Autophagy in infection, inflammation and immunity

Abstract

Autophagy is a fundamental eukaryotic pathway that has multiple effects on immunity. Autophagy is induced by pattern recognition receptors and, through autophagic adaptors, it provides a mechanism for the elimination of intracellular microorganisms. Autophagy controls inflammation through regulatory interactions with innate immune signalling pathways, by removing endogenous inflammasome agonists and through effects on the secretion of immune mediators. Moreover, autophagy contributes to antigen presentation and to T cell homeostasis, and it affects T cell repertoires and polarization. Thus, as we discuss in this Review, autophagy has multitiered immunological functions that influence infection, inflammation and immunity.

Figure 1. Four principal roles of autophagy in immunity

a | The role of autophagy in the elimination of microorganisms is shown. An incoming microorganism can induce autophagy by competing for nutrients or by stimulating innate immune receptors, such as Toll-like receptors (TLRs). When the microorganism is taken up by phagocytosis and remains in an intact vacuole, an autophagic process termed LC3-associated phagocytosis (LAP) can promote the maturation of autophagosomes into autolysosomes. Xenophagy of pathogens that enter the cytosol can be initiated by sequestosome 1-like receptors (SLRs) or other mechanisms, including nucleotide-binding oligomerization domain-containing protein 2 (NOD2)–autophagy-related protein 16-like 1 (ATG16L1) interactions. b Several examples of the role of autophagy in the control of pro-inflammatory signalling (see also FIG. 3) are shown. Failure to remove SLRs by autophagy can increase the levels of these receptors and the levels of pro-inflammatory signalling. Autophagy can deliver cytoplasmic pathogen-associated molecular patterns (PAMPs) to endocytic TLRs and can stimulate their activity. NOD-like receptors (NLRs; such as NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3)) and RIG-I-like receptors (RLRs; such as absent in melanoma 2 (AIM2)) show complex positive and negative co-regulation with autophagy: the ATG5–ATG12 complex inhibits retinoic acid-inducible gene I (RIG-I) signalling, and autophagy limits inflammasome activation by removing damaged mitochondria, which then release the inflammasome activators reactive oxygen species (ROS) and mitochondrial DNA. c The role of autophagy in adaptive immunity is shown. Autophagy can increase the MHC class II presentation of cytoplasmic antigens, including self or viral antigens, as well as promoting the citrullination of antigens. LAP can enhance the processing of particulate antigens for MHC class II presentation. NOD2 enhances autophagic antigen presentation. Autophagy may directly or indirectly affect MHC class I presentation by competing with the proteasome for substrates, by influencing the peptidome pools through the control of levels of components of microRNA (miRNA) machinery (for example, argonaute (AGO) and DICER), or by supporting unconventional MHC class I presentation. In addition, autophagy affects the self-renewal of haematopoietic stem cells (HSCs), B1 cell development, plasma cell survival and IgG secretion. Autophagy affects T cell survival following T cell receptor (TCR) activation, and it destabilizes the immunological synapse. It also controls innate immune cell (such as macrophage) signalling through the release of interleukin-1α _(IL-1α)_ _and IL-1β, which influence the polarization of T cells into T helper 17 (T_H17) cells. Autophagy also affects naive T cell repertoire selection in the thymus and the survival and function of maturing T cells by removing the mitochondria and endoplasmic reticulum (ER), thus ensuring calcium homeostasis. d The role of autophagy in the secretion of immune mediators is shown. Autophagy affects the quality of regulated secretion from pre-stored granules. Autophagy affects the quality and the quantity of the output of the constitutive secretory pathway (which is the conventional pathway of protein secretion via the ER, the Golgi apparatus and the plasma membrane). Autophagy supports a form of unconventional secretion that captures cytoplasmic proteins for extracellular release. Note that secretory protein cargo in the regulated and constitutive secretory pathways contains conventional leader peptides for co-translational import into the ER lumen, whereas protein cargo that enters the unconventional secretory pathway lacks leader peptides and does not enter the ER. Dashed arrow indicates that this pathway remains to be defined. DAMPs, damage-associated molecular patterns; HMGB1, high-mobility group box 1 protein; IPS1, IFNβ _promoter stimulator protein 1; mtDNA, mitochondrial DNA; mTOR, mammalian target of rapamycin; NOX2, NADPH oxidase 2; PRRs, pattern recognition receptors; ssRNA, single-stranded RNA; TRAF6, TNF receptor-associated factor 6.

Figure 2. Autophagy-mediated clearance of intracellular pathogens

a| Protein domains of sequestosome 1-like receptors (SLRs) are shown. The LC3-interacting region (LIR) motif of an SLR binds to autophagy-related LC3 proteins through its consensus sequence at amino acids 332–342 in sequestosome 1 (also known as p62). The conserved residues are shown. X/(D,E,S,T) indicates that any amino acid (X) is allowed but that acidic (D,E) or phosphorylatable amino acids (S,T) are often present (usually at least one or more within the entire consensus sequence). The core LIR motif residues are aromatic pocket-filling W (or F or Y) residues and aliphatic pocket-filling L (or I or V). They form an intermolecular parallel β-_sheet with LC3 proteins or γ-aminobutyric acid receptor-associated proteins (GABARAPs). The CLIR motif, which is a LIR motif that is specific for LC3C, lacks the aromatic residue found in the LIR motif and, instead, uses hydrophobic contacts provided by additional aliphatic residues located between the W and L position anchors to stabilize interactions with LC3C. All human SLRs also contain a ubiquitin-binding domain (UBD): UBA (as found in sequestosome 1 and NBR1) is a three-helix bundle UBD that has affinity for monoubiquitin and K63 ubiquitin linkages; UBAN (as found in optineurin) is a parallel coiled-coiled dimer UBD that has specificity for linear ubiquitin chains; and UBZ (as found in nuclear dot protein 52 (NDP52)) is a zinc finger ββα-fold UBD that binds to monoubiquitin and polyubiquitin. b A model of cooperative action between different SLRs and E3 ligases in bacterial targeting for xenophagy is shown. The schematic shows a parasitophorous vacuole with glycosylated molecules (in this case β-galactosides) facing the lumen of the vacuole that contains a bacterium and that is experiencing membrane damage. This membrane tear exposes β-galactosides to galectins (for example, galectin 8) which in turn bind to the galectin-interacting region (GIR) motif of NDP52. NDP52 also directly interacts with the E3 ligase LRSAM1 and indirectly with the serine/threonine protein kinase TANK-binding kinase 1 (TBK1), which interacts with optineurin. The CLIR motif of NDP52 binds to LC3C, which is a proposed initiator in the LC3 and GABARAP cascade during bacterial xenophagy. LRSAM1 or other E3 ubiquitin ligases polymerize ubiquitin at molecular targets that are yet to be identified. The hypothetical model includes the putative recognition of bacterial pathogen-associated molecular patterns (PAMPs) by LRSAM1 through its leucine-rich repeat domain. Ubiquitin tags are recognized by UBDs of NDP52, optineurin and sequestosome 1. The LIR motif of optineurin is phosphorylated by TBK1 and this improves LC3 and GABARAP binding. The UBA of sequestosome 1 is also phosphorylated by TBK1 and this improves ubiquitin chain binding. As a consequence, the autophagic isolation membrane initiates at the appropriate location and grows to capture the bacterium and to eliminate it through autophagy. CC, coiled-coil domain; FW, four W domain (also known as the NBR1 domain); KIR, KEAP1 interacting region; NES, nuclear export signal; NLS, nuclear localization signal; P, phosphorylation; PB1, protein-binding domain 1; SKICH, skeletal muscle and kidney enriched inositol phosphatase carboxyl homology domain; TAX1BP1, TAX1-binding protein 1; Ub, ubiquitylation; ZnF, zinc finger domain; ZZ, ZZ-type ZnF domain.

Figure 3. Autophagy controls inflammatory processes

a Autophagy promotes Toll-like receptor 9 (TLR9) signalling in B cells and type I interferon (IFN) production by plasmacytoid dendritic cells (pDCs). b The autophagy protein complex autophagy-related protein 5 (ATG5)–ATG12 inhibits RIG-I-like receptor (RLR) signalling by binding to the caspase recruitment domains of retinoic acid-inducible gene I (RIG-I) and IFNβ _promoter stimulator protein 1 (IPS1), which is the mitochondrial adaptor of RIG-I signalling. The NOD-like receptor X1 (NLRX1)-interacting partner mitochondrial Tu elongation factor (TUFM) associates with the ATG5–ATG12 complex to promote autophagy while inhibiting RLR-dependent type I IFN activation. c Autophagy factors negatively regulate the caspase recruitment domain-containing protein 9 (CARD9)–B cell lymphoma 10 (BCL-10)– mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) complex. RUBICON (run domain beclin 1-interacting and cysteine-rich-containing protein), which is a binding partner and a negative regulator of beclin 1, inhibits CARD9, whereas sequestosome 1 leads to the degradation of BCL-10. d Excessive production of reactive oxygen species (ROS) by depolarized mitochondria that are not cleared by autophagy enhance RLR signalling. e Viral, mitochondrial or bacterial DNA lead to the activation of stimulator of IFN genes protein (STING), probably through cGAMP synthase and cyclic GMP–AMP (cGAMP) production, which increases the type I IFN response. Autophagy removes sources of agonists that stimulate STING, whereas autophagic factors (for example, ATG9) inhibit the activation of STING by affecting its cytoplasmic translocation. Bacterial cyclic dinucleotides (di-AMP and di-GMP) can activate autophagy, thereby functioning as a regulatory loop that amplifies the removal of infectious or endogenous irritants. BCR, B cell receptor; IL, interleukin; LAP, LC3-associated phagocytosis; NK-κB, nuclear factor-κB; TBK1, TANK-binding kinase 1; Ub, ubiquitylation.