng Yang.

A persistent accumulation of damaged mitochondria is part of prion disease pathogenesis. Normally, damaged mitochondria are cleared via a major pathway that involves the E3 ubiquitin ligase parkin and PTEN-induced kinase 1 (PINK1) that together initiate mitophagy, recognize and eliminate damaged mitochondria. However, the precise mechanisms underlying mitophagy in prion disease remain largely unknown. Using prion disease cell models, we observed PINK1-parkin-mediated mitophagy deficiency in which parkin depletion aggravated blocked mitochondrial colocalization with LC3-II-labeled autophagosomes, and significantly increased mitochondrial protein levels, which led to inhibited mitophagy. Parkin overexpression directly induced LC3-II colocalization with mitochondria and alleviated defective mitophagy. Moreover, parkin-mediated mitophagy was dependent on PINK1, since PINK1 depletion blocked mitochondrial Parkin recruitment and reduced optineurin and LC3-II proteins levels, thus inhibiting mitophagy. PINK1 overexpression induced parkin recruitment to the mitochondria, which then stimulated mitophagy. In addition, overexpressed parkin and PINK1 also protected neurons from apoptosis. Furthermore, we found that supplementation with two mitophagy-inducing agents, nicotinamide mononucleotide (NMN) and urolithin A (UA), significantly stimulated PINK1-parkin-mediated mitophagy. However, compared with NMN, UA could not alleviate prion-induced mitochondrial fragmentation and dysfunction, and neuronal apoptosis. These findings show that PINK1-parkin-mediated mitophagy defects lead to an accumulation of damaged mitochondria, thus suggesting that interventions that stimulate mitophagy may be potential therapeutic targets for prion diseases.

DOI: https://doi.org/10.1038/s41419-022-04613-2
Nat Biotechnol. 2022 Feb 24.

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.

Tyler E Miller, Caleb A Lareau, Julia A Verga, Erica A K DePasquale, Vincent Liu, Daniel Ssozi, Katalin Sandor, Yajie Yin, Leif S Ludwig, Chadi A El Farran, Duncan M Morgan, Ansuman T Satpathy, Gabriel K Griffin, Andrew A Lane, J Christopher Love, Bradley E Bernstein, Vijay G Sankaran, Peter van Galen.

The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogate complex tissues. Here, we combine common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling high-confidence mutation detection. The method successfully identifies skewed immune-cell expansions in primary human clonal hematopoiesis.

DOI: https://doi.org/10.1038/s41587-022-01210-8
Autophagy. 2022 Feb 23. 1-3

A new role of the early endosome in restricting NLRP3 inflammasome via mitophagy.

Kelvin Ka Lok Wu, Kenneth King Yip Cheng.

  NLRP3 (NLR family pyrin domain containing 3) inflammasome is a potent mediator of inflammation due to its ability to produce the pro-inflammatory cytokines IL1B (interleukin 1 beta) and IL18 in response to numerous danger signals and pathogens. Mitophagy, a selective form of autophagy, restricts NLRP3 inflammasome activation by limiting the mitochondrial-derived danger signals. Here, we demonstrated that the adaptor protein APPL1 together with its interaction partner RAB5 in early endosomes negatively regulate NLRP3 inflammasome activation via induction of mitophagy in macrophages. Hematopoietic-deletion of Appl1 exacerbates systemic NLRP3 inflammasome activation in rodent models under obese or septic conditions. Our study identified a new regulatory network between early endosomes and mitochondria in control of NLRP3 inflammasome activation.

Keywords:  APPL1; NLRP3 inflammasome; RAB5; early endosome; mitochondria; mitophagy

DOI:  https://doi.org/10.1080/15548627.2022.2040314
iScience. 2022 Feb 18. 25(2): 103823

Aberrant cyclin C nuclear release induces mitochondrial fragmentation and dysfunction in MED13L syndrome fibroblasts.

Kai-Ti Chang, Jan Jezek, Alicia N Campbell, David C Stieg, Zachary A Kiss, Kevin Kemper, Ping Jiang, Hyung-Ok Lee, Warren D Kruger, Peter M van Hasselt, Randy Strich.

  MED13L syndrome is a haploinsufficiency developmental disorder characterized by intellectual disability, heart malformation, and hypotonia. MED13L controls transcription by tethering the cyclin C-Cdk8 kinase module (CKM) to the Mediator complex. In addition, cyclin C has CKM-independent roles in the cytoplasm directing stress-induced mitochondrial fragmentation and regulated cell death. Unstressed MED13L S1497 F/fs patient fibroblasts exhibited aberrant cytoplasmic cyclin C localization, mitochondrial fragmentation, and a 6-fold reduction in respiration. In addition, the fibroblasts exhibited reduced mtDNA copy number, reduction in mitochondrial membrane integrity, and hypersensitivity to oxidative stress. Finally, transcriptional analysis of MED13L mutant fibroblasts revealed reduced mRNA levels for several genes necessary for normal mitochondrial function. Pharmacological or genetic approaches preventing cyclin C-mitochondrial localization corrected the fragmented mitochondrial phenotype and partially restored organelle function. In conclusion, this study found that mitochondrial dysfunction is an underlying defect in cells harboring the MED13L S1497 F/fs allele and identified cyclin C mis-localization as the likely cause. These results provide a new avenue for understanding this disorder.

Keywords:  Biochemistry; Biological sciences; Cell biology

DOI:  https://doi.org/10.1016/j.isci.2022.103823
Biochem J. 2022 Feb 17. 479(4): 525-536

FoxO transcription factors in mitochondrial homeostasis.

Zhiyong Cheng.

  Mitochondria play essential roles in cellular energetics, biosynthesis, and signaling transduction. Dysfunctional mitochondria have been implicated in different diseases such as obesity, diabetes, cardiovascular disease, nonalcoholic fatty liver disease, neurodegenerative disease, and cancer. Mitochondrial homeostasis is controlled by a triad of mitochondrial biogenesis, dynamics (fusion and fission), and autophagy (mitophagy). Studies have underscored FoxO transcription factors as key mitochondrial regulators. Specifically, FoxOs regulate mitochondrial biogenesis by dampening NRF1-Tfam and c-Myc-Tfam cascades directly, and inhibiting NAD-Sirt1-Pgc1α cascade indirectly by inducing Hmox1 or repressing Fxn and Urod. In addition, FoxOs mediate mitochondrial fusion (via Mfn1 and Mfn2) and fission (via Drp1, Fis1, and MIEF2), during which FoxOs elicit regulatory mechanisms at transcriptional, posttranscriptional (e.g. via miR-484/Fis1), and posttranslational (e.g. via Bnip3-calcineurin mediated Drp1 dephosphorylation) levels. Furthermore, FoxOs control mitochondrial autophagy in the stages of autophagosome formation and maturation (e.g. initiation, nucleation, and elongation), mitochondria connected to and engulfed by autophagosome (e.g. via PINK1 and Bnip3 pathways), and autophagosome-lysosome fusion to form autolysosome for cargo degradation (e.g. via Tfeb and cathepsin proteins). This article provides an up-to-date view of FoxOs regulating mitochondrial homeostasis and discusses the potential of targeting FoxOs for therapeutics.

Keywords:  FoxO; autophagy; fusion and fission; homeostasis; mitochondrial biogenesis; mitophagy

DOI:  https://doi.org/10.1042/BCJ20210777
Methods Mol Biol. 2022 ;2459 65-72

Measurement of Inflammasome-Induced Mitochondrial Dysfunction by Flow Cytometry.

Mayoorey M Thasan, Ali A Abdul-Sater.

  A growing body of work has recently highlighted the pivotal role of mitochondria in the initiation and modulation of inflammasome activation. Specifically, mitochondrial dysfunction can induce NLRP3 inflammasome activation, where loss of mitochondrial potential leads to production of reactive oxygen species (ROS) and release of Ca2+, which in turn trigger inflammasome assembly. Therefore, several measures of mitochondrial parameters and components are routinely utilized in studies assessing mechanisms of inflammasome activation. In this chapter, we show detailed protocols on how to employ flow cytometry using three distinct mitochondria-specific dyes to measure mitochondrial ROS (MitoSOX), mitochondrial respiration (Mitotracker deep red), and total mitochondria (Mitotracker green), as well as a dye that measures reduced glutathione (mBBr ).

Keywords:  Bone marrow–derived macrophages (BMDM); Flow cytometry; Glutathione (GSH); Inflammasomes; MitoSOX; Mitochondria; Mitotracker; Monobromobimane (mBBr); Reactive oxygen species (ROS)

DOI:  https://doi.org/10.1007/978-1-0716-2144-8_6
Elife. 2022 Feb 22. pii: e74606. [Epub ahead of print]11

Frequency- and spike-timing-dependent mitochondrial Ca2+ signaling regulates the metabolic rate and synaptic efficacy in cortical.

Ohad Stoler, Alexandra Stavsky, Yana Khrapunsky, Israel Melamed, Grace E Stutzmann, Daniel Gitler, Israel Sekler, Ilya Fleidervish.

  Mitochondrial activity is crucial for the plasticity of central synapses, but how the firing pattern of pre- and postsynaptic neurons affects the mitochondria remains elusive. We recorded changes in the fluorescence of cytosolic and mitochondrial Ca2+ indicators in cell bodies, axons, and dendrites of cortical pyramidal neurons in mouse brain slices while evoking pre- and postsynaptic spikes. Postsynaptic spike firing elicited fast mitochondrial Ca2+ responses that were about threefold larger in the somas and apical dendrites than in basal dendrites and axons. The amplitude of these responses and metabolic activity were extremely sensitive to the firing frequency. Furthermore, while an EPSP alone caused no detectable Ca2+ elevation in the dendritic mitochondria, the coincidence of EPSP with a backpropagating spike produced prominent, highly localized mitochondrial Ca2+ hotspots. Our results indicate that mitochondria decode the spike firing frequency and the Hebbian temporal coincidences into the Ca2+ signals, which are further translated into the metabolic output and most probably lead to long-term changes in synaptic efficacy.

Keywords:  mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.74606
FEBS J. 2022 Feb 25.

Mitochondrial and metabolic remodeling in human skin fibroblasts in response to glucose availability.

Sónia A Pinho, Cláudio F Costa, Cláudia M Deus, Sonia L C Pinho, Inês Miranda-Santos, Gonçalo Afonso, Olivia Bagshaw, Jeffrey Stuart, Paulo J Oliveira, Teresa Cunha-Oliveira.

  Cell culture conditions highly influence cell metabolism in vitro. This is relevant for preclinical assays, for which fibroblasts are an interesting cell model, with applications in regenerative medicine, diagnostics and therapeutic development for personalized medicine, and the validation of ingredients for cosmetics. Given these cells' short lifespan in culture, we aimed to identify the best cell culture conditions and promising markers to study mitochondrial health and stress in Normal Human Dermal Fibroblasts (NHDF). We tested the effect of reducing glucose concentration in the cell medium from high glucose (HGm) to a more physiological level (LGm), or its complete removal and replacement by galactose (OXPHOSm), always in the presence of glutamine and pyruvate. We have demonstrated that only with OXPHOSm was it possible to observe the selective inhibition of mitochondrial ATP production. This reliance on mitochondrial ATP was accompanied by changes in oxygen consumption rate (OCR) and extracellular acidification rate (ECAR), oxidation of citric acid cycle substrates, fatty acids, lactate, and other substrates, increased mitochondrial network extension and polarization, increased protein content of VDAC and PGC1α and changes in several key transcripts related to energy metabolism. LGm did not promote significant metabolic changes in NHDF, although mitochondrial network extension and VDAC protein content were increased compared to HGm-cultured cells. Our results indicate that short-term adaptation to OXPHOSm is ideal for studying mitochondrial health and stress in NHDF.

Keywords:  bioenergetics; human fibroblasts; metabolic remodeling; metabolism; mitochondrial health

DOI:  https://doi.org/10.1111/febs.16413
FASEB J. 2022 03;36(3): e22219

RNA-binding protein YBX1 promotes brown adipogenesis and thermogenesis via PINK1/PRKN-mediated mitophagy.

Ruifan Wu, Shuting Cao, Fan Li, Shengchun Feng, Gang Shu, Lina Wang, Ping Gao, Xiaotong Zhu, Canjun Zhu, Songbo Wang, Qingyan Jiang.

  Promoting the thermogenic function of brown adipose tissue (BAT) is a promising strategy to combat obesity and metabolic disorders. While much is known about the transcriptional regulation of BAT activation, however, the underlying mechanism of post-transcriptional control by RNA binding proteins remains largely unknown. Here, we found that RNA binding protein Y-box binding protein 1 (YBX1) expression was abundant in BAT and induced by cold exposure and a β-adrenergic agonist in mice. Loss-of-function experiments showed that YBX1 deficiency inhibited mouse primary brown adipocyte differentiation and thermogenic function. Further study showed that YBX1 positively regulates thermogenesis through enhancing mitophagy. Mechanistically, RNA immunoprecipitation identified that YBX1 directly targeted the transcripts of PTEN-induced kinase 1 (Pink1) and parkin RBR E3 ubiquitin-protein ligase (Prkn), two key regulators of mitophagy. RNA decay assay proved that loss of YBX1 decreased mRNA stability of Pink1 and Prkn, leading to reduced protein expression, thereby alleviating mitophagy and inhibiting thermogenic program. Importantly, in vivo experiments demonstrated that YBX1 overexpression in BAT promoted thermogenesis and mitophagy in mice. Collectively, our results reveal novel insight into the molecular mechanism of YBX1 in post-transcriptional regulation of PINK1/PRKN-mediated mitophagy and highlight the critical role of YBX1 in brown adipogenesis and thermogenesis.

Keywords:  PINK1/PRKN; YBX1; adipogenesis; mitophagy; thermogenesis

DOI:  https://doi.org/10.1096/fj.202101810RR