bims-mikwok 2021-10-17 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2021–10–17
ten papers selected by
Avinash N. Mukkala, University of Toronto

ULK1 promotes mitophagy via phosphorylation and stabilization of BNIP3.
The protein N-terminal acetyltransferase A complex contributes to yeast mitophagy via promoting expression and phosphorylation of Atg32.
Phase separation of Nur77 mediates celastrol-induced mitophagy by promoting the liquidity of p62/SQSTM1 condensates.
Generating stable isolated mitochondrial recipient clones in mammalian cells using MitoPunch mitochondrial transfer.
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity.
Downregulation of mitochondrial biogenesis by virus infection triggers antiviral responses by cyclic GMP-AMP synthase.
Mitochondrial translation is required for sustained killing by cytotoxic T cells.
In vitro models of insulin resistance: mitochondrial coupling is differently affected in liver and muscle cells.
Estrogen alleviates hepatocyte necroptosis depending on GPER in hepatic ischemia reperfusion injury.
Diminished YAP1 affects mitochondrial dynamics in IDH1 mutant glioma.

Sci Rep. 2021 Oct 15. 11(1): 20526

ULK1 promotes mitophagy via phosphorylation and stabilization of BNIP3.

Logan P Poole, Althea Bock-Hughes, Damian E Berardi, Kay F Macleod.

UNC51-like kinase-1 (ULK1) is the catalytic component of the autophagy pre-initiation complex that stimulates autophagy via phosphorylation of ATG14, BECLN1 and other autophagy proteins. ULK1 has also been shown to specifically promote mitophagy but the mechanistic basis of how has remained unclear. Here we show that ULK1 phosphorylates the BNIP3 mitochondrial cargo receptor on a critical serine residue (S17) adjacent to its amino terminal LIR motif. ULK1 similarly phosphorylates BNIP3L on S35. Phosphorylation of BNIP3 on S17 by ULK1 promotes interaction with LC3 and mitophagy. ULK1 interaction also promotes BNIP3 protein stability by limiting its turnover at the proteasome. The ability of ULK1 to regulate BNIP3 protein stability depends on an intact "BH3" domain and deletion of its "BH3" domain reduces BNIP3 turnover and increases BNIP3 protein levels independent of ULK1. In summary ULK1 promotes mitophagy by both stabilization of BNIP3 protein and via phosphorylation of S17 to stimulate interaction with LC3.

DOI: https://doi.org/10.1038/s41598-021-00170-4
J Biochem. 2021 Oct 11. 170(2): 175-182

The protein N-terminal acetyltransferase A complex contributes to yeast mitophagy via promoting expression and phosphorylation of Atg32.

Mitsutaka Kubota, Koji Okamoto.

  Mitophagy is an evolutionarily conserved catabolic process that selectively degrades damaged or superfluous mitochondria via autophagy. Although mitophagy is considered to be critical to maintain cellular homeostasis, detailed mechanisms of mitophagy remain largely unknown. In the budding yeast Saccharomyces cerevisiae, the protein N-terminal acetyltransferase A (NatA) complex is important for transcriptional induction of the pro-mitophagic factor Atg32 and efficient degradation of mitochondria under prolonged respiratory conditions. Overexpression of Atg32 only partially recovers mitophagy in cells lacking NatA, raising the possibility that NatA may contribute to mitophagy via additional mechanisms. Here, we demonstrate that Atg32 phosphorylation, which is required for facilitating mitophagy, is altered in respiring NatA-deficient cells. Hyperphosphorylation of Atg32 partially rescues mitophagy in cells lacking NatA. Notably, mitophagy is mostly restored in NatA-null cells overexpressing hyperphosphorylated Atg32. Loss of NatA does not impair the interaction of phosphorylated Atg32 with Atg11, a scaffold protein critical for selective autophagy, suggesting that NatA-dependent Atg32 phosphorylation promotes mitophagy independently of Atg32-Atg11 interactions. We propose that NatA-mediated protein N-terminal acetylation acts in Atg32 expression and phosphorylation to drive mitophagy.

Keywords:  Atg32; NatA; Ppg1; autophagy; mitochondria; yeast

DOI:  https://doi.org/10.1093/jb/mvab068
Nat Commun. 2021 Oct 13. 12(1): 5989

Phase separation of Nur77 mediates celastrol-induced mitophagy by promoting the liquidity of p62/SQSTM1 condensates.

Shuang-Zhou Peng, Xiao-Hui Chen, Si-Jie Chen, Jie Zhang, Chuan-Ying Wang, Wei-Rong Liu, Duo Zhang, Ying Su, Xiao-Kun Zhang.

Liquid-liquid phase separation promotes the formation of membraneless condensates that mediate diverse cellular functions, including autophagy of misfolded proteins. However, how phase separation participates in autophagy of dysfunctional mitochondria (mitophagy) remains obscure. We previously discovered that nuclear receptor Nur77 (also called TR3, NGFI-B, or NR4A1) translocates from the nucleus to mitochondria to mediate celastrol-induced mitophagy through interaction with p62/SQSTM1. Here, we show that the ubiquitinated mitochondrial Nur77 forms membraneless condensates capable of sequestrating damaged mitochondria by interacting with the UBA domain of p62/SQSTM1. However, tethering clustered mitochondria to the autophagy machinery requires an additional interaction mediated by the N-terminal intrinsically disordered region (IDR) of Nur77 and the N-terminal PB1 domain of p62/SQSTM1, which confers Nur77-p62/SQSTM1 condensates with the magnitude and liquidity. Our results demonstrate how composite multivalent interaction between Nur77 and p62/SQSTM1 coordinates to sequester damaged mitochondria and to connect targeted cargo mitochondria for autophagy, providing mechanistic insight into mitophagy.

DOI: https://doi.org/10.1038/s41467-021-26295-8
STAR Protoc. 2021 Dec 17. 2(4): 100850

Generating stable isolated mitochondrial recipient clones in mammalian cells using MitoPunch mitochondrial transfer.

Alexander J Sercel, Alexander J Napior, Alexander N Patananan, Ting-Hsiang Wu, Pei-Yu Chiou, Michael A Teitell.

  This protocol describes the assembly and use of MitoPunch to deliver mitochondria containing mitochondrial DNA (mtDNA) into cells lacking mtDNA (ρ0 cells). MitoPunch generates stable isolated mitochondrial recipient clones with restored mtDNA and recovered respiration, enabling investigation of mtDNA mutations and mtDNA-nuclear DNA interactions in a range of cell types. For complete details on the use and execution of this protocol, please refer to Sercel et al. (2021) and Patananan et al. (2020).

Keywords:  Biotechnology and bioengineering; Cell Biology; Cell culture; Cell-based Assays; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2021.100850
Biosystems. 2021 Oct 07. pii: S0303-2647(21)00201-X. [Epub ahead of print]210 104559

Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity.

Igor Khmelinskii, Vladimir Makarov.

  An extended biophysical model was obtained by upgrading the previously reported one (Khmelinskii and Makarov, 2021). The upgraded model accommodates variations of solute transport rates through the inner mitochondrial membrane (IMM) within the mitochondrial population, described by a Gaussian distribution. However, the model may be used for any functional form of the distribution. The dynamics of system parameters as predicted by the current model differed from that predicted by the previous model in the same initial conditions (Khmelinskii and Makarov, 2021). The amount of change varied from one parameter to the other, remaining in the 1-38% range. The upgraded model fitted the available experimental data with a better accuracy (R = 0.993) compared to the previous model (R = 0.978) using the same experimental data (Khmelinskii and Makarov, 2021). The fitting procedure also estimated the Gaussian distribution parameters. The new model requires much larger computational resources, but given its higher accuracy, it may be used for better analysis of experimental data and for better prediction of MS dynamics in different initial conditions. Note that activities of individual mitochondria in mitochondrial populations should vary within biological tissues. Thus, the currently upgraded model is a better tool for biological and bio-medical applications. We believe that this model is much better adapted to the analysis of MS dynamics in vivo.

Keywords:  Biophysical model; Computation analysis; Irreversible swelling; Mitochondrion; Reversible swelling; Swelling

DOI:  https://doi.org/10.1016/j.biosystems.2021.104559
PLoS Pathog. 2021 Oct;17(10): e1009841

Downregulation of mitochondrial biogenesis by virus infection triggers antiviral responses by cyclic GMP-AMP synthase.

Hiroki Sato, Miho Hoshi, Fusako Ikeda, Tomoko Fujiyuki, Misako Yoneda, Chieko Kai.

In general, in mammalian cells, cytosolic DNA viruses are sensed by cyclic GMP-AMP synthase (cGAS), and RNA viruses are recognized by retinoic acid-inducible gene I (RIG-I)-like receptors, triggering a series of downstream innate antiviral signaling steps in the host. We previously reported that measles virus (MeV), which possesses an RNA genome, induces rapid antiviral responses, followed by comprehensive downregulation of host gene expression in epithelial cells. Interestingly, gene ontology analysis indicated that genes encoding mitochondrial proteins are enriched among the list of downregulated genes. To evaluate mitochondrial stress after MeV infection, we first observed the mitochondrial morphology of infected cells and found that significantly elongated mitochondrial networks with a hyperfused phenotype were formed. In addition, an increased amount of mitochondrial DNA (mtDNA) in the cytosol was detected during progression of infection. Based on these results, we show that cytosolic mtDNA released from hyperfused mitochondria during MeV infection is captured by cGAS and causes consequent priming of the DNA sensing pathway in addition to canonical RNA sensing. We also ascertained the contribution of cGAS to the in vivo pathogenicity of MeV. In addition, we found that other viruses that induce downregulation of mitochondrial biogenesis as seen for MeV cause similar mitochondrial hyperfusion and cytosolic mtDNA-priming antiviral responses. These findings indicate that the mtDNA-activated cGAS pathway is critical for full innate control of certain viruses, including RNA viruses that cause mitochondrial stress.

DOI: https://doi.org/10.1371/journal.ppat.1009841
Science. 2021 Oct 15. 374(6565): eabe9977

Mitochondrial translation is required for sustained killing by cytotoxic T cells.

Miriam Lisci, Philippa R Barton, Lyra O Randzavola, Claire Y Ma, Julia M Marchingo, Doreen A Cantrell, Vincent Paupe, Julien Prudent, Jane C Stinchcombe, Gillian M Griffiths.

[Figure: see text].

DOI: https://doi.org/10.1126/science.abe9977
Mitochondrion. 2021 Oct 08. pii: S1567-7249(21)00141-0. [Epub ahead of print]

In vitro models of insulin resistance: mitochondrial coupling is differently affected in liver and muscle cells.

Nina Krako Jakovljevic, Kasja Pavlovic, Tijana Zujovic, Tamara Kravic-Stevovic, Aleksandra Jotic, Ivanka Markovic, Nebojsa M Lalic.

  Mitochondrial dysfunction in diabetes is a widely studied topic, but inconsistency in literature data suggests a need for valid and reproducible models that will help to clarify this interaction. We aimed to establish insulin resistance models using chronic high insulin treatment in two cell types: myocytes and hepatocytes, characterise them in terms of mitochondrial function and compare them to the widely used palmitate-induced model of insulin resistance. We found that insulin lowered phosphorylation of Akt while not affecting cell viability, ROS production, mitochondrial morphology or respiration, and caused decrease in mitochondrial coupling only in muscle but not in liver cells.

Keywords:  cell models; hepatocytes; insulin resistance; mitochondria; myocytes; respiration

DOI:  https://doi.org/10.1016/j.mito.2021.10.001
J Physiol Biochem. 2021 Oct 15.

Estrogen alleviates hepatocyte necroptosis depending on GPER in hepatic ischemia reperfusion injury.

Zhonglin Li, Liuying Chen, Huikuan Chu, Weijun Wang, Ling Yang.

  Hepatic ischemia reperfusion injury (IRI) occurs in liver transplantation, complex liver resection, and hemorrhagic shock, which causes donor organ shortage and hepatic damage. The burst of reactive oxygen species (ROS) during reperfusion leads to cell apoptosis and necroptosis. It has been reported that estrogen could attenuate hepatic IRI. G protein estrogen receptor (GPER) mediates estrogen effects via nonclassic receptor systems. Here, we investigate whether estrogen protecting liver from hepatic IRI depends on GPER and the influence of GPER activation on hepatocyte necroptosis. We proved that estrogen had a protective effect on both hepatocyte hypoxia re-oxygen (H/R) challenge and mouse hepatic ischemia reperfusion model. However, the application of GPER specific antagonist G15 before estrogen inhibited this beneficial effect. The results of mitochondria functional measurement revealed that estrogen improved hepatocyte mitochondria function by activating GPER, which might benefit from the increased expression of connexin 43 (Cx43) in mitochondria. To investigate the relationship between GPER activation and necroptosis, we used caspase-3/7 inhibitor benzyloxycarbonyl-Asp(OMe)-Glu(OMe)-Val-Asp(OMe)-chloromethylketone (Z-DEVD-FMK) to eliminate the interference of apoptosis. Estrogen showed a protective effect on hepatic IRI after using Z-DEVD-FMK, which could be suppressed by G15. GPER activation decreased the level of receptor interacting protein kinase (RIPK) 3, phosphorylated (p-) RIPK1, and p-mixed lineage kinase domain-like (MLKL). The co-immunoprecipitation result indicated that GPER could bind with RIPK3. GPER is indispensable in estrogen protecting liver from IRI. GPER activation attenuates hepatocyte necroptosis by decreasing the level of RIPK3, p-RIPK1, and p-MLKL.

Keywords:  Estrogen; GPER; Hepatic ischemia reperfusion injury; Necroptosis

DOI:  https://doi.org/10.1007/s13105-021-00846-5
J Cell Sci. 2021 Oct 15. pii: jcs.259188. [Epub ahead of print]

Diminished YAP1 affects mitochondrial dynamics in IDH1 mutant glioma.

Shruti Patrick, Pruthvi Gowda, Kirti Lathoria, Vaishali Suri, Ellora Sen.

  Mutation in isocitrate dehydrogenase 1 (IDH1) gene, leading to the production of oncometabolite D-2-hydroxyglutarate (2-HG) from α-ketoglutarate, is associated with better prognosis in glioma. As Yes-associated protein 1 (YAP1) is an important regulator of tumor progression, its role in glioma expressing IDH1 R132H mutation was investigated. Diminished nuclear YAP1 in IDH1 mutant patient gliomas and cell lines was accompanied by decreased TFAM levels. Luciferase reporter assays and chromatin immunoprecipitation indicated the functionality of TEAD2 site on TFAM promoter in mediating its YAP1-dependent expression. YAP1-dependent mitochondrial fragmentation and ROS generation was accompanied by decreased TERT levels and increased mitochondrial TERT localization in IDH1 R132H cells. Treatment with Bosutinib that prevents extranuclear TERT shuttle, further elevated ROS in IDH1 R132H cells and triggered apoptosis. Importantly, Bosutinib elevated ROS levels and induced apoptosis in IDH1 WT cells upon concurrent depletion of YAP1. These findings highlight the involvement of YAP1 in coupling mitochondrial dysfunction with TERT mitochondrial shuttle to constitute an essential non-canonical function of YAP1 in regulating redox homeostasis.

Keywords:  Glioma; IDH1; Mitochondria; TERT; TFAM; YAP1

DOI:  https://doi.org/10.1242/jcs.259188