KEGG   PATHWAY: gfr04141
Entry
gfr04141                    Pathway                                
Name
Protein processing in endoplasmic reticulum - Geospiza fortis (medium ground-finch)
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
gfr04141  Protein processing in endoplasmic reticulum
gfr04141

Other DBs
GO: 0030433 0034976
Organism
Geospiza fortis (medium ground-finch) [GN:gfr]
Gene
102043686  SEC61A1; Sec61 translocon alpha 1 subunit [KO:K10956]
102045195  SEC61A2; Sec61 translocon alpha 2 subunit [KO:K10956]
102038066  SEC61G; Sec61 translocon gamma subunit [KO:K07342]
102043941  SEC62; SEC62 homolog, preprotein translocation factor [KO:K12275]
102033653  SEC63; SEC63 homolog, protein translocation regulator [KO:K09540]
102039983  RPN1; ribophorin I [KO:K12666]
102032217  RPN2; ribophorin II [KO:K12667]
102034969  DDOST; dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit [KO:K12670]
102035202  STT3A; STT3A, catalytic subunit of the oligosaccharyltransferase complex [KO:K07151] [EC:2.4.99.18]
102040723  STT3B; STT3B, catalytic subunit of the oligosaccharyltransferase complex [KO:K07151] [EC:2.4.99.18]
102044041  MAGT1; magnesium transporter 1 [KO:K19478]
102043875  TUSC3; tumor suppressor candidate 3 [KO:K19478]
102034776  OSTC; oligosaccharyltransferase complex non-catalytic subunit [KO:K26501]
102036381  TMEM258; transmembrane protein 258 [KO:K26502]
102045298  CKAP4; cytoskeleton associated protein 4 [KO:K13999]
102044081  RRBP1; ribosome binding protein 1 [KO:K14000]
102032406  SIL1; SIL1 nucleotide exchange factor [KO:K14001]
102045431  nucleotide exchange factor SIL1-like [KO:K14001]
102037286  HYOU1; hypoxia up-regulated 1 [KO:K09486]
102035853  HSPA5; heat shock protein family A (Hsp70) member 5 [KO:K09490] [EC:3.6.4.10]
102033895  DNAJB11; DnaJ heat shock protein family (Hsp40) member B11 [KO:K09517]
102034441  DNAJC1; DnaJ heat shock protein family (Hsp40) member C1 [KO:K09521]
102035232  DNAJC3; DnaJ heat shock protein family (Hsp40) member C3 [KO:K09523]
102038989  DNAJC10; DnaJ heat shock protein family (Hsp40) member C10 [KO:K09530] [EC:1.8.4.-]
102035424  HSP90B1; heat shock protein 90 beta family member 1 [KO:K09487]
102035899  neutral alpha-glucosidase AB-like [KO:K05546] [EC:3.2.1.207]
102044555  CANX; calnexin [KO:K08054]
102038630  PDIA3; protein disulfide isomerase family A member 3 [KO:K08056] [EC:5.3.4.1]
102039799  calreticulin-like [KO:K08057]
102038714  MAN1A1; mannosidase alpha class 1A member 1 [KO:K01230] [EC:3.2.1.113]
102039998  MAN1C1; mannosidase alpha class 1C member 1 [KO:K01230] [EC:3.2.1.113]
102039589  MAN1A2; mannosidase alpha class 1A member 2 [KO:K01230] [EC:3.2.1.113]
102031555  MAN1B1; mannosidase alpha class 1B member 1 [KO:K23741] [EC:3.2.1.209]
102032159  LMAN2; lectin, mannose binding 2 [KO:K10082]
102034036  LMAN1; lectin, mannose binding 1 [KO:K10080]
102039059  SAR1B; secretion associated Ras related GTPase 1B [KO:K07953] [EC:3.6.5.-]
102038698  SAR1A; secretion associated Ras related GTPase 1A [KO:K07953] [EC:3.6.5.-]
102036100  SEC13; SEC13 homolog, nuclear pore and COPII coat complex component [KO:K14004]
102039339  SEC31B; SEC31 homolog B, COPII coat complex component [KO:K14005]
102041087  SEC31A; SEC31 homolog A, COPII coat complex component [KO:K14005]
102034496  SEC23A; Sec23 homolog A, coat complex II component [KO:K14006]
102033223  SEC23B; Sec23 homolog B, coat complex II component [KO:K14006]
102035952  SEC24C; SEC24 homolog C, COPII coat complex component [KO:K14007]
102037094  SEC24A; SEC24 homolog A, COPII coat complex component [KO:K14007]
102035107  SEC24B; SEC24 homolog B, COPII coat complex component [KO:K14007]
102045363  SEC24D; SEC24 homolog D, COPII coat complex component [KO:K14007]
102039086  UGGT1; UDP-glucose glycoprotein glucosyltransferase 1 [KO:K11718] [EC:2.4.1.-]
102035399  UGGT2; UDP-glucose glycoprotein glucosyltransferase 2 [KO:K11718] [EC:2.4.1.-]
102034907  EDEM1; ER degradation enhancing alpha-mannosidase like protein 1 [KO:K10084]
102038524  EDEM2; ER degradation enhancing alpha-mannosidase like protein 2 [KO:K10085]
102044740  EDEM3; ER degradation enhancing alpha-mannosidase like protein 3 [KO:K10086]
102032637  P4HB; prolyl 4-hydroxylase subunit beta [KO:K09580] [EC:5.3.4.1]
102041292  PDIA4; protein disulfide isomerase family A member 4 [KO:K09582] [EC:5.3.4.1]
102032995  PDIA6; protein disulfide isomerase family A member 6 [KO:K09584] [EC:5.3.4.1]
102043073  ERP29; endoplasmic reticulum protein 29 [KO:K09586]
102039016  TXNDC5; thioredoxin domain containing 5 [KO:K13984] [EC:5.3.4.1]
102031323  ERO1A; endoplasmic reticulum oxidoreductase 1 alpha [KO:K10950] [EC:1.8.4.-]
102039985  ERO1B; endoplasmic reticulum oxidoreductase 1 beta [KO:K10976] [EC:1.8.4.-]
102041004  ERLEC1; endoplasmic reticulum lectin 1 [KO:K14008]
102041639  SSR1; signal sequence receptor subunit 1 [KO:K13249]
102034308  translocon-associated protein subunit beta [KO:K13250]
102038263  translocon-associated protein subunit beta-like [KO:K13250]
102042058  SSR3; signal sequence receptor subunit 3 [KO:K13251]
102040382  TRAM1; translocation associated membrane protein 1 [KO:K14010]
102045398  DERL1; derlin 1 [KO:K11519]
102043986  DERL3; derlin 3 [KO:K13989]
102043989  DERL2; derlin 2 [KO:K13989]
102041258  UBXN4; UBX domain protein 4 [KO:K24348]
102033093  UBXN2A; UBX domain protein 2A [KO:K24349]
102045266  UBXN6; UBX domain protein 6 [KO:K14011]
102036137  NSFL1C; NSFL1 cofactor [KO:K14012]
102044420  SVIP; small VCP interacting protein [KO:K14014]
102036274  VCP; valosin containing protein [KO:K13525]
102032750  transitional endoplasmic reticulum ATPase [KO:K13525]
102042329  NPLOC4; NPL4 homolog, ubiquitin recognition factor [KO:K14015]
102042729  UFD1L; ubiquitin fusion degradation 1 like (yeast) [KO:K14016]
102044992  HSPA8; heat shock protein family A (Hsp70) member 8 [KO:K03283]
102041861  DNAJA1; DnaJ heat shock protein family (Hsp40) member A1 [KO:K09502]
102034917  dnaJ homolog subfamily A member 1-like [KO:K09502]
102039023  DNAJA2; DnaJ heat shock protein family (Hsp40) member A2 [KO:K09503]
102037804  DNAJB2; DnaJ heat shock protein family (Hsp40) member B2 [KO:K09508]
102041835  DNAJB12; DnaJ heat shock protein family (Hsp40) member B12 [KO:K09518]
102033272  DNAJC5; DnaJ heat shock protein family (Hsp40) member C5 [KO:K09525]
102037548  dnaJ homolog subfamily C member 5-like [KO:K09525]
102032319  HSP90AA1; heat shock protein 90 alpha family class A member 1 [KO:K04079]
102034985  HSP90AB1; heat shock protein 90 alpha family class B member 1 [KO:K04079]
102042692  HSPH1; heat shock protein family H (Hsp110) member 1 [KO:K09485]
102034199  HSPA4L; heat shock protein family A (Hsp70) member 4 like [KO:K09485]
102043456  BAG1; BCL2 associated athanogene 1 [KO:K09555]
102041619  BAG2; BCL2 associated athanogene 2 [KO:K09556]
102033292  CRYAA; crystallin alpha A [KO:K09541]
102040461  CRYAB; crystallin alpha B [KO:K09542]
102045096  YOD1; YOD1 deubiquitinase [KO:K13719] [EC:3.1.2.-]
102043142  PLAA; phospholipase A2 activating protein [KO:K14018]
102042701  RAD23B; RAD23 homolog B, nucleotide excision repair protein [KO:K10839]
102045128  UBQLN1; ubiquilin 1 [KO:K04523]
102036446  UBQLN4; ubiquilin 4 [KO:K04523]
102040046  NGLY1; N-glycanase 1 [KO:K01456] [EC:3.5.1.52]
102038613  ATXN3; ataxin 3 [KO:K11863] [EC:3.4.22.-]
102031908  UBE4B; ubiquitination factor E4B [KO:K10597] [EC:2.3.2.27]
102039323  EIF2AK3; eukaryotic translation initiation factor 2 alpha kinase 3 [KO:K08860] [EC:2.7.11.1]
102041037  EIF2S1; eukaryotic translation initiation factor 2 subunit alpha [KO:K03237]
102036230  NFE2L2; nuclear factor, erythroid 2 like 2 [KO:K05638]
102036875  ATF4; activating transcription factor 4 [KO:K04374]
102032008  BCL2; BCL2, apoptosis regulator [KO:K02161]
102038347  ATF6; activating transcription factor 6 [KO:K09054]
102032466  WFS1; wolframin ER transmembrane glycoprotein [KO:K14020]
102042134  MBTPS1; membrane bound transcription factor peptidase, site 1 [KO:K08653] [EC:3.4.21.112]
102036374  MBTPS2; membrane bound transcription factor peptidase, site 2 [KO:K07765] [EC:3.4.24.85]
102038226  XBP1; X-box binding protein 1 [KO:K09027]
102037392  ERN1; endoplasmic reticulum to nucleus signaling 1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
102042914  ERN2; endoplasmic reticulum to nucleus signaling 2 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
102033115  TRAF2; TNF receptor associated factor 2 [KO:K03173] [EC:2.3.2.27]
102034507  MAP3K5; mitogen-activated protein kinase kinase kinase 5 [KO:K04426] [EC:2.7.11.25]
102038813  MAP2K7; mitogen-activated protein kinase kinase 7 [KO:K04431] [EC:2.7.12.2]
102036009  MAPK8; mitogen-activated protein kinase 8 [KO:K04440] [EC:2.7.11.24]
102043776  MAPK10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
102043222  MAPK9; mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
102040914  BAK1; BCL2 antagonist/killer 1 [KO:K14021]
102043510  CAPN1; calpain 1 [KO:K01367] [EC:3.4.22.52]
102035321  CAPN11; calpain 11 [KO:K01367] [EC:3.4.22.52]
102045030  CAPN2; calpain 2 [KO:K03853] [EC:3.4.22.53]
102043469  MARCH6; membrane associated ring-CH-type finger 6 [KO:K10661] [EC:2.3.2.27]
102038731  UBE2J1; ubiquitin conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
102039441  UBE2J2; ubiquitin conjugating enzyme E2 J2 [KO:K04554] [EC:2.3.2.23]
102036375  UBE2G2; ubiquitin conjugating enzyme E2 G2 [KO:K04555] [EC:2.3.2.23]
102043337  SYVN1; synoviolin 1 [KO:K10601] [EC:2.3.2.27]
102033717  RNF185; ring finger protein 185 [KO:K10666] [EC:2.3.2.27]
102043582  SELENOS; selenoprotein S [KO:K14025]
102034825  SEL1L; SEL1L ERAD E3 ligase adaptor subunit [KO:K14026]
102032886  HERPUD1; homocysteine inducible ER protein with ubiquitin like domain 1 [KO:K14027]
102042966  AMFR; autocrine motility factor receptor [KO:K10636] [EC:2.3.2.36]
102040454  STUB1; STIP1 homology and U-box containing protein 1 [KO:K09561] [EC:2.3.2.27]
102032895  UBE2D1; ubiquitin conjugating enzyme E2 D1 [KO:K06689] [EC:2.3.2.23]
102032455  UBE2D2; ubiquitin conjugating enzyme E2 D2 [KO:K06689] [EC:2.3.2.23]
102037811  UBE2D3; ubiquitin conjugating enzyme E2 D3 [KO:K06689] [EC:2.3.2.23]
102043879  PARK2; parkin RBR E3 ubiquitin protein ligase [KO:K04556] [EC:2.3.2.31]
102037823  RBX1; ring-box 1 [KO:K03868] [EC:2.3.2.32]
102038503  CUL1; cullin 1 [KO:K03347]
102038546  SKP1; S-phase kinase associated protein 1 [KO:K03094]
102033685  FBXO2; F-box only protein 2 [KO:K10099]
102039786  FBXO6; F-box only protein 6 [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
gfr00510  N-Glycan biosynthesis
gfr03050  Proteasome
gfr03060  Protein export
gfr04210  Apoptosis
KO pathway
ko04141   
LinkDB

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