KEGG   PATHWAY: sdu04140
Entry
sdu04140                    Pathway                                
Name
Autophagy - animal - Seriola dumerili (greater amberjack)
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
sdu04140  Autophagy - animal
sdu04140

Other DBs
GO: 0006914
Organism
Seriola dumerili (greater amberjack) [GN:sdu]
Gene
111216331  rubcn; run domain Beclin-1-interacting and cysteine-rich domain-containing protein isoform X1 [KO:K19330]
111216431  pik3ca; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform [KO:K00922] [EC:2.7.1.153]
111216444  vps18; vacuolar protein sorting-associated protein 18 homolog [KO:K20181]
111216673  [KO:K23611]
111216736  [KO:K08852] [EC:2.7.11.1 3.1.26.-]
111216835  atg16l1; autophagy-related protein 16-1 isoform X1 [KO:K17890]
111216921  [KO:K08268]
111216925  [KO:K20868]
111217001  uba52; ubiquitin-60S ribosomal protein L40 [KO:K02927]
111217083  [KO:K07925]
111217084  hmgb1; high mobility group protein B1 [KO:K10802]
111217176  supt20h; transcription factor SPT20 homolog isoform X1 [KO:K21245]
111217299  atg4c; cysteine protease ATG4C [KO:K08342] [EC:3.4.22.-]
111217320  raf1; RAF proto-oncogene serine/threonine-protein kinase isoform X1 [KO:K04366] [EC:2.7.11.1]
111217583  akt1s1; proline-rich AKT1 substrate 1 [KO:K16184]
111217738  [KO:K05087] [EC:2.7.10.1]
111217916  [KO:K04688] [EC:2.7.11.1]
111217934  rptor; regulatory-associated protein of mTOR [KO:K07204]
111218114  cflar; CASP8 and FADD-like apoptosis regulator [KO:K04724]
111218153  mras; ras-related protein M-Ras [KO:K07831]
111218308  irs2; insulin receptor substrate 2 [KO:K07187]
111218350  [KO:K07920]
111218840  tank; TRAF family member-associated NF-kappa-B activator [KO:K12650]
111218856  gorasp2; Golgi reassembly-stacking protein 2 [KO:K26797]
111218880  [KO:K06528]
111219094  pik3cd; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform [KO:K00922] [EC:2.7.1.153]
111219313  tp53inp2; tumor protein p53-inducible nuclear protein 2 isoform X1 [KO:K21247]
111219327  [KO:K01363] [EC:3.4.22.1]
111219463  map1lc3a; microtubule-associated proteins 1A/1B light chain 3A [KO:K10435]
111219534  [KO:K04440] [EC:2.7.11.24]
111219550  wipi1; WD repeat domain phosphoinositide-interacting protein 1 isoform X1 [KO:K17908]
111219708  becn1; beclin-1 [KO:K08334]
111219974  calcoco2; calcium-binding and coiled-coil domain-containing protein 2 isoform X1 [KO:K21348]
111219998  [KO:K17987]
111220111  ddit4; DNA damage-inducible transcript 4 protein [KO:K08270]
111220177  [KO:K01110] [EC:3.1.3.16 3.1.3.48 3.1.3.67]
111220260  epas1; endothelial PAS domain-containing protein 1 [KO:K08268]
111220282  plekhm1; pleckstrin homology domain-containing family M member 1 isoform X1 [KO:K23282]
111220405  [KO:K21247]
111220408  wdr45b; WD repeat domain phosphoinositide-interacting protein 3 [KO:K22991]
111220410  pdpk1; 3-phosphoinositide-dependent protein kinase 1 [KO:K06276] [EC:2.7.11.1]
111220607  [KO:K07874]
111220870  prkacb; cAMP-dependent protein kinase catalytic subunit beta isoform X1 [KO:K04345] [EC:2.7.11.11]
111220995  [KO:K26797]
111221377  ins; insulin [KO:K04526]
111221456  [KO:K04958]
111221504  [KO:K07897]
111221542  [KO:K04570]
111221638  [KO:K07208]
111221645  [KO:K07897]
111221681  prkcd; protein kinase C delta type [KO:K06068] [EC:2.7.11.13]
111221688  mtmr14; myotubularin-related protein 14 isoform X1 [KO:K18086] [EC:3.1.3.64 3.1.3.95]
111221709  [KO:K06068] [EC:2.7.11.13]
111221715  [KO:K07897]
111221798  [KO:K04958]
111221882  [KO:K20402]
111222182  mtmr4; myotubularin-related protein 4 isoform X1 [KO:K18082] [EC:3.1.3.48 3.1.3.64 3.1.3.95]
111222200  [KO:K04688] [EC:2.7.11.1]
111222250  vmp1; vacuole membrane protein 1 isoform X1 [KO:K21248]
111222366  vps11; vacuolar protein sorting-associated protein 11 homolog [KO:K20179]
111222367  uvrag; UV radiation resistance-associated gene protein [KO:K21249]
111222378  atg101; autophagy-related protein 101 [KO:K19730]
111222381  ubc; polyubiquitin-C [KO:K08770]
111222457  atg5; autophagy protein 5 isoform X1 [KO:K08339]
111222710  [KO:K07187]
111223137  [KO:K16186]
111223177  [KO:K21347]
111223324  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
111223588  traf6; TNF receptor-associated factor 6 isoform X1 [KO:K03175] [EC:2.3.2.27]
111224015  atg7; ubiquitin-like modifier-activating enzyme ATG7 [KO:K08337]
111224188  rps27a; ubiquitin-40S ribosomal protein S27a isoform X1 [KO:K02977]
111224270  wdr45; WD repeat domain phosphoinositide-interacting protein 4 [KO:K22991]
111224364  [KO:K08803] [EC:2.7.11.1]
111224459  [KO:K10802]
111224634  prkcq; protein kinase C theta type isoform X1 [KO:K18052] [EC:2.7.11.13]
111224855  [KO:K08341]
111225058  optn; optineurin [KO:K19946]
111225231  [KO:K10435]
111225274  eif2ak4; eIF-2-alpha kinase GCN2 [KO:K16196] [EC:2.7.11.1]
111225342  hif1a; LOW QUALITY PROTEIN: hypoxia-inducible factor 1-alpha [KO:K08268]
111225465  akt1; RAC-alpha serine/threonine-protein kinase [KO:K04456] [EC:2.7.11.1]
111225644  atg2b; autophagy-related protein 2 homolog B isoform X1 [KO:K17906]
111225703  [KO:K17603]
111225856  [KO:K01365] [EC:3.4.22.15]
111225869  atg9a; autophagy-related protein 9A [KO:K17907]
111226008  [KO:K04427] [EC:2.7.11.25]
111226074  vps39; vam6/Vps39-like protein isoform X1 [KO:K20183]
111226127  eif2ak3; eukaryotic translation initiation factor 2-alpha kinase 3 [KO:K08860] [EC:2.7.11.1]
111226191  cunh9orf72; guanine nucleotide exchange C9orf72 homolog [KO:K23609]
111226203  [KO:K16186]
111226280  ulk2; serine/threonine-protein kinase ULK2 isoform X1 [KO:K08269] [EC:2.7.11.1]
111226317  prkaa2; 5'-AMP-activated protein kinase catalytic subunit alpha-2 isoform X1 [KO:K07198] [EC:2.7.11.31]
111226333  [KO:K01365] [EC:3.4.22.15]
111226417  [KO:K04440] [EC:2.7.11.24]
111226526  [KO:K04382] [EC:3.1.3.16]
111226678  [KO:K04526]
111226711  epg5; ectopic P granules protein 5 homolog [KO:K23883]
111227008  [KO:K04345] [EC:2.7.11.11]
111227244  ern1; serine/threonine-protein kinase/endoribonuclease IRE1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
111227486  pik3r3; phosphatidylinositol 3-kinase regulatory subunit gamma isoform X1 [KO:K02649]
111227586  mtor; serine/threonine-protein kinase mTOR isoform X1 [KO:K07203] [EC:2.7.11.1]
111227677  deptor; DEP domain-containing mTOR-interacting protein isoform X1 [KO:K20402]
111227963  rras; ras-related protein R-Ras [KO:K07830]
111227986  dapk1; death-associated protein kinase 1 [KO:K08803] [EC:2.7.11.1]
111227987  ctsl; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
111227988  wdfy3; WD repeat and FYVE domain-containing protein 3 [KO:K22262]
111228252  sh3glb1; endophilin-B1 isoform X1 [KO:K11248]
111228368  dapk2; death-associated protein kinase 2 isoform X1 [KO:K08803] [EC:2.7.11.1]
111228382  hras; GTPase HRas [KO:K02833]
111228410  [KO:K08512]
111228418  [KO:K08512]
111228455  kras; GTPase KRas isoform X1 [KO:K07827]
111228471  map2k1; dual specificity mitogen-activated protein kinase kinase 1 [KO:K04368] [EC:2.7.12.2]
111228731  [KO:K05087] [EC:2.7.10.1]
111228751  vps33a; vacuolar protein sorting-associated protein 33A [KO:K20182]
111228782  [KO:K02927]
111228803  [KO:K26797]
111228846  [KO:K02649]
111228886  [KO:K00922] [EC:2.7.1.153]
111228977  stk11; serine/threonine-protein kinase STK11 [KO:K07298] [EC:2.7.11.1]
111228984  [KO:K02649]
111229041  [KO:K04369] [EC:2.7.12.2]
111229174  [KO:K26797]
111229195  tsc2; tuberin isoform X1 [KO:K07207]
111229212  prkaca; cAMP-dependent protein kinase catalytic subunit alpha [KO:K04345] [EC:2.7.11.11]
111229372  [KO:K07920]
111229518  tbk1; serine/threonine-protein kinase TBK1 isoform X1 [KO:K05410] [EC:2.7.11.10]
111230109  [KO:K08341]
111230134  atg12; ubiquitin-like protein ATG12 [KO:K08336]
111230214  [KO:K04371] [EC:2.7.11.24]
111230220  [KO:K07827]
111230321  wipi2; WD repeat domain phosphoinositide-interacting protein 2 isoform X1 [KO:K17908]
111230342  smcr8; guanine nucleotide exchange protein SMCR8 [KO:K23611]
111230367  [KO:K01379] [EC:3.4.23.5]
111230376  igbp1; immunoglobulin-binding protein 1 [KO:K17606]
111230383  rab33b; ras-related protein Rab-33B [KO:K07920]
111230605  [KO:K08803] [EC:2.7.11.1]
111230994  [KO:K17907]
111231003  [KO:K07901]
111231006  mtmr3; myotubularin-related protein 3 isoform X1 [KO:K18082] [EC:3.1.3.48 3.1.3.64 3.1.3.95]
111231008  rb1cc1; RB1-inducible coiled-coil protein 1 isoform X1 [KO:K17589]
111231088  [KO:K07208]
111231263  dapk3; death-associated protein kinase 3 [KO:K08803] [EC:2.7.11.1]
111231315  bad; bcl2-associated agonist of cell death [KO:K02158]
111231550  [KO:K08342] [EC:3.4.22.-]
111231860  [KO:K21357] [EC:2.7.11.1]
111231992  atg4b; cysteine protease ATG4B isoform X1 [KO:K08342] [EC:3.4.22.-]
111232134  rab8a; ras-related protein Rab-8A [KO:K07901]
111232170  [KO:K04369] [EC:2.7.12.2]
111232227  atg3; ubiquitin-like-conjugating enzyme ATG3 [KO:K08343]
111232381  [KO:K10435]
111232476  atg2a; autophagy-related protein 2 homolog A isoform X1 [KO:K17906]
111232692  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
111232818  pik3cb; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform [KO:K00922] [EC:2.7.1.153]
111232820  [KO:K17603]
111232964  map1lc3c; microtubule-associated proteins 1A/1B light chain 3C [KO:K10435]
111233019  [KO:K16172]
111233024  gabarap; gamma-aminobutyric acid receptor-associated protein [KO:K08341]
111233068  ulk1; serine/threonine-protein kinase ULK1 isoform X1 [KO:K21357] [EC:2.7.11.1]
111233301  atg10; ubiquitin-like-conjugating enzyme ATG10 [KO:K17888]
111233400  [KO:K04456] [EC:2.7.11.1]
111233454  rab39b; ras-related protein Rab-39B [KO:K07925]
111233462  [KO:K07187]
111233501  sqstm1; sequestosome-1 isoform X1 [KO:K14381]
111233666  pik3r4; phosphoinositide 3-kinase regulatory subunit 4 isoform X1 [KO:K08333] [EC:2.7.11.1]
111233714  ambra1; activating molecule in BECN1-regulated autophagy protein 1 isoform X1 [KO:K17985]
111234315  [KO:K04456] [EC:2.7.11.1]
111234362  ppp2ca; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
111234582  [KO:K04526]
111234619  [KO:K16185]
111234720  mapk10; mitogen-activated protein kinase 10 isoform X1 [KO:K04440] [EC:2.7.11.24]
111234723  bcl2l1; bcl-2-like protein 1 [KO:K04570]
111235092  [KO:K04440] [EC:2.7.11.24]
111235195  bnip3; BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 [KO:K15464]
111235327  [KO:K01110] [EC:3.1.3.16 3.1.3.48 3.1.3.67]
111235342  [KO:K02649]
111235348  [KO:K08270]
111235389  [KO:K04456] [EC:2.7.11.1]
111235574  vps16; vacuolar protein sorting-associated protein 16 homolog [KO:K20180]
111235652  pik3c3; phosphatidylinositol 3-kinase catalytic subunit type 3 [KO:K00914] [EC:2.7.1.137]
111235659  eif2s1; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
111235821  rragc; ras-related GTP-binding protein C [KO:K16186]
111236140  [KO:K07206]
111236255  [KO:K17987]
111236271  [KO:K17908]
111236425  birc6; baculoviral IAP repeat-containing protein 6 isoform X1 [KO:K10586] [EC:2.3.2.23]
111236493  snap29; synaptosomal-associated protein 29 [KO:K08509]
111236545  ykt6; synaptobrevin homolog YKT6 [KO:K08516]
111236562  rras2; ras-related protein R-Ras2 [KO:K07830]
111236831  [KO:K00922] [EC:2.7.1.153]
111236845  [KO:K04371] [EC:2.7.11.24]
111236887  [KO:K02161]
111236920  stx17; syntaxin-17 [KO:K08491]
111236941  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
111236942  [KO:K02649]
111237095  nrbf2; nuclear receptor-binding factor 2 [KO:K21246]
111237164  atg14; beclin 1-associated autophagy-related key regulator [KO:K17889]
111237369  prkaa1; 5'-AMP-activated protein kinase catalytic subunit alpha-1 [KO:K07198] [EC:2.7.11.31]
111237415  [KO:K07208]
111237576  [KO:K07874]
111237627  [KO:K17603]
111237842  vps41; vacuolar protein sorting-associated protein 41 homolog [KO:K20184]
111238063  [KO:K08342] [EC:3.4.22.-]
111238251  [KO:K04456] [EC:2.7.11.1]
111238358  lamp1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
111238487  [KO:K07206]
111238781  map3k7; mitogen-activated protein kinase kinase kinase 7 isoform X1 [KO:K04427] [EC:2.7.11.25]
111238800  [KO:K21347]
111238835  [KO:K08341]
111238941  [KO:K07359] [EC:2.7.11.17]
111239004  bcl2; apoptosis regulator Bcl-2 [KO:K02161]
111239022  pik3r1; phosphatidylinositol 3-kinase regulatory subunit alpha isoform X1 [KO:K02649]
111239031  [KO:K08512]
111239036  wdr41; WD repeat-containing protein 41 [KO:K23610]
111239086  [KO:K04688] [EC:2.7.11.1]
111239111  [KO:K21248]
111239355  [KO:K01363] [EC:3.4.22.1]
111239640  stx7; syntaxin-7 [KO:K08488]
111239883  [KO:K15464]
111239927  atg13; autophagy-related protein 13 isoform X1 [KO:K08331]
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
sdu04010  MAPK signaling pathway
sdu04141  Protein processing in endoplasmic reticulum
sdu04142  Lysosome
sdu04150  mTOR signaling pathway
sdu04910  Insulin signaling pathway
KO pathway
ko04140   

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