bims-mikwok 2020-11-15 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2020‒11‒15
fifteen papers selected by
Avinash N. Mukkala
University of Toronto

Deletion of mitochondrial uncoupling protein 2 exacerbates mitophagy and cell apoptosis after cerebral ischemia and reperfusion injury in mice.
Phosphoglycerate mutase 5 exacerbates cardiac ischemia-reperfusion injury through disrupting mitochondrial quality control.
Macrophage mitochondrial MFN2 (mitofusin 2) links immune stress and immune response through reactive oxygen species (ROS) production.
Parkin overexpression alleviates cardiac aging through facilitating K63-polyubiquitination of TBK1 to facilitate mitophagy.
Mitochondrial translation inhibition triggers ATF4 activation, leading to integrated stress response but not to mitochondria unfolded protein response.
Mono-2-ethylhexyl phthalate drives progression of PINK1-parkin-mediated mitophagy via increasing mitochondrial ROS to exacerbate cytotoxicity.
Computational Modeling Analysis of Generation of Reactive Oxygen Species by Mitochondrial Assembled and Disintegrated Complex II.
MAVS is energized by Mff which senses mitochondrial metabolism via AMPK for acute antiviral immunity.
The eIF2α kinase HRI triggers the autophagic clearance of cytosolic protein aggregates.
Glaucocalyxin A Protects H9c2 Cells Against Hypoxia/Reoxygenation-Induced Injury Through the Activation of Akt/Nrf2/HO-1 Pathway.
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations.
Sirtuin 5 is Regulated by the SCF-Cyclin F Ubiquitin Ligase and is Involved in Cell Cycle Control.
An Endoplasmic Reticulum ATPase Safeguards Endoplasmic Reticulum Identity by Removing Ectopically Localized Mitochondrial Proteins.
A Systematic Protein Turnover Map for Decoding Protein Degradation.
TBK1-Mediated DRP1 Targeting Confers Nucleic Acid Sensing to Reprogram Mitochondrial Dynamics and Physiology.

Int J Med Sci. 2020 ;17(17): 2869-2878

Deletion of mitochondrial uncoupling protein 2 exacerbates mitophagy and cell apoptosis after cerebral ischemia and reperfusion injury in mice.

Maotao He, Ting Zhang, Yucheng Fan, Yanmei Ma, Jianzhong Zhang, Li Jing, P Andy Li.

  Objective: Uncoupling protein 2 (UCP2) is a member of inner mitochondrial membrane proteins and deletion of UCP2 exacerbates brain damage after cerebral ischemia/reperfusion (I/R). Nevertheless, its functional role during cerebral I/R is not entirely understood. The objective of present study was to explore the influence of UCP2 deletion on mitochondrial autophagy (mitophagy) and mitochondria-mediated cell death pathway after cerebral I/R. Methods: UCP2-/- and wildtype (WT) mice were subjected to 60 min middle cerebral artery occlusion (MCAO) and allowed reperfusion for 24 hours. Infarct volume and histological outcomes were assessed, reactive oxygen species (ROS) and autophagy markers were measured, and mitochondrial ultrastructure was examined. Results: Deletion of UCP2 enlarged infarct volume, increased numbers of necrotic and TUNEL positive cells, and significantly increased pro-apoptotic protein levels in UCP2-/- mice compared with WT mice subjected to the same duration of I/R. Further, deletion of UCP2 increased ROS production, elevated LC3, Beclin1 and PINK1, while it suppressed p62 compared with respective WT ischemic controls. Electron microscopic study demonstrated the number of autophagosomes was higher in the UCP2-/- group, compared with the WT group. Conclusions: It is concluded that deletion of UCP2 exacerbates cerebral I/R injury via reinforcing mitophagy and cellular apoptosis in mice.

Keywords:  ROS; apoptosis; autophagy; cerebral ischemia/reperfusion; mitophagy; uncoupling protein 2

DOI:  https://doi.org/10.7150/ijms.49849
Redox Biol. 2020 Nov 01. pii: S2213-2317(20)30982-4. [Epub ahead of print]38 101777

Phosphoglycerate mutase 5 exacerbates cardiac ischemia-reperfusion injury through disrupting mitochondrial quality control.

Hang Zhu, Ying Tan, Wenjun Du, Yang Li, Sam Toan, David Mui, Feng Tian, Hao Zhou.

  The death of cardiomyocytes either through apoptosis or necroptosis is the pathological feature of cardiac ischemia-reperfusion (I/R) injury. Phosphoglycerate mutase 5 (PGAM5), a mitochondrially-localized serine/threonine-protein phosphatase, functions as a novel inducer of necroptosis. However, intense debate exists regarding the effect of PGAM5 on I/R-related cardiomyocyte death. Using cardiac-specific PGAM5 knockout (PGAM5CKO) mice, we comprehensively investigated the precise contribution and molecular mechanism of PGAM5 in cardiomyocyte death. Our data showed that both PGAM5 transcription and expression were upregulated in reperfused myocardium. Genetic ablation of PGAM5 suppressed I/R-mediated necroptosis but failed to prevent apoptosis activation, a result that went along with improved heart function and decreased inflammation response. Regardless of PGAM5 status, mitophagy-related cell death was not apparent following I/R. Under physiological conditions, PGAM5 overexpression in primary cardiomyocytes was sufficient to induce cardiomyocyte necroptosis rather than apoptosis. At the sub-cellular levels, PGAM5 deficiency increased mitochondrial DNA copy number and transcript levels, normalized mitochondrial respiration, repressed mitochondrial ROS production, and prevented abnormal mPTP opening upon I/R. Molecular investigation demonstrated that PGAM5 deletion interrupted I/R-mediated DrpS637 dephosphorylation but failed to abolish I/R-induce Drp1S616 phosphorylation, resulting in partial inhibition of mitochondrial fission. In addition, declining Mfn2 and OPA1 levels were restored in PGAM5CKO cardiomyocytes following I/R. Nevertheless, PGAM5 depletion did not rescue suppressed mitophagy upon I/R injury. In conclusion, our results provide an insight into the specific role and working mechanism of PGAM5 in driving cardiomyocyte necroptosis through imposing mitochondrial quality control in cardiac I/R injury.

Keywords:  Cardiac I/R injury; Death; Mitochondrial fission; Mitochondrial quality control; Mitophagy; Necroptosis; PGAM5

DOI:  https://doi.org/10.1016/j.redox.2020.101777
Autophagy. 2020 Nov 10. 1-3

Macrophage mitochondrial MFN2 (mitofusin 2) links immune stress and immune response through reactive oxygen species (ROS) production.

Jorge Lloberas, Juan P Muñoz, María Isabel Hernández-Álvarez, Pere-Joan Cardona, Antonio Zorzano, Antonio Celada.

  MFN2 (mitofusin 2) is required for mitochondrial fusion and for mitochondria-endoplasmic reticulum interaction. Using myeloid-conditional KO mice models, we found that MFN2 but not MFN1 is a prerequisite for the adaptation of mitochondrial respiration to stress conditions as well as for the production of reactive oxygen species (ROS). The deficient ROS production in the absence of MFN2 impairs the induction of cytokines and nitric oxide, and is associated with dysfunctional autophagy, apoptosis, phagocytosis, and antigen processing. The lack of MFN2 in macrophages causes an impaired response in a model of non-septic inflammation in mice, as well as a failure in protection from Listeria, Mycobacterium tuberculosis or LPS endotoxemia. These results reveal an unexpected role of MFN2 to ROS production in macrophages affecting natural and acquired immunity and the immune response.

Keywords:  Autophagy; ROS; bactericidal activity; cytokine; inflammation; macrophages; phagocytosis

DOI:  https://doi.org/10.1080/15548627.2020.1839191
Biochim Biophys Acta Mol Basis Dis. 2020 Oct 22. pii: S0925-4439(20)30345-8. [Epub ahead of print]1867(1): 165997

Parkin overexpression alleviates cardiac aging through facilitating K63-polyubiquitination of TBK1 to facilitate mitophagy.

Beilei Gao, Wenjun Yu, Ping Lv, Xinyue Liang, Shiqun Sun, Yingmei Zhang.

  Cumulative clinical and experimental evidence has revealed a cardinal role for mitochondrial integrity in cardiac aging. Parkin-mediated mitophagy is essential to ensure mitochondrial quality control in myocardium. This study was designed to examine the impact of Parkin overexpression on aging-induced myocardial anomalies and the underlying mechanisms with a focus on Parkin-regulated mitophagy. Cardiac function, myocardial apoptosis, mitochondrial ultrastructure and mitophagy were examined in young (3 mo) and old (24-26 mo) wild-type (WT) and Parkin transgenic mice. Our data revealed compromised myocardial function and mitochondrial morphology along with overtly apoptosis with advanced aging, the effects of which were attenuated by Parkin overexpression. Advanced aging dampened mitophagy as evidenced by decreased levels of Parkin, LC3II, phosphorylation of p62 and TBK1 in isolated mitochondria as well as reduced mitochondria autophagosomes, the effects of which were mitigated by restoration of mitophagy via Parkin overexpression. Using the low-dose doxorubicin (DOX) in vitro model of cell senescence, we noted that Parkin-offered beneficial effect against senescence was abolished by the TBK1 kinase inhibitor BX795. With TBK1 overexpression in cardiomyocytes, we uncovered the interaction of Parkin with TBK1 using a Co-immunoprecipitation (Co-IP) assay. The interaction of Parkin with TBK1 contributed to K63-linked polyubiquitination of TBK1. Our study also noted that DOX disturbed K63-linked polyubiquitination of TBK1 with downregulation of Parkin. Parkin overexpression promoted K63-linked polyubiquitination of TBK1 through Lys30 and Lys401 residues to foster TBK1 phosphorylation to facilitate efficient mitophagy. In summary, these findings suggested that Parkin effectively rescued cardiac aging through promoting K63-linked polyubiquitination of TBK1 to facilitate mitophagy.

Keywords:  Aging; K63-linked polyubiquitination; Mitophagy; Parkin; TBK1

DOI:  https://doi.org/10.1016/j.bbadis.2020.165997
Biosci Rep. 2020 Nov 09. pii: BSR20201289. [Epub ahead of print]

Mitochondrial translation inhibition triggers ATF4 activation, leading to integrated stress response but not to mitochondria unfolded protein response.

Katsuhiko Sasaki, Takeshi Uchiumi, Takahiro Toshima, Mikako Yagi, Yura Do, Haruka Hirai, Ko Igami, Kazuhito Gotoh, Dongchon Kang.

  Mitochondrial-nuclear communication, known as retrograde signaling, is important for regulating nuclear gene expression in response to mitochondrial dysfunction. Previously, we have found that p32/C1qbp-deficient mice, which have a mitochondrial translation defect, show ER stress response and integrated stress response (ISR) gene expression in the heart and brain. However, the mechanism by which mitochondrial translation inhibition elicits these responses is not clear. Among the transcription factors that respond to mitochondrial stress, ATF4 is a key transcription factor in the ISR. Herein, chloramphenicol, which inhibits mitochondrial DNA-encoded protein expression, induced eIF2a phosphorylation and ATF4 induction, leading to ISR gene expression. However, the expression of the mitochondrial unfolded protein response genes, which has been shown in Caenorhabditis Elegans, was not induced. Short hairpin RNA-based knockdown of ATF4 markedly inhibited the chloramphenicol-induced ISR gene expression. We also observed by ChIP analysis that induced ATF4 bound to the promoter region of several ISR genes, suggesting that mitochondrial translation inhibition induces ISR gene expression through ATF4 activation. In this study, we showed that mitochondrial translation inhibition induced the ISR through ATF4 activation rather than the mitochondrial unfolded protein response.

Keywords:  ATF4; integratad stress responce; mitochondria; mtUPR

DOI:  https://doi.org/10.1042/BSR20201289
Redox Biol. 2020 Nov 01. pii: S2213-2317(20)30981-2. [Epub ahead of print]38 101776

Mono-2-ethylhexyl phthalate drives progression of PINK1-parkin-mediated mitophagy via increasing mitochondrial ROS to exacerbate cytotoxicity.

Jian Xu, Liming Wang, Lihuan Zhang, Fang Zheng, Fang Wang, Jianhang Leng, Keyi Wang, Paul Héroux, Han-Ming Shen, Yihua Wu, Dajing Xia.

  Phthalate ester plasticizers are used to improve the plasticity and strength of plastics. One of the most widely used and studied, di-2-ethylhexyl phthalate (DEHP), has been labeled as an endocrine disruptor. The major and toxic metabolic derivative of DEHP, mono-2-ethylhexyl phthalate (MEHP), is capable of interfering with mitochondrial function, but its mechanism of action on mitophagy remains elusive. Here, we report that MEHP exacerbates cytotoxicity by amplifying the PINK1-Parkin-mediated mitophagy pathway. First, MEHP exacerbated mitochondrial damage induced by low-dose CCCP via increased reactive oxygen species (ROS) production, decreased mitochondrial membrane potential (MMP), and enhanced fragmentation in mitochondria. Second, co-exposure to MEHP and CCCP ("MEHP-CCCP") induced robust mitophagy. Mechanistically, MEHP-CCCP stabilized PINK1, increased the level of phosphorylated ubiquitin (pSer 65-Ub), and led to Parkin mitochondrial translocation and activation. Third, MEHP-CCCP synergistically caused more cell death, while inhibition of mitophagy, either through chemical or gene silencing, reduced cell death. Finally and importantly, co-treatment with N-acetyl cysteine (NAC) completely counteracted the effects of MEHP-CCCP, suggesting that mitochondrial ROS played a vital role in this process. Our results link mitophagy and MEHP cytotoxicity, providing an insight into the potential roles of endocrine disrupting chemicals (EDCs) in human diseases such as Parkinson's disease.

Keywords:  Cell death; Cytotoxicity; MEHP; Mitochondrial ROS; PINK1-Parkin-mediated mitophagy

DOI:  https://doi.org/10.1016/j.redox.2020.101776
Front Physiol. 2020 ;11 557721

Computational Modeling Analysis of Generation of Reactive Oxygen Species by Mitochondrial Assembled and Disintegrated Complex II.

Nikolay I Markevich, Lubov N Markevich, Jan B Hoek.

  Reactive oxygen species (ROS) function as critical mediators in a broad range of cellular signaling processes. The mitochondrial electron transport chain is one of the major contributors to ROS formation in most cells. Increasing evidence indicates that the respiratory Complex II (CII) can be the predominant ROS generator under certain conditions. A computational, mechanistic model of electron transfer and ROS formation in CII was developed in the present study to facilitate quantitative analysis of mitochondrial ROS production. The model was calibrated by fitting the computer simulated results to experimental data obtained on submitochondrial particles (SMP) prepared from bovine and rat heart mitochondria upon inhibition of the ubiquinone (Q)-binding site by atpenin A5 (AA5) and Complex III by myxothiazol, respectively. The model predicts that only reduced flavin adenine dinucleotide (FADH2) in the unoccupied dicarboxylate state and flavin semiquinone radical (FADH•) feature the experimentally observed bell-shaped dependence of the rate of ROS production on the succinate concentration upon inhibition of respiratory Complex III (CIII) or Q-binding site of CII, i.e., suppression of succinate-Q reductase (SQR) activity. The other redox centers of CII such as Fe-S clusters and Q-binding site have a hyperbolic dependence of ROS formation on the succinate concentration with very small maximal rate under any condition and cannot be considered as substantial ROS generators in CII. Computer simulation results show that CII disintegration (which results in dissociation of the hydrophilic SDHA/SDHB subunits from the inner membrane to the mitochondrial matrix) causes crucial changes in the kinetics of ROS production by CII that are qualitatively and quantitatively close to changes in the kinetics of ROS production by assembled CII upon inhibition of CIII or Q-binding site of CII. Thus, the main conclusions from the present computational modeling study are the following: (i) the impairment of the SQR activity of CII resulting from inhibition of CIII or Q-binding site of CII and (ii) CII disintegration causes a transition in the succinate-dependence of ROS production from a small-amplitude sigmoid (hyperbolic) shape, determined by Q-binding site or [3Fe-4S] cluster to a high-amplitude bell-shaped kinetics with a shift to small subsaturated concentrations of succinate, determined by the flavin site.

Keywords:  assembled; complex II; computational model; disintegrated; reactive oxygen species

DOI:  https://doi.org/10.3389/fphys.2020.557721
Nat Commun. 2020 11 11. 11(1): 5711

MAVS is energized by Mff which senses mitochondrial metabolism via AMPK for acute antiviral immunity.

Yuki Hanada, Naotada Ishihara, Lixiang Wang, Hidenori Otera, Takaya Ishihara, Takumi Koshiba, Katsuyoshi Mihara, Yoshihiro Ogawa, Masatoshi Nomura.

Mitochondria are multifunctional organelles that produce energy and are critical for various signaling pathways. Mitochondrial antiviral signaling (MAVS) is a mitochondrial outer membrane protein essential for the anti-RNA viral immune response, which is regulated by mitochondrial dynamics and energetics; however, the molecular link between mitochondrial metabolism and immunity is unclear. Here we show in cultured mammalian cells that MAVS is activated by mitochondrial fission factor (Mff), which senses mitochondrial energy status. Mff mediates the formation of active MAVS clusters on mitochondria, independent of mitochondrial fission and dynamin-related protein 1. Under mitochondrial dysfunction, Mff is phosphorylated by the cellular energy sensor AMP-activated protein kinase (AMPK), leading to the disorganization of MAVS clusters and repression of the acute antiviral response. Mff also contributes to immune tolerance during chronic infection by disrupting the mitochondrial MAVS clusters. Taken together, Mff has a critical function in MAVS-mediated innate immunity, by sensing mitochondrial energy metabolism via AMPK signaling.

DOI: https://doi.org/10.1038/s41467-020-19287-7
J Biol Chem. 2020 Nov 09. pii: jbc.RA120.014415. [Epub ahead of print]

The eIF2α kinase HRI triggers the autophagic clearance of cytosolic protein aggregates.

Tapas Mukherjee, Valeria Ramaglia, Mena Abdel-Nour, Athanasia A Bianchi, Jessica Tsalikis, Hien N Chau, Suneil K Kalia, Lorraine V Kalia, Jane-Jane Chen, Damien Arnoult, Jennifer L Gommerman, Dana J Philpott, Stephen E Girardin.

  Large cytosolic protein aggregates are removed by two main cellular processes, autophagy and the ubiquitin-proteasome system (UPS), and defective clearance of these protein aggregates results in proteotoxicity and cell death. Recently, we found that the eIF2α kinase heme-regulated inhibitory (HRI) induced a cytosolic unfolded protein response (cUPR) to prevent aggregation of innate immune signalosomes, but whether HRI acts as a general sensor of proteotoxicity in the cytosol remains unclear. Here we show that HRI controls autophagy to clear cytosolic protein aggregates when the UPS is inhibited. We further report that silencing HRI expression resulted in decreased levels of BAG3 and HSPB8, two proteins involved in chaperone-assisted selective autophagy (CASA), suggesting that HRI controls proteostasis in the cytosol at least in part through CASA. Moreover, knocking down the expression of HRI resulted in cytotoxic accumulation of over-expressed α-synuclein, a protein known to aggregate in Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. In agreement with these data, protein aggregate accumulation and microglia activation were observed in the spinal cord white matter of 7-month old Hri-/- mice as compared to Hri+/+ littermates. Moreover, aged Hri-/- mice showed accumulation of misfolded α-synuclein, indicative of misfolded proteins, in the lateral collateral pathway, a region of the sacral spinal cord horn that receives visceral sensory afferents from the bladder and distal colon, a pathological feature common to α-synucleinopathies in humans. Together, these results suggest that HRI contributes to a general cUPR that could be leveraged to bolster the clearance of cytotoxic protein aggregates.

Keywords:  Integrated Stress Response; Parkinson disease; autophagy; eIF2alpha; synuclein; ubiquitin-dependent protease; unfolded protein response (UPR)

DOI:  https://doi.org/10.1074/jbc.RA120.014415
Cell Transplant. 2020 Jan-Dec;29:29 963689720967672

Glaucocalyxin A Protects H9c2 Cells Against Hypoxia/Reoxygenation-Induced Injury Through the Activation of Akt/Nrf2/HO-1 Pathway.

Zhuo Peng, Rui Zhang, Longfei Pan, Honghong Pei, Zequn Niu, Hai Wang, Junhua Lv, Xiaoyan Dang.

  Myocardial infarction (MI) is one of the most serious cardiovascular diseases associated with myocardial ischemia/reperfusion (I/R) injury. Glaucocalyxin A (GLA) is a biologically active ent-kauranoid diterpenoid that has been found to ameliorate myocardial I/R injury in mice. However, the mechanism has not been fully investigated. In the present study, we aimed to investigate the effect of GLA on rat cardiomyocytes H9c2 cells exposed to hypoxia/reoxygenation (H/R). The results showed that GLA treatment improved cell viability of H/R-stimulated H9c2 cells. Administration with GLA suppressed the H/R-stimulated reactive oxygen species (ROS) production in H9c2 cells. GLA also elevated the activities of antioxidant enzymes, including superoxide dismutase and glutathione peroxidase in H/R-stimulated H9c2 cells. Moreover, GLA prevented H/R-stimulated cell apoptosis in H9c2 cells, as evidenced by increased bcl-2 expression, decreased bax expression, as well as reduced caspase-3 activity. Furthermore, GLA enhanced the activation of protein kinase B (Akt)/nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling pathway in H9c2 cells exposed to H/R. Additionally, treatment with LY294002 reserved the protective effects of GLA on H/R-stimulated oxidative injury in H9c2 cells. In conclusion, these findings suggested that GLA protected H9c2 cells from H/R-stimulated oxidative damage, which was mediated by the Akt/Nrf2/HO-1 signaling pathway. Thus, GLA might be a promising therapeutic agent for the prevention and treatment of myocardial I/R.

Keywords:  Akt/Nrf2/HO-1 signaling pathway; glaucocalyxin A (GLA); myocardial infarction (MI); myocardial ischemia/reperfusion (I/R) injury; oxidative stress

DOI:  https://doi.org/10.1177/0963689720967672
Nucleic Acids Res. 2020 Nov 11. pii: gkaa1011. [Epub ahead of print]

MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations.

Sneha Rath, Rohit Sharma, Rahul Gupta, Tslil Ast, Connie Chan, Timothy J Durham, Russell P Goodman, Zenon Grabarek, Mary E Haas, Wendy H W Hung, Pallavi R Joshi, Alexis A Jourdain, Sharon H Kim, Anna V Kotrys, Stephanie S Lam, Jason G McCoy, Joshua D Meisel, Maria Miranda, Apekshya Panda, Anupam Patgiri, Robert Rogers, Shayan Sadre, Hardik Shah, Owen S Skinner, Tsz-Leung To, Melissa A Walker, Hong Wang, Patrick S Ward, Jordan Wengrod, Chen-Ching Yuan, Sarah E Calvo, Vamsi K Mootha.

The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.

DOI: https://doi.org/10.1093/nar/gkaa1011
Mol Cell Biol. 2020 Nov 09. pii: MCB.00269-20. [Epub ahead of print]

Sirtuin 5 is Regulated by the SCF-Cyclin F Ubiquitin Ligase and is Involved in Cell Cycle Control.

Christine A Mills, Xianxi Wang, Dhaval P Bhatt, Paul A Grimsrud, Jacob Peter Matson, Debojyoti Lahiri, Daniel J Burke, Jeanette Gowen Cook, Matthew D Hirschey, Michael J Emanuele.

The ubiquitin-proteasome system is essential for cell cycle progression. Cyclin F is a cell cycle regulated substrate adapter F-box protein for the SKP1/CUL1/F-box (SCF) family of E3 ubiquitin ligases. Despite its importance in cell cycle progression, identifying SCFCyclin F substrates has remained challenging. Since Cyclin F overexpression rescues a yeast mutant in the cdc4 gene, we considered the possibility that other genes that genetically modify cdc4 mutant lethality could also encode Cyclin F substrates. We identified the mitochondrial and cytosolic deacylating enzyme Sirtuin 5 (SIRT5) as a novel Cyclin F substrate. SIRT5 has been implicated in metabolic processes, but its connection to the cell cycle is not known. We show that Cyclin F interacts with, and controls the ubiquitination, abundance, and stability of SIRT5. We show SIRT5 knockout results in a diminished G1 population, and subsequent increase in both S and G2/M. Global proteomic analyses reveal CDK signaling changes congruent with the cell cycle changes in SIRT5 knockout cells. Together these data demonstrate that SIRT5 is regulated by Cyclin F and suggest a connection between SIRT5, cell cycle regulation, and metabolism.

DOI: https://doi.org/10.1128/MCB.00269-20
Cell Rep. 2020 Nov 10. pii: S2211-1247(20)31352-8. [Epub ahead of print]33(6): 108363

An Endoplasmic Reticulum ATPase Safeguards Endoplasmic Reticulum Identity by Removing Ectopically Localized Mitochondrial Proteins.

Qing Qin, Ting Zhao, Wei Zou, Kang Shen, Xiangming Wang.

Stringent targeting of membrane proteins to corresponding organelles is essential for organelle identity and functions. In addition to molecular pathways that target proteins to appropriate organelles, surveillance mechanisms clear mistargeted proteins from undesired destinations. Although Msp1 functions on the mitochondrial membrane to remove mistargeted proteins, the surveillance mechanism for the endoplasmic reticulum (ER) is not well understood. Here, we show that a conserved P5A-type ATPase CATP-8, which localizes to ER, removes ectopic mitochondrial tail-anchored (TA) and signal-anchored (SA) proteins from the ER. In catp-8 mutant, mitochondria fission protein FIS-1 mislocalizes to the ER membrane. Together with another mitochondria fission protein MFF-2, FIS-1 causes ER fragmentation in a Dynamin-related protein (DRP-1)-dependent manner. In addition, CATP-8 is essential for dendrite development. catp-8 mutant dramatically reduces the level of the dendrite guidance receptor DMA-1, leading to diminished dendritic arbors. Hence, P5A ATPase safeguards ER morphology and functions by preventing mitochondrial proteins mislocalization.

DOI: https://doi.org/10.1016/j.celrep.2020.108363
Cell Rep. 2020 Nov 10. pii: S2211-1247(20)31367-X. [Epub ahead of print]33(6): 108378

A Systematic Protein Turnover Map for Decoding Protein Degradation.

Romain Christiano, Henning Arlt, Sonja Kabatnik, Niklas Mejhert, Zon Weng Lai, Robert V Farese, Tobias C Walther.

  Protein degradation is mediated by an expansive and complex network of protein modification and degradation enzymes. Matching degradation enzymes with their targets and determining globally which proteins are degraded by the proteasome or lysosome/vacuole have been a major challenge. Furthermore, an integrated view of protein degradation for cellular pathways has been lacking. Here, we present an analytical platform that combines systematic gene deletions with quantitative measures of protein turnover to deconvolve protein degradation pathways for Saccharomyces cerevisiae. The resulting turnover map (T-MAP) reveals target candidates of nearly all E2 and E3 ubiquitin ligases and identifies the primary degradation routes for most proteins. We further mined this T-MAP to identify new substrates of ER-associated degradation (ERAD) involved in sterol biosynthesis and to uncover regulatory nodes for sphingolipid biosynthesis. The T-MAP approach should be broadly applicable to the study of other cellular processes, including mammalian systems.

Keywords:  E2; E3 ligases; ERAD; SILAC; mass spectrometry; proteasome; protein turnover; proteomics; ubiquitin

DOI:  https://doi.org/10.1016/j.celrep.2020.108378
Mol Cell. 2020 Oct 29. pii: S1097-2765(20)30725-5. [Epub ahead of print]

TBK1-Mediated DRP1 Targeting Confers Nucleic Acid Sensing to Reprogram Mitochondrial Dynamics and Physiology.

Shasha Chen, Shengduo Liu, Junxian Wang, Qirou Wu, Ailian Wang, Hongxin Guan, Qian Zhang, Dan Zhang, Xiaojian Wang, Hai Song, Jun Qin, Jian Zou, Zhengfan Jiang, Songying Ouyang, Xin-Hua Feng, Tingbo Liang, Pinglong Xu.

  Mitochondrial morphology shifts rapidly to manage cellular metabolism, organelle integrity, and cell fate. It remains unknown whether innate nucleic acid sensing, the central and general mechanisms of monitoring both microbial invasion and cellular damage, can reprogram and govern mitochondrial dynamics and function. Here, we unexpectedly observed that upon activation of RIG-I-like receptor (RLR)-MAVS signaling, TBK1 directly phosphorylated DRP1/DNM1L, which disabled DRP1, preventing its high-order oligomerization and mitochondrial fragmentation function. The TBK1-DRP1 axis was essential for assembly of large MAVS aggregates and healthy antiviral immunity and underlay nutrient-triggered mitochondrial dynamics and cell fate determination. Knockin (KI) strategies mimicking TBK1-DRP1 signaling produced dominant-negative phenotypes reminiscent of human DRP1 inborn mutations, while interrupting the TBK1-DRP1 connection compromised antiviral responses. Thus, our findings establish an unrecognized function of innate immunity governing both morphology and physiology of a major organelle, identify a lacking loop during innate RNA sensing, and report an elegant mechanism of shaping mitochondrial dynamics.

Keywords:  DRP1; RLR-MAVS; TBK1; antiviral immunity; cell fate determination; innate immunity; mitochondrial dynamics; mitochondrion; nucleic acid sensing; phosphorylation

DOI:  https://doi.org/10.1016/j.molcel.2020.10.018