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      Suppression of autophagic activity by Rubicon is a signature of aging

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          Abstract

          Autophagy, an evolutionarily conserved cytoplasmic degradation system, has been implicated as a convergent mechanism in various longevity pathways. Autophagic activity decreases with age in several organisms, but the underlying mechanism is unclear. Here, we show that the expression of Rubicon, a negative regulator of autophagy, increases in aged worm, fly and mouse tissues at transcript and/or protein levels, suggesting that an age-dependent increase in Rubicon impairs autophagy over time, and thereby curtails animal healthspan. Consistent with this idea, knockdown of Rubicon extends worm and fly lifespan and ameliorates several age-associated phenotypes. Tissue-specific experiments reveal that Rubicon knockdown in neurons has the greatest effect on lifespan. Rubicon knockout mice exhibits reductions in interstitial fibrosis in kidney and reduced α-synuclein accumulation in the brain. Rubicon is suppressed in several long-lived worms and calorie restricted mice. Taken together, our results suggest that suppression of autophagic activity by Rubicon is one of signatures of aging.

          Abstract

          Autophagic activity decreases with age via unknown mechanisms. Here the authors show that expression of the negative autophagy regulator Rubicon increases with age, that its genetic ablation improves lifespan and ameliorates a number of age-associated phenotypes in invertebrates and in mouse models.

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          Most cited references36

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          Trehalose, a novel mTOR-independent autophagy enhancer, accelerates the clearance of mutant huntingtin and alpha-synuclein.

          Trehalose, a disaccharide present in many non-mammalian species, protects cells against various environmental stresses. Whereas some of the protective effects may be explained by its chemical chaperone properties, its actions are largely unknown. Here we report a novel function of trehalose as an mTOR-independent autophagy activator. Trehalose-induced autophagy enhanced the clearance of autophagy substrates like mutant huntingtin and the A30P and A53T mutants of alpha-synuclein, associated with Huntington disease (HD) and Parkinson disease (PD), respectively. Furthermore, trehalose and mTOR inhibition by rapamycin together exerted an additive effect on the clearance of these aggregate-prone proteins because of increased autophagic activity. By inducing autophagy, we showed that trehalose also protects cells against subsequent pro-apoptotic insults via the mitochondrial pathway. The dual protective properties of trehalose (as an inducer of autophagy and chemical chaperone) and the combinatorial strategy with rapamycin may be relevant to the treatment of HD and related diseases, where the mutant proteins are autophagy substrates.
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            Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex.

            Beclin 1, a mammalian autophagy protein that has been implicated in development, tumour suppression, neurodegeneration and cell death, exists in a complex with Vps34, the class III phosphatidylinositol-3-kinase (PI(3)K) that mediates multiple vesicle-trafficking processes including endocytosis and autophagy. However, the precise role of the Beclin 1-Vps34 complex in autophagy regulation remains to be elucidated. Combining mouse genetics and biochemistry, we have identified a large in vivo Beclin 1 complex containing the known proteins Vps34, p150/Vps15 and UVRAG, as well as two newly identified proteins, Atg14L (yeast Atg14-like) and Rubicon (RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein). Characterization of the new proteins revealed that Atg14L enhances Vps34 lipid kinase activity and upregulates autophagy, whereas Rubicon reduces Vps34 activity and downregulates autophagy. We show that Beclin 1 and Atg14L synergistically promote the formation of double-membraned organelles that are associated with Atg5 and Atg12, whereas forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation. We hypothesize that by forming distinct protein complexes, Beclin 1 and its binding proteins orchestrate the precise function of the class III PI(3)K in regulating autophagy at multiple steps.
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              Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans.

              Impaired mitochondrial maintenance in disparate cell types is a shared hallmark of many human pathologies and ageing. How mitochondrial biogenesis coordinates with the removal of damaged or superfluous mitochondria to maintain cellular homeostasis is not well understood. Here we show that mitophagy, a selective type of autophagy targeting mitochondria for degradation, interfaces with mitochondrial biogenesis to regulate mitochondrial content and longevity in Caenorhabditis elegans. We find that DCT-1 is a key mediator of mitophagy and longevity assurance under conditions of stress in C. elegans. Impairment of mitophagy compromises stress resistance and triggers mitochondrial retrograde signalling through the SKN-1 transcription factor that regulates both mitochondrial biogenesis genes and mitophagy by enhancing DCT-1 expression. Our findings reveal a homeostatic feedback loop that integrates metabolic signals to coordinate the biogenesis and turnover of mitochondria. Uncoupling of these two processes during ageing contributes to overproliferation of damaged mitochondria and decline of cellular function.
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                Author and article information

                Contributors
                tamyoshi@fbs.osaka-u.ac.jp
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                19 February 2019
                19 February 2019
                2019
                : 10
                : 847
                Affiliations
                [1 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Department of Genetics, Graduate School of Medicine, , Osaka University, ; Osaka, 565-0871 Japan
                [2 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, , Osaka University, ; Osaka, 565-0871 Japan
                [3 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Institute for Advanced Co-Creation Studies, , Osaka University, ; Osaka, 565-0871 Japan
                [4 ]GRID grid.272456.0, Diabetic Neuropathy Project, Department of Sensory and Motor Systems, , Tokyo Metropolitan Institute of Medical Science, Setagaya, ; Tokyo, 156-8506 Japan
                [5 ]ISNI 0000 0001 0166 4675, GRID grid.419152.a, Department of Bioscience and Engineering, , Shibaura Institute of Technology, ; Saitama, 337-8570 Japan
                [6 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Department of Nephrology, Graduate School of Medicine, , Osaka University, ; Osaka, 565-0871 Japan
                [7 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Department of Neurology, , Graduate School of Medicine, Osaka University, ; Osaka, 565-0871 Japan
                [8 ]Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047 Japan
                [9 ]ISNI 0000 0004 0372 2033, GRID grid.258799.8, Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, , Kyoto University, ; Kyoto, 606-8501 Japan
                [10 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Laboratory of Biomolecular Informatics, Graduate School of Science, , Osaka University, ; Osaka, 560-0043 Japan
                [11 ]ISNI 0000 0004 0373 3971, GRID grid.136593.b, Department of Statistical Genetics, Graduate School of Medicine, , Osaka University, ; Osaka, 565-0871 Japan
                [12 ]ISNI 0000 0000 8902 2273, GRID grid.174567.6, Department of Stem Cell Biology, Atomic Bomb Disease Institute, , Nagasaki University, ; Nagasaki, 852-8523 Japan
                [13 ]ISNI 0000 0001 0667 4960, GRID grid.272458.e, Department of Basic Geriatrics, Graduate School of Medical Science, , Kyoto Prefectural University of Medicine, ; Kyoto, 602-8566 Japan
                [14 ]ISNI 0000 0004 0373 6590, GRID grid.419502.b, Department of Molecular Genetics of Ageing, , Max Planck Institute for Biology of Ageing, ; Cologne, 50931 Germany
                [15 ]ISNI 0000 0000 8580 3777, GRID grid.6190.e, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), , University of Cologne, ; Cologne, 50931 Germany
                Author information
                http://orcid.org/0000-0002-1488-8317
                http://orcid.org/0000-0001-7495-1675
                http://orcid.org/0000-0002-8912-2316
                http://orcid.org/0000-0002-6486-7143
                http://orcid.org/0000-0002-0311-8472
                http://orcid.org/0000-0002-0874-7542
                Article
                8729
                10.1038/s41467-019-08729-6
                6381146
                30783089
                ddfb5138-89fd-4657-9dba-d3992920d916
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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                : 20 February 2018
                : 11 January 2019
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