autophagy , ancient system necessary to maintain homeostasis in eukaryotic cells , degrades long - lived cytoplasmic proteins and organelles and provides nutrients in starvation or stress conditions ( 1 )
. there are at least three types of autophagy in eukaryotic cells : macroautophagy , microautophagy , and chaperone - mediated autophagy ( 2 ) .
microautophagy involves the continuous degradation of cytosolic constituents close to the lysosomes via budding of the lysosomal membrane . in chaperone - mediated autophagy ,
proteins containing a kferq motif , which is recognized by hsc70 , are transported into the lysosomal lumen via lamp-2a to be degraded ( 3 - 6 ) .
macroautophagy is the primary route of degradation and has been most widely studied . in this process , cellular components such as protein aggregates and organelles ( e.g. , mitochondria ) are wrapped by an elongated cup - shaped membrane , which forms a double - membrane structure called an autophagosome ( 7 ) .
autophagosomes mature and fuse with lysosomes to facilitate the degradation of the internal contents . recently
autophagic adaptors such as p62 targets polyubiquitylated substrates and are selectively degraded by autophagy ( 8) . the autophagic pathway consists of three distinct stages .
initially , an isolation membrane is formed through complex interaction of the autophagic protein atg6 ( beclin-1 ) and type - iii phosphatidylinositol 3-kinase , along with membrane components .
elongation of the isolation membrane and completion of autophagosome formation are regulated by at least two ubiquitin - like systems : the microtubule - associated protein 1 light chain 3 ( lc3 ; mammalian homolog of the yeast autophagic protein atg8 ) and the atg12 conjugation systems ( 9,10 ) .
atg12 is transferred to the e1- and e2-like enzyme atg7 and atg10 sequentially , and is finally conjugated with a lysine residue of atg5 through its c - terminal glycine residue .
the atg12-atg5 conjugates facilitate the elongation of the isolation membrane and catalyze the lc3 conjugation with the help of atg16 .
the c - terminal amino acids of lc3 are cleaved by atg4 and conjugated with phosphatidylethanolamine ( pe ) by the e1- and e2-like enzymes atg7 and atg3 , respectively .
the lipidated lc3 ( lc3-ii ) is incorporated into the newly formed autophagosomal membrane . upon autophagosome closure , the atg12-atg5-atg16 complex dissociates from the outer autophagosomal membrane , but lc3 remains in the autophagosomal lumen as an autophagosomal marker .
interestingly , lc3 binds to the adaptor protein p62 , which interacts with polyubiquitylated structures to facilitate their autophagic degradation ( 11 ) . finally , the outer membrane of the autophagosome fuses with the lysosomal membrane , followed by degradation of the membrane and its contents
although autophagy is necessary for cellular homeostasis , it is involved in biological processes including development , aging , and degeneration ( 12 ) .
aberrant regulation of autophagy is related to many diseases , such as cancer and neurodegenerative disease ( 13,14 ) .
autophagy can directly eliminate intracellular pathogens or enhance pathogen recognition and elimination ( 15 - 19 ) , and can regulate autoimmunity and inflammatory disorders ( 20 ) .
moreover , autophagy affects the adaptive immune system by contributing to antigen presentation and controlling t- and b - cell homeostasis ( 21 - 26 ) . here , we briefly review the role of autophagy in innate immune control .
because autophagy removes large cytoplasmic proteins and organelles , intracellular pathogens such as bacteria and parasites are cleared by autophagic machinery .
autophagy can target free microbes in the cytosol and pathogens contained in phagosomes ( 27 ) .
( 15 ) showed that group a streptococcus ( gas ) that escapes from endosomes into the cytoplasm becomes enveloped by autophagosome - like compartments and is killed upon fusion of these compartments with lysosomes ( fig .
1 ) . gas survives and multiplies in atg5-deficient cells , which indicates that elimination of gas is autophagy - dependent . in cases of intracellular pathogens that persist within phagosomes such as mycobacterium tuberculosis
, autophagy promotes the maturation of mycobacterial phagosomes into phagolysosomes . using mycobacterium bovis bacille calmette - gurin ( bcg ) , starvation- or rapamycin - induced autophagy leads to mycobacterial phagosome colocalization with the lc3 , resulting in fusion of phagosomes with autophagosomes , which in turn deliver the pathogen - containing vacuoles for lysosomal degradation ( 16 ) . in case of human macrophages ,
it induces promoter activation of the autophagy - related genes atg5 and beclin-1 , and promotes colocalization of bacterial phagosomes and autophagosomes ( 28 ) .
however , the mechanism of autophagy targeting and its role in natural infection without exogenous induction of autophagy remains unclear .
interestingly , a recent study using wild type mycobacterium tuberculosis revealed how m. tuberculosis interfaces with the selective autophagy pathway from within the phagosomes in resting macrophages ( fig .
, m. tuberculosis includes several virulence factors such as the extraembryonic spermatogenic homeobox 1 ( esx-1 ) secretion system ( 30 , 31 ) .
the bacterial esx-1 facilitates the exposure of bacterial dna to the host by permeabilizing the phagosome membrane ( 32 ) .
the exposed bacterial dna is recognized by the cytosolic dna pathway , including stimulator of interferon ( ifn ) genes ( sting ) , and surrounded by a ubiquitin chain .
ubiquitin and lc3-binding autophagy adaptors p62 and nuclear dot protein 52 ( ndp52 ) recruit autophagy components to target the bacilli to the selective autophagy pathway . in this process , atg5 and tank - binding kinase 1 are also required .
consequently , bacilli - containing autophagosomes are fused with lysosomes to facilitate the elimination of mycobacteria .
other intracellular bacteria and parasites such as listeria monocytogenes and salmonella species are also limited by autophagy with various strategies including selective autophagy activation ( 33 - 36 ) .
the innate immune system recognizes conserved microbial molecular structures , so called pathogen - associated molecular patterns ( pamps ) .
pattern recognition receptors ( prrs ) bind to these conserved structures and initiate downstream signaling pathways ( 37 ) . in addition , signaling initiated by prr activation can promote the autophagy induction .
studies have shown that activation of toll - like receptors ( tlrs ) facilitates pathogen elimination by autophagy induction ( 17 , 18 ) .
tlr4 stimulated with lipopolysaccharide ( lps ) induces autophagy in primary human macrophages and the murine macrophage cell line , raw 264.7 .
redistribution of lc3 protein from a diffuse to a punctate pattern and increased levels of the lipidated form of lc3 ( lc3ii ) , both of which are reliable markers of autophagy induction , were observed after stimulation with lps .
this process occurred via the toll / interleukin-1 receptor domain - containing adapter - inducing interferon  ( trif)-p38 axis , but not via myd88 , and resulted in formation of the autophagosome colocalized with mycobacteria ( fig .
thus , it was suggested that autophagy induced by tlr activation enhances the elimination of mycobacteria . according to a report showing the effect of tlr agonists on autophagy induction in raw264.7 ( 18 ) , ligands of tlr3 , tlr4 , and
tlr7 signaling activated by two different ligands , single - stranded rna ( ssrna ) and imiquimod , induces the formation of autophagosomes characterized by lc3 puncta formation in murine macrophages ( fig .
tlr7-induced autophagy activation promotes the killing of intracellular mycobacteria , even though mycobacteria are normally not associated with tlr signaling ( 18 ) .
in addition to the formation of autophagosomes fused with pathogen - containing phagosomes , tlr signaling could enhance the maturation of phagosomes into phagolysosomes via autophagic machinery ( 19 ) .
when zymosan ( a component of the fungal cell wall ) is phagocytosed , phagosomes rapidly recruit lc3 and fuse with lysosomes ( fig .
lc3 translocation to phagosomes was dependent on tlr2 but not myd88 , and requires atg 5 and atg7 .
interestingly , lc3 recruitment to phagosomal membranes is not associated with the double - membrane structures characteristic of autophagosomes .
thus , this study identified a new way of using the autophagic machinery to enhance conventional functions of phagocytes after tlr activation ( 38 ) .
nucleotide oligomerization domain ( nod)-like receptors ( nlrs ) are a family of cytoplasmic molecules that recognize bacterial cell wall components , such as peptidoglycan , in the cytosol . upon bacterial invasion ,
nlrs recognize bacterial peptidoglycan by their c - terminal leucine - rich repeat and initiate signal transduction by their n - terminal effector domain .
downstream signals activate nuclear factor kappa - light - chain - enhancer of activated b cells ( nf-b ) and activator protein 1 , and lead to the production of cytokines involved in innate defense ( 39 ) .
studies have shown that nod1 and nod2 are critical for the autophagic response to bacterial invasion ( 40 , 41 ) . in mouse
embryonic fibroblasts ( mefs ) , nod2 recruits atg16l1 to the plasma membrane at the bacterial entry site , which facilitates bacterial trafficking to the autophagosomes .
this process does not require the adaptor receptor interacting protein 2 and the transcription factor nf-b ( 41 ) .
another study showed that nod2 activation by muramyl dipeptide ( mdp ) induces autophagosome formation and subsequently promotes major histocompatibility complex ( mhc ) class ii - associated antigen presentation in human dendritic cells ( dcs ) . in this process ,
atg5 , atg7 , atg16l1 , and receptor - interacting serine - threonine kinase 2 are required ( 40 ) .
thus , autophagy mediates bacterial clearance and bacterial antigen presentation , which are initiated by nod sensing of invasive bacteria ( fig .
interestingly , nod2 and atg16l1 are two of the most important genes associated with crohn 's disease ( 42 - 44 ) , a complicated inflammatory condition .
dcs isolated from patients with crohn 's disease expressing risk alleles for nod2 and atg16l1 are impaired in autophagy induction , bacterial trafficking , and antigen presentation .
overexpression or neuron - specific deletion of atg proteins resulted in increased or decreased survival following intracranial injection with sindbis virus , respectively ( 45,46 ) . in another study , intracranial infection with hsv-1 beclin-1
virulence factor , icp 34.5 , encoded by herpes simplex virus 1 ( hsv-1 ) blocks autophagy induction through binding and inhibiting beclin-1 .
most viral sensing is mediated by viral nucleic acids , which is different from other pathogens containing particular cell wall components triggering tlr activation .
tlr3 , tlr7 , tlr8 , and tlr9 sense endocytosed viral nucleic acids in the endosomal compartment ( 49 ) . in plasmacytoid dcs ( pdcs ) , viral rna or dna recognized by tlr7 or tlr9 , respectively , induces ifn regulatory factor 7 ( irf7 ) activation via myd88 , leading to type - i ifn production . in vesicular stomatitis virus ( vsv ) ,
pdcs recognize replicating virus in cytosol rather than the viral genome via tlr7 in endosomes .
however , how these cytosolic replication intermediates gain entry to the endosomal compartment where tlr7 resides is not completely known .
a study demonstrated that autophagy mediates the delivery of the cytosolic pamp to the lysosomes to activate tlr7 signaling ( fig .
atg5-deficient pdcs are unable to produce ifn- and interleukin ( il)-12p40 in response to vsv .
in addition to vsv , pdcs lacking atg5 failed to produce ifn- in response to hsv-1 , which is recognized by tlr9 , whereas the il-12 response was not impaired in these cells .
autophagy plays an important role in the antiviral response by delivering viral replication intermediates from the cytosol to the endosome .
however , the precise mechanism of the differential control of nf-b versus ifn- induction pathways in pdcs by autophagy remains to be determined ( 50 - 52 ) .
most cell types other than pdcs use cytosolic receptors , retinoic acid - inducible gene ( rig)-i - like receptors ( rlrs ) and melanoma differentiation associated gene 5 ( mda-5 ) , to sense the viral invasion ( 53 - 55 ) . via their caspase - recruiting domains ( cards ) , rlrs recognize double - stranded rna , which is synthesized during active viral replication in the cytosol and signal through ifn- promoter stimulator-1 ( ips-1 ; also known as mavs , visa , or cardif ) , and activate transcription factors irf-3 and nf-b , subsequently leading to the production of type - i ifn and proinflammatory cytokines ( 39 ) .
a study showed that atg5-atg12 conjugates negatively regulate innate viral recognition by rig - i and mda-5 in mefs ( 56 ) .
the atg5-atg12 conjugates , which are directly associated with card domains of rig - i and ips-1 , block rlr signaling and suppress type - i ifn production ( fig .
, atg5- and atg7-deficient mefs , lacking atg5-atg12 conjugates , overproduce type - i ifn in response to vsv .
similarly , atg5-deficient cells show increased ifn production through enhanced rlr signaling in response to vsv infection . in this study ,
in addition , dysfunctional mitochondria and mitochondria - associated ips-1 are accumulated in the absence of autophagy .
collectively , accumulation of ros associated with dysfunctional mitochondria may potentiate rlr signaling in atg5-deficient cells ( fig .
inflammasomes are molecular machinery that promote innate immune defenses by triggering the maturation of proinflammatory cytokines such as il-1 ( 58 ) .
stimulation of tlr4 by lps is unable to induce inflammasome activation in macrophages if lps is not contaminated with other ligands .
however , atg16l1-deficient macrophages exhibit enhanced il-1 and il-18 production in response to lps ( fig .
5a ) , suggesting that autophagy normally suppresses inflammasome activation by lps ( 20 ) .
atg16l1 is an essential component of the autophagosome , forming a complex with atg5-atg12 conjugates and inducing lc3-pe conjugation .
interestingly , atg16l1 is one of the most important genes associated with crohn 's disease .
thus , endotoxin - induced inflammasome activation in atg16l1 deficiency could be involved in the occurrence of crohn 's disease . in a recent study detailing the complex reciprocal regulation of inflammasome and autophagic pathways , blocking autophagy
the activation of absent in melanoma 2 ( aim2 ) or nlr pyrin domain containing 3 ( nlrp3 ) inflammasomes trigger autophagy induction by activating ralb to bind to exo84 , which serves as platform for the formation of isolation membrane ( 60 ) .
autophagy engulfs ubiquitylated assembled inflammasomes through p62 , an autophagic adaptor including both ubiquitin - associated domains and lc3-interacting regions , that recognizes ubiquitinated molecules and assists their degradation by autophagy ( fig .
thus , activation of inflammasomes induces autophagy , which in turn limits the inflammasome activity by physical engulfment .
this may represent a negative regulation of autophagy in maintaining homeostasis by returning to a basal state in some inflammatory conditions .
recent advances in the characterization of autophagic machinery enable us to identify the role of autophagy in immune systems . by virtue of its ability to degrade cytosolic constituents ,
autophagy has been shown to eliminate intracellular pathogens regardless of their location ( cytosol or phagosome ) . moreover ,
autophagic machinery induced by tlr activation facilitates clearance of pathogens through autophagosome formation or maturation of phagosomes .
autophagy also mediates bacterial clearance and adaptive immune responses including antigen presentation to mhc class ii after bacterial sensing via nlrs . in viral infection , autophagy promotes the production of antiviral type - i ifn by delivering the cytosolic replication intermediates to the lysosomes , enabling recognition of virus by endosomal tlrs .
autophagy may also play a critical role in regulating inflammatory conditions including crohn 's disease by controlling inflammasome activity .
autophagy prevents excessive activation of inflammasomes to maintain basal status against endogenous / exogenous irritants .
collectively , autophagy plays multiple roles in immunity , either activating or suppressing immune responses .
comprehensive understanding of autophagy will therefore provide a more integrated picture of how this system controls immune responses .
 autophagy is a fundamental cellular process in eukaryotic cells for maintaining homeostasis by degrading cellular proteins and organelles . 
 recently , the roles of autophagy have been expanded to immune systems , which in turn modulate innate immune responses . 
 more specifically , autophagy acts as a direct effector for protection against pathogens , as well as a modulator of pathogen recognition and downstream signaling in innate immune responses . 
 in addition , autophagy controls autoimmunity and inflammatory disorders by negative regulation of immune signaling . in this review , 
 we focus on recent advances in the role of autophagy in innate immune systems . 
INTRODUCTION
DIRECT ELIMINATION OF PATHOGENS BY AUTOPHAGY
INTERACTION BETWEEN AUTOPHAGY AND TOLL-LIKE RECEPTORS
AUTOPHAGY IN NUCLEOTIDE OLIGOMERIZATION DOMAIN-LIKE RECEPTOR SIGNALING
AUTOPHAGY IN ANTIVIRAL IMMUNITY
AUTOPHAGY IN REGULATION OF INFLAMMASOME
CONCLUSION