AUTOPHAGY PATHWAY (PW:0000278)

View Ontology Report

Description

Autophagy, the catabolic pathway of cytoplasmic degradation is essential for cellular and tissue homeostasis and it can act as a source of nutrients under starvation or stress conditions. Autophagy encompasses macro and microautophagy, conserved across species, and the chaperone-mediated autophagy (CMA) which appears to be confined to mammalian cells. Macroautophagy (autophagy hereafter) is the pathway described here and shown in the diagram. It involves the sequestration of damaged organelles a

Pathway Diagram:

Ariadne Genomics Inc. Lamp members SNARE, ESCRT, Rabs Atg4 members Atg9 members LC3 conjugation system Atg12 conjugation system Pik3c3 Pik3r4 Atg14 Rb1cc1 Ulk1 mTOR signaling pathway PtdIns3P Atg4 members ---> LC3 conjugation system starvation ---| mTOR signaling pathway nutrient-rich --+> mTOR signaling pathway starvation nutrient-rich Becn1 ---- Uvrag Ulk2 --+> Atg13 Ulk1 --+> Rb1cc1 Becn1 class III PI3K complex Becn1 ---- Rubicon mTOR signaling pathway ---| Ulk1 mTOR signaling pathway ---| Ulk2 Rubicon Uvrag Atg12 conjugation system ---> LC3 conjugation system Acp2 ---> degradation Acp2 degradation Lamp members ---> degradation Ulk2 Atg13 Atg13 ---- Rb1cc1 Pik3c3 ---> PtdIns3P PE Ulk/Atg13/Atg17 complex class III PI3K complex ---> Atg12 conjugation system
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Genes in Pathway:

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autophagy pathway term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Acp2 acid phosphatase 2, lysosomal JBrowse link 3 80,020,346 80,030,365 RGD:4892631
G Atg10 autophagy related 10 JBrowse link 2 19,853,546 20,152,918 RGD:1643329
RGD:4889529
G Atg12 autophagy related 12 JBrowse link 18 40,721,799 40,732,143 RGD:1643329
RGD:6907045
RGD:4889529
RGD:2301217
G Atg13 autophagy related 13 JBrowse link 3 80,580,549 80,614,554 RGD:4889529
G Atg14 autophagy related 14 JBrowse link 15 24,343,418 24,374,776 RGD:4889529
G Atg16l1 autophagy related 16-like 1 JBrowse link 9 94,879,876 94,915,231 RGD:1643329
RGD:4889529
G Atg16l2 autophagy related 16-like 2 JBrowse link 1 166,401,271 166,415,078 RGD:1643329
RGD:4889529
G Atg3 autophagy related 3 JBrowse link 11 60,585,192 60,613,706 RGD:1643237
RGD:6907045
RGD:4889529
RGD:1643329
G Atg4a autophagy related 4A, cysteine peptidase JBrowse link X 112,328,907 112,403,157 RGD:1643329
G Atg4b autophagy related 4B, cysteine peptidase JBrowse link 9 100,888,457 100,920,123 RGD:1643329
RGD:6907045
G Atg4c autophagy related 4C, cysteine peptidase JBrowse link 5 117,861,517 117,932,116 RGD:1643329
RGD:6907045
G Atg4d autophagy related 4D, cysteine peptidase JBrowse link 8 22,291,445 22,301,331 RGD:1643329
RGD:6907045
G Atg5 autophagy related 5 JBrowse link 20 49,301,783 49,393,147 RGD:2301217
RGD:6907045
RGD:4889529
G Atg7 autophagy related 7 JBrowse link 4 146,570,113 146,777,093 RGD:1643329
RGD:1643198
RGD:6907045
RGD:4889529
G Atg9a autophagy related 9A JBrowse link 9 82,382,800 82,393,429 RGD:4889529
G Atg9b autophagy related 9B JBrowse link 4 7,314,369 7,322,095 RGD:4889529
G Becn1 beclin 1 JBrowse link 10 89,209,944 89,225,297 RGD:1643194
RGD:6907045
RGD:4889529
RGD:1643329
G Chmp2b charged multivesicular body protein 2B JBrowse link 11 2,666,405 2,692,213 RGD:4892619
G Chmp3 charged multivesicular body protein 3 JBrowse link 4 99,449,213 99,496,156 RGD:4892619
G Gabarap GABA type A receptor-associated protein JBrowse link 10 56,601,288 56,604,223 RGD:1643329
RGD:6907045
RGD:4890444
G Gabarapl1 GABA type A receptor associated protein like 1 JBrowse link 4 163,293,724 163,302,866 RGD:4890444
RGD:6907045
G Gabarapl2 GABA type A receptor associated protein like 2 JBrowse link 19 44,164,935 44,175,771 RGD:1643329
RGD:6907045
RGD:4890444
G Hgs hepatocyte growth factor-regulated tyrosine kinase substrate JBrowse link 10 109,638,944 109,657,460 RGD:4892619
G Ifna1 interferon, alpha 1 JBrowse link 5 106,951,822 106,952,908 RGD:6907045
G Ifna11 interferon alpha family, gene 11 JBrowse link 5 107,504,741 107,505,783 RGD:6907045
G Ifna2 interferon alpha 2 JBrowse link 5 107,416,117 107,416,695 RGD:6907045
G Ifna4 interferon, alpha 4 JBrowse link 5 106,922,563 106,923,132 RGD:6907045
G Ifna5 interferon, alpha 5 JBrowse link 5 107,039,347 107,039,925 RGD:6907045
G Ifng interferon gamma JBrowse link 7 61,337,383 61,341,419 RGD:6907045
G Ins1 insulin 1 JBrowse link 1 272,799,784 272,800,351 RGD:6907045
G Ins2 insulin 2 JBrowse link 1 215,856,967 215,858,034 RGD:6907045
G Lamp1 lysosomal-associated membrane protein 1 JBrowse link 16 81,689,576 81,714,341 RGD:4892310
RGD:4892631
G Lamp2 lysosomal-associated membrane protein 2 JBrowse link X 124,722,628 124,766,079 RGD:4892310
G LOC100911527 interferon alpha-12-like JBrowse link 5 87,328,395 87,328,946 RGD:6907045
G Map1lc3a microtubule-associated protein 1 light chain 3 alpha JBrowse link 3 150,801,289 150,802,935 RGD:1643198
RGD:4890444
RGD:1643329
G Map1lc3b microtubule-associated protein 1 light chain 3 beta JBrowse link 19 53,635,449 53,643,970 RGD:1643329
RGD:4890444
G Pik3c3 phosphatidylinositol 3-kinase, catalytic subunit type 3 JBrowse link 18 22,964,121 23,047,896 RGD:4889529
RGD:6907045
G Pik3r4 phosphoinositide-3-kinase, regulatory subunit 4 JBrowse link 8 114,300,248 114,350,686 RGD:4889529
RGD:6907045
G Prkaa1 protein kinase AMP-activated catalytic subunit alpha 1 JBrowse link 2 54,857,688 54,893,404 RGD:6907045
G Prkaa2 protein kinase AMP-activated catalytic subunit alpha 2 JBrowse link 5 124,568,845 124,642,569 RGD:6907045
G Rab11a RAB11a, member RAS oncogene family JBrowse link 8 70,192,975 70,215,719 RGD:4892310
G Rab33b RAB33B, member RAS oncogene family JBrowse link 2 140,541,619 140,552,220 RGD:4892310
G Rab5a RAB5A, member RAS oncogene family JBrowse link 9 5,910 6,065 RGD:4892310
G Rab7a RAB7A, member RAS oncogene family JBrowse link 4 119,910,461 119,963,065 RGD:4892310
G Rb1cc1 RB1-inducible coiled-coil 1 JBrowse link 5 13,033,918 13,097,369 RGD:4889529
G Rubcn RUN and cysteine rich domain containing beclin 1 interacting protein JBrowse link 11 71,150,506 71,199,254 RGD:4889529
G Snf8 SNF8, ESCRT-II complex subunit JBrowse link 10 83,856,331 83,868,621 RGD:4892619
G Tsg101 tumor susceptibility 101 JBrowse link 1 102,941,151 102,971,017 RGD:4892619
G Ulk1 unc-51 like autophagy activating kinase 1 JBrowse link 12 51,908,105 51,934,704 RGD:1643329
RGD:6907045
RGD:4889529
G Ulk2 unc-51 like autophagy activating kinase 2 JBrowse link 10 48,050,079 48,129,377 RGD:4889529
RGD:6907045
G Ulk3 unc-51 like kinase 3 JBrowse link 8 62,368,548 62,375,229 RGD:6907045
G Uvrag UV radiation resistance associated JBrowse link 1 163,844,804 164,101,568 RGD:4889529
G Vamp3 vesicle-associated membrane protein 3 JBrowse link 5 168,126,157 168,136,628 RGD:4892310
G Vamp7 vesicle-associated membrane protein 7 JBrowse link 12 18,996,566 19,033,714 RGD:4892310
G Vps4a vacuolar protein sorting 4 homolog A JBrowse link 19 39,230,050 39,243,298 RGD:4892619

Additional Elements in Pathway:

(includes Gene Groups, Small Molecules, Other Pathways..etc.)
Object TypePathway ObjectPathway Object Description
Gene GroupAtg4 membersmembers of Atg4 proteases that prime Lc3/Atg8
Small MoleculePEphosphatidylethanolamine
Small MoleculePtdIns3Pphosphatidylinositol 3-phosphate
Gene GroupAtg9 membersthe transmembrane Atg9 proteins

Pathway Gene Annotations

Pathway Annotations Associated with Genes in the autophagy pathway
Pathway TermsGene Symbols
adenosine monophosphate-activated protein kinase (AMPK) signaling pathwayPrkaa1 , Prkaa2
aldosterone signaling pathwayIns1 , Ins2
allograft rejection pathwayIfng
altered insulin signaling pathwayIns2
amyotrophic lateral sclerosis disease pathwayRab5a
antigen processing and presentation pathwayIfng
autoimmune thyroid disease pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , LOC100911527
autophagy pathwayAcp2 , Atg10 , Atg12 , Atg13 , Atg14 , Atg16l1 , Atg16l2 , Atg3 , Atg4a , Atg4b , Atg4c , Atg4d , Atg5 , Atg7 , Atg9a , Atg9b , Becn1 , Chmp2b , Chmp3 , Gabarap , Gabarapl1 , Gabarapl2 , Hgs , Ifna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , Ins1 , Ins2 , Lamp1 , Lamp2 , LOC100911527 , Map1lc3a , Map1lc3b , Pik3c3 , Pik3r4 , Prkaa1 , Prkaa2 , Rab11a , Rab33b , Rab5a , Rab7a , Rb1cc1 , Rubcn , Snf8 , Tsg101 , Ulk1 , Ulk2 , Ulk3 , Uvrag , Vamp3 , Vamp7 , Vps4a
chaperone mediated autophagy pathwayLamp2
cytokine mediated signaling pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , LOC100911527
eicosanoid signaling pathwayRab11a
endocytosis pathwayChmp2b , Hgs , Rab11a , Rab5a , Rab7a , Snf8 , Tsg101 , Vps4a
Entamoeba histolyca infection pathwayIfng , Rab5a , Rab7a
forkhead class A signaling pathwayIns2
gliclazide pharmacodynamics pathwayIns2
glyburide pharmacodynamics pathwayIns2
graft-versus-host disease pathwayIfng
hepatitis C virus infection pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , LOC100911527
hypertrophic cardiomyopathy pathwayPrkaa1 , Prkaa2
influenza A virus infection pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , LOC100911527
inositol metabolic pathwayBecn1 , Pik3c3 , Pik3r4
inositol phosphate metabolic pathwayPik3c3
insulin responsive facilitative sugar transporter mediated glucose transport pathwayIns2 , Rab11a , Rab5a
insulin signaling pathwayIns1 , Ins2 , Prkaa1 , Prkaa2
interleukin-12 signaling pathwayIfng , Rab7a
interleukin-2 signaling pathwayIfng
interleukin-23 signaling pathwayIfng
interleukin-27 signaling pathwayIfng
Jak-Stat signaling pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , LOC100911527
Leishmania infection pathwayIfng
maturity onset diabetes of the young pathwayIns1 , Ins2
measles infection pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , LOC100911527
mitochondrial autophagy pathwayAtg7 , Becn1 , Ulk1
mTOR signaling pathwayAtg13 , Ins1 , Ins2 , Prkaa1 , Prkaa2 , Rb1cc1 , Ulk1 , Ulk2 , Ulk3
Mycobacterium tuberculosis infection pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , Ifng , Lamp1 , Lamp2 , LOC100911527 , Pik3c3 , Rab5a , Rab7a
Notch signaling pathwayRab11a
phagocytosis pathwayHgs , Lamp1 , Lamp2 , Pik3c3 , Rab5a , Rab7a , Vamp3
phosphatidylinositol 3-kinase signaling pathwayPik3c3
phosphoinositide metabolic pathwayBecn1 , Pik3c3 , Pik3r4
Plasmodium infection pathwayIfng
platelet-derived growth factor signaling pathwayIfng
potassium channel inhibitors pharmacodynamics pathwayIns2
prostate cancer pathwayIns1 , Ins2
Rab family mediated signaling pathwayRab11a , Rab5a
Retinoic acid-inducible gene (RIG) I-like receptor signaling pathwayAtg12 , Atg5 , Ifna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , LOC100911527
rheumatoid arthritis disease pathwayIfng
riboflavin metabolic pathwayAcp2
systemic lupus erythematosus pathwayIfng
T cell receptor signaling pathwayIfng
Toll-like receptor signaling pathwayIfna1 , Ifna11 , Ifna2 , Ifna4 , Ifna5 , LOC100911527
Toxoplasma gondii infection pathwayIfng
transforming growth factor-beta superfamily mediated signaling pathwayIfng
Trypanosoma brucei infection pathwayIfng
Trypanosoma cruzi infection pathwayIfng
type 1 diabetes mellitus pathwayIfng , Ins1 , Ins2
type 2 diabetes mellitus pathwayIns1 , Ins2
type II interferon signaling pathwayIfng
ubiquitin/proteasome degradation pathwayIfng
vascular endothelial growth factor signaling pathwayHgs , Prkaa1 , Prkaa2
vasopressin signaling pathwayRab11a
vasopressin signaling pathway via receptor type 2Rab11a , Rab5a

References Associated with the autophagy pathway:

Ontology Path Diagram:

paths to the root

Import into Pathway Studio: