Diverse Cellular Roles of Autophagy.pdf

CB35CH03_MizushimaARjats.clsJune 26,201913:0Annual Review of Cell and Developmental BiologyDiverse Cellular Rolesof AutophagyHideaki Morishitaand Noboru MizushimaDepartment of Biochemistry and Molecular Biology,Graduate School and Faculty of Medicine,The University of Tokyo,Tokyo 113-0033,Japan;email:morishitam.u-tokyo.ac.jp,nmizum.u-tokyo.ac.jpAnnu.Rev.Cell Dev.Biol.2019.35:3.13.23The Annual Review of Cell and Developmental Biologyis online at cellbio.annualreviews.orghttps:/doi.org/10.1146/annurev-cellbio-100818-125300Copyright 2019 by Annual Reviews.All rights reservedThese authors contributed equally to this articleKeywordsautophagosome,selective autophagy,mitophagy,ER-phagy,nutrientstarvationAbstractMacroautophagy is an intracellular degradation system that delivers diversecytoplasmic materials to lysosomes via autophagosomes.Recent advanceshave enabled identification of several selective autophagy substrates andreceptors,greatly expanding our understanding of the cellular functionsof autophagy.In this review,we describe the diverse cellular functions ofmacroautophagy,including its essential contribution to metabolic adapta-tion and cellular homeostasis.We also discuss emerging findings on themechanisms and functions of various types of selective autophagy.3.1Review in Advance first posted on July 5,2019.(Changes may still occur before final publication.)Annu.Rev.Cell Dev.Biol.2019.35.Downloaded from www.annualreviews.org Access provided by Lund University Libraries,Head Office on 07/20/19.For personal use only.CB35CH03_MizushimaARjats.clsJune 26,201913:0Autophagosome:a double-membranestructure enclosingcytoplasmic materialsContentsINTRODUCTION.3.2MECHANISM OF AUTOPHAGY.3.3Autophagosome Formation and Maturation.3.3Selective Autophagy.3.4APPROACHES TO UNDERSTANDING CELLULAR ROLESOF AUTOPHAGY.3.6Monitoring of Autophagy.3.6Loss-of-Function Analysis of Autophagy.3.7Identification of Selective Cargos and Receptors.3.8AUTOPHAGY FOR SELF-NOURISHMENTAND METABOLIC RECYCLING.3.9Supply of Amino Acids.3.9Supply of Lipids.3.10Supply of Iron.3.10Supply of Nucleosides.3.11AUTOPHAGY FOR CELLULAR HOMEOSTASIS AND ELIMINATIONOF UNWANTED MATERIALS.3.11Regulation of the Levels of Specific Proteins.3.11Selective Degradation of Mitochondria.3.12Selective Degradation of the ER.3.13Selective Degradation of Peroxisomes.3.14Selective Degradation of Lysosomes.3.14Selective Degradation of Intracellular Bacteria.3.15CLOSING REMARKS AND FUTURE ISSUES.3.15INTRODUCTIONAutophagy is an intracellular degradation system that delivers cytoplasmic materials to lysosomes(Mizushima et al.2011,Nakatogawa et al.2009,Soreng et al.2018).Autophagy can be classifiedinto three types:macroautophagy,microautophagy(uptake of cytoplasmic components by inwardinvagination of lysosomal membranes)(Oku&Sakai 2018),and chaperone-mediated autophagy(direct transport of cytosolic proteins into lysosomes through translocons)(Kaushik&Cuervo2018).The best-characterized class of autophagy is macroautophagy(hereafter referred to as au-tophagy),whichisthefocusofthisreview.Duringautophagy,theisolationmembrane(alsoknownas the phagophore)nucleates,elongates,and encloses a small portion of the cytoplasm,forming adouble-membrane organelle termed the autophagosome(Figure 1).Autophagosomes fuse withlysosomes to form autolysosomes in which lysosomal hydrolases digest internal contents.Degra-dation products are recycled after being released into the cytosol.The molecular mechanisms and functions of autophagy have been extensively investigatedsince the discovery of autophagy-related(ATG)genes in yeast in the 1990s(Klionsky et al.2003,Takeshige et al.1992,Tsukada&Ohsumi 1993).To date,42 ATG genes have been identified,andmany of them are conserved among eukaryotes(Mizushima et al.2011,Nakatogawa et al.2009).Additional genes essential for autophagy in most eukaryotes,but not present in yeast,have alsobeen identified:ATG101,EI24,EPG5,TMEM41B,and VMP1(Mizushima et al.2011,Moretti3.2MorishitaMizushimaReview in Advance first posted on July 5,2019.(Changes may still occur before final publication.)Annu.Rev.Cell Dev.Biol.2019.35.Downloaded from www.annualreviews.org Access provided by Lund University Libraries,Head Office on 07/20/19.For personal use only.CB35CH03_MizushimaARjats.clsJune 26,201913:0Selective autophagy:a form of autophagythat can selectivelysequester specificcargos into theautophagosomeLysosomeIsolationmembraneAutophagosomeAutolysosomeAmino acidsLipidsMetalsNucleosidesOthersSelf-nourishment and metabolic recyclingCellular homeostasis and elimination of unwanted or excess materialsFigure 1Processes and functions of autophagy.Membrane dynamics of macroautophagy in mammals are shown.Upon induction of autophagy,a small portion of the cytoplasm is enclosed by the isolation membrane.Then,the isolation membrane is closed,forming a double-membrane structure termed the autophagosome.Theautophagosome fuses with the lysosome to degrade internal contents,forming the autolysosome,from whichamino acids,lipids,metals(e.g.,iron),nucleosides,and other materials are recycled back into the cytosol.Ingeneral,autophagy has two major functions:(1)self-nourishment and metabolic recycling and(2)cellularhomeostasis and elimination of unwanted or excess materials.et al.2018,Morita et al.2018,Shoemaker et al.2019,Tian et al.2010).Reverse-genetic ap-proaches using mice and cell cultures have revealed two major roles of autophagy(Figure 1):(1)self-nourishment and metabolic recycling and(2)maintaining cellular homeostasis and elim-inating unwanted materials(Gatica et al.2018,Kaur&Debnath 2015,Levine et al.2015,Mizushima&Komatsu 2011).In this review,we describe these functions at the cellular rather than the organismal level,par-ticularly emphasizing the roles and molecular mechanisms of various types of selective autophagy.We do not include the roles of autophagy in general physiology and diseases(e.g.,degenerativedisorders,cancers,inflammatory disorders,and aging),which have been reviewed in detail else-where(Amaravadi et al.2016,Deretic et al.2013,Hansen et al.2018,Kroemer 2015,Leidal et al.2018,Mizushima&Komatsu 2011).MECHANISM OF AUTOPHAGYOver the last two decades,a large body of research has revealed the functions of ATG pro-teins.Autophagosome formation requires a subset of core ATG proteins comprising severalfunctional units:(1)Atg1/Unc-51-like kinase(ULK)complexes,(2)ATG9 vesicles,(3)class IIIphosphatidylinositol 3-kinase(PtdIns3K)complexes,(4)ATG2-Atg18/WIPI complexes,(5)theATG12conjugationsystem,and(6)theAtg8/microtubule-associatedprotein1lightchain3(LC3)conjugation system(Mizushima et al.2011,Nakatogawa et al.2009,Soreng et al.2018).Here,wesummarize the principal mechanisms of the formation and maturation of autophagosomes andrecognition of selective substrates.Autophagosome Formation and MaturationIn mammals,the most upstream autophagy factors are the ULK complex consisting of ATG101,ATG13,FIP200(also termed RB1CC1),and ULK1/2 and ATG9 vesicles,both of whichwww.annualreviews.orgDiverse Cellular Roles of Autophagy3.3Review in Advance first posted on July 5,2019.(Changes may still occur before final publication.)Annu.Rev.Cell Dev.Biol.2019.35.Downloaded from www.annualreviews.org Access provided by Lund University Libraries,Head Office on 07/20/19.For personal use only.CB35CH03_MizushimaARjats.clsJune 26,201913:0Autophagy receptor:a factor that tethers acargo to autophagicmembranes and isdegraded togetherwith the cargotranslocate independently to the autophagosome formation site on or close to the endoplasmicreticulum(ER)(Axe et al.2008,Itakura et al.2012,Karanasios et al.2016).The ULK complexis responsible for nucleating the isolation membrane(Zachari&Ganley 2017).ATG9 vesicleslikely compose a portion of the autophagosome membrane(Noda 2017).These upstream factorsthen recruit a subtype of the class III PtdIns3K complex(consisting of ATG14,Beclin 1,VPS15,and VPS34)to generate phosphatidylinositol 3-phosphate(PtdIns3P).ATG2A/B and PtdIns3P-binding WIPI2 and two ER transmembrane proteins,VMP1 and TMEM41B,are required toform isolation membranes(Dooley et al.2014,Mizushima et al.2011,Moretti et al.2018,Moritaet al.2018,Shoemaker et al.2019).In yeast,the Atg1 complex is composed of Atg1,Atg13,Atg17,Atg29,and Atg31,and Atg18 is a WIPI2 homolog(Mizushima et al.2011).Two ATG conjugation systems lead to the covalent attachment of Atg8/LC3 to phos-phatidylethanolamine on autophagic membranes.The Atg8/LC3 family in mammals consists oftwosubfamilies:theLC3andgamma-aminobutyricacidreceptorassociatedprotein(GABARAP)families.Atg8/LC3promotesthematurationofautophagosomes,includingexpansionandclosureof the isolation membrane,fusion with the lysosome,and degradation of the inner autophago-some membrane(Nguyen et al.2016,Noda et al.2009,Tsuboyama et al.2016).The closure ofthe isolation membrane is mediated by the ESCRT machinery(Takahashi et al.2018).Once au-tophagosomes are closed,they undergo maturation to fuse with lysosomes(Bas et al.2018,Zhao&Zhang 2018).Selective AutophagyDiverse cargos have been recognized as substrates for selective autophagy,including proteins,or-ganelles,and pathogens(Farr&Subramani 2016,Gatica et al.2018,Khaminets et al.2016)(Table 1).Cargo selectivity can be conferred by direct or indirect interaction of cargo withAtg8/LC3 on autophagic membranes(Figure 2).Indirect interactions are achieved by autophagyreceptors,which can tether cargo to autophagic membranes by binding to both the cargo andAtg8/LC3 on autophagic membranes.Although both cargos and receptors are subjected to lyso-somaldegradation,onlythelatterfunctionaspartoftheautophagyapparatus(Galluzzietal.2017).The interaction of the cargo or receptor with Atg8/LC3 is mostly mediated by Atg8-interactingmotifs(AIMs),LC3-interacting regions(LIRs),or GABARAP-interacting motifs(GIMs)on thecargo or receptor(Noda et al.2010,Rogov et al.2017).The canonical AIM/LIR/GIMs are com-posed of a consensus motif W/F/YxxL/I/V(where x is any amino acid),surrounded by one ormore proximal acidic residues(Noda et al.2010,Rogov et al.2017).Two hydrophobic bindingpockets in Atg8/LC3s recognize the first and fourth hydrophobic residues in the AIM/LIR/GIM(Noda et al.2010).The autophagic receptors recognize cargos in a ubiquitin-dependent or-independent man-ner(Figure 2).When cargos(e.g.,damaged mitochondria or lysosomes)are polyubiquiti-nated,the ubiquitin tag is recognized by autophagy receptors that can bind ubiquitinatedproteins(Khaminets et al.2016).For example,during PTEN-induced putative kinase 1(PINK1)PARKIN-mediated mitophagy,ubiquitinated mitochondrial proteins are recognized by twocytosolic autophagy receptors,NDP52 and optineurin(OPTN),which have both LIR andubiquitin-binding domains(Lazarou et al.2015).One example of ubiquitin-independent recogni-tion is the binding of yeast aminopeptidase I precursors by the AIM-containing autophagy recep-tor Atg19 for transport to the vacuole by the autophagy-related cytoplasm-to-vacuole targeting(Cvt)pathway(Gatica et al.2018).However,cargo selectivity can be achieved by other mechanisms that are not necessarily mutu-allyexclusiveoftheabovemechanism(Mizushima2018).Somecargoscantriggerautophagosome3.4MorishitaMizushimaReview in Advance first posted on July 5,2019.(Changes may still occur before final publication.)Annu.Rev.Cell Dev.Biol.2019.35.Downloaded from www.annualreviews.org Access provided by Lund University Libraries,Head Office on 07/20/19.For personal use only.CB35CH03_MizushimaARjats.clsJune 26,201913:0Table 1Cargos and receptors of selective autophagyCargo(process)Receptor species,ubiquitin(Ub)dependencyReference(s)Ams1,prApe1(Cvt pathway)Atg19(yeast)Gatica et al.2018Bacterial and viral pathogens(xenophagy)OPTN,p62,NDP52,TAX1BP1(mammals,Ub)TRIM5(mammals)Mandell et al.2014;Thurston et al.2009,2012;Wild et al.2011;Zheng et al.2009Endoplasmic reticulum(ER-phagy,reticulophagy)Atg39,Atg40(yeast)Mochida et al.2015ATL3,CCPG1,FAM134B,RTN3,SEC62,TEX264(mammals)p62(mammals,Ub)An et al.2019,Chen et al.2019,Chino et al.2019,Fumagalli et al.2016,Grumati et al.2017,Khaminets et al.2015,Smith et al.2018,Yanget al.2016Ferritin(ferritinophagy)NCOA4(mammals)Dowdle et al.2014,Mancias et al.2014Glycogen(glycophagy)STBD1(mammals)Jiang et al.2010Lipid droplet(lipophagy)UnknownSingh et al.2009Lysosome(lysophagy)p62(mammals,Ub)TRIM16(mammals)Chauhan et al.2016,Maejima et al.2013,Papadopoulos et al.2017Membranous organelles inCaenorhabditis elegans spermALLO-1(C.elegans,Ub)Sato et al.2018Mitochondria(mitophagy)Atg32(yeast)Kanki et al.2009,Okamoto et al.2009ALLO-1(C.elegans,Ub)Sato et al.2018BCL2L13,BNIP3,BNIP3L/NIX,FKBP8,FUNDC1,PHB2(mammals)Bhujabal et al.2017,Hanna et al.2012,Liu et al.2012,Murakawa et al.2015,Novak et al.2010,Schweers et al.2007,Wei et al.2017NDP52,OPTN(mammals,Ub)Lazarou et al.2015,Wong&Holzbaur 2014Cardiolipin(mammals)Chu et al.2013Nuclear envelope(nucleophagy)Atg39(yeast)Mochida et al.2015Peroxisome(pexophagy)Atg36,PpAtg30,PpAtg37,Pex3,PpPex14,PpPex3 yeast(Pp denotesPichia pastoris)Farr&Subramani 2016,Farr et al.2008,Motleyet al.2012,Nazarko et al.2014NBR1,p62(mammals,Ub)Deosaran et al.2013,Yamashita et al.2014P granules(aggrephagy)SEPA-1(C.elegans)Zhang et al.2009Proteasome(proteaphagy)RPN10(plants,Ub)Marshall et al.2015Cue5(yeast,Ub)Marshall et al.2016p62(mammals,Ub)Cohen-Kaplan et al.2016Stress granules and P-bodies(granulophagy)p62(mammals)Buchan et al.2013Ubiquitinated proteinaggregates(aggrephagy)Cue5(yeast,Ub)Lu et al.2014NBR1,OPTN,p62,TOLLIP(mammals,Ub)Kirkin et al.2009,Korac et al.2013,Lu et al.2014,Pankiv et al.2007formation by recruiting upstream autophagy-initiating ATG factors such as the Atg1/ULK com-plex(Figures 2 and 3).For example,in yeast,several cargo receptors e.g.,Atg19(the Cvtpathway),Atg32(mitophagy),Atg36,Pichia pastoris(Pp)Atg30(pexophagy),Atg39,and Atg40(ER-phagy)interact with the scaffold protein Atg11,which can recruit ATG1 complexes to in-duce autophagy(Gatica et al.2018).In mammals,during PINK1PARKIN-mediated mitophagy,www.annualreviews.orgDiverse Cellular Roles of Autophagy3.5Review in Advance first posted on July 5,2019.(Changes may still occur before final publication.)Annu.Rev.Cell Dev.Biol.2019.35.Downloaded from www.annualreviews.org Access provided by Lund University Libraries,Head Office on 07/20/19.For personal use only.CB35CH03_MizushimaARjats.clsJune 26,201913:0Autophagic flux:the rate at whichlysosomes degradeautophagic substratesabcdCargoAutophagicmembraneAIM/LIR/GIMSelective autophagyUbiquitindependentUbiquitinindependentDirectIndirectInteraction of cargos withAtg8/LC3/GABARAPs:UbiquitinchainsReceptorAtg8,LC3s,GABARAPsUbAtg1/ULKcomplexNonselectiveautophagyReceptorFigure 2Types of cargo selection for autophagy.(a)When cargos have AIM/LIR/GIMs(e.g.,p62 and NCoR1),they can directly bind toAtg8/LC3/GABARAPs on autophagic membranes.(b)When cargos lack AIM/LIR/GIMs or ubiquitin tags(e.g.,ApeI and ferritin),they use autophagy receptors with AIM/LIR/GIMs(e.g.,Atg19