KEGG   PATHWAY: rtp04140
Entry
rtp04140                    Pathway                                
Name
Autophagy - animal - Rhincodon typus (whale shark)
Description
Autophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily conserved among eukaryotes and exquisitely regulated. This progress initiates with production of the autophagosome, a double-membrane intracellular structure of reticular origin that engulfs cytoplasmic contents and ultimately fuses with lysosomes for cargo degradation. Autophagy is regulated in response to extra- or intracellular stress and signals such as starvation, growth factor deprivation and ER stress. Constitutive level of autophagy plays an important role in cellular homeostasis and maintains quality control of essential cellular components.
Class
Cellular Processes; Transport and catabolism
Pathway map
rtp04140  Autophagy - animal
rtp04140

Other DBs
GO: 0006914
Organism
Rhincodon typus (whale shark) [GN:rtp]
Gene
109921259  insulin [KO:K04526]
109916967  insulin receptor substrate 1-B-like [KO:K16172]
109924087  irs1; insulin receptor substrate 1-B [KO:K16172]
109921559  insulin receptor substrate 2 [KO:K07187]
109919326  insulin receptor substrate 2-A [KO:K07187]
109915990  pik3cb; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform [KO:K00922] [EC:2.7.1.153]
109916739  phosphatidylinositol 3-kinase regulatory subunit gamma-like [KO:K02649]
109917303  pik3r3b; phosphoinositide-3-kinase, regulatory subunit 3b (gamma) isoform X3 [KO:K02649]
109931632  RAC-beta serine/threonine-protein kinase isoform X1 [KO:K04456] [EC:2.7.11.1]
109916533  akt3a; RAC-gamma serine/threonine-protein kinase isoform X1 [KO:K04456] [EC:2.7.11.1]
109913977  ptenb; phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN [KO:K01110] [EC:3.1.3.16 3.1.3.48 3.1.3.67]
109915744  GTPase HRas [KO:K02833]
109919287  GTPase HRas [KO:K07827]
109931543  GTPase KRas isoform X1 [KO:K07827]
109917328  nras; GTPase NRas [KO:K07828]
109932084  mrasa; ras-related protein M-Ras [KO:K07831]
109919272  rras2; ras-related protein R-Ras2 isoform X1 [KO:K07830]
109920125  ras-related protein R-Ras2-like isoform X1 [KO:K07830]
109911534  raf1b; RAF proto-oncogene serine/threonine-protein kinase [KO:K04366] [EC:2.7.11.1]
109922810  map2k1; dual specificity mitogen-activated protein kinase kinase 1 [KO:K04368] [EC:2.7.12.2]
109918415  mapk1; mitogen-activated protein kinase 1 [KO:K04371] [EC:2.7.11.24]
109915465  hif1aa; hypoxia inducible factor 1 subunit alpha a isoform X1 [KO:K08268]
109922714  ddit4; DNA damage-inducible transcript 4 protein [KO:K08270]
109913050  tsc2; tuberin [KO:K07207]
109916041  tsc1b; TSC complex subunit 1b isoform X3 [KO:K07206]
109924930  BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like isoform X1 [KO:K15464]
109929749  rptor; regulatory-associated protein of mTOR [KO:K07204]
109919177  deptor; DEP domain-containing mTOR-interacting protein isoform X1 [KO:K20402]
109914403  mtor; serine/threonine-protein kinase mTOR [KO:K07203] [EC:2.7.11.1]
109923030  akt1s1; proline-rich AKT1 substrate 1 isoform X1 [KO:K16184]
109936398  mlst8; target of rapamycin complex subunit lst8 [KO:K08266]
109911139  ribosomal protein S6 kinase beta-1-like [KO:K04688] [EC:2.7.11.1]
109921033  igbp1; immunoglobulin-binding protein 1 [KO:K17606]
109912238  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
109934366  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
109928757  ulk2; serine/threonine-protein kinase ULK2 isoform X1 [KO:K08269] [EC:2.7.11.1]
109933952  atg101; autophagy-related protein 101 [KO:K19730]
109913419  wipi1; WD repeat domain phosphoinositide-interacting protein 1 isoform X1 [KO:K17908]
109920337  wipi2; WD repeat domain phosphoinositide-interacting protein 2 isoform X1 [KO:K17908]
109917816  wdr45b; WD repeat domain phosphoinositide-interacting protein 3 isoform X1 [KO:K22991]
109920516  atg9b; autophagy-related protein 9B [KO:K17907]
109923599  supt20; transcription factor SPT20 homolog [KO:K21245]
109928660  smcr8a; guanine nucleotide exchange protein smcr8a isoform X1 [KO:K23611]
109932001  wdr41; WD repeat-containing protein 41 [KO:K23610]
109922847  ras-related protein Rab-39B isoform X1 [KO:K07925]
109927682  sqstm1; sequestosome-1 isoform X2 [KO:K14381]
109935579  serine/threonine-protein kinase TBK1-like [KO:K05410] [EC:2.7.11.10]
109938939  serine/threonine-protein kinase TBK1-like isoform X1 [KO:K05410] [EC:2.7.11.10]
109923490  TRAF family member-associated NF-kappa-B activator isoform X1 [KO:K12650]
109920871  ras-related protein ORAB-1 [KO:K07874]
109934848  ras-related protein ORAB-1-like [KO:K07874]
109937457  rraga; ras-related GTP-binding protein A [KO:K16185]
109934795  ras-related GTP-binding protein D-like isoform X2 [KO:K16186]
109934237  ras-related GTP-binding protein C [KO:K16186]
109931437  stk11; serine/threonine-protein kinase STK11 [KO:K07298] [EC:2.7.11.1]
109937292  prkaa2; 5'-AMP-activated protein kinase catalytic subunit alpha-2 isoform X1 [KO:K07198] [EC:2.7.11.31]
109910402  cAMP-dependent protein kinase catalytic subunit alpha-like isoform X1 [KO:K04345] [EC:2.7.11.11]
109937447  prkacba; protein kinase, cAMP-dependent, catalytic, beta a isoform X1 [KO:K04345] [EC:2.7.11.11]
109918618  protein kinase C delta type-like [KO:K06068] [EC:2.7.11.13]
109927876  mapk10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
109917844  mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
109917855  mapk8a; mitogen-activated protein kinase 8 isoform X1 [KO:K04440] [EC:2.7.11.24]
109930204  apoptosis regulator Bcl-2-like isoform X2 [KO:K02161]
109912276  becn1; beclin-1 [KO:K08334]
125480996  nuclear receptor-binding factor 2-like [KO:K21246]
109910531  pik3r4; phosphoinositide 3-kinase regulatory subunit 4 [KO:K08333] [EC:2.7.11.1]
109924008  phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform-like [KO:K00914] [EC:2.7.1.137]
109918745  pik3c3; phosphatidylinositol 3-kinase catalytic subunit type 3 [KO:K00914] [EC:2.7.1.137]
109927348  atg14; beclin 1-associated autophagy-related key regulator [KO:K17889]
109936672  traf6; TNF receptor-associated factor 6 [KO:K03175] [EC:2.3.2.27]
109935985  vmp1; vacuole membrane protein 1 [KO:K21248]
109938455  stx17; syntaxin-17 [KO:K08491]
109938448  rubcn; run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1 [KO:K19330]
109913953  calcium/calmodulin-dependent protein kinase kinase 2 [KO:K07359] [EC:2.7.11.17]
109927672  map3k7; mitogen-activated protein kinase kinase kinase 7 isoform X1 [KO:K04427] [EC:2.7.11.25]
109910482  ern2; serine/threonine-protein kinase/endoribonuclease IRE1 isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
109914380  itpr1b; inositol 1,4,5-trisphosphate receptor type 1 isoform X1 [KO:K04958]
109927259  dapk1; death-associated protein kinase 1 isoform X1 [KO:K08803] [EC:2.7.11.1]
109912840  death-associated protein kinase 3 [KO:K08803] [EC:2.7.11.1]
109933600  dapk2b; death-associated protein kinase 2 [KO:K08803] [EC:2.7.11.1]
109928820  eif2ak3; eukaryotic translation initiation factor 2-alpha kinase 3 isoform X1 [KO:K08860] [EC:2.7.11.1]
109914026  eIF-2-alpha kinase GCN2-like isoform X1 [KO:K16196] [EC:2.7.11.1]
109933548  eif2s1b; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
109911088  mtmr3; myotubularin-related protein 3 isoform X1 [KO:K18082] [EC:3.1.3.48 3.1.3.64 3.1.3.95]
109917731  mtmr4; myotubularin-related protein 4 isoform X1 [KO:K18082] [EC:3.1.3.48 3.1.3.64 3.1.3.95]
109912378  mtmr14; myotubularin-related protein 14 isoform X1 [KO:K18086] [EC:3.1.3.64 3.1.3.95]
109938103  si:ch211-11n16.2; zinc finger FYVE domain-containing protein 1 [KO:K17603]
109926691  atg5; autophagy protein 5 isoform X1 [KO:K08339]
109914974  autophagy-related protein 16-1-like isoform X1 [KO:K17890]
109914975  uncharacterized protein LOC109914975 isoform X1 [KO:K17890]
109933135  autophagy-related protein 16-1-like [KO:K17890]
125485140  atg7; ubiquitin-like modifier-activating enzyme ATG7 [KO:K08337]
109916111  atg3; ubiquitin-like-conjugating enzyme ATG3 [KO:K08343]
109929742  CASP8 and FADD-like apoptosis regulator [KO:K04724]
109919567  rab33ba; RAB33B, member RAS oncogene family a [KO:K07920]
109925439  gamma-aminobutyric acid receptor-associated protein [KO:K08341]
109921630  gabarapl2; gamma-aminobutyric acid receptor-associated protein-like 2 [KO:K08341]
109910840  map1lc3b; microtubule-associated proteins 1A/1B light chain 3B [KO:K10435]
109910943  microtubule-associated proteins 1A/1B light chain 3A [KO:K10435]
109914331  microtubule-associated proteins 1A/1B light chain 3C-like [KO:K10435]
109924806  map1lc3c; microtubule-associated proteins 1A/1B light chain 3C [KO:K10435]
109914282  atg4c; cysteine protease ATG4C isoform X1 [KO:K08342] [EC:3.4.22.-]
109919349  atg4da; cysteine protease atg4da [KO:K08342] [EC:3.4.22.-]
109918283  nbr1a; NBR1 autophagy cargo receptor a isoform X1 [KO:K17987]
109910505  optineurin-like [KO:K19946]
109919084  calcium-binding and coiled-coil domain-containing protein 2-like [KO:K21348]
109938042  tax1bp1b; tax1-binding protein 1 homolog B [KO:K21347]
109926050  uba52; ubiquitin-60S ribosomal protein L40 [KO:K02927]
109938877  rps27a; ubiquitin-40S ribosomal protein S27a [KO:K02977]
109911986  snap29; synaptosomal-associated protein 29 [KO:K08509]
109911530  si:ch73-234b20.5; vesicle-associated membrane protein 8 isoform X3 [KO:K08512]
109924072  syntaxin-7-like isoform X1 [KO:K08488]
109922570  vps11; vacuolar protein sorting-associated protein 11 homolog [KO:K20179]
109924053  vps16; vacuolar protein sorting-associated protein 16 homolog [KO:K20180]
109931608  vps33a; vacuolar protein sorting-associated protein 33A isoform X1 [KO:K20182]
109937106  vps39; vam6/Vps39-like protein [KO:K20183]
109935310  vps41; vacuolar protein sorting-associated protein 41 homolog isoform X2 [KO:K20184]
109933463  birc6; baculoviral IAP repeat-containing protein 6 [KO:K10586] [EC:2.3.2.23]
109912773  Golgi reassembly-stacking protein 1 [KO:K26797]
109910534  gorasp2; Golgi reassembly-stacking protein 2 isoform X1 [KO:K26797]
109926017  Golgi reassembly-stacking protein 2-like [KO:K26797]
109925048  ras-related protein Rab-7a-like [KO:K07897]
109922896  rab7a; ras-related protein Rab-7a [KO:K07897]
109934029  LOW QUALITY PROTEIN: ras-related protein Rab-7b-like [KO:K07898]
109938316  lamp1a; lysosome-associated membrane glycoprotein 1a [KO:K06528]
109919738  lysosome-associated membrane glycoprotein 2-like isoform X1 [KO:K06528]
109925695  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
109913218  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
109926453  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
109919201  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
109921459  ctsl.1; cathepsin L.1 [KO:K01365] [EC:3.4.22.15]
109923998  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
109927260  ctsla; cathepsin La isoform X1 [KO:K01365] [EC:3.4.22.15]
109930144  procathepsin L-like isoform X3 [KO:K01365] [EC:3.4.22.15]
109930146  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
109925170  cathepsin B [KO:K01363] [EC:3.4.22.1]
Compound
C00035  GDP
C00044  GTP
C00350  Phosphatidylethanolamine
C01194  1-Phosphatidyl-D-myo-inositol
C04549  1-Phosphatidyl-1D-myo-inositol 3-phosphate
C05981  Phosphatidylinositol-3,4,5-trisphosphate
Reference
PMID:15325584
  Authors
Meijer AJ, Codogno P.
  Title
Regulation and role of autophagy in mammalian cells.
  Journal
Int J Biochem Cell Biol 36:2445-62 (2004)
DOI:10.1016/j.biocel.2004.02.002
Reference
PMID:16099218
  Authors
Deretic V.
  Title
Autophagy in innate and adaptive immunity.
  Journal
Trends Immunol 26:523-8 (2005)
DOI:10.1016/j.it.2005.08.003
Reference
PMID:16200202
  Authors
Levine B, Yuan J.
  Title
Autophagy in cell death: an innocent convict?
  Journal
J Clin Invest 115:2679-88 (2005)
DOI:10.1172/JCI26390
Reference
PMID:15325588
  Authors
Tanida I, Ueno T, Kominami E.
  Title
LC3 conjugation system in mammalian autophagy.
  Journal
Int J Biochem Cell Biol 36:2503-18 (2004)
DOI:10.1016/j.biocel.2004.05.009
Reference
PMID:15928708
  Authors
Lum JJ, DeBerardinis RJ, Thompson CB.
  Title
Autophagy in metazoans: cell survival in the land of plenty.
  Journal
Nat Rev Mol Cell Biol 6:439-48 (2005)
DOI:10.1038/nrm1660
Reference
PMID:15978794
  Authors
Reggiori F, Klionsky DJ.
  Title
Autophagosomes: biogenesis from scratch?
  Journal
Curr Opin Cell Biol 17:415-22 (2005)
DOI:10.1016/j.ceb.2005.06.007
Reference
PMID:11099404
  Authors
Klionsky DJ, Emr SD.
  Title
Autophagy as a regulated pathway of cellular degradation.
  Journal
Science 290:1717-21 (2000)
DOI:10.1126/science.290.5497.1717
Reference
PMID:16125113
  Authors
Bechet D, Tassa A, Taillandier D, Combaret L, Attaix D.
  Title
Lysosomal proteolysis in skeletal muscle.
  Journal
Int J Biochem Cell Biol 37:2098-114 (2005)
DOI:10.1016/j.biocel.2005.02.029
Reference
PMID:19653858
  Authors
He C, Klionsky DJ
  Title
Regulation mechanisms and signaling pathways of autophagy.
  Journal
Annu Rev Genet 43:67-93 (2009)
DOI:10.1146/annurev-genet-102808-114910
Reference
PMID:19802558
  Authors
Yang Z, Klionsky DJ
  Title
An overview of the molecular mechanism of autophagy.
  Journal
Curr Top Microbiol Immunol 335:1-32 (2009)
DOI:10.1007/978-3-642-00302-8_1
Reference
PMID:20034776
  Authors
Yang Z, Klionsky DJ
  Title
Mammalian autophagy: core molecular machinery and signaling regulation.
  Journal
Curr Opin Cell Biol 22:124-31 (2010)
DOI:10.1016/j.ceb.2009.11.014
Reference
PMID:21187343
  Authors
Chen Y, Klionsky DJ
  Title
The regulation of autophagy - unanswered questions.
  Journal
J Cell Sci 124:161-70 (2011)
DOI:10.1242/jcs.064576
Reference
PMID:21801009
  Authors
Mizushima N, Yoshimori T, Ohsumi Y
  Title
The role of Atg proteins in autophagosome formation.
  Journal
Annu Rev Cell Dev Biol 27:107-32 (2011)
DOI:10.1146/annurev-cellbio-092910-154005
Reference
PMID:24343578
  Authors
Russell RC, Yuan HX, Guan KL
  Title
Autophagy regulation by nutrient signaling.
  Journal
Cell Res 24:42-57 (2014)
DOI:10.1038/cr.2013.166
Reference
PMID:25948417
  Authors
Noda NN, Fujioka Y
  Title
Atg1 family kinases in autophagy initiation.
  Journal
Cell Mol Life Sci 72:3083-96 (2015)
DOI:10.1007/s00018-015-1917-z
Related
pathway
rtp04010  MAPK signaling pathway
rtp04141  Protein processing in endoplasmic reticulum
rtp04142  Lysosome
rtp04150  mTOR signaling pathway
rtp04910  Insulin signaling pathway
KO pathway
ko04140   
LinkDB

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