KEGG   PATHWAY: tben04141
Entry
tben04141                   Pathway                                
Name
Protein processing in endoplasmic reticulum - Trematomus bernacchii (emerald rockcod)
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
tben04141  Protein processing in endoplasmic reticulum
tben04141

Other DBs
GO: 0030433 0034976
Organism
Trematomus bernacchii (emerald rockcod) [GN:tben]
Gene
117489571  sec61a1; protein transport protein Sec61 subunit alpha-like 1 [KO:K10956]
117475338  protein transport protein Sec61 subunit alpha-like [KO:K10956]
117475343  protein transport protein Sec61 subunit alpha-like [KO:K10956]
117475477  protein transport protein Sec61 subunit alpha [KO:K10956]
117480694  sec61b; protein transport protein Sec61 subunit beta [KO:K09481]
117484147  sec61g; protein transport protein Sec61 subunit gamma [KO:K07342]
117500222  sec62; LOW QUALITY PROTEIN: translocation protein SEC62 [KO:K12275]
117492844  sec63; translocation protein SEC63 homolog [KO:K09540]
117475474  rpn1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 [KO:K12666]
117475519  rpn2; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 [KO:K12667]
117488456  dad1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
117494203  ddost; dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
117472138  stt3a; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
117470780  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B-like [KO:K07151] [EC:2.4.99.18]
117477539  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
117485670  magnesium transporter protein 1-like [KO:K19478]
117474758  tusc3; tumor suppressor candidate 3 isoform X1 [KO:K19478]
117487948  ostc; oligosaccharyltransferase complex subunit ostc [KO:K26501]
117491964  tmem258; transmembrane protein 258 [KO:K26502]
117482144  mogs; mannosyl-oligosaccharide glucosidase [KO:K01228] [EC:3.2.1.106]
117485093  ckap4; cytoskeleton-associated protein 4 [KO:K13999]
117484608  rrbp1b; ribosome-binding protein 1b [KO:K14000]
117499895  rrbp1a; ribosome-binding protein 1a isoform X1 [KO:K14000]
117470862  sil1; nucleotide exchange factor SIL1 [KO:K14001]
117472160  hyou1; hypoxia up-regulated protein 1 [KO:K09486]
117476471  hspa5; endoplasmic reticulum chaperone BiP [KO:K09490] [EC:3.6.4.10]
117496032  dnajb11; dnaJ homolog subfamily B member 11 [KO:K09517]
117469454  dnajc1; LOW QUALITY PROTEIN: dnaJ homolog subfamily C member 1 [KO:K09521]
117481120  dnajc3a; dnaJ homolog subfamily C member 3a [KO:K09523]
117488149  dnajc3b; dnaJ homolog subfamily C member 3b [KO:K09523]
117476979  dnajc10; dnaJ homolog subfamily C member 10 [KO:K09530] [EC:1.8.4.-]
117494951  hsp90b1; endoplasmin [KO:K09487]
117488142  ganab; LOW QUALITY PROTEIN: neutral alpha-glucosidase AB [KO:K05546] [EC:3.2.1.207]
117492353  prkcsh; glucosidase 2 subunit beta isoform X1 [KO:K08288]
117487879  glucosidase 2 subunit beta-like [KO:K08288]
117474445  calnexin-like [KO:K08054]
117486844  canx; LOW QUALITY PROTEIN: calnexin [KO:K08054]
117497230  pdia3; protein disulfide-isomerase A3 [KO:K08056] [EC:5.3.4.1]
117482801  protein disulfide-isomerase A3-like [KO:K08056] [EC:5.3.4.1]
117495613  calreticulin-like [KO:K08057]
117495706  calr3a; calreticulin 3a [KO:K08057]
117500225  calreticulin-like [KO:K08057]
117495845  man1a2; mannosyl-oligosaccharide 1,2-alpha-mannosidase IB [KO:K01230] [EC:3.2.1.113]
117486858  mannosyl-oligosaccharide 1,2-alpha-mannosidase IA-like [KO:K01230] [EC:3.2.1.113]
117486989  man1a1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IA [KO:K01230] [EC:3.2.1.113]
117500575  mannosyl-oligosaccharide 1,2-alpha-mannosidase IA isoform X1 [KO:K01230] [EC:3.2.1.113]
117478935  man1b1a; LOW QUALITY PROTEIN: endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase [KO:K23741] [EC:3.2.1.209]
117472485  man1b1b; mannosidase, alpha, class 1B, member 1b isoform X1 [KO:K23741] [EC:3.2.1.209]
117472544  lman2; vesicular integral-membrane protein VIP36 [KO:K10082]
117476762  lman1; protein ERGIC-53 [KO:K10080]
117470769  preb; prolactin regulatory element-binding protein [KO:K14003]
117490326  sar1b; GTP-binding protein SAR1b [KO:K07953] [EC:3.6.5.-]
117473543  sar1aa; GTP-binding protein SAR1b [KO:K07953] [EC:3.6.5.-]
117499587  sar1ab; secretion associated, Ras related GTPase 1Ab [KO:K07953] [EC:3.6.5.-]
117486829  sec13; protein SEC13 homolog [KO:K14004]
117473686  sec31b; protein transport protein Sec31A isoform X1 [KO:K14005]
117476488  sec31a; protein transport protein Sec31A isoform X1 [KO:K14005]
117474664  sec23b; protein transport protein Sec23B [KO:K14006]
117495028  protein transport protein Sec23A [KO:K14006]
117490353  sec24a; protein transport protein Sec24A isoform X1 [KO:K14007]
117485223  sec24b; protein transport protein Sec24B isoform X1 [KO:K14007]
117473235  si:dkey-13n15.2; protein transport protein Sec24C [KO:K14007]
117474103  sec24c; protein transport protein Sec24C isoform X1 [KO:K14007]
117487914  sec24d; LOW QUALITY PROTEIN: protein transport protein Sec24D [KO:K14007]
117481119  uggt2; UDP-glucose:glycoprotein glucosyltransferase 2 isoform X1 [KO:K11718] [EC:2.4.1.-]
117492186  uggt1; UDP-glucose:glycoprotein glucosyltransferase 1 [KO:K11718] [EC:2.4.1.-]
117489559  edem1; ER degradation-enhancing alpha-mannosidase-like protein 1 [KO:K10084]
117478537  edem2; ER degradation-enhancing alpha-mannosidase-like protein 2 isoform X1 [KO:K10085]
117495426  edem3; ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1 [KO:K10086]
117476575  si:ch211-282j22.3; ER degradation-enhancing alpha-mannosidase-like protein 3 [KO:K10086]
117481538  p4hb; LOW QUALITY PROTEIN: protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
117484014  pdia4; protein disulfide-isomerase A4 [KO:K09582] [EC:5.3.4.1]
117492674  pdia6; protein disulfide-isomerase A6 [KO:K09584] [EC:5.3.4.1]
117484062  txndc5; thioredoxin domain-containing protein 5 [KO:K13984] [EC:5.3.4.1]
117471338  ero1a; LOW QUALITY PROTEIN: ERO1-like protein alpha [KO:K10950] [EC:1.8.4.-]
117481778  ero1b; ERO1-like protein beta isoform X1 [KO:K10976] [EC:1.8.4.-]
117489653  os9; protein OS-9 [KO:K10088]
117499859  erlec1; endoplasmic reticulum lectin 1 [KO:K14008]
117496083  LOW QUALITY PROTEIN: translocon-associated protein subunit alpha-like [KO:K13249]
117486566  translocon-associated protein subunit alpha-like [KO:K13249]
117479201  ssr2; translocon-associated protein subunit beta [KO:K13250]
117470098  ssr3; translocon-associated protein subunit gamma [KO:K13251]
117494178  ssr4; translocon-associated protein subunit delta [KO:K04571]
117483850  bcap31; B-cell receptor-associated protein 31 [KO:K14009]
117484039  tram1; translocating chain-associated membrane protein 1 [KO:K14010]
117479554  zgc:113278; translocating chain-associated membrane protein 1-like 1 isoform X1 [KO:K14010]
117480183  derl1; derlin-1 [KO:K11519]
117472372  derl3; derlin-3 [KO:K13989]
117484741  derl2; derlin-2 [KO:K13989]
117485707  ubxn4; UBX domain-containing protein 4 [KO:K24348]
117487848  ubxn1; UBX domain-containing protein 1 [KO:K24348]
117498583  ubxn2a; UBX domain-containing protein 2A [KO:K24349]
117495126  ubxn6; UBX domain-containing protein 6 [KO:K14011]
117494378  nsfl1c; NSFL1 cofactor p47 [KO:K14012]
117491933  svip; small VCP/p97-interacting protein [KO:K14014]
117474762  zgc:136908; transitional endoplasmic reticulum ATPase [KO:K13525]
117476032  vcp; transitional endoplasmic reticulum ATPase [KO:K13525]
117473709  nploc4; nuclear protein localization protein 4 homolog [KO:K14015]
117473061  ufd1l; ubiquitin recognition factor in ER-associated degradation protein 1 [KO:K14016]
117472121  hspa8; heat shock cognate 71 kDa protein isoform X1 [KO:K03283]
117480296  LOW QUALITY PROTEIN: heat shock cognate 71 kDa protein-like [KO:K03283]
117492278  heat shock 70 kDa protein 1 [KO:K03283]
117468761  hspa8b; heat shock protein family A (Hsp70) member 8b [KO:K03283]
117476294  heat shock cognate 71 kDa protein-like [KO:K03283]
117494474  hspa1b; heat shock 70 kDa protein 1B [KO:K03283]
117474565  dnaja1; dnaJ homolog subfamily A member 1 [KO:K09502]
117484271  dnaja2a; dnaJ homolog subfamily A member 2a [KO:K09503]
117491469  dnaja2b; dnaJ homolog subfamily A member 2b [KO:K09503]
117474618  dnajb1b; dnaJ homolog subfamily B member 1b [KO:K09507]
117493418  dnajb1a; dnaJ homolog subfamily B member 1a [KO:K09507]
117485746  dnajb2; dnaJ homolog subfamily B member 2 isoform X1 [KO:K09508]
117473555  dnajb12b; dnaJ homolog subfamily B member 12b [KO:K09518]
117499582  dnajb12a; dnaJ homolog subfamily B member 12a [KO:K09518]
117483710  dnaJ homolog subfamily C member 5-like isoform X1 [KO:K09525]
117497115  dnajc5gb; dnaJ (Hsp40) homolog, subfamily C, member 5 gamma b isoform X1 [KO:K09525]
117474996  dnajc5ga; dnaJ (Hsp40) homolog, subfamily C, member 5 gamma a isoform X1 [KO:K09525]
117483395  dnaJ homolog subfamily C member 5-like [KO:K09525]
117486867  hsp90ab1; heat shock protein HSP 90-beta [KO:K04079]
117498481  hsp90aa1.1; heat shock protein HSP 90-alpha 1 [KO:K04079]
117498483  hsp90aa1.2; heat shock protein 90, alpha (cytosolic), class A member 1, tandem duplicate 2 [KO:K04079]
117477786  hspa4l; heat shock 70 kDa protein 4L [KO:K09485]
117482536  bag1; BAG family molecular chaperone regulator 1 [KO:K09555]
117499868  bag2; BAG family molecular chaperone regulator 2 [KO:K09556]
117492403  hspbp1; hsp70-binding protein 1 [KO:K09562]
117477445  cryaa; alpha-crystallin A chain [KO:K09541]
117490226  LOW QUALITY PROTEIN: alpha-crystallin B chain-like [KO:K09542]
117480323  hspb6; heat shock protein beta-6 [KO:K09542]
117489871  yod1; ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
117487873  plaa; phospholipase A-2-activating protein [KO:K14018]
117492088  rad23aa; RAD23 homolog A, nucleotide excision repair protein a isoform X1 [KO:K10839]
117476750  rad23b; UV excision repair protein RAD23 homolog B [KO:K10839]
117472911  ubiquilin-1-like [KO:K04523]
117468533  ubqln4; ubiquilin-4 [KO:K04523]
117478029  ubiquilin-4-like [KO:K04523]
117482848  ngly1; peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase [KO:K01456] [EC:3.5.1.52]
117476563  atxn3; ataxin-3 [KO:K11863] [EC:3.4.22.-]
117494200  ube4b; ubiquitin conjugation factor E4 B isoform X1 [KO:K10597] [EC:2.3.2.27]
117469677  eif2ak3; LOW QUALITY PROTEIN: eukaryotic translation initiation factor 2-alpha kinase 3 [KO:K08860] [EC:2.7.11.1]
117486954  eif2s1b; eukaryotic translation initiation factor 2 subunit 1b [KO:K03237]
117481164  nfe2l2a; nuclear factor erythroid 2-related factor 2a [KO:K05638]
117496522  atf4a; cyclic AMP-dependent transcription factor ATF-4 isoform X1 [KO:K04374]
117492616  atf4b; activating transcription factor 4b [KO:K04374]
117489480  ddit3; DNA damage-inducible transcript 3 protein [KO:K04452]
117488347  bcl2b; apoptosis regulator Bcl-2 [KO:K02161]
117495197  atf6; cyclic AMP-dependent transcription factor ATF-6 alpha [KO:K09054]
117478312  atf6b; LOW QUALITY PROTEIN: cyclic AMP-dependent transcription factor ATF-6 beta [KO:K09049]
117474807  wfs1a; wolframin isoform X1 [KO:K14020]
117477234  wolframin-like isoform X1 [KO:K14020]
117491635  mbtps1; membrane-bound transcription factor site-1 protease [KO:K08653] [EC:3.4.21.112]
117497407  mbtps2; membrane-bound transcription factor site-2 protease [KO:K07765] [EC:3.4.24.85]
117472674  xbp1; LOW QUALITY PROTEIN: X-box-binding protein 1 [KO:K09027]
117481653  ern2; serine/threonine-protein kinase/endoribonuclease IRE1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
117492323  serine/threonine-protein kinase/endoribonuclease IRE1-like isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
117472809  TNF receptor-associated factor 2-like [KO:K03173] [EC:2.3.2.27]
117476319  TNF receptor-associated factor 2-like [KO:K03173] [EC:2.3.2.27]
117476522  traf2b; TNF receptor-associated factor 2 [KO:K03173] [EC:2.3.2.27]
117486921  map3k5; mitogen-activated protein kinase kinase kinase 5 [KO:K04426] [EC:2.7.11.25]
117468561  si:ch211-1i11.3; mitogen-activated protein kinase kinase kinase 5 [KO:K04426] [EC:2.7.11.25]
117481609  map2k7; dual specificity mitogen-activated protein kinase kinase 7 isoform X1 [KO:K04431] [EC:2.7.12.2]
117486395  mapk8b; LOW QUALITY PROTEIN: mitogen-activated protein kinase 8 [KO:K04440] [EC:2.7.11.24]
117499592  mapk8a; mitogen-activated protein kinase 8 isoform X1 [KO:K04440] [EC:2.7.11.24]
117475749  mapk9; mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
117476691  mapk10; mitogen-activated protein kinase 10 isoform X1 [KO:K04440] [EC:2.7.11.24]
117491122  zgc:153993; apoptosis regulator BAX [KO:K02159]
117493224  apoptosis regulator BAX-like [KO:K02159]
117490139  calpain-1 catalytic subunit-like [KO:K01367] [EC:3.4.22.52]
117490140  calpain-1 catalytic subunit-like isoform X1 [KO:K01367] [EC:3.4.22.52]
117486632  calpain-1 catalytic subunit-like isoform X1 [KO:K01367] [EC:3.4.22.52]
117486640  calpain-1 catalytic subunit-like [KO:K01367] [EC:3.4.22.52]
117486643  calpain-1 catalytic subunit-like [KO:K01367] [EC:3.4.22.52]
117486661  calpain-A-like [KO:K01367] [EC:3.4.22.52]
117486706  calpain-1 catalytic subunit-like [KO:K01367] [EC:3.4.22.52]
117497617  capn1b; calpain-1 catalytic subunit b [KO:K01367] [EC:3.4.22.52]
117497989  capn1; calpain-1 catalytic subunit [KO:K01367] [EC:3.4.22.52]
117499889  capn1a; calpain 1, (mu/I) large subunit a [KO:K01367] [EC:3.4.22.52]
117499311  calpain-2 catalytic subunit-like [KO:K03853] [EC:3.4.22.53]
117499313  calpain-2 catalytic subunit-like [KO:K03853] [EC:3.4.22.53]
117499673  capn8; calpain-8 [KO:K03853] [EC:3.4.22.53]
117499674  calpain-2 catalytic subunit-like [KO:K03853] [EC:3.4.22.53]
117484072  E3 ubiquitin-protein ligase MARCHF6 isoform X1 [KO:K10661] [EC:2.3.2.27]
117488776  E3 ubiquitin-protein ligase MARCHF6-like isoform X1 [KO:K10661] [EC:2.3.2.27]
117498418  ube2j1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
117486553  ube2j2; ubiquitin-conjugating enzyme E2 J2 [KO:K04554] [EC:2.3.2.23]
117484798  ubiquitin-conjugating enzyme E2 G1-like [KO:K10575] [EC:2.3.2.23]
117470311  ube2g1a; ubiquitin-conjugating enzyme E2 G1a [KO:K10575] [EC:2.3.2.23]
117476450  ube2g1b; ubiquitin-conjugating enzyme E2G 1b [KO:K10575] [EC:2.3.2.23]
117489197  ube2g2; ubiquitin-conjugating enzyme E2 G2 [KO:K04555] [EC:2.3.2.23]
117475169  syvn1; LOW QUALITY PROTEIN: E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
117478321  rnf5; E3 ubiquitin-protein ligase RNF5 isoform X1 [KO:K10666] [EC:2.3.2.27]
117476688  rnf185; E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
117491136  selenos; selenoprotein S [KO:K14025]
117498400  sel1l; protein sel-1 homolog 1 isoform X1 [KO:K14026]
117484460  herpud1; homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein [KO:K14027]
117471347  E3 ubiquitin-protein ligase AMFR-like [KO:K10636] [EC:2.3.2.36]
117473821  stub1; E3 ubiquitin-protein ligase CHIP isoform X1 [KO:K09561] [EC:2.3.2.27]
117496911  ube2d4; ubiquitin-conjugating enzyme E2 D4 [KO:K06689] [EC:2.3.2.23]
117473848  ubiquitin-conjugating enzyme E2 D4-like [KO:K06689] [EC:2.3.2.23]
117475108  ube2d2; ubiquitin-conjugating enzyme E2 D2 [KO:K06689] [EC:2.3.2.23]
117499812  ubiquitin-conjugating enzyme E2 D4-like [KO:K06689] [EC:2.3.2.23]
117493918  ubiquitin-conjugating enzyme E2 D2-like [KO:K06689] [EC:2.3.2.23]
117482564  ubiquitin-conjugating enzyme E2-17 kDa-like [KO:K06689] [EC:2.3.2.23]
117486002  prkn; E3 ubiquitin-protein ligase parkin [KO:K04556] [EC:2.3.2.31]
117492884  rbx1; E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
117495941  cullin-1 [KO:K03347]
117490737  skp1; S-phase kinase-associated protein 1 isoform X1 [KO:K03094]
117475362  fbxo2; F-box only protein 2 [KO:K10099]
117483421  F-box only protein 6-like [KO:K10100]
117483498  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
tben00510  N-Glycan biosynthesis
tben03050  Proteasome
tben03060  Protein export
tben04210  Apoptosis
KO pathway
ko04141   
LinkDB

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