151
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Genetic aberrations in macroautophagy genes leading to diseases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018. [PMID: 29524522 DOI: 10.1016/j.bbamcr.2018.03.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The catabolic process of macroautophagy, through the rapid degradation of unwanted cellular components, is involved in a multitude of cellular and organismal functions that are essential to maintain homeostasis. Those functions include adaptation to starvation, cell development and differentiation, innate and adaptive immunity, tumor suppression, autophagic cell death, and maintenance of stem cell stemness. Not surprisingly, an impairment or block of macroautophagy can lead to severe pathologies. A still increasing number of reports, in particular, have revealed that mutations in the autophagy-related (ATG) genes, encoding the key players of macroautophagy, are either the cause or represent a risk factor for the development of several illnesses. The aim of this review is to provide a comprehensive overview of the diseases and disorders currently known that are or could be caused by mutations in core ATG proteins but also in the so-called autophagy receptors, which provide specificity to the process of macroautophagy. Our compendium underlines the medical relevance of this pathway and underscores the importance of the eventual development of therapeutic approaches aimed at modulating macroautophagy.
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152
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Crosstalk of Autophagy and the Secretory Pathway and Its Role in Diseases. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 337:153-184. [DOI: 10.1016/bs.ircmb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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153
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Cui Y, He Y, Cao W, Gao J, Jiang L. The Multivesicular Body and Autophagosome Pathways in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1837. [PMID: 30619408 PMCID: PMC6299029 DOI: 10.3389/fpls.2018.01837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/27/2018] [Indexed: 05/03/2023]
Abstract
In eukaryotic cells, the endomembrane system consists of multiple membrane-bound organelles, which play essential roles in the precise transportation of various cargo proteins. In plant cells, vacuoles are regarded as the terminus of catabolic pathways whereas the selection and transport of vacuolar cargoes are mainly mediated by two types of organelles, multivesicular bodies (MVBs) also termed prevacuolar compartments (PVCs) and autophagosomes. MVBs are single-membrane bound organelles with intraluminal vesicles and mediate the transport between the trans-Golgi network (TGN) and vacuoles, while autophagosomes are double-membrane bound organelles, which mediate cargo delivery to the vacuole for degradation and recycling during autophagy. Great progress has been achieved recently in identification and characterization of the conserved and plant-unique regulators involved in the MVB and autophagosome pathways. In this review, we present an update on the current knowledge of these key regulators and pay special attention to their conserved protein domains. In addition, we discuss the possible interplay between the MVB and autophagosome pathways in regulating vacuolar degradation in plants.
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Affiliation(s)
- Yong Cui
- Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Yong Cui, Liwen Jiang,
| | - Yilin He
- Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wenhan Cao
- Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jiayang Gao
- Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- *Correspondence: Yong Cui, Liwen Jiang,
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154
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Wang B, Iyengar R, Li-Harms X, Joo JH, Wright C, Lavado A, Horner L, Yang M, Guan JL, Frase S, Green DR, Cao X, Kundu M. The autophagy-inducing kinases, ULK1 and ULK2, regulate axon guidance in the developing mouse forebrain via a noncanonical pathway. Autophagy 2017; 14:796-811. [PMID: 29099309 DOI: 10.1080/15548627.2017.1386820] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mammalian ULK1 (unc-51 like kinase 1) and ULK2, Caenorhabditis elegans UNC-51, and Drosophila melanogaster Atg1 are serine/threonine kinases that regulate flux through the autophagy pathway in response to various types of cellular stress. C. elegans UNC-51 and D. melanogaster Atg1 also promote axonal growth and defasciculation; disruption of these genes results in defective axon guidance in invertebrates. Although disrupting ULK1/2 function impairs normal neurite outgrowth in vitro, the role of ULK1 and ULK2 in the developing brain remains poorly characterized. Here, we show that ULK1 and ULK2 are required for proper projection of axons in the forebrain. Mice lacking Ulk1 and Ulk2 in their central nervous systems showed defects in axonal pathfinding and defasciculation affecting the corpus callosum, anterior commissure, corticothalamic axons and thalamocortical axons. These defects impaired the midline crossing of callosal axons and caused hypoplasia of the anterior commissure and disorganization of the somatosensory cortex. The axon guidance defects observed in ulk1/2 double-knockout mice and central nervous system-specific (Nes-Cre) Ulk1/2-conditional double-knockout mice were not recapitulated in mice lacking other autophagy genes (i.e., Atg7 or Rb1cc1 [RB1-inducible coiled-coil 1]). The brains of Ulk1/2-deficient mice did not show stem cell defects previously attributed to defective autophagy in ambra1 (autophagy/Beclin 1 regulator 1)- and Rb1cc1-deficient mice or accumulation of SQSTM1 (sequestosome 1)+ or ubiquitin+ deposits. Together, these data demonstrate that ULK1 and ULK2 regulate axon guidance during mammalian brain development via a noncanonical (i.e., autophagy-independent) pathway.
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Affiliation(s)
- Bo Wang
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA.,f Integrated Biomedical Sciences Program , the University of Tennessee Health Science Center , Memphis , TN , USA
| | - Rekha Iyengar
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Xiujie Li-Harms
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Joung Hyuck Joo
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Christopher Wright
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Alfonso Lavado
- b Department of Developmental Neurobiology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Linda Horner
- d Cell and Tissue Imaging Center , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Mao Yang
- c Department of Immunology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Jun-Lin Guan
- e Department of Cancer Biology , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Sharon Frase
- d Cell and Tissue Imaging Center , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Douglas R Green
- c Department of Immunology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Xinwei Cao
- b Department of Developmental Neurobiology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Mondira Kundu
- a Department of Pathology , St. Jude Children's Research Hospital , Memphis , TN , USA
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155
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Lindqvist LM, Tandoc K, Topisirovic I, Furic L. Cross-talk between protein synthesis, energy metabolism and autophagy in cancer. Curr Opin Genet Dev 2017; 48:104-111. [PMID: 29179096 DOI: 10.1016/j.gde.2017.11.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Translation is a pivotal step in the regulation of gene expression as well as one of the most energy consuming processes in the cell. Dysregulation of translation caused by the aberrant function of upstream signaling pathways and/or perturbations in the expression or function of components of the translation machinery is frequent in cancer. In this review, we discuss emerging findings that highlight hitherto unappreciated aspects of signaling to the translation apparatus with the particular focus on emerging connections between protein synthesis, autophagy and energy homeostasis in cancer.
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Affiliation(s)
- Lisa M Lindqvist
- Cell Signalling and Cell Death Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3050, Australia.
| | - Kristofferson Tandoc
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada H3T 1E2; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3T2, Canada
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada H3T 1E2; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3T2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada; Department of Biochemistry, McGill University, Montreal, QC H4A 3T2, Canada
| | - Luc Furic
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia.
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156
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Autophagy in the context of the cellular membrane-trafficking system: the enigma of Atg9 vesicles. Biochem Soc Trans 2017; 45:1323-1331. [PMID: 29150528 PMCID: PMC5730941 DOI: 10.1042/bst20170128] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/15/2022]
Abstract
Macroautophagy is an intracellular degradation system that involves the de novo formation of membrane structures called autophagosomes, although the detailed process by which membrane lipids are supplied during autophagosome formation is yet to be elucidated. Macroautophagy is thought to be associated with canonical membrane trafficking, but several mechanistic details are still missing. In this review, the current understanding and potential mechanisms by which membrane trafficking participates in macroautophagy are described, with a focus on the enigma of the membrane protein Atg9, for which the proximal mechanisms determining its movement are disputable, despite its key role in autophagosome formation.
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157
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Wen JK, Wang YT, Chan CC, Hsieh CW, Liao HM, Hung CC, Chen GC. Atg9 antagonizes TOR signaling to regulate intestinal cell growth and epithelial homeostasis in Drosophila. eLife 2017; 6:29338. [PMID: 29144896 PMCID: PMC5690286 DOI: 10.7554/elife.29338] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/29/2017] [Indexed: 02/06/2023] Open
Abstract
Autophagy is essential for maintaining cellular homeostasis and survival under various stress conditions. Autophagy-related gene 9 (Atg9) encodes a multipass transmembrane protein thought to act as a membrane carrier for forming autophagosomes. However, the molecular regulation and physiological importance of Atg9 in animal development remain largely unclear. Here, we generated Atg9 null mutant flies and found that loss of Atg9 led to shortened lifespan, locomotor defects, and increased susceptibility to stress. Atg9 loss also resulted in aberrant adult midgut morphology with dramatically enlarged enterocytes. Interestingly, inhibiting the TOR signaling pathway rescued the midgut defects of the Atg9 mutants. In addition, Atg9 interacted with PALS1-associated tight junction protein (Patj), which associates with TSC2 to regulate TOR activity. Depletion of Atg9 caused a marked decrease in TSC2 levels. Our findings revealed an antagonistic relationship between Atg9 and TOR signaling in the regulation of cell growth and tissue homeostasis.
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Affiliation(s)
- Jung-Kun Wen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Program, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chih-Chiang Chan
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Cheng-Wen Hsieh
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsiao-Man Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chin-Chun Hung
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Program, College of Life Science, National Taiwan University, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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158
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Structure and function of yeast Atg20, a sorting nexin that facilitates autophagy induction. Proc Natl Acad Sci U S A 2017; 114:E10112-E10121. [PMID: 29114050 DOI: 10.1073/pnas.1708367114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Atg20 and Snx4/Atg24 proteins have been identified in a screen for mutants defective in a type of selective macroautophagy/autophagy. Both proteins are connected to the Atg1 kinase complex, which is involved in autophagy initiation, and bind phosphatidylinositol-3-phosphate. Atg20 and Snx4 contain putative BAR domains, suggesting a possible role in membrane deformation, but they have been relatively uncharacterized. Here we demonstrate that, in addition to its function in selective autophagy, Atg20 plays a critical role in the efficient induction of nonselective autophagy. Atg20 is a dynamic posttranslationally modified protein that engages both structurally stable (PX and BAR) and intrinsically disordered domains for its function. In addition to its PX and BAR domains, Atg20 uses a third membrane-binding module, a membrane-inducible amphipathic helix present in a previously undescribed location in Atg20 within the putative BAR domain. Taken together, these findings yield insights into the molecular mechanism of the autophagy machinery.
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159
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MicroRNA-93 Regulates Hypoxia-Induced Autophagy by Targeting ULK1. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2709053. [PMID: 29109831 PMCID: PMC5646326 DOI: 10.1155/2017/2709053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/13/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
The expression of the core autophagy kinase, Unc51-like kinase 1 (ULK1), is regulated transcriptionally and translationally by starvation-induced autophagy. However, how ULK1 is regulated during hypoxia is not well understood. Previously, we showed that ULK1 expression is induced by hypoxia stress. Here, we report a new ULK1-modulating microRNA, miR-93; its transcription is negatively correlated with the translation of ULK1 under hypoxic condition. miR-93 targets ULK1 and reduces its protein levels under hypoxia condition. miR-93 also inhibits hypoxia-induced autophagy by preventing LC3-I to LC3-II transition and P62 degradation; these processes are reversed by the overexpression of an endogenous miR-93 inhibitor. Re-expression of ULK1 without miR-93 response elements restores the hypoxia-induced autophagy which is inhibited by miR-93. Finally, we detected the effects of miR-93 on cell viability and apoptosis in noncancer cell lines and cancer cells. We found that miR-93 sustains the viability of MEFs (mouse embryonic fibroblasts) and inhibits its apoptosis under hypoxia. Thus, we conclude that miR-93 is involved in hypoxia-induced autophagy by regulating ULK1. Our results provide a new angle to understand the complicated regulation of the key autophagy kinase ULK1 during different stress conditions.
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160
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A Rab5 GTPase module is important for autophagosome closure. PLoS Genet 2017; 13:e1007020. [PMID: 28934205 PMCID: PMC5626503 DOI: 10.1371/journal.pgen.1007020] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 10/03/2017] [Accepted: 09/14/2017] [Indexed: 02/03/2023] Open
Abstract
In the conserved autophagy pathway, the double-membrane autophagosome (AP) engulfs cellular components to be delivered for degradation in the lysosome. While only sealed AP can productively fuse with the lysosome, the molecular mechanism of AP closure is currently unknown. Rab GTPases, which regulate all intracellular trafficking pathways in eukaryotes, also regulate autophagy. Rabs function in GTPase modules together with their activators and downstream effectors. In yeast, an autophagy-specific Ypt1 GTPase module, together with a set of autophagy-related proteins (Atgs) and a phosphatidylinositol-3-phosphate (PI3P) kinase, regulates AP formation. Fusion of APs and endosomes with the vacuole (the yeast lysosome) requires the Ypt7 GTPase module. We have previously shown that the Rab5-related Vps21, within its endocytic GTPase module, regulates autophagy. However, it was not clear which autophagy step it regulates. Here, we show that this module, which includes the Vps9 activator, the Rab5-related Vps21, the CORVET tethering complex, and the Pep12 SNARE, functions after AP expansion and before AP closure. Whereas APs are not formed in mutant cells depleted for Atgs, sealed APs accumulate in cells depleted for the Ypt7 GTPase module members. Importantly, depletion of individual members of the Vps21 module results in a novel phenotype: accumulation of unsealed APs. In addition, we show that Vps21-regulated AP closure precedes another AP maturation step, the previously reported PI3P phosphatase-dependent Atg dissociation. Our results delineate three successive steps in the autophagy pathway regulated by Rabs, Ypt1, Vps21 and Ypt7, and provide the first insight into the upstream regulation of AP closure. In autophagy, a cellular recycling pathway, the double-membrane autophagosome (AP) engulfs excess or damaged cargo and delivers it for degradation in the lysosome for the reuse of its building blocks. While plenty of information is currently available regarding AP formation, expansion and fusion, not much is known about the regulation of AP closure, which is required for fusion of APs with the lysosome. Here, we use yeast genetics to characterize a novel mutant phenotype, accumulation of unsealed APs, and identify a role for the Rab5-related Vps21 GTPase in this process. Rab GTPases function in modules that include upstream activators and downstream effectors. We have previously shown that the same Vps21 module that regulates endocytosis also plays a role in autophagy. Using single and double mutant analyses, we find that this module is important for AP closure. Moreover, we delineate three Rab GTPase-regulated steps in the autophagy pathway: AP formation, closure, and fusion, which are regulated by Ypt1, Vps21 and Ypt7, respectively. This study provides the first insight into the mechanism of the elusive process of AP closure.
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161
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Abstract
Macroautophagy is an intracellular pathway used for targeting of cellular components to the lysosome for their degradation and involves sequestration of cytoplasmic material into autophagosomes formed from a double membrane structure called the phagophore. The nucleation and elongation of the phagophore is tightly regulated by several autophagy-related (ATG) proteins, but also involves vesicular trafficking from different subcellular compartments to the forming autophagosome. Such trafficking must be tightly regulated by various intra- and extracellular signals to respond to different cellular stressors and metabolic states, as well as the nature of the cargo to become degraded. We are only starting to understand the interconnections between different membrane trafficking pathways and macroautophagy. This review will focus on the membrane trafficking machinery found to be involved in delivery of membrane, lipids, and proteins to the forming autophagosome and in the subsequent autophagosome fusion with endolysosomal membranes. The role of RAB proteins and their regulators, as well as coat proteins, vesicle tethers, and SNARE proteins in autophagosome biogenesis and maturation will be discussed.
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162
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Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A, Kraft C. Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Mol Cell 2017; 64:221-235. [PMID: 27768871 DOI: 10.1016/j.molcel.2016.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022]
Abstract
Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
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Affiliation(s)
- Raffaela Torggler
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thorsten Brach
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thaddäus Pfaffenwimmer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Tamara Matzhold
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - David Schweida
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Andrea Brezovich
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria.
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163
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Palmisano NJ, Rosario N, Wysocki M, Hong M, Grant B, Meléndez A. The recycling endosome protein RAB-10 promotes autophagic flux and localization of the transmembrane protein ATG-9. Autophagy 2017; 13:1742-1753. [PMID: 28872980 DOI: 10.1080/15548627.2017.1356976] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Macroautophagy/autophagy involves the formation of an autophagosome, a double-membrane vesicle that delivers sequestered cytoplasmic cargo to lysosomes for degradation and recycling. Closely related, endocytosis mediates the sorting and transport of cargo throughout the cell, and both processes are important for cellular homeostasis. However, how endocytic proteins functionally intersect with autophagy is not clear. Mutations in the DAF-2/insulin-like IGF-1 (INSR) receptor at the permissive temperature result in a small increase in GFP::LGG-1 foci, i.e. autophagosomes, but a large increase at the nonpermissive temperature, allowing us to control the level of autophagy. In a RNAi screen for endocytic genes that alter the expression of GFP::LGG-1 in daf-2 mutants, we identified RAB-10, a small GTPase that regulates basolateral endocytosis. Loss of rab-10 in daf-2 mutants results in more GFP::LGG-1-positive foci at the permissive, but less GFP::LGG-1 or SQST-1::GFP foci at the nonpermissive temperature. As previously reported, loss of rab-10 alone resulted in an increase of GFP:LGG-1 foci. Exposure of rab-10 mutant animals to chloroquine, a known inhibitor of autophagic flux, failed to increase the number of GFP::LGG-1 foci. Moreover, colocalization between LMP-1::tagRFP and GFP::LGG-1 (the lysosome and autophagosome reporters) was decreased in daf-2; rab-10 dauers at the nonpermissive temperature. Intriguingly, RAB-10 was required to maintain the normal size of GFP::ATG-9-positive structures in daf-2 mutants at both the permissive and nonpermissive temperature. Finally, we found that RAB-10 GTPase cycling was required to control the size of GFP::ATG-9 foci. Collectively, our data support a model where rab-10 controls autophagic flux by regulating autophagosome formation and maturation.
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Affiliation(s)
- N J Palmisano
- a Biology Department, Queens College, CUNY , Flushing , NY , USA.,b Biology and Biochemistry Ph.D. Programs , The Graduate Center of the City University of New York , NY , USA
| | - N Rosario
- a Biology Department, Queens College, CUNY , Flushing , NY , USA
| | - M Wysocki
- a Biology Department, Queens College, CUNY , Flushing , NY , USA
| | - M Hong
- a Biology Department, Queens College, CUNY , Flushing , NY , USA
| | - B Grant
- c Department of Molecular Biology and Biochemistry , Rutgers University , Piscataway , NJ , USA
| | - A Meléndez
- a Biology Department, Queens College, CUNY , Flushing , NY , USA.,b Biology and Biochemistry Ph.D. Programs , The Graduate Center of the City University of New York , NY , USA
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164
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Schmidt O, Weyer Y, Fink MJ, Müller M, Weys S, Bindreither M, Teis D. Regulation of Rab5 isoforms by transcriptional and post-transcriptional mechanisms in yeast. FEBS Lett 2017; 591:2803-2815. [PMID: 28792590 PMCID: PMC5637908 DOI: 10.1002/1873-3468.12785] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 12/15/2022]
Abstract
Rab5 GTPases are master regulators of early endosome biogenesis and transport. The genome of Saccharomyces cerevisiae encodes three Rab5 proteins: Vps21, the major isoform, Ypt52 and Ypt53. Here, we show that Vps21 is the most abundant Rab5 protein and Ypt53 is the least abundant. In stressed cells, Ypt53 levels increase but never exceed that of Vps21. Its induction requires the transcription factors Crz1 and Gis1. In growing cells, the expression of Ypt53 is suppressed by post-transcriptional mechanisms mediated by the untranslated regions of the YPT53 mRNA. Based on genetic experiments, these sequences appear to stimulate deadenylation, Pat1-activated decapping and Xrn1-mediated mRNA degradation. Once this regulation is bypassed, Ypt53 protein levels surpass Vps21, and Ypt53 is sufficient to maintain endosomal function and cell growth.
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Affiliation(s)
- Oliver Schmidt
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | - Yannick Weyer
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | - Matthias J. Fink
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | - Martin Müller
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | - Sabine Weys
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | | | - David Teis
- Division of Cell Biology, BiocenterMedical University of InnsbruckAustria
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165
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Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
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Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
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166
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Pengo N, Agrotis A, Prak K, Jones J, Ketteler R. A reversible phospho-switch mediated by ULK1 regulates the activity of autophagy protease ATG4B. Nat Commun 2017; 8:294. [PMID: 28821708 PMCID: PMC5562857 DOI: 10.1038/s41467-017-00303-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 06/20/2017] [Indexed: 12/26/2022] Open
Abstract
Upon induction of autophagy, the ubiquitin-like protein LC3 is conjugated to phosphatidylethanolamine (PE) on the inner and outer membrane of autophagosomes to allow cargo selection and autophagosome formation. LC3 undergoes two processing steps, the proteolytic cleavage of pro-LC3 and the de-lipidation of LC3-PE from autophagosomes, both executed by the same cysteine protease ATG4. How ATG4 activity is regulated to co-ordinate these events is currently unknown. Here we find that ULK1, a protein kinase activated at the autophagosome formation site, phosphorylates human ATG4B on serine 316. Phosphorylation at this residue results in inhibition of its catalytic activity in vitro and in vivo. On the other hand, phosphatase PP2A-PP2R3B can remove this inhibitory phosphorylation. We propose that the opposing activities of ULK1-mediated phosphorylation and PP2A-mediated dephosphorylation provide a phospho-switch that regulates the cellular activity of ATG4B to control LC3 processing.Upon autophagy induction, LC3 is cleaved by the protease ATG4 and conjugated to the autophagosomal membrane; however, its removal is mediated by the same protease. Here the authors show that ULK1-mediated phosphorylation and PP2A-mediated dephosphorylation of ATG4 regulates its cellular activity to control LC3 processing.
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Affiliation(s)
- N Pengo
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - A Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - K Prak
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - J Jones
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - R Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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167
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Sánchez-Wandelmer J, Kriegenburg F, Rohringer S, Schuschnig M, Gómez-Sánchez R, Zens B, Abreu S, Hardenberg R, Hollenstein D, Gao J, Ungermann C, Martens S, Kraft C, Reggiori F. Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation. Nat Commun 2017; 8:295. [PMID: 28821724 PMCID: PMC5562703 DOI: 10.1038/s41467-017-00302-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 06/19/2017] [Indexed: 11/09/2022] Open
Abstract
The biogenesis of autophagosomes depends on the conjugation of Atg8-like proteins with phosphatidylethanolamine. Atg8 processing by the cysteine protease Atg4 is required for its covalent linkage to phosphatidylethanolamine, but it is also necessary for Atg8 deconjugation from this lipid to release it from membranes. How these two cleavage steps are coordinated is unknown. Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. These results are consistent with a model where the Atg8-phosphatidylethanolamine pool essential for autophagosome formation is protected at least in part by Atg4 phosphorylation by Atg1 while newly synthesized cytoplasmic Atg8 remains susceptible to constitutive Atg4 processing.The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at autophagosome formation sites.
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Affiliation(s)
- Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | | | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Bettina Zens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - David Hollenstein
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Jieqiong Gao
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands.
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168
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Joshi AS, Zhang H, Prinz WA. Organelle biogenesis in the endoplasmic reticulum. Nat Cell Biol 2017; 19:876-882. [DOI: 10.1038/ncb3579] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/21/2017] [Indexed: 12/16/2022]
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169
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Torggler R, Papinski D, Kraft C. Assays to Monitor Autophagy in Saccharomyces cerevisiae. Cells 2017; 6:cells6030023. [PMID: 28703742 PMCID: PMC5617969 DOI: 10.3390/cells6030023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022] Open
Abstract
Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of cytoplasmic components. While research over the last decades has led to the discovery of the key factors involved in autophagy, the pathway is not yet completely understood. The first studies of autophagy on a molecular level were conducted in the yeast Saccharomyces cerevisiae. Building up on these studies, many homologs have been found in higher eukaryotes. Yeast remains a highly relevant model organism for studying autophagy, with a wide range of established methods to elucidate the molecular details of the autophagy pathway. In this review, we provide an overview of methods to study both selective and bulk autophagy, including intermediate steps in the yeast Saccharomyces cerevisiae. We compare different assays, discuss their advantages and limitations and list potential applications.
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Affiliation(s)
- Raffaela Torggler
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.
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170
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Noda T. Regulation of Autophagy through TORC1 and mTORC1. Biomolecules 2017; 7:biom7030052. [PMID: 28686223 PMCID: PMC5618233 DOI: 10.3390/biom7030052] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 12/27/2022] Open
Abstract
Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated by the target of rapamycin complex 1 (TORC1/mTORC1). In this review, a history of this regulation and recent advances in such regulation both in yeast and mammals will be discussed. Recently, the mechanism of autophagy initiation in yeast has been deduced. The autophagy-related gene 13 (Atg13) and the unc-51 like autophagy activating kinase 1 (Ulk1) are the most crucial substrates of TORC1 in autophagy, and by its dephosphorylation, autophagosome formation is initiated. Phosphorylation/dephosphorylation of Atg13 is regulated spatially inside the cell. Another TORC1-dependent regulation lies in the expression of autophagy genes and vacuolar/lysosomal hydrolases. Several transcriptional and post-transcriptional regulations are controlled by TORC1, which affects autophagy activity in yeast and mammals.
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Affiliation(s)
- Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Osaka 565-0871, Japan.
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171
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Galluzzi L, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cecconi F, Choi AM, Chu CT, Codogno P, Colombo MI, Cuervo AM, Debnath J, Deretic V, Dikic I, Eskelinen EL, Fimia GM, Fulda S, Gewirtz DA, Green DR, Hansen M, Harper JW, Jäättelä M, Johansen T, Juhasz G, Kimmelman AC, Kraft C, Ktistakis NT, Kumar S, Levine B, Lopez-Otin C, Madeo F, Martens S, Martinez J, Melendez A, Mizushima N, Münz C, Murphy LO, Penninger JM, Piacentini M, Reggiori F, Rubinsztein DC, Ryan KM, Santambrogio L, Scorrano L, Simon AK, Simon HU, Simonsen A, Tavernarakis N, Tooze SA, Yoshimori T, Yuan J, Yue Z, Zhong Q, Kroemer G. Molecular definitions of autophagy and related processes. EMBO J 2017; 36:1811-1836. [PMID: 28596378 PMCID: PMC5494474 DOI: 10.15252/embj.201796697] [Citation(s) in RCA: 1222] [Impact Index Per Article: 152.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/15/2022] Open
Abstract
Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.
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Affiliation(s)
- Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Université Paris Descartes/Paris V, Paris, France
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics, Department of Pediatrics, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Manuel Bravo-San Pedro
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Francesco Cecconi
- Department of Biology, University of Tor Vergata, Rome, Italy
- Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Augustine M Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patrice Codogno
- Université Paris Descartes/Paris V, Paris, France
- Institut Necker-Enfants Malades (INEM), Paris, France
- INSERM, U1151, Paris, France
- CNRS, UMR8253, Paris, France
| | - Maria Isabel Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jayanta Debnath
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt Main, Germany
- Department of Immunology and Medical Genetics, University of Split School of Medicine, Split, Croatia
| | | | - Gian Maria Fimia
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David A Gewirtz
- Department of Pharmacology and Toxicology and Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marja Jäättelä
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Gabor Juhasz
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest, Hungary
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Claudine Kraft
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | | | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute (HHMI), Dallas, TX, USA
| | - Carlos Lopez-Otin
- Department de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer, Oviedo, Spain
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Sascha Martens
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Jennifer Martinez
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alicia Melendez
- Department of Biology, Queens College, Queens, NY, USA
- Graduate Center, City University of New York, New York, NY, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Leon O Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Campus Vienna BioCentre, Vienna, Austria
| | - Mauro Piacentini
- Department of Biology, University of Tor Vergata, Rome, Italy
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine, Padova, Italy
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka, Japan
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qing Zhong
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guido Kroemer
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
- Pôle de Biologie, Hopitâl Européen George Pompidou, AP-HP, Paris, France
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172
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Davis S, Wang J, Ferro-Novick S. Crosstalk between the Secretory and Autophagy Pathways Regulates Autophagosome Formation. Dev Cell 2017; 41:23-32. [PMID: 28399396 DOI: 10.1016/j.devcel.2017.03.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/26/2017] [Accepted: 03/16/2017] [Indexed: 12/26/2022]
Abstract
The induction of autophagy by nutrient deprivation leads to a rapid increase in the formation of autophagosomes, unique organelles that replenish the cellular pool of nutrients by sequestering cytoplasmic material for degradation. The urgent need for membranes to form autophagosomes during starvation to maintain homeostasis leads to a dramatic rearrangement of intracellular membranes. Here we discuss recent findings that have begun to uncover how different parts of the secretory pathway directly and indirectly contribute to autophagosome formation during starvation.
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Affiliation(s)
- Saralin Davis
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA
| | - Juan Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA.
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173
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Yamamoto H, Fujioka Y, Suzuki SW, Noshiro D, Suzuki H, Kondo-Kakuta C, Kimura Y, Hirano H, Ando T, Noda NN, Ohsumi Y. The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes. Dev Cell 2017; 38:86-99. [PMID: 27404361 DOI: 10.1016/j.devcel.2016.06.015] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 05/11/2016] [Accepted: 06/12/2016] [Indexed: 12/21/2022]
Abstract
Autophagosome formation in yeast entails starvation-induced assembly of the pre-autophagosomal structure (PAS), in which multiple Atg1 complexes (composed of Atg1, Atg13, and the Atg17-Atg29-Atg31 subcomplex) are initially engaged. However, the molecular mechanisms underlying the multimeric assembly of these complexes remain unclear. Using structural and biological techniques, we herein demonstrate that Atg13 has a large intrinsically disordered region (IDR) and interacts with two distinct Atg17 molecules using two binding regions in the IDR. We further reveal that these two binding regions are essential not only for Atg1 complex assembly in vitro, but also for PAS organization in vivo. These findings underscore the structural and functional significance of the IDR of Atg13 in autophagy initiation: Atg13 provides intercomplex linkages between Atg17-Atg29-Atg31 complexes, thereby leading to supramolecular self-assembly of Atg1 complexes, in turn accelerating the initial events of autophagy, including autophosphorylation of Atg1, recruitment of Atg9 vesicles, and phosphorylation of Atg9 by Atg1.
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Affiliation(s)
- Hayashi Yamamoto
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Sho W Suzuki
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Daisuke Noshiro
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hironori Suzuki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Chika Kondo-Kakuta
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Toshio Ando
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
| | - Yoshinori Ohsumi
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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174
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Nishimura T, Tamura N, Kono N, Shimanaka Y, Arai H, Yamamoto H, Mizushima N. Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains. EMBO J 2017; 36:1719-1735. [PMID: 28495679 DOI: 10.15252/embj.201695189] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 03/28/2017] [Accepted: 04/11/2017] [Indexed: 11/09/2022] Open
Abstract
The autophagosome, a double-membrane structure mediating degradation of cytoplasmic materials by macroautophagy, is formed in close proximity to the endoplasmic reticulum (ER). However, how the ER membrane is involved in autophagy initiation and to which membrane structures the autophagy-initiation complex is localized have not been fully characterized. Here, we were able to biochemically analyze autophagic intermediate membranes and show that the autophagy-initiation complex containing ULK and FIP200 first associates with the ER membrane. To further characterize the ER subdomain, we screened phospholipid biosynthetic enzymes and found that the autophagy-initiation complex localizes to phosphatidylinositol synthase (PIS)-enriched ER subdomains. Then, the initiation complex translocates to the ATG9A-positive autophagosome precursors in a PI3P-dependent manner. Depletion of phosphatidylinositol (PI) by targeting bacterial PI-specific phospholipase C to the PIS domain impairs recruitment of downstream autophagy factors and autophagosome formation. These findings suggest that the autophagy-initiation complex, the PIS-enriched ER subdomain, and ATG9A vesicles together initiate autophagosome formation.
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Affiliation(s)
- Taki Nishimura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norito Tamura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuta Shimanaka
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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175
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Zhang N, Yang Y, Lu H, Xiang Y, Huang X, Hu R, Chen Z, Yuan W, Peng R, Peng J, Ai H, Liu K. Spodoptera litura autophagy-related protein 1 interacts with autophagy-related protein 5 and enhances its degradation. INSECT MOLECULAR BIOLOGY 2017; 26:190-203. [PMID: 27902874 DOI: 10.1111/imb.12284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
It is known that the autophagy-related protein 1 (ATG1) plays critical roles in the regulation of autophagy in mammals and yeast, whereas the function of ATG1 in lepidopteran insects is not well elucidated. Here Spodoptera litura ATG1 (SlATG1) and its interactions with other ATG proteins were characterized. Alternative splicing of SlAtg1 produced at least four transcript variants. Over-expression and RNA interference knockdown of SlAtg1 demonstrated that SlATG1 enhanced autophagy. SlATG1A-Green fluorescent protein (GFP) tagged localized in the cytoplasm and formed some punctuate dots, which were colocalized with red fluorescent protein mCherry tagged Spodoptera exigua ATG5 (SeATG5). SlATG1A-GFP over-expression reduced the nuclear abundance of mCherry-SeATG5 but increased its cytoplasmic abundance. Pull-down, co-immunoprecipitation and bimolecular fluorescence complementation assays showed that SlATG1A bound to SeATG5 through the N-terminus of SlATG1A. The over-expression of FLAG epitope tagged SlATG1A significantly increased the accumulation of the cleaved GFP from GFP-SeATG5, suggesting the enhanced degradation of GFP-SeATG5. In addition, we confirmed that the interactions of SlATG1 with other autophagy-related proteins were conserved. These results provide the first evidence that ATG1 interacts with ATG5 and enhances its degradation in lepidopteran insect cells, which may have important physiological functions.
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Affiliation(s)
- N Zhang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Y Yang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - H Lu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Y Xiang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - X Huang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - R Hu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Z Chen
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - W Yuan
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - R Peng
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - J Peng
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - H Ai
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - K Liu
- School of Life Sciences, Central China Normal University, Wuhan, China
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176
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Philipp O, Hamann A, Osiewacz HD, Koch I. The autophagy interaction network of the aging model Podospora anserina. BMC Bioinformatics 2017; 18:196. [PMID: 28347269 PMCID: PMC5369006 DOI: 10.1186/s12859-017-1603-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/15/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autophagy plays a key role in the degradation of damaged cellular components and thereby affects aging and lifespan control. In earlier studies, it was found that autophagy in the aging model Podospora anserina acts as a longevity assurance mechanism. However, only little is known about the individual components controlling autophagy in this aging model. Here, we report a biochemical and bioinformatics study to detect the protein-protein interaction (PPI) network of P. anserina combining experimental and theoretical methods. RESULTS We constructed the PPI network of autophagy in P. anserina based on the corresponding networks of yeast and human. We integrated PaATG8 interaction partners identified in an own yeast two-hybrid analysis using ATG8 of P. anserina as bait. Additionally, we included age-dependent transcriptome data. The resulting network consists of 89 proteins involved in 186 interactions. We applied bioinformatics approaches to analyze the network topology and to prove that the network is not random, but exhibits biologically meaningful properties. We identified hub proteins which play an essential role in the network as well as seven putative sub-pathways, and interactions which are likely to be evolutionary conserved amongst species. We confirmed that autophagy-associated genes are significantly often up-regulated and co-expressed during aging of P. anserina. CONCLUSIONS With the present study, we provide a comprehensive biological network of the autophagy pathway in P. anserina comprising PPI and gene expression data. It is based on computational prediction as well as experimental data. We identified sub-pathways, important hub proteins, and evolutionary conserved interactions. The network clearly illustrates the relation of autophagy to aging processes and enables further specific studies to understand autophagy and aging in P. anserina as well as in other systems.
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Affiliation(s)
- Oliver Philipp
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics and Cluster of Excellence ‘Macromolecular Complexes’, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, Frankfurt am Main, 60325 Germany
- Molecular Developmental Biology, Institute of Molecular Biosciences, Faculty for Biosciences & Cluster of Excellence ‘Macromolecular Complexes’, Johann Wolfgang Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438 Germany
| | - Andrea Hamann
- Molecular Developmental Biology, Institute of Molecular Biosciences, Faculty for Biosciences & Cluster of Excellence ‘Macromolecular Complexes’, Johann Wolfgang Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438 Germany
| | - Heinz D. Osiewacz
- Molecular Developmental Biology, Institute of Molecular Biosciences, Faculty for Biosciences & Cluster of Excellence ‘Macromolecular Complexes’, Johann Wolfgang Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438 Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics and Cluster of Excellence ‘Macromolecular Complexes’, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, Frankfurt am Main, 60325 Germany
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177
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Abstract
Autophagy is the process of cellular self-eating by a double-membrane organelle, the autophagosome. A range of signaling processes converge on two protein complexes to initiate autophagy: the ULK1 (unc51-like autophagy activating kinase 1) protein kinase complex and the PI3KC3-C1 (class III phosphatidylinositol 3-kinase complex I) lipid kinase complex. Some 90% of the mass of these large protein complexes consists of noncatalytic domains and subunits, and the ULK1 complex has essential noncatalytic activities. Structural studies of these complexes have shed increasing light on the regulation of their catalytic and noncatalytic activities in autophagy initiation. The autophagosome is thought to nucleate from vesicles containing the integral membrane protein Atg9 (autophagy-related 9), COPII (coat protein complex II) vesicles, and possibly other sources. In the wake of reconstitution and super-resolution imaging studies, we are beginning to understand how the ULK1 and PI3KC3-C1 complexes might coordinate the nucleation and fusion of Atg9 and COPII vesicles at the start of autophagosome biogenesis.
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Affiliation(s)
- James H Hurley
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, California, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| | - Lindsey N Young
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, California, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
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178
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Wang B, Kundu M. Canonical and noncanonical functions of ULK/Atg1. Curr Opin Cell Biol 2017; 45:47-54. [PMID: 28292700 DOI: 10.1016/j.ceb.2017.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/09/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023]
Abstract
Mammalian Unc-51-like kinases 1 and 2 (ULK1 and ULK2) belong to the ULK/Atg1 family of serine/threonine kinases, which are conserved from yeast to mammals. Although ULK/Atg1 is best known for regulating flux through the autophagy pathway, it has evolutionarily conserved noncanonical functions in protein trafficking that are essential for maintaining cellular homeostasis. As a direct target of energy- and nutrient-sensing kinases, ULK/Atg1 is positioned to regulate the distribution and use of cellular resources in response to metabolic cues. In this review, we provide an overview of the molecular mechanisms through which ULK/Atg1 carries out its canonical and noncanonical functions and the signaling pathways that link its function to metabolism. We also highlight potential contributions of ULK/Atg1 in human diseases, including cancer and neurodegeneration.
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Affiliation(s)
- Bo Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Mondira Kundu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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179
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Santana-Codina N, Mancias JD, Kimmelman AC. The Role of Autophagy in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2017; 1:19-39. [PMID: 31119201 DOI: 10.1146/annurev-cancerbio-041816-122338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autophagy is a highly conserved and regulated process that targets proteins and damaged organelles for lysosomal degradation to maintain cell metabolism, genomic integrity, and cell survival. The role of autophagy in cancer is dynamic and depends, in part, on tumor type and stage. Although autophagy constrains tumor initiation in normal tissue, some tumors rely on autophagy for tumor promotion and maintenance. Studies in genetically engineered mouse models support the idea that autophagy can constrain tumor initiation by regulating DNA damage and oxidative stress. In established tumors, autophagy can also be required for tumor maintenance, allowing tumors to survive environmental stress and providing intermediates for cell metabolism. Autophagy can also be induced in response to chemotherapeutics, acting as a drug-resistance mechanism. Therefore, targeting autophagy is an attractive cancer therapeutic option currently undergoing validation in clinical trials.
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Affiliation(s)
- Naiara Santana-Codina
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016;
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180
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Nguyen N, Shteyn V, Melia TJ. Sensing Membrane Curvature in Macroautophagy. J Mol Biol 2017; 429:457-472. [PMID: 28088480 PMCID: PMC5276735 DOI: 10.1016/j.jmb.2017.01.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/07/2017] [Accepted: 01/08/2017] [Indexed: 10/20/2022]
Abstract
In response to intracellular stress events ranging from starvation to pathogen invasion, the cell activates one or more forms of macroautophagy. The key event in these related pathways is the de novo formation of a new organelle called the autophagosome, which either surrounds and sequesters random portions of the cytoplasm or selectively targets individual intracellular challenges. Thus, the autophagosome is a flexible membrane platform with dimensions that ultimately depend upon the target cargo. The intermediate membrane, termed the phagophore or isolation membrane, is a cup-like structure with a clear concave face and a highly curved rim. The phagophore is largely devoid of integral membrane proteins; thus, its shape and size are governed by peripherally associated membrane proteins and possibly by the lipid composition of the membrane itself. Growth along the phagophore rim marks the progress of both organelle expansion and ultimately organelle closure around a particular cargo. These two properties, a reliance on peripheral membrane proteins and a structurally distinct membrane architecture, suggest that the ability to target or manipulate membrane curvature might be an essential activity of proteins functioning in this pathway. In this review, we discuss the extent to which membranes are naturally curved at each of the cellular sites believed to engage in autophagosome formation, review basic mechanisms used to sense this curvature, and then summarize the existing literature concerning which autophagy proteins are capable of curvature recognition.
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Affiliation(s)
- Nathan Nguyen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Vladimir Shteyn
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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181
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Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell 2017; 65:761-774.e5. [PMID: 28132844 DOI: 10.1016/j.molcel.2016.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 11/21/2016] [Accepted: 12/22/2016] [Indexed: 12/15/2022]
Abstract
We have developed a general progressive procedure, Active Interaction Mapping, to guide assembly of the hierarchy of functions encoding any biological system. Using this process, we assemble an ontology of functions comprising autophagy, a central recycling process implicated in numerous diseases. A first-generation model, built from existing gene networks in Saccharomyces, captures most known autophagy components in broad relation to vesicle transport, cell cycle, and stress response. Systematic analysis identifies synthetic-lethal interactions as most informative for further experiments; consequently, we saturate the model with 156,364 such measurements across autophagy-activating conditions. These targeted interactions provide more information about autophagy than all previous datasets, producing a second-generation ontology of 220 functions. Approximately half are previously unknown; we confirm roles for Gyp1 at the phagophore-assembly site, Atg24 in cargo engulfment, Atg26 in cytoplasm-to-vacuole targeting, and Ssd1, Did4, and others in selective and non-selective autophagy. The procedure and autophagy hierarchy are at http://atgo.ucsd.edu/.
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182
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Abstract
One of the key questions regarding macroautophagy/autophagy is the mechanism through which the transmembrane protein ATG9 functions in delivering membrane to the expanding phagophore, the sequestering compartment that matures into an autophagosome. In a recent study, Zhou et al. identified a novel mechanism that regulates ATG9 trafficking from the plasma membrane and trans-Golgi network, which involves two conserved sorting signals required for ATG9 interaction with the AP1/2 adaptor complex and phosphorylation of ATG9 at Tyr8 by SRC kinase and at Ser14 by ULK1 for proper function during basal and starvation-induced autophagy.
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Affiliation(s)
- Yuchen Feng
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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183
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ATG9 regulates autophagosome progression from the endoplasmic reticulum in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E426-E435. [PMID: 28053229 DOI: 10.1073/pnas.1616299114] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Autophagy is a conserved pathway for bulk degradation of cytoplasmic material by a double-membrane structure named the autophagosome. The initiation of autophagosome formation requires the recruitment of autophagy-related protein 9 (ATG9) vesicles to the preautophagosomal structure. However, the functional relationship between ATG9 vesicles and the phagophore is controversial in different systems, and the molecular function of ATG9 remains unknown in plants. Here, we demonstrate that ATG9 is essential for endoplasmic reticulum (ER)-derived autophagosome formation in plants. Through a combination of genetic, in vivo imaging and electron tomography approaches, we show that Arabidopsis ATG9 deficiency leads to a drastic accumulation of autophagosome-related tubular structures in direct membrane continuity with the ER upon autophagic induction. Dynamic analyses demonstrate a transient membrane association between ATG9 vesicles and the autophagosomal membrane during autophagy. Furthermore, trafficking of ATG18a is compromised in atg9 mutants during autophagy by forming extended tubules in a phosphatidylinositol 3-phosphate-dependent manner. Taken together, this study provides evidence for a pivotal role of ATG9 in regulating autophagosome progression from the ER membrane in Arabidopsis.
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184
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Hayat M. Overview of Autophagy. AUTOPHAGY: CANCER, OTHER PATHOLOGIES, INFLAMMATION, IMMUNITY, INFECTION, AND AGING 2017:3-90. [DOI: 10.1016/b978-0-12-805420-8.00001-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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185
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186
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Gómez-Sánchez R, Sánchez-Wandelmer J, Reggiori F. Monitoring the Formation of Autophagosomal Precursor Structures in Yeast Saccharomyces cerevisiae. Methods Enzymol 2017; 588:323-365. [DOI: 10.1016/bs.mie.2016.09.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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187
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Hayat M. Overview of Autophagy. AUTOPHAGY: CANCER, OTHER PATHOLOGIES, INFLAMMATION, IMMUNITY, INFECTION, AND AGING 2017:1-122. [DOI: 10.1016/b978-0-12-812146-7.00001-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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188
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Feng Y, Backues SK, Baba M, Heo JM, Harper JW, Klionsky DJ. Phosphorylation of Atg9 regulates movement to the phagophore assembly site and the rate of autophagosome formation. Autophagy 2016; 12:648-58. [PMID: 27050455 DOI: 10.1080/15548627.2016.1157237] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Macroautophagy is primarily a degradative process that cells use to break down their own components to recycle macromolecules and provide energy under stress conditions, and defects in macroautophagy lead to a wide range of diseases. Atg9, conserved from yeast to mammals, is the only identified transmembrane protein in the yeast core macroautophagy machinery required for formation of the sequestering compartment termed the autophagosome. This protein undergoes dynamic movement between the phagophore assembly site (PAS), where the autophagosome precursor is nucleated, and peripheral sites that may provide donor membrane for expansion of the phagophore. Atg9 is a phosphoprotein that is regulated by the Atg1 kinase. We used stable isotope labeling by amino acids in cell culture (SILAC) to identify phosphorylation sites on this protein and identified an Atg1-independent phosphorylation site at serine 122. A nonphosphorylatable Atg9 mutant showed decreased autophagy activity, whereas the phosphomimetic mutant enhanced activity. Electron microscopy analysis suggests that the different levels of autophagy activity reflect differences in autophagosome formation, correlating with the delivery of Atg9 to the PAS. Finally, this phosphorylation regulates Atg9 interaction with Atg23 and Atg27.
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Affiliation(s)
- Yuchen Feng
- a Life Sciences Institute and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor , MI , USA
| | - Steven K Backues
- a Life Sciences Institute and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor , MI , USA
| | - Misuzu Baba
- b Research Institute for Science and Technology, Kogakuin University , Tokyo , Japan
| | - Jin-mi Heo
- c Department of Cell Biology , Harvard Medical School , Boston , MA USA
| | - J Wade Harper
- c Department of Cell Biology , Harvard Medical School , Boston , MA USA
| | - Daniel J Klionsky
- a Life Sciences Institute and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor , MI , USA
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189
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Wold MS, Lim J, Lachance V, Deng Z, Yue Z. ULK1-mediated phosphorylation of ATG14 promotes autophagy and is impaired in Huntington's disease models. Mol Neurodegener 2016; 11:76. [PMID: 27938392 PMCID: PMC5148922 DOI: 10.1186/s13024-016-0141-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/03/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Autophagy is a bulk degradation pathway for long-lived proteins, protein aggregates, and damaged organelles. ULK1 protein kinase and Vps34 lipid kinase are two key autophagy regulators that are critical for autophagosome biogenesis. However, it isn't fully understood how ULK1 regulates Vps34, especially in the context of disease. Polyglutamine expansion in huntingtin (Htt) causes aberrant accumulation of the aggregated protein and disrupts various cellular pathways including autophagy, a lysosomal degradation pathway, underlying the pathogenesis of Huntington's disease (HD). Although autophagic clearance of Htt aggregates is under investigation as therapeutic strategy for HD, the precise mechanism of autophagy impairment remains poorly understood. Moreover, in-vivo assays of autophagy have been particularly challenging due to lack of reliable and robust molecular biomarkers. METHOD We generated anti-phosphorylated ATG14 antibody to determine ATG14-mediated autophagy regulation; we employed Huntington's disease (HD) genetic cell models and animal models as well as autophagy reporter animal model to understand autophagy signaling and regulation in vivo. We applied biochemical analysis and molecular biology approaches to dissect the alteration of autophagy kinase activity and regulation. RESULTS Here, we demonstrate that ULK1 phosphorylates ATG14 at serine 29 in an mTOR-dependent manner. This phosphorylation critically regulates ATG14-Vps34 lipid kinase activity to control autophagy level. We also show that ATG14-associated Vps34 activity and ULK1-mediated phosphorylation of ATG14 and Beclin 1 are compromised in the Q175 mouse model of Huntington's disease. Finally, we show that ATG14 phosphorylation is decreased during general proteotoxic stress caused by proteasomal inhibition. This reduction of the specific phosphorylation of ATG14 and Beclin 1 is mediated, in part, by p62-induced sequestration of ULK1 to an insoluble cellular fraction. We show that increased ULK1 levels and phosphor-mimetic mutant ATG14 facilitate the clearance of polyQ mutant in cells. CONCLUSION Our study identifies a new regulatory mechanism for ATG14-Vps34 kinase activity by ULK1, which can be used as valuable molecular markers for in-vivo autophagic activity as well as potential therapeutic target for the clearance of polyglutamine disease protein.
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Affiliation(s)
- Mitchell S Wold
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Junghyun Lim
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Present Address: Genentech, Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Véronik Lachance
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiqiang Deng
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, and Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Zhenyu Yue
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Leon and Norma Hess Center for Science and Medicine, 9-106, 1470 Madison Ave, New York, NY, 10029, USA.
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190
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Abstract
Macroautophagy/autophagy is an evolutionarily conserved cellular degradation process that targets cytoplasmic materials including cytosol, macromolecules and unwanted organelles. The discovery and analysis of autophagy-related (Atg) proteins have unveiled much of the machinery of autophagosome formation. Although initially autophagy was regarded as a survival response to stress, recent studies have revealed its significance in cellular and organismal homeostasis, development and immunity. Autophagic dysfunction and dysregulation are implicated in various diseases. In this review, we briefly summarize the physiological roles, molecular mechanism, regulatory network, and pathophysiological roles of autophagy.
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Affiliation(s)
- Zhangyuan Yin
- Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology; University of Michigan, Ann Arbor, MI, USA 48109
| | - Clarence Pascual
- Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology; University of Michigan, Ann Arbor, MI, USA 48109
| | - Daniel J Klionsky
- Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology; University of Michigan, Ann Arbor, MI, USA 48109
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191
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Lebesgue N, Megyeri M, Cristobal A, Scholten A, Chuartzman SG, Voichek Y, Scheltema RA, Mohammed S, Futerman AH, Schuldiner M, Heck AJR, Lemeer S. Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. J Proteome Res 2016; 16:571-582. [PMID: 28152593 DOI: 10.1021/acs.jproteome.6b00691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sphingolipids (SLs) are essential components of cell membranes and are broad-range bioactive signaling molecules. SL levels must be tightly regulated as imbalances affect cellular function and contribute to pathologies ranging from neurodegenerative and metabolic disorders to cancer and aging. Deciphering how SL homeostasis is maintained and uncovering new regulators is required for understanding lipid biology and for identifying new targets for therapeutic interventions. Here we combine omics technologies to identify the changes of the transcriptome, proteome, and phosphoproteome in the yeast Saccharomyces cerevisiae upon SL depletion induced by myriocin. Surprisingly, while SL depletion triggers important changes in the expression of regulatory proteins involved in SL homeostasis, the most dramatic regulation occurs at the level of the phosphoproteome, suggesting that maintaining SL homeostasis demands rapid responses. To discover which of the phosphoproteomic changes are required for the cell's first-line response to SL depletion, we overlaid our omics results with systematic growth screens for genes required during growth in myriocin. By following the rate of SL biosynthesis in those candidates that are both affecting growth and are phosphorylated in response to the drug, we uncovered Atg9, Stp4, and Gvp36 as putative new regulators of SL homeostasis.
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Affiliation(s)
- Nicolas Lebesgue
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Márton Megyeri
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel.,Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anthony H Futerman
- Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
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192
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Fracchiolla D, Sawa-Makarska J, Zens B, Ruiter AD, Zaffagnini G, Brezovich A, Romanov J, Runggatscher K, Kraft C, Zagrovic B, Martens S. Mechanism of cargo-directed Atg8 conjugation during selective autophagy. eLife 2016; 5. [PMID: 27879200 PMCID: PMC5148612 DOI: 10.7554/elife.18544] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
Selective autophagy is mediated by cargo receptors that link the cargo to the isolation membrane via interactions with Atg8 proteins. Atg8 proteins are localized to the membrane in an ubiquitin-like conjugation reaction, but how this conjugation is coupled to the presence of the cargo is unclear. Here we show that the S. cerevisiae Atg19, Atg34 and the human p62, Optineurin and NDP52 cargo receptors interact with the E3-like enzyme Atg12~Atg5-Atg16, which stimulates Atg8 conjugation. The interaction of Atg19 with the Atg12~Atg5-Atg16 complex is mediated by its Atg8-interacting motifs (AIMs). We identify the AIM-binding sites in the Atg5 subunit and mutation of these sites impairs selective autophagy. In a reconstituted system the recruitment of the E3 to the prApe1 cargo is sufficient to drive accumulation of conjugated Atg8 at the cargo. The interaction of the Atg12~Atg5-Atg16 complex and Atg8 with Atg19 is mutually exclusive, which may confer directionality to the system. DOI:http://dx.doi.org/10.7554/eLife.18544.001 A living cell must remove unhealthy or excess material from its interior in order to remain healthy and operational. Cells pack this waste into membrane-bound compartments named autophagosomes in a process called autophagy. So-called autophagy proteins make sure that only the unwanted material is eliminated. However, it was not completely clear how these proteins achieve this. What was known was that proteins called cargo receptors recognize and bind to specific waste materials. At the same time, so-called autophagy enzymes tag the membranes of the autophagosome with a protein known as Atg8, so that cargo receptor molecules can bind this membrane. Now, Fracchiolla, Sawa-Makarska et al. report that, in yeast, an autophagy enzyme links these two events by binding to the cargo receptor and promoting the tagging of the autophagosome’s membrane at the same place. The enzyme in question is a complex made from three autophagy proteins (called Atg12, Atg5 and Atg16), and its activity ensures that the membrane is tagged only next to those materials that need to be disposed of. Although it is now clearer how a cell’s waste ends up in the autophagosome, it is still puzzling how this process is regulated and how the other autophagy-related components contribute to this highly coordinated process. In particular, an important next step will be to find out what is the source of membrane that gives rise to the autophagosome. DOI:http://dx.doi.org/10.7554/eLife.18544.002
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Affiliation(s)
- Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Bettina Zens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Anita de Ruiter
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Gabriele Zaffagnini
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Andrea Brezovich
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Julia Romanov
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Kathrin Runggatscher
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Claudine Kraft
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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193
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Chen YD, Fang YT, Chang CP, Lin CF, Hsu LJ, Wu SR, Chiu YC, Anderson R, Lin YS. S100A10 Regulates ULK1 Localization to ER-Mitochondria Contact Sites in IFN-γ-Triggered Autophagy. J Mol Biol 2016; 429:142-157. [PMID: 27871932 DOI: 10.1016/j.jmb.2016.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/28/2016] [Accepted: 11/15/2016] [Indexed: 01/07/2023]
Abstract
During the process of autophagy, the autophagy-related proteins are translocated to autophagosome formation sites. Here, we demonstrate that S100A10 is required for ULK1 localization to autophagosome formation sites. Silencing of S100A10 reduces IFN-γ-induced autophagosome formation. We also determined the role of annexin A2 (ANXA2), a binding partner of S100A10, which has been reported to promote phagophore assembly. Silencing of ANXA2 reduced S100A10 expression. However, overexpression of S100A10 in ANXA2-silenced cells was still able to enhance autophagosome formation, suggesting that ANXA2 regulates IFN-γ-induced autophagy through S100A10. We also observed that S100A10 interacted with ULK1 after IFN-γ stimulation, and S100A10 knockdown prevented ULK1 localization to autophagosome formation sites. Finally, the release of high mobility group protein B1, one of the functions mediated by IFN-γ-induced autophagy, was inhibited in S100A10 knockdown cells. These results elucidate the importance of S100A10 in autophagosome formation and reveal the relationship between S100A10 and ULK1 in IFN-γ-induced autophagy.
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Affiliation(s)
- Ying-Da Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Ting Fang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chih-Peng Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chiou-Feng Lin
- Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Department of Microbiology and Immunology, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Li-Jin Hsu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Shang-Rung Wu
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Yen-Chi Chiu
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Robert Anderson
- Departments of Microbiology & Immunology and Pediatrics, and Canadian Center for Vaccinology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Yee-Shin Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.
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194
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Mesquita A, Cardenal-Muñoz E, Dominguez E, Muñoz-Braceras S, Nuñez-Corcuera B, Phillips BA, Tábara LC, Xiong Q, Coria R, Eichinger L, Golstein P, King JS, Soldati T, Vincent O, Escalante R. Autophagy in Dictyostelium: Mechanisms, regulation and disease in a simple biomedical model. Autophagy 2016; 13:24-40. [PMID: 27715405 DOI: 10.1080/15548627.2016.1226737] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Autophagy is a fast-moving field with an enormous impact on human health and disease. Understanding the complexity of the mechanism and regulation of this process often benefits from the use of simple experimental models such as the social amoeba Dictyostelium discoideum. Since the publication of the first review describing the potential of D. discoideum in autophagy, significant advances have been made that demonstrate both the experimental advantages and interest in using this model. Since our previous review, research in D. discoideum has shed light on the mechanisms that regulate autophagosome formation and contributed significantly to the study of autophagy-related pathologies. Here, we review these advances, as well as the current techniques to monitor autophagy in D. discoideum. The comprehensive bioinformatics search of autophagic proteins that was a substantial part of the previous review has not been revisited here except for those aspects that challenged previous predictions such as the composition of the Atg1 complex. In recent years our understanding of, and ability to investigate, autophagy in D. discoideum has evolved significantly and will surely enable and accelerate future research using this model.
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Affiliation(s)
- Ana Mesquita
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain.,b University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Elena Cardenal-Muñoz
- c Départment de Biochimie , Faculté des Sciences, Université de Genève , Switzerland
| | - Eunice Dominguez
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain.,d Departamento de Genética Molecular , Instituto de Fisiología Celular, Universidad Nacional Autónoma de México , Mexico City , México
| | - Sandra Muñoz-Braceras
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain
| | | | - Ben A Phillips
- e Department of Biomedical Sciences , University of Sheffield , UK
| | - Luis C Tábara
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain
| | - Qiuhong Xiong
- f Center for Biochemistry, Medical Faculty, University of Cologne , Cologne , Germany
| | - Roberto Coria
- d Departamento de Genética Molecular , Instituto de Fisiología Celular, Universidad Nacional Autónoma de México , Mexico City , México
| | - Ludwig Eichinger
- f Center for Biochemistry, Medical Faculty, University of Cologne , Cologne , Germany
| | - Pierre Golstein
- g Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2 , Inserm, U1104, CNRS UMR7280, Marseille , France
| | - Jason S King
- e Department of Biomedical Sciences , University of Sheffield , UK
| | - Thierry Soldati
- c Départment de Biochimie , Faculté des Sciences, Université de Genève , Switzerland
| | - Olivier Vincent
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain
| | - Ricardo Escalante
- a Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM) , Madrid , Spain
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195
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Suzuki H, Osawa T, Fujioka Y, Noda NN. Structural biology of the core autophagy machinery. Curr Opin Struct Biol 2016; 43:10-17. [PMID: 27723509 DOI: 10.1016/j.sbi.2016.09.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/13/2016] [Accepted: 09/21/2016] [Indexed: 02/08/2023]
Abstract
In autophagy, which is an intracellular degradation system that is conserved among eukaryotes, degradation targets are sequestered through the de novo synthesis of a double-membrane organelle, the autophagosome, which delivers them to the lysosomes for degradation. The core autophagy machinery comprising 18 autophagy-related (Atg) proteins in yeast plays an essential role in autophagosome formation; however, the molecular role of each Atg factor and the mechanism of autophagosome formation remain elusive. Recent years have seen remarkable progress in structural biological studies on the core autophagy machinery, opening new avenues for autophagy research. This review summarizes recent advances in structural biological and mechanistic studies on the core autophagy machinery and discusses the molecular mechanisms of autophagosome formation.
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Affiliation(s)
- Hironori Suzuki
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Takuo Osawa
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan.
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196
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Wang DW, Peng ZJ, Ren GF, Wang GX. The different roles of selective autophagic protein degradation in mammalian cells. Oncotarget 2016; 6:37098-116. [PMID: 26415220 PMCID: PMC4741918 DOI: 10.18632/oncotarget.5776] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/31/2015] [Indexed: 01/01/2023] Open
Abstract
Autophagy is an intracellular pathway for bulk protein degradation and the removal of damaged organelles by lysosomes. Autophagy was previously thought to be unselective; however, studies have increasingly confirmed that autophagy-mediated protein degradation is highly regulated. Abnormal autophagic protein degradation has been associated with multiple human diseases such as cancer, neurological disability and cardiovascular disease; therefore, further elucidation of protein degradation by autophagy may be beneficial for protein-based clinical therapies. Macroautophagy and chaperone-mediated autophagy (CMA) can both participate in selective protein degradation in mammalian cells, but the process is quite different in each case. Here, we summarize the various types of macroautophagy and CMA involved in determining protein degradation. For this summary, we divide the autophagic protein degradation pathways into four categories: the post-translational modification dependent and independent CMA pathways and the ubiquitin dependent and independent macroautophagy pathways, and describe how some non-canonical pathways and modifications such as phosphorylation, acetylation and arginylation can influence protein degradation by the autophagy lysosome system (ALS). Finally, we comment on why autophagy can serve as either diagnostics or therapeutic targets in different human diseases.
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Affiliation(s)
- Da-wei Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhen-ju Peng
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
| | - Guang-fang Ren
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
| | - Guang-xin Wang
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
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197
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Farré JC, Subramani S. Mechanistic insights into selective autophagy pathways: lessons from yeast. Nat Rev Mol Cell Biol 2016; 17:537-52. [PMID: 27381245 PMCID: PMC5549613 DOI: 10.1038/nrm.2016.74] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Autophagy has burgeoned rapidly as a field of study because of its evolutionary conservation, the diversity of intracellular cargoes degraded and recycled by this machinery, the mechanisms involved, as well as its physiological relevance to human health and disease. This self-eating process was initially viewed as a non-selective mechanism used by eukaryotic cells to degrade and recycle macromolecules in response to stress; we now know that various cellular constituents, as well as pathogens, can also undergo selective autophagy. In contrast to non-selective autophagy, selective autophagy pathways rely on a plethora of selective autophagy receptors (SARs) that recognize and direct intracellular protein aggregates, organelles and pathogens for specific degradation. Although SARs themselves are not highly conserved, their modes of action and the signalling cascades that activate and regulate them are. Recent yeast studies have provided novel mechanistic insights into selective autophagy pathways, revealing principles of how various cargoes can be marked and targeted for selective degradation.
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Affiliation(s)
- Jean-Claude Farré
- University of California, 3326 Bonner Hall, 9500 Gilman Drive, San Diego, La Jolla, California 92093-0322, USA
| | - Suresh Subramani
- University of California, 3326 Bonner Hall, 9500 Gilman Drive, San Diego, La Jolla, California 92093-0322, USA
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198
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Coutts AS, La Thangue NB. Regulation of actin nucleation and autophagosome formation. Cell Mol Life Sci 2016; 73:3249-63. [PMID: 27147468 PMCID: PMC4967107 DOI: 10.1007/s00018-016-2224-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
Autophagy is a process of self-eating, whereby cytosolic constituents are enclosed by a double-membrane vesicle before delivery to the lysosome for degradation. This is an important process which allows for recycling of nutrients and cellular components and thus plays a critical role in normal cellular homeostasis as well as cell survival during stresses such as starvation or hypoxia. A large number of proteins regulate various stages of autophagy in a complex and still incompletely understood series of events. In this review, we will discuss recent studies which provide a growing body of evidence that actin dynamics and proteins that influence actin nucleation play an important role in the regulation of autophagosome formation and maturation.
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Affiliation(s)
- Amanda S Coutts
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nicholas B La Thangue
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.
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199
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Li M, Lindblad JL, Perez E, Bergmann A, Fan Y. Autophagy-independent function of Atg1 for apoptosis-induced compensatory proliferation. BMC Biol 2016; 14:70. [PMID: 27542914 PMCID: PMC4992243 DOI: 10.1186/s12915-016-0293-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ATG1 belongs to the Uncoordinated-51-like kinase protein family. Members of this family are best characterized for roles in macroautophagy and neuronal development. Apoptosis-induced proliferation (AiP) is a caspase-directed and JNK-dependent process which is involved in tissue repair and regeneration after massive stress-induced apoptotic cell loss. Under certain conditions, AiP can cause tissue overgrowth with implications for cancer. RESULTS Here, we show that Atg1 in Drosophila (dAtg1) has a previously unrecognized function for both regenerative and overgrowth-promoting AiP in eye and wing imaginal discs. dAtg1 acts genetically downstream of and is transcriptionally induced by JNK activity, and it is required for JNK-dependent production of mitogens such as Wingless for AiP. Interestingly, this function of dAtg1 in AiP is independent of its roles in autophagy and in neuronal development. CONCLUSION In addition to a role of dAtg1 in autophagy and neuronal development, we report a third function of dAtg1 for AiP.
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Affiliation(s)
- Mingli Li
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
| | - Jillian L Lindblad
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, LRB419, Worcester, MA, 01605, USA
| | - Ernesto Perez
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, LRB419, Worcester, MA, 01605, USA
| | - Andreas Bergmann
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, LRB419, Worcester, MA, 01605, USA.
| | - Yun Fan
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK.
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200
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Dengjel J, Abeliovich H. Roles of mitophagy in cellular physiology and development. Cell Tissue Res 2016; 367:95-109. [PMID: 27488107 DOI: 10.1007/s00441-016-2472-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/04/2016] [Indexed: 12/19/2022]
Abstract
The autophagic degradation of mitochondria, or mitophagy, has been shown to occur in eukaryotic cells under various physiological conditions. Broadly, these fall into two categories: quality-control related mitophagy and developmentally induced mitophagy. Quality-control related mitophagy, which is the lysosomal/vacuolar degradation of malfunctioning or superfluous mitochondria, is an important housekeeping function in respiring eukaryotic cells. It plays an essential role in physiological homeostasis and its deregulation has been linked to the progression of late-onset diseases. On the other hand, developmental processes such as reticulocyte maturation have also been shown to involve mitophagy. Importantly, there are clear differences between these processes. Unlike our knowledge of the more general degradation of soluble cytosolic content during starvation-induced macroautophagy, the mechanisms involved in the selective autophagic degradation of mitochondria have only recently begun to receive significant attention. Here, we review the current literature on these topics and proceed to provide specific examples from yeast and mammalian systems. Finally, we cover experimental approaches, with a focus on proteomic methods dedicated to the study of mitophagy in different systems.
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Affiliation(s)
- Jörn Dengjel
- Department of Dermatology, Medical Center, Freiburg Institute for Advanced Studies (FRIAS), ZBSA Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany.,Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland
| | - Hagai Abeliovich
- Department of Biochemistry and Food Science, Hebrew University of Jerusalem, Rehovot, 76100, Israel. .,FRIAS Senior Fellow and Marie Curie Fellow of the European Union Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstr. 19, 79104, Freiburg, Germany.
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