KEGG   PATHWAY: tru04141
Entry
tru04141                    Pathway                                
Name
Protein processing in endoplasmic reticulum - Takifugu rubripes (torafugu)
Description
The endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylated. Correctly folded proteins are packaged into transport vesicles that shuttle them to the Golgi complex. Misfolded proteins are retained within the ER lumen in complex with molecular chaperones. Proteins that are terminally misfolded bind to BiP and are directed toward degradation through the proteasome in a process called ER-associated degradation (ERAD). Accumulation of misfolded proteins in the ER causes ER stress and activates a signaling pathway called the unfolded protein response (UPR). In certain severe situations, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis.
Class
Genetic Information Processing; Folding, sorting and degradation
Pathway map
tru04141  Protein processing in endoplasmic reticulum
tru04141

Other DBs
GO: 0030433 0034976
Organism
Takifugu rubripes (torafugu) [GN:tru]
Gene
101061140  sec61a1; protein transport protein Sec61 subunit alpha [KO:K10956]
101075256  protein transport protein Sec61 subunit alpha-like 1 [KO:K10956]
101076269  sec61b; protein transport protein Sec61 subunit beta [KO:K09481]
115251207  sec61g; protein transport protein Sec61 subunit gamma [KO:K07342]
101079550  sec62; translocation protein SEC62 [KO:K12275]
101074362  sec63; translocation protein SEC63 homolog [KO:K09540]
101076301  rpn1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 [KO:K12666]
101073027  rpn2; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 isoform X2 [KO:K12667]
101077296  dad1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
101067153  ddost; dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
101076802  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
101077895  stt3a; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
101073975  LOW QUALITY PROTEIN: dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
101066134  magnesium transporter protein 1 [KO:K19478]
101063622  tumor suppressor candidate 3 [KO:K19478]
101061270  ostc; oligosaccharyltransferase complex subunit OSTC [KO:K26501]
115251023  tmem258; transmembrane protein 258 [KO:K26502]
101061971  mogs; mannosyl-oligosaccharide glucosidase [KO:K01228] [EC:3.2.1.106]
101075696  ckap4; cytoskeleton-associated protein 4 isoform X1 [KO:K13999]
101065193  rrbp1; ribosome-binding protein 1 isoform X1 [KO:K14000]
101063920  sil1; nucleotide exchange factor SIL1 [KO:K14001]
101065326  hyou1; hypoxia up-regulated protein 1 [KO:K09486]
101063130  hspa5; endoplasmic reticulum chaperone BiP [KO:K09490] [EC:3.6.4.10]
101077464  dnajb11; dnaJ homolog subfamily B member 11 [KO:K09517]
101064950  dnaJ homolog subfamily C member 1 [KO:K09521]
115247908  dnaJ homolog subfamily C member 1-like [KO:K09521]
101061949  dnaJ homolog subfamily C member 3-like [KO:K09523]
101063494  dnajc3; dnaJ homolog subfamily C member 3 [KO:K09523]
101070494  dnajc10; dnaJ homolog subfamily C member 10 [KO:K09530] [EC:1.8.4.-]
101078160  hsp90b1; endoplasmin [KO:K09487]
101062108  ganab; neutral alpha-glucosidase AB isoform X1 [KO:K05546] [EC:3.2.1.207]
101061409  prkcsh; glucosidase 2 subunit beta isoform X1 [KO:K08288]
101070859  calnexin-like [KO:K08054]
101079898  pdia3; protein disulfide-isomerase A3 [KO:K08056] [EC:5.3.4.1]
101067334  protein disulfide-isomerase A3-like [KO:K08056] [EC:5.3.4.1]
101072647  calr; calreticulin [KO:K08057]
101074526  calreticulin [KO:K08057]
101071492  man1a2; LOW QUALITY PROTEIN: mannosyl-oligosaccharide 1,2-alpha-mannosidase IB [KO:K01230] [EC:3.2.1.113]
101068067  mannosyl-oligosaccharide 1,2-alpha-mannosidase IA isoform X2 [KO:K01230] [EC:3.2.1.113]
101064343  LOW QUALITY PROTEIN: mannosyl-oligosaccharide 1,2-alpha-mannosidase IA-like [KO:K01230] [EC:3.2.1.113]
101072461  endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase-like [KO:K23741] [EC:3.2.1.209]
105418968  endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase-like isoform X1 [KO:K23741] [EC:3.2.1.209]
101070027  lman2; vesicular integral-membrane protein VIP36 [KO:K10082]
101075962  lman1; protein ERGIC-53 [KO:K10080]
101069970  preb; prolactin regulatory element-binding protein [KO:K14003]
101072837  GTP-binding protein SAR1b-like isoform X2 [KO:K07953] [EC:3.6.5.-]
101069304  sar1b; GTP-binding protein SAR1b [KO:K07953] [EC:3.6.5.-]
101062656  sec13; protein SEC13 homolog [KO:K14004]
101061108  sec31a; protein transport protein Sec31A isoform X2 [KO:K14005]
101073109  protein transport protein Sec31A-like isoform X1 [KO:K14005]
101070501  sec23a; protein transport protein Sec23A [KO:K14006]
101067573  protein transport protein Sec23B isoform X1 [KO:K14006]
101061950  sec24d; protein transport protein Sec24D [KO:K14007]
101073617  protein transport protein Sec24B-like isoform X2 [KO:K14007]
101077197  sec24a; protein transport protein Sec24A isoform X2 [KO:K14007]
105418056  protein transport protein Sec24C-like isoform X2 [KO:K14007]
101061925  LOW QUALITY PROTEIN: protein transport protein Sec24C [KO:K14007]
101078292  uggt2; UDP-glucose:glycoprotein glucosyltransferase 2 isoform X1 [KO:K11718] [EC:2.4.1.-]
101061848  uggt1; UDP-glucose:glycoprotein glucosyltransferase 1 [KO:K11718] [EC:2.4.1.-]
101061518  edem1; ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X2 [KO:K10084]
101062875  ER degradation-enhancing alpha-mannosidase-like protein 2 [KO:K10085]
101079995  edem3; ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X3 [KO:K10086]
101067969  ER degradation-enhancing alpha-mannosidase-like protein 3 [KO:K10086]
101076214  p4hb; protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
101064319  pdia4; protein disulfide-isomerase A4 [KO:K09582] [EC:5.3.4.1]
101077277  pdia6; protein disulfide-isomerase A6 isoform X1 [KO:K09584] [EC:5.3.4.1]
101079902  txndc5; thioredoxin domain-containing protein 5 [KO:K13984] [EC:5.3.4.1]
101064419  ero1a; ERO1-like protein alpha [KO:K10950] [EC:1.8.4.-]
101065233  ero1b; ERO1-like protein beta isoform X1 [KO:K10976] [EC:1.8.4.-]
101070773  os9; protein OS-9 isoform X1 [KO:K10088]
101077698  erlec1; endoplasmic reticulum lectin 1 isoform X1 [KO:K14008]
101066901  translocon-associated protein subunit alpha-like [KO:K13249]
101079864  ssr1; translocon-associated protein subunit alpha isoform X2 [KO:K13249]
101063218  ssr2; translocon-associated protein subunit beta [KO:K13250]
101075017  ssr3; translocon-associated protein subunit gamma [KO:K13251]
101063784  ssr4; translocon-associated protein subunit delta [KO:K04571]
115248179  translocon-associated protein subunit delta-like [KO:K04571]
101073353  bcap31; B-cell receptor-associated protein 31 [KO:K14009]
101067090  translocating chain-associated membrane protein 1-like 1 [KO:K14010]
101065979  tram1; translocating chain-associated membrane protein 1 isoform X1 [KO:K14010]
101061860  derl1; derlin-1 [KO:K11519]
101070971  derl2; derlin-2 [KO:K13989]
101070958  ubxn4; UBX domain-containing protein 4 isoform X1 [KO:K24348]
101075469  ubxn1; UBX domain-containing protein 1 [KO:K24348]
101076897  ubxn2a; UBX domain-containing protein 2A isoform X1 [KO:K24349]
101074819  ubxn6; UBX domain-containing protein 6 isoform X1 [KO:K14011]
101072983  nsfl1c; NSFL1 cofactor p47 isoform X1 [KO:K14012]
105416963  svip; small VCP/p97-interacting protein [KO:K14014]
101075785  vcp; transitional endoplasmic reticulum ATPase [KO:K13525]
101075431  nploc4; nuclear protein localization protein 4 homolog [KO:K14015]
101063535  ufd1; ubiquitin recognition factor in ER-associated degradation protein 1 [KO:K14016]
101071708  heat shock 70 kDa protein 1-like [KO:K03283]
101067097  heat shock 70 kDa protein 1-like [KO:K03283]
101067989  heat shock 70 kDa protein-like [KO:K03283]
101075813  heat shock cognate 71 kDa protein-like [KO:K03283]
101077308  heat shock 70 kDa protein 1-like [KO:K03283]
101067318  heat shock 70 kDa protein 1 [KO:K03283]
101063324  hspa8; heat shock cognate 71 kDa protein [KO:K03283]
101073999  heat shock 70 kDa protein 1 isoform X1 [KO:K03283]
101073900  dnaJ homolog subfamily A member 2-like [KO:K09503]
101073610  dnaJ homolog subfamily A member 2 [KO:K09503]
101074424  dnajb1; dnaJ homolog subfamily B member 1 [KO:K09507]
101070194  dnaJ homolog subfamily B member 1-like [KO:K09507]
101067222  dnajb2; dnaJ homolog subfamily B member 2 isoform X1 [KO:K09508]
101061766  dnajb12; dnaJ homolog subfamily B member 12 [KO:K09518]
101079430  dnaJ homolog subfamily B member 12-like isoform X2 [KO:K09518]
101073355  dnaJ homolog subfamily C member 5 [KO:K09525]
101071682  dnajc5g; dnaJ homolog subfamily C member 5G isoform X2 [KO:K09525]
101061153  LOW QUALITY PROTEIN: dnaJ homolog subfamily C member 5-like [KO:K09525]
101073875  dnaJ homolog subfamily C member 5-like isoform X1 [KO:K09525]
115247922  dnaJ homolog subfamily C member 5B-like [KO:K09525]
101076976  heat shock protein HSP 90-beta [KO:K04079]
101069079  heat shock protein HSP 90-alpha 1 [KO:K04079]
101068853  heat shock protein HSP 90-alpha [KO:K04079]
101075949  heat shock 70 kDa protein 4L [KO:K09485]
101070094  bag1; BAG family molecular chaperone regulator 1 [KO:K09555]
101072767  bag2; BAG family molecular chaperone regulator 2 [KO:K09556]
101070193  hspbp1; hsp70-binding protein 1 [KO:K09562]
101064246  alpha-crystallin A chain-like [KO:K09541]
101076268  hspb6; heat shock protein beta-6 isoform X2 [KO:K09542]
101066139  alpha-crystallin B chain [KO:K09542]
101075181  yod1; ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
101061044  plaa; phospholipase A-2-activating protein [KO:K14018]
101075890  rad23a; UV excision repair protein RAD23 homolog A isoform X2 [KO:K10839]
101073063  UV excision repair protein RAD23 homolog B [KO:K10839]
101073227  ubqln4; ubiquilin-4 [KO:K04523]
101075603  peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase [KO:K01456] [EC:3.5.1.52]
115248097  peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase-like [KO:K01456] [EC:3.5.1.52]
101073729  ataxin-3-like [KO:K11863] [EC:3.4.22.-]
101077319  ube4b; ubiquitin conjugation factor E4 B isoform X3 [KO:K10597] [EC:2.3.2.27]
101068654  eif2ak3; eukaryotic translation initiation factor 2-alpha kinase 3 [KO:K08860] [EC:2.7.11.1]
101076750  eif2s1; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
101077394  nfe2; transcription factor NF-E2 45 kDa subunit [KO:K05638]
101064613  nfe2l2; nuclear factor erythroid 2-related factor 2 [KO:K05638]
101075957  cyclic AMP-dependent transcription factor ATF-4-like [KO:K04374]
101070714  atf4; cyclic AMP-dependent transcription factor ATF-4 isoform X2 [KO:K04374]
101061813  ddit3; DNA damage-inducible transcript 3 protein [KO:K04452]
101071405  bcl2; apoptosis regulator Bcl-2 [KO:K02161]
101078942  atf6; cyclic AMP-dependent transcription factor ATF-6 alpha [KO:K09054]
101073153  cyclic AMP-dependent transcription factor ATF-6 beta [KO:K09049]
101062334  wfs1; wolframin [KO:K14020]
101064513  wolframin-like isoform X1 [KO:K14020]
101067515  mbtps1; membrane-bound transcription factor site-1 protease isoform X1 [KO:K08653] [EC:3.4.21.112]
101072394  mbtps2; membrane-bound transcription factor site-2 protease isoform X2 [KO:K07765] [EC:3.4.24.85]
654272  xbp1; X-box-binding protein 1 [KO:K09027]
101067048  serine/threonine-protein kinase/endoribonuclease IRE1-like [KO:K08852] [EC:2.7.11.1 3.1.26.-]
101071946  serine/threonine-protein kinase/endoribonuclease IRE1-like isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
101076265  traf2; TNF receptor-associated factor 2 [KO:K03173] [EC:2.3.2.27]
101064444  TNF receptor-associated factor 2-like [KO:K03173] [EC:2.3.2.27]
101075779  TNF receptor-associated factor 2-like isoform X1 [KO:K03173] [EC:2.3.2.27]
101071039  mitogen-activated protein kinase kinase kinase 5-like isoform X1 [KO:K04426] [EC:2.7.11.25]
101061432  map3k5; mitogen-activated protein kinase kinase kinase 5 [KO:K04426] [EC:2.7.11.25]
101064650  map2k7; dual specificity mitogen-activated protein kinase kinase 7 isoform X1 [KO:K04431] [EC:2.7.12.2]
101073575  mitogen-activated protein kinase 8 isoform X1 [KO:K04440] [EC:2.7.11.24]
101070190  mitogen-activated protein kinase 8 isoform X3 [KO:K04440] [EC:2.7.11.24]
101067839  mapk10; mitogen-activated protein kinase 10 isoform X2 [KO:K04440] [EC:2.7.11.24]
101078548  mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
101068139  bax; apoptosis regulator BAX [KO:K02159]
101069964  apoptosis regulator BAX-like [KO:K02159]
101067511  apoptosis regulator BAX-like [KO:K02159]
101070832  calpain-1 catalytic subunit-like isoform X2 [KO:K01367] [EC:3.4.22.52]
101075956  calpain-1 catalytic subunit [KO:K01367] [EC:3.4.22.52]
101063922  calpain-1 catalytic subunit-like [KO:K01367] [EC:3.4.22.52]
101072522  calpain-1 catalytic subunit-like isoform X1 [KO:K01367] [EC:3.4.22.52]
101080097  LOW QUALITY PROTEIN: calpain-8-like [KO:K01367] [EC:3.4.22.52]
115247065  calpain-8-like isoform X1 [KO:K01367] [EC:3.4.22.52]
101064754  calpain-2 catalytic subunit-like [KO:K03853] [EC:3.4.22.53]
101076184  calpain-2 catalytic subunit-like isoform X2 [KO:K03853] [EC:3.4.22.53]
101076595  calpain-2 catalytic subunit-like isoform X2 [KO:K03853] [EC:3.4.22.53]
101066351  march6; E3 ubiquitin-protein ligase MARCH6 isoform X1 [KO:K10661] [EC:2.3.2.27]
101075280  E3 ubiquitin-protein ligase MARCH6-like [KO:K10661] [EC:2.3.2.27]
101076776  ube2j1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
101075623  ube2j2; ubiquitin-conjugating enzyme E2 J2 isoform X1 [KO:K04554] [EC:2.3.2.23]
101076431  ubiquitin-conjugating enzyme E2 G1 [KO:K10575] [EC:2.3.2.23]
101074150  ubiquitin-conjugating enzyme E2 G1-like isoform X2 [KO:K10575] [EC:2.3.2.23]
101069640  ubiquitin-conjugating enzyme E2 G1-like [KO:K10575] [EC:2.3.2.23]
115252688  ubiquitin-conjugating enzyme E2 G1-like [KO:K10575] [EC:2.3.2.23]
115252689  ubiquitin-conjugating enzyme E2 G1-like [KO:K10575] [EC:2.3.2.23]
101068397  syvn1; E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
101076913  rnf5; E3 ubiquitin-protein ligase RNF5 [KO:K10666] [EC:2.3.2.27]
101065746  rnf185; E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
101067820  selenos; selenoprotein S [KO:K14025]
115251939  selenoprotein S-like [KO:K14025]
115251968  selenoprotein S-like [KO:K14025]
101065768  sel1l; protein sel-1 homolog 1 isoform X1 [KO:K14026]
101077032  homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein [KO:K14027]
101064558  amfr; E3 ubiquitin-protein ligase AMFR [KO:K10636] [EC:2.3.2.36]
101075352  stub1; E3 ubiquitin-protein ligase CHIP [KO:K09561] [EC:2.3.2.27]
101062529  ubiquitin-conjugating enzyme E2 D2 [KO:K06689] [EC:2.3.2.23]
101069170  ubiquitin-conjugating enzyme E2 D4 [KO:K06689] [EC:2.3.2.23]
101070684  ubiquitin-conjugating enzyme E2 D2 [KO:K06689] [EC:2.3.2.23]
101078814  ubiquitin-conjugating enzyme E2 2-like isoform X1 [KO:K06689] [EC:2.3.2.23]
101078887  ubiquitin-conjugating enzyme E2-17 kDa-like isoform X2 [KO:K06689] [EC:2.3.2.23]
101073892  prkn; E3 ubiquitin-protein ligase parkin [KO:K04556] [EC:2.3.2.31]
101079814  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
115248454  E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
115249889  E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
115249890  RING-box protein 1-like [KO:K03868] [EC:2.3.2.32]
101068951  cul1; LOW QUALITY PROTEIN: cullin-1 [KO:K03347]
101068627  skp1; S-phase kinase-associated protein 1 [KO:K03094]
101068318  F-box only protein 2-like [KO:K10099]
101066414  F-box only protein 6-like [KO:K10100]
Compound
C00076  Calcium cation
G00009   
G00010   
G00011   
G00012   
G10694   
Reference
PMID:19491040
  Authors
Naidoo N
  Title
ER and aging-Protein folding and the ER stress response.
  Journal
Ageing Res Rev 8:150-9 (2009)
DOI:10.1016/j.arr.2009.03.001
Reference
PMID:18023214
  Authors
Malhotra JD, Kaufman RJ
  Title
The endoplasmic reticulum and the unfolded protein response.
  Journal
Semin Cell Dev Biol 18:716-31 (2007)
DOI:10.1016/j.semcdb.2007.09.003
Reference
PMID:20347046
  Authors
Maattanen P, Gehring K, Bergeron JJ, Thomas DY
  Title
Protein quality control in the ER: the recognition of misfolded proteins.
  Journal
Semin Cell Dev Biol 21:500-11 (2010)
DOI:10.1016/j.semcdb.2010.03.006
Reference
PMID:20219571
  Authors
Stolz A, Wolf DH
  Title
Endoplasmic reticulum associated protein degradation: a chaperone assisted journey to hell.
  Journal
Biochim Biophys Acta 1803:694-705 (2010)
DOI:10.1016/j.bbamcr.2010.02.005
Reference
PMID:20112977
  Authors
Dejgaard K, Theberge JF, Heath-Engel H, Chevet E, Tremblay ML, Thomas DY
  Title
Organization of the Sec61 translocon, studied by high resolution native electrophoresis.
  Journal
J Proteome Res 9:1763-71 (2010)
DOI:10.1021/pr900900x
Related
pathway
tru00510  N-Glycan biosynthesis
tru03050  Proteasome
tru03060  Protein export
tru04210  Apoptosis
KO pathway
ko04141   
LinkDB

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