DefinitionThis section has been translated automatically.
The term"autophagy genes", also known as ATG genes, refers to a family of genes involved in the orchestration of autophagy . The lysosomal "disposal" of cytological "waste" (misfolded proteins, portions of cell organelles) involves approximately 20 evolutionarily conserved ATG core genes encoding proteinsof the same name(ATG proteins) (Klionsky et al. 2003).
The ATG genes were originally discovered in yeast genetic screens (Mizushima 2018). With few exceptions, all ATG genes are required for the efficient formation of membrane-enveloped autophagosomes that fuse with lysosomes after autophagosome formation. The proteins encoded by ATG genes are traditionally classified into different biochemical and functional groups that are effective at specific stages of autophagosome assembly.
General informationThis section has been translated automatically.
The process of autophagy is highly conserved in all eukaryotic organisms and is enhanced by various intra- and extracellular stimuli. Autophagy is essential for cellular homeostasis, cellular protein and organelle quality control and disposal, and adaptation of the organism to environmental stress. (Levine and Kroemer, 2008; Mizushima and Komatsu, 2011). In autophagy initiation, the ULK1-serine-threonine kinase complex (involving ULK1, FIP200, ATG13, and ATG101) plays a major role by phosphorylating and thereby activating several downstream proteins. In higher eukaryotes, many autophagy genes have additionally functionally diversified to
- facilitate the transport of extracellular cargo to the lysosome
- promote plasma membrane localization or extracellular release of intracellular cargo
- coordinate intracellular communication with various cell signaling pathways.
These downstream functions are in the true sense, not autophagy. Accordingly, they are referred to as ATG gene-dependent pathways.
- The nuclear ATG proteins are necessary but not sufficient for intact degradative autophagy in human cells. Degradation of autophagosomal cargo can only occur via successful fusion of the autophagosome with a functional lysosome. Prerequisite for these essential processes are: on the one hand an intact lysosomal biogenesis
- an undisturbed autophagolysosomal fusion process per se (Yu et al. 2018)
- an unimpaired lysosomal (enzymatic) function (Shen and Mizushima, 2014)
- and ultimately a restoration of intact lysosomal function (Chen and Yu, 2017).
Mutations in genes required for autophagy and lysosomal function that regulate these processes lead to frequent lines of dysfunction in cellular metabolism and to entirely different, often severe, disease patterns.
Clinical pictureThis section has been translated automatically.
Mutations in genes required for autophagy and lysosomal function.
- ATG 16L1(Crohn's disease): ATGL16L1 T300A is a major risk allele for CD. The T300A polymorphism has a caspase-3 cleavage site that reduces protein levels. T300A knock-in or hypomorphic or intestinal knockout mice show decreased intestinal bacterial clearance; increased cytokine responses; decreased Paneth cell lysozyme secretion and clearance of IRE la protein aggregates during ER stress; increased enterocytic TNFa-induced necroptosis; dendritic cell defects in regulatory T cell induction and suppression of mucosal inflammation (Chu et al., 2016)
- ATG16L2(Systemic lupus erythematosus; Crohn's disease): The ATG16L2 gene encodes a protein of the same name that interacts with Atg5 in a large protein complex consisting of Atg5, Atg12, and Atg16L1. This protein complex has been shown to be essential for stretching isolation membranes (also called phagophores) during autophagy in mammals. To date, however, the precise function and regulation of the Atg12-5-16L1 complex has remained largely unknown. The ATG16L2 protein is an isoform of ATG16 whose function remains unclear (Molineros et al. 2017)
- ATG5 (childhood ataxia, systemic sclerosis, SLE): A loss-of-function mutation reduces autophagy and causes ataxia. Intronic variants are associated with susceptibility to systemic sclerosis. Versch. Polymorphisms are associated with susceptibility to SLE; mouse studies suggest that the mechanism involves deficient LC3-associated phagocytosis (Martinez et al. 2016)
- ATP6AP2(X-linked parkinsonism with spasticity. Multisystem disorder): exon skipping mutations are associated with parkinsonism; missense mutations associated with immunodeficiency, liver disease, and psychomotor impairment result in defective lysosomal acidification due to impaired v-ATPase assembly, leading to defects in autophagy (Rujano et al. 2017)
- BECN1(breast and ovarian cancer): Monoallelic deletion associated with risk and poor prognosis of sporadic breast and ovarian cancer; monoallelic deletion in mice leads to decreased autophagy and increased tumor incidence, including basal breast cancer (Tang et al. 2015)
- CLEC16A(diabetes, multiple sclerosis): CLEC16A variants are associated with several autoimmune diseases. Mice, with Clecl6a deficiencies, suffer from autophagy defects associated with Purkinje degeneration and ataxia, impaired β-cell mitophagy, and autoimmunity (Redmann et al. 2016)
- CTNS gene(cystinosis): Recessive loss-of-function mutations in the CTNS gene, which encodes a transporter that exports cysteine from lysosomes and is associated with renal lysosomal storage disease; gene deletion in mice results in deficient autophagy, altered lysosomal dynamics, and accumulation of dysfunctional, ROS overproducing mitochondria (Festa et al. 2018)
- EPG5 (Vici syndrome): Recessive mutations in EPG5, a gene required for autophagolysosomal fusion, lead to a neurodevelopmental disorder with multisystem involvement (Hori et al. 2017)
- GBA (Gaucher disease; Parkinson disease): GBA1 encodes the lysosomal enzyme glucocerebrosidase. Homozygous GBA defects cause Gaucher's disease and heterozygous defects predispose to Parkinson's disease (Afiaki et al. 2017).
- GRN(Frontotemporal dementia (heterozygous) or neuronal ceroid lipofuscinosis (homozygous): Loss-of-function mutations impair lysosomal function and autophagic flux.
- LAMP2 (Danon's cardiomyopathy; Hypertrophic cardiomyopathy): X-linked deletion leads to vacuolar cardiomyopathy and myopathy; Lamp2 deletion in mice leads to autophagosome accumulation and cardiomyopathy.
- PIK3R4 (VPSI 5): Cortical atrophy and epilepsy Mutations in PIK3R4, a component of the Beclin-1 complex required for endosomal-lysosomal trafficking and autophagy, are associated with human neurodevelopmental diseases (Gstrein et al. 2018).
- SNX14(Autosomal recessive spinocerebellar ataxia): SNX14 binds lysosomal phosphatidylinositol(3,5)-bisphosphate and is required for autophagosomal clearance (Akizu et al. 2015;
- SPG11, SPG15 (ZFYVE26), SPG49 (TECPR)(Hereditary spastic paraplegia): SPG15 binds phosphatidylinositol-3-phosphate and SPG49 binds LC3 to function in autophagolysosomal trafficking (Ebrahimi-Fakhari et al., 2016).
- WDR45 (WIPI4)(beta-propeller protein-associated neurodegeneration): WDR45 (WIPI4) binds to phosphoinositide-3-phosphate and interacts with ATG2 and ATG9; disease-associated mutations impair autophagy (Ebrahimi-Fakhari et al. 2016).
Mutations in genes regulating autophagy and lysosomal function.
- APP(Alzheimer's disease): Mutant amyloid precursor protein expressed in mouse hippocampal neurons inhibits mitophagy and autophagy.
- AT-1 (SLC33A1)(spastic paraplegia, developmental delay, autism spectrum disorders): AT-1 translocates cytosolic acetyl-CoA into the ER lumen; mutations and duplications are associated with a variety of CNS phenotypes in humans; in mice, overexpression blocks Atg9a-Faml34b-LC3 interactions, leading to defective ER phagy and progeria (Peng et al. 2018).
- C9orf72(Amyotrophic lateral sclerosis -ALS; Frontotemporal dementia -FTD): Hexanucleotide repeat expansion in the C9orf72 gene is the most common genetic cause of ALS and FTD. Regulates autophagy and lysosomal homeostasis through interactions with SMCR8, ULK1, and Rab GTPases (Corrionero et al. 2018).
- ERBB2(breast cancer): amplification of ERBB2 and resulting overexpression of ERBB2 (HER2) interacts with Beclin 1 and inhibits autophagy (Vega-Rubin-de-Celis et al., 2018)
- GBA1(Gaucher disease; Parkinson's disease): mutations in GBA1 decrease glucocerebrosidase activity, leading to defects in autophagy-lysosomal function and accumulation of a-synuclein aggregates (Afiaki et al. 2017)
- GPR65(Inflammatory bowel disease):GPR65 I231L risk variant of this proton-sensitive G protein-coupled receptor impairs lysosomal acidification, decreases intracellular bacterial clearance, and alters lipid droplet turnover.
- HTT (Huntingtin; Huntington's disease): PolyQ expansion in HTT competitively disrupts the interaction between the deubiquitinase ataxin 3 and Beclin 1, leading to increased proteasomal degradation of Beclin 1 and reduced autophagy (Ashkenazi et al. 2017).
- IRGM (non-alcoholic fatty liver disease (NAFLD); Crohn's disease; tuberculosis): IRGM functions in assembly and activation of the autophagy machinery; a synonymous variant reduces protein expression, leading to reduced autophagy and lipophagy in NAFLD; polymorphisms are associated with risk for Crohn's disease and tuberculosis (Lin et al. 2016)
- LRRK2(Crohn's disease; Parkinson's disease): risk alleles for CD and PD increase kinase activity of leucine-rich repeat kinase 2 and reduce autophagic flux; a protective allele increases flux (Hui et al. 2018)
- MeCP2 (Rett syndrome - X-linked neurodevelopmental disorder-): Deficiency of methyl-CpG-binding protein-2 (MeCP2), a transcriptional regulator, leads to defective autophagy in patient fibroblasts and in the cerebellum of knockout mice, as well as mitochondrial retention in erythrocytes (Sbardella et al. 2017)
- MTMR3(Inflammatory bowel disease): MMTR is a PI3P phosphatase that decreases autophagy. Macrophages from carriers of the risk allele express higher MTMR3 protein levels and have increased pathogen recognition receptor-induced caspase-1 activation and IL-1β secretion (Lahiri et al. 2015)
- PLEKHM1(osteopetrosis): associated mutants impair binding to RAB7A and secretory lysosome trafficking in osteoclasts.
- RAB7A(Charcot-Marie-Tooth disease type 2B): disease-associated RAB7A mutants reduce autophagic flux in HeLa cells and patient-derived fibroblasts are autophagy-deficient.
- PS1(Alzheimer's disease): mutations in presenilin 1 that disrupt v-ATPase assembly, lysosomal acidification, and autophagy cause early-onset Alzheimer's disease (Lee et al. 2010).
- PTPN2(type 1 diabetes; juvenile arthritis): Disease-associated SNP in PTPN2, a gene encoding protein tyrosine phosphatase non-receptor type 2, causes impaired autophagosome formation and defective bacterial handling in macrophages and intestinal epithelial cells.
- SMS(Snyder-Robinson syndrome): Loss-of-function mutations in spermine synthase (SMS) cause SRS, an X-linked syndrome with mental retardation; deficiency of SMS produces toxic metabolites that impair lysosomal function and autophagic flux
- TMEM230(Parkinson's disease): transmembrane protein involved in retromer function; loss reduces autophagic cargo degradation and secretory autophagy (Kim et al. 2017)
- v-ATPase(Autosomal Recessive Osteoporosis): Mutations in the α3-subunit encoded by TCIRG1 impair lysosomal acidification at the grooved border of osteoclasts, leading to defects in bone resorption.
- WASP(Wiskott-Aldrich syndrome) Deficiency of the actin cytoskeleton-regulating WASP protein impairs autophagosome formation, leading to deficient xenophagy and excessive inflammasome activation and pyroptosis.
Mutations in genes required for cargo delivery during selective autophagy.
- ALFY (Primary microcephaly) Dominant mutation in this autophagy scaffold protein causes human microcephaly (Kadir et al. 2016).
- CALC0C02 (NDP52) (Crohn's disease): Missense mutation of this autophagy adaptor reduces its function and enhances NF-kB activation of inflammatory genes (Ellinghaus et al. 2013)
- FAM134B (hereditary sensory and autonomic neuropathy type II): mutations disrupt the interaction of this ER protein with LC3 and GABARP and impair ER phagy.
- FANC genes (Fanconi anemia; Hereditary breast and ovarian cancer): FA pathway genes are required for clearance of damaged mitochondria (mitophagy) and prevention of aberrant inflammasome activation (Sumpter et al. 2016).
- OPTN1 (amyotrophic lateral sclerosis; primary open-angle glaucoma; Paget's disease of bone): Mutations in ALS reduce interaction of this autophagy adaptor with TBK1 and decrease Parkin-dependent mitophagy; mutations in POAG increase interaction with TBK1, activate Bax-dependent apoptosis, and are associated with mitochondrial dysfunction. Truncated protein mutations occur in association with Paget's disease of bone (Silva et al. 2018)
- PARK2/Parkin (Autosomal recessive and sporadic early-onset Parkinson's disease; colon, lung, and brain cancers): Parkin is an E3 ligase that functions in mitophagy and xenophagy; mutations are associated with PD and cancer risk; polymorphisms are associated with increased susceptibility to intracellular bacterial infections.
- PARK6/PINK1 Autosomal recessive and sporadic early-onset Parkinson's disease PINK1 is a serine-threonine kinase that translocates to the outer mitochondrial membrane upon damage and mediates parkin recruitment and mitophagy.
- PEX13 (Zellweger syndrome): Disease-associated mutations impair mitophagy and patients with mutations have accumulation of abnormal mitochondria.
- SQSTM1 (p62) (ALS; FTD; Paget's disease; Distal myopathy) SQSTM1 is an autophagy adaptor that binds ubiquitin and LC3; mutations in the ubiquitin-binding association domain result in a spectrum of multisystem proteinopathies.
- SMURF1 (ulcerative colitis) SMURF1, a susceptibility gene for ulcerative colitis, encodes an E3 ligase that functions in the mitophagy, virophagy, and xenophagy of intracellular bacteria (Franco et al. 2017)
- TBK1 (ALS; Frontotemporal Dementia; Other Neurodegenerative Phenotypes; POAG) TBK1 kinase phosphorylates the autophagy receptor OPTN1 and increases its interaction with ATG8 proteins and polyubiquitinated proteins.
- TRIM20 (Familial Mediterranean fever): Disease-associated TRIM20 mutants do not interact with inflammasome components and target them for autophagic destruction (Kimura et al.2017).
- VPS13D (ataxia with spasticity) Recessively inherited defects in this ubiquitin-binding protein cause mitophagy failure and mitochondrial dysfunction
LiteratureThis section has been translated automatically.
- Aflaki E et al (2017). The complicated relationship between Gaucher disease and Parkinsonism: Insights from a rare disease. Neuron 93: 737-746.
- Ashkenazi A et al. (2017) Polyglutamine tracts regulate beclin 1-dependent autophagy. Nature 545: 108-111.
- Chen Y et al (2017). Recent progress in autophagic lysosome reformation. Traffic 18: 358-361.
- Chu H et al (2016). Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science 352: 1116-1120.
- Corrionero A et al (2018). A C9orf72 ALS/FTD ortholog acts in endolysosomal degradation and lysosomal homeostasis. Curr Biol 28: 1522-1535 e1525.
- Ebrahimi-Fakhari D et al (2016). Congenital disorders of autophagy: an emerging novel class of inborn errors of neuro-metabolism. Brain 139: 317-337.
- Ellinghaus D et al (2013). Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology 145: 339-347.
- Festa BP et al (2018). Impaired autophagy bridges lysosomal storage disease and epithelial dysfunction in the kidney. Nat Commun 9: 161.
- Franco LH et al. (2017) The ubiquitin ligase Smurf1 functions in selective autophagy of Mycobacterium tuberculosis and anti-tuberculous host defense. Cell Host Microbe 21: 59-72.
- Gstrein T et al (2018). Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nat Neurosci 21: 207-217.
- Hori I et al (2017). Defects in autophagosome-lysosome fusion underlie Vici syndrome, a neurodevelopmental disorder with multisystem involvement. Sci Rep 7: 3552.
- Hui KY et al (2018). Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 10, pii: eaai7795.
- Kadir R et al (2016). ALFY-controlled DVL3 autophagy regulates Wnt signaling, determining human brain size. PLoS Genet 12: e1005919.
- Kimura T et al (2017). Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy. EMBO J 36: 42-60.
- Levine B et al. (2019) Biological Functions of Autophagy Genes: A Disease PerspectiveCell 176 P11-42.
- Klionsky DJ et al (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5, 539-545.
- Kroemer G et al (2010). Autophagy and the integrated stress response. Mol Cell 40: 280-293.
- Lahiri A et al (2015). MTMR3 risk allele enhances innate receptor-induced signaling and cytokines by decreasing autophagy and increasing caspase-1 activation. Proc Natl Acad Sci U S A 112: 10461-10466.
- Lee JH et al (2010). Lysosomal proteolysis and autophagy require presenilin 1 and are disrupted by Alzheimer-related PS1 mutations. Cell 141: 1146-1158.
- Lee PPet al (2017b). Wiskott-Aldrich syndrome protein regulates autophagy and inflammasome activity in innate immune cells. Nat Commun 8: 1576.
- Lin YC et al. (2016) Variants in the autophagy-related gene IRGM confer susceptibility to non-alcoholic fatty liver disease by modulating lipophagy. J Hepatol 65: 1209-1216.
- Martinez J et al (2016) Noncanonical autophagy inhibits the autoinflammatory, lupus-like response to dying cells. Nature 533: 115-119.
- Mizushima N et al (2011). Autophagy: renovation of cells and tissues. Cell 147: 728-741.
- Mizushima N (2018). A brief history of autophagy from cell biology to physiology and disease. Nat Cell Biol 20: 521-527.
- Molineros JE et al. (2017) Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Hum Mol Genet 26: 1205-1216.
- Peng Y et al (2018). Increased transport of acetyl-CoA into the endoplasmic reticulum causes a progeria-like phenotype. Aging Cell, e12820.
- Redmann V et al (2016). Clec16a is critical for autolysosome function and Purkinje cell survival. Sci Rep 6: 23326.
- Rujano MA et al (2017). Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects. J Exp Med 214. 3707-3729.
- Sbardella D et al (2017). Retention of mitochondria in mature human red blood cells as the result of autophagy impairment in Rett Syndrome. Sci Rep 7: 12297.
- Shen HM et al (2014). At the end of the autophagic road: an emerging understanding of lysosomal functions in autophagy. Trends Biochem Sci 39: 61-71.
- Sumpter R Jr et al (2016). Fanconi anemia proteins function in mitophagy and immunity. Cell 165: 867-881.
- Yu L et al (2018). Autophagy pathway: Cellular and molecular mechanisms. Autophagy 14: 207-215.