Regulation and repurposing of nutrient sensing and autophagy in innate immunity

Abstract

Nutrients not only act as building blocks but also as signaling molecules. Nutrient-availability promotes cell growth and proliferation and suppresses catabolic processes, such as macroautophagy/autophagy. These effects are mediated by checkpoint kinases such as MTOR (mechanistic target of rapamycin kinase), which is activated by amino acids and growth factors, and AMP-activated protein kinase (AMPK), which is activated by low levels of glucose or ATP. These kinases have wide-ranging activities that can be co-opted by immune cells upon exposure to danger signals, cytokines or pathogens. Here, we discuss recent insight into the regulation and repurposing of nutrient-sensing responses by the innate immune system during infection. Moreover, we examine how natural mutations and pathogen-mediated interventions can alter the balance between anabolic and autophagic pathways leading to a breakdown in tissue homeostasis and/or host defense.Abbreviations: AKT1/PKB: AKT serine/threonine kinase 1; ATG: autophagy related; BECN1: beclin 1; CGAS: cyclic GMP-AMP synthase; EIF2AK4/GCN2: eukaryotic translation initiation factor 2 alpha kinase 4; ER: endoplasmic reticulum; FFAR: free fatty acid receptor; GABARAP: GABA type A receptor-associated protein; IFN: interferon; IL: interleukin; LAP: LC3-associated phagocytosis; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; NLR: NOD (nucleotide-binding oligomerization domain) and leucine-rich repeat containing proteins; PI3K, phosphoinositide 3-kinase; PRR: pattern-recognition receptor; PtdIns3K: phosphatidylinositol 3-kinase; RALB: RAS like proto-oncogene B; RHEB: Ras homolog, MTORC1 binding; RIPK1: receptor interacting serine/threonine kinase 1; RRAG: Ras related GTP binding; SQSTM1/p62: sequestosome 1; STING1/TMEM173: stimulator of interferon response cGAMP interactor 1; STK11/LKB1: serine/threonine kinase 11; TBK1: TANK binding kinase 1; TLR: toll like receptor; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; TRIM: tripartite motif protein; ULK1: unc-51 like autophagy activating kinase 1; V-ATPase: vacuolar-type H⁺-proton-translocating ATPase.

Keywords: AMPK; LC3-associated phagocytosis; MTOR; immunity; microbial pathogenesis; unconventional secretion.

Figure 1.

Nutrient sensing and autophagy. (A) Amino acids transported across the plasma membrane or from lysosomes are detected by various receptors (not shown; also see Box 1) that promote the lysosomal localization of MTORC1 and RRAG GTPases. Receptor signaling uses adaptors to activate class I PI3K (PI3K-C1), which produces PtdIns(3,4,5)P₃ and activates AKT1 through PDPK1 and MTORC2. AKT1 phosphorylates TSC2 and inhibits its GAP activity toward RHEB GTPase. During amino acid starvation, uncharged tRNAs bind and activate EIF2AK4/GCN2. Glucose import stimulates enhanced ATP production through glycolysis and oxidative phosphorylation (OxPhos). In low-energy conditions, elevated cellular AMP binds AMPK, which results in its phosphorylation and activation by STK11/LKB1. (B) Nutrient starvation activates autophagy via the ULK1 complex by preventing its inhibition by MTORC1 and promoting its activation by AMPK. The steps involved in autophagy are labeled on the left. The BECN1-PIK3C3-PIK3R4 complex is a class III PtdIns3K (PtdIns3K-C3), which generates PtdIns3P on phagophores to recruit the Atg8 (LC3/GABARAP subfamilies) lipidation machinery, expand the membrane and engulf cargo. Ubiquitin-binding SQSTM1-like receptors (SLRs) and vesicle tethering and fusion machineries promote cargo-capture, vesicle transport and fusion with lysosomes. See Boxes 1 and 3. PI3K, phosphoinositide 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns(3,4,5)P₃: phosphatidylinositol-3,4-5,-triphosphate; PtdIns3K: phosphatidylinositol-3ʹ-phosphate kinase

Figure 2.

MTORC1 and AMPK regulation during infection and innate immune signaling. (A) TLR activation results in the recruitment of the adaptors PIK3AP1/BCAP or BANK1 that activate PI3K-C1 and PtdIns(3,4,5)P₃ production. Infection by Salmonella or Helicobacter or exposure to TNFSF10/TRAIL, TNFSF11/RANKL and TLR9 stimulate MAP3K7/TAK1-dependent phosphorylation and activation of AMPK, which stimulates ULK1-dependent autophagy. (B) Activation of endosomal TLRs such as TLR3 or TLR7 results in MTORC1-dependent activation of TBK1 and type I IFN production. During TLR3 signaling, PKC activation by MTORC2 promotes trafficking to cell periphery to lysosomes that are positive for RAB7A. TLR7 activation results in its trafficking to ARL5B/ARL8-positive lysosomes for TBK1 activation. TBK1 may also contribute to MTORC1 activation. Amino acids may promote lysosomal localization of MTORC1; however, this remains to be tested. (C) TLR3 signaling through its adaptor TICAM1/TRIF triggers the cleavage of SQSTM1/p62 via RIPK1 and CASP8 at Asp329. The trimmed protein, SQSTM1/p62^TRM, is required for MTORC1 activation in response to amino acids and leucine. Full-length SQSTM1 selectively participates in autophagy maturation, whereas SQSTM1/p62^TRM promotes MTORC1 and suppresses autophagy

Figure 3.

Redirection of ULK1 and BECN1-PtdIns3K-C3 complexes. (A) Damage of pathogen-containing vacuoles exposes luminal glycans that recruit galectins. Galectins, such as LGALS8 (galectin 8) and LGALS3 (galectin 3), can recruit the ULK1 complex through the SQSTM1-like protein (SLR) CALCOCO2/NDP52. TRIMs can detect microbial components or endosome damage through galectins and recruit the ULK1 complex. The subsequent recruitment of BECN1-PtdIns3K-C3 complexes promotes ATG12–ATG5-ATG16L1-driven LC3 lipidation. Ubiquitination of pathogens or associated membranes with polyubiquitin chains of different topologies further enhances the recruitment of the autophagy machinery through SLRs. In contrast, the V-ATPase complex can directly recruit ATG16L1 for MAP1LC3B (LC3B) deposition on Salmonella. Both pathways result in vacuole maturation, fusion with lysosomes and restriction of bacterial replication. (B) During infection by Salmonella or RNA virus or exposure to cytosolic dsRNA, the RALB GTPase differentially promotes autophagy and innate immune signaling. Active RALB promotes xenophagy through the EXOC8 subcomplex of the EXOCYST, which activates ULK1 and BECN1. RALB can be ubiquitinated at Lys47, which sterically hinders its interaction with EXOC8 and enhances binding to the EXOC2 subcomplex of the EXOCYST. This complex promotes the activation of TBK1 and type I IFNs during viral infection. USP33 can remove ubiquitin chains and alter the balance between the two pathways

Figure 4.

Autophagy via CGAS-STING1 and non-canonical roles of autophagy proteins. (A) ULK1-independent autophagy via STING1. The detection of dsDNA by CGAS generates cGAMP that binds and activates STING1 in the ER. Trafficking of STING1-cGAMP through the ERGIC promotes PtdIns3P production independently of ULK1 and BECN1-PtdIns3K-C3 complexes. The PtdIns3P-binding protein WIPI2 assists in ATG5-dependent LC3 lipidation and autophagosome formation. CGAS and STING1 are turned over within autophagosomes. A separate subcellular compartment containing STING1 and TBK1 (not shown) promotes type I IFN signaling. (B) ULK1-dependent STING1 and CGAS turnover. cGAMP produced by CGAS can induce STING1-dependent autophagy via CGAS ubiquitination or BECN1 interactions and through cGAMP-mediated STK11/LKB1-AMPK activation. The detection of c-diAMP, produced by Gram-positive bacteria such as Listeria innocua (not shown), promotes STING1-dependent ER-stress through unknown mechanisms. The activation of the unfolded protein response (UPR) results in EIF2S1 phosphorylation and the selective translation of ATF4 targets, such as DDIT4/REDD1, which inhibit MTORC1 (dotted red line). Autophagy is thus activated directly through ULK1 and BECN1-PtdIns3K-C3 complexes, or MTORC1 inhibition in these settings. (C) Some receptors, especially FCGR2A/FcγR2A, CLEC7A/Dectin 1 and some TLRs, use autophagy-related proteins during phagocytosis in a process that involves LC3 lipidation. In this pathway, the BECN1-PIK3C3-PIK3R4 complex containing RUBCN and UVRAG generates PtdIns3P. Phagosomes, which are enclosed by a single bilayer, are coated with LC3 and fuse with lysosomes. NADPH oxidase, whose subunits bind PtdIns3P and recruit it to phagosomes, produces ROS for LC3-associated phagocytosis (LAP). ULK1 complex, AMBRA1 and ATG14, and therefore nutrient signals, are dispensable in this process. (D) Unconventional secretion of mature IL1B. Expression of CASP1 and proIL1B in fibroblasts results in mature IL1B production upon starvation. IL1B is translocated into LC3-positive vesicles through HSP90AA1 and independently of ATG2B, RB1CC1 and ATG5 activities. This suggests CMA-like threading of IL1B directly into vesicles followed by secretion of soluble IL1B protein, which requires GORASP2/GRASP55, GORASP1/GRASP65 and multivesicular bodies (MVBs). IL1B resides within the inter-membrane space. In macrophages, lysosomal damage-induced IL1B is captured by TRIM16, which also interacts with LGALS8 and HSP90AA1 to transfer IL1B into vesicles. RAB8A is required for vesicle trafficking and the TRIM16-partner SEC22B SNARE mediates fusion of vesicles to plasma membrane through SNAP23, SNAP29, STX3 and STX4. An outstanding question is how vesicles containing cargo do not fuse with lysosomes

Figure 5.

Pathogen-driven manipulation of host nutrient sensing and autophagy. Schematics in (A) and (B) show proteins used by microbial pathogens (within parenthesis) that act at the indicated steps. Pathogen-driven activation or inhibition are colored in blue and violet, respectively. See text for details and compare with Figure 1, which depicts core-pathways (blue arrows/lines). (A) Pathogens manipulate MTOR signaling through RRAGs and/or RHEB, AMPK or affect EIF2AK4/GCN2 signaling. Activation of MTORC1 promotes membrane synthesis for maintaining intracellular microbial vacuoles, biogenesis for building blocks, selective protein translation and gene transcription. Inhibition of MTORC1 blocks the host from utilizing nutrients, prevents anti-microbial gene transcription and induces autophagy. Some pathogens affect these pathways temporally and use other effectors to additionally manipulate autophagy, as shown in (B). See refs [44,125–149]. PFT: Pore Forming Toxin; SLO: streptolysin O; T3SS: Type III Secretion System; T4SS: Type IV Secretion System. (B) Several pathogens upregulate or inhibit xenophagy to avoid the harsh lysosomal environment. Intracellular pathogens can block the fusion of vacuoles with lysosomes or alter lysosomal contents to develop a less hostile niche and promote fusion with endosomes and/or detoxified lysosomes to obtain nutrients. See refs [150–173]