ENTRY       sly04141                    Pathway
NAME        Protein processing in endoplasmic reticulum - Solanum lycopersicum (tomato)
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 sly04141  Protein processing in endoplasmic reticulum
DBLINKS     GO: 0030433 0034976
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101245021  protein transport protein Sec61 subunit alpha [KO:K10956]
            101259292  protein transport protein Sec61 subunit alpha [KO:K10956]
            101263722  preprotein translocase subunit SCY1, chloroplastic [KO:K10956]
            101245632  protein transport protein Sec61 subunit beta [KO:K09481]
            101268397  protein transport protein Sec61 subunit beta [KO:K09481]
            101268107  protein transport protein Sec61 subunit beta-like [KO:K09481]
            101245464  protein transport protein Sec61 subunit beta-like [KO:K09481]
            101247903  protein transport protein Sec61 subunit gamma-1 [KO:K07342]
            101243898  protein transport protein Sec61 subunit gamma-1-like [KO:K07342]
            101265358  uncharacterized protein LOC101265358 [KO:K12275]
            101248267  translocation protein SEC62 isoform X1 [KO:K12275]
            101257737  dnaJ protein ERDJ2A [KO:K09540]
            101268712  dnaJ protein ERDJ2 [KO:K09540]
            101264927  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1A [KO:K12666]
            101250991  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1B [KO:K12666]
            101265028  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 [KO:K12667]
            101252001  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 [KO:K12667]
            543753  DAD1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
            101256748  probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3B [KO:K12669]
            101261758  probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3B [KO:K12669]
            101261568  probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3B [KO:K12669]
            101245405  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit precursor [KO:K12670]
            101256652  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
            101259924  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
            101267114  mannosyl-oligosaccharide glucosidase GCS1 [KO:K01228] [EC:3.2.1.106]
            101252901  heat shock 70 kDa protein 17 [KO:K09486]
            101252822  mediator of RNA polymerase II transcription subunit 37a [KO:K09490] [EC:3.6.4.10]
            543957  BiP/grp78; luminal-binding protein precursor [KO:K09490] [EC:3.6.4.10]
            101263797  luminal-binding protein 5 [KO:K09490] [EC:3.6.4.10]
            101246562  dnaJ protein ERDJ3B [KO:K09517]
            543872  P58IPK-like protein [KO:K09523]
            101265819  endoplasmin homolog [KO:K09487]
            101255395  heat shock protein 90-5, chloroplastic [KO:K09487]
            101254814  heat shock protein 90-6, mitochondrial [KO:K09487]
            543798  gluII; alpha glucosidase II precursor [KO:K05546] [EC:3.2.1.207]
            101257751  glucosidase 2 subunit beta isoform X1 [KO:K08288]
            778323  CNX61.0; calnexin-like protein precursor [KO:K08054]
            101247033  calnexin homolog 1-like isoform X1 [KO:K08054]
            101246093  calreticulin [KO:K08057]
            101248677  calreticulin-3 [KO:K08057]
            101262304  calreticulin-3-like [KO:K08057]
            101264908  mannosyl-oligosaccharide 1,2-alpha-mannosidase MNS1-like isoform X1 [KO:K01230] [EC:3.2.1.113]
            101262322  mannosyl-oligosaccharide 1,2-alpha-mannosidase MNS1-like isoform X1 [KO:K01230] [EC:3.2.1.113]
            101246787  mannosyl-oligosaccharide 1,2-alpha-mannosidase MNS3 [KO:K23741] [EC:3.2.1.209]
            101258215  SEC12-like protein 1 [KO:K14003]
            101251489  SEC12-like protein 2 [KO:K14003]
            101244805  GTP-binding protein SAR1A [KO:K07953] [EC:3.6.5.-]
            543958  SAR2; GTP-binding protein SAR2 [KO:K07953] [EC:3.6.5.-]
            101244997  GTP-binding protein SAR1A-like [KO:K07953] [EC:3.6.5.-]
            101267027  GTP-binding protein SAR1A [KO:K07953] [EC:3.6.5.-]
            101265789  protein transport protein SEC13 homolog B [KO:K14004]
            101257847  protein transport protein SEC13 homolog B [KO:K14004]
            101261454  protein transport protein SEC31 homolog B isoform X1 [KO:K14005]
            101255531  protein transport protein SEC23 [KO:K14006]
            101259216  protein transport protein SEC23 [KO:K14006]
            101255494  protein transport protein SEC23 [KO:K14006]
            101254944  protein transport protein SEC23-like [KO:K14006]
            101243662  protein transport protein Sec24-like At3g07100 [KO:K14007]
            101260822  protein transport protein Sec24-like At4g32640 isoform X1 [KO:K14007]
            101253501  protein transport protein Sec24-like CEF [KO:K14007]
            101252027  UDP-glucose:glycoprotein glucosyltransferase isoform X1 [KO:K11718] [EC:2.4.1.-]
            101257158  alpha-mannosidase I MNS5 [KO:K10084]
            101256095  alpha-mannosidase I MNS4 isoform X2 [KO:K10085]
            101262499  protein disulfide isomerase-like 1-6 [KO:K09580] [EC:5.3.4.1]
            101244079  protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
            101257163  protein disulfide isomerase-like 1-4 [KO:K09580] [EC:5.3.4.1]
            101257830  protein disulfide isomerase-like 1-4 [KO:K09580] [EC:5.3.4.1]
            101247779  protein disulfide-isomerase 5-2 [KO:K09580] [EC:5.3.4.1]
            101247321  protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
            101261717  protein disulfide isomerase-like 1-4 [KO:K09580] [EC:5.3.4.1]
            101262222  protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
            101252596  protein disulfide isomerase-like 5-2 [KO:K09580] [EC:5.3.4.1]
            101262921  protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
            101244123  protein disulfide-isomerase like 2-1 precursor [KO:K09584] [EC:5.3.4.1]
            101266349  protein disulfide isomerase-like 2-3 [KO:K09584] [EC:5.3.4.1]
            101246644  endoplasmic reticulum oxidoreductin-1 [KO:K10950] [EC:1.8.4.-]
            101256100  protein OS-9 homolog [KO:K10088]
            101256722  translocon-associated protein subunit alpha isoform X2 [KO:K13249]
            101253329  translocon-associated protein subunit alpha [KO:K13249]
            101259897  translocon-associated protein subunit beta isoform X1 [KO:K13250]
            101264411  translocon-associated protein subunit beta-like [KO:K13250]
            101258207  B-cell receptor-associated protein 31-like [KO:K14009]
            101255462  uncharacterized protein LOC101255462 [KO:K14009]
            101251810  uncharacterized protein LOC101251810 [KO:K14009]
            101250189  uncharacterized protein LOC101250189 [KO:K14009]
            101256736  derlin-2.2 [KO:K13989]
            101266220  derlin-1 [KO:K13989]
            101261210  troponin T, fast skeletal muscle [KO:K24348]
            101253939  plant UBX domain-containing protein 11 isoform X5 [KO:K24348]
            101251912  plant UBX domain-containing protein 2 [KO:K14011]
            101244442  plant UBX domain-containing protein 4-like [KO:K14012]
            101252989  plant UBX domain-containing protein 4 isoform X2 [KO:K14012]
            101245776  plant UBX domain-containing protein 4 [KO:K14012]
            101259229  cell division cycle protein 48 homolog isoform X1 [KO:K13525]
            101246391  cell division cycle protein 48 homolog [KO:K13525]
            101266255  cell division cycle protein 48 homolog [KO:K13525]
            101266129  cell division cycle protein 48 homolog [KO:K13525]
            101265798  cell division cycle protein 48 homolog isoform X1 [KO:K13525]
            101248688  NPL4-like protein 2 [KO:K14015]
            101248524  ubiquitin fusion degradation protein 1 homolog isoform 1 [KO:K14016]
            101265681  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
            100134914  HSP70; heat shock protein 70 [KO:K03283]
            100736433  Hsc70.1; heat shock cognate 70 kDa protein 1 [KO:K03283]
            101055596  hsc70.3; heat shock protein 70-3 [KO:K03283]
            101247772  Hsc70.2; heat shock cognate 70 kDa protein 2 [KO:K03283]
            101248309  heat shock 70 kDa protein-like [KO:K03283]
            101247151  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101254866  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101255164  heat shock cognate 70 kDa protein [KO:K03283]
            101255185  heat shock 70 kDa protein 5 [KO:K03283]
            101262751  dnaJ protein homolog 2 [KO:K09503]
            101252869  dnaJ protein homolog isoform X1 [KO:K09503]
            101248484  dnaJ protein homolog [KO:K09503]
            101258610  DnaJ-like protein [KO:K09503]
            101259708  dnaJ protein homolog [KO:K09503]
            101255429  chaperone protein dnaJ 49 [KO:K09518]
            101261306  chaperone protein dnaJ 49 [KO:K09518]
            101246246  chaperone protein dnaJ 49 [KO:K09518]
            101264183  heat shock protein 83 [KO:K04079]
            101260143  HSP90; heat shock protein 90 [KO:K04079]
            543902  Hsp90-1; molecular chaperone Hsp90-1 [KO:K04079]
            543903  HSC80; heat shock cognate protein 80 [KO:K04079]
            101253115  hsp70-binding protein 1 [KO:K09562]
            101261804  hsp70 nucleotide exchange factor FES1-like protein precursor [KO:K09562]
            543572  HSP17.4; cytosolic class II small heat shock protein HCT2 [KO:K13993]
            544205  er-sHSP; small heat shock protein precursor [KO:K13993]
            543848  HSP17-6; heat shock protein HSP 17-6 [KO:K13993]
            101264936  Hsp20.0; class I small heat shock protein [KO:K13993]
            101254946  22.7 kDa class IV heat shock protein-like [KO:K13993]
            101254323  14.7 kDa heat shock protein [KO:K13993]
            101256444  15.4 kDa class V heat shock protein [KO:K13993]
            101256536  class I heat shock protein [KO:K13993]
            101248279  17.4 kDa class III heat shock protein [KO:K13993]
            101256272  22.7 kDa class IV heat shock protein [KO:K13993]
            101268271  15.7 kDa heat shock protein, peroxisomal [KO:K13993]
            101261225  16.9 kDa class I heat shock protein 1-like [KO:K13993]
            101263239  18.1 kDa class I heat shock protein [KO:K13993]
            101268307  18.2 kDa class I heat shock protein [KO:K13993]
            101261304  26.5 kDa heat shock protein, mitochondrial [KO:K13993]
            101266231  HSP17.8; 17.8 kDa class I heat shock protein [KO:K13993]
            543846  vis1; small heat shock protein [KO:K13993]
            544282  class II small heat shock protein Le-HSP17.6 [KO:K13993]
            544024  HSP21; small heat shock protein, chloroplastic [KO:K13993]
            543507  MTSHP; mitochondrial small heat shock protein [KO:K13993]
            101266525  17.7 kDa class I heat shock protein [KO:K13993]
            101263227  LOW QUALITY PROTEIN: class I heat shock protein-like [KO:K13993]
            101250041  heat shock 22 kDa protein, mitochondrial-like [KO:K13993]
            101268020  17.3 kDa class I heat shock protein-like [KO:K13993]
            101248409  ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
            101264260  phospholipase A-2-activating protein isoform X1 [KO:K14018]
            101258124  ubiquitin receptor RAD23d isoform X1 [KO:K10839]
            101251966  ubiquitin receptor RAD23b isoform X1 [KO:K10839]
            101249452  ubiquitin receptor RAD23c [KO:K10839]
            101246007  RAD23d; ubiquitin receptor RAD23d [KO:K10839]
            101258726  ubiquitin domain-containing protein DSK2b-like [KO:K04523]
            101259610  ubiquitin domain-containing protein DSK2b-like [KO:K04523]
            109119473  ubiquitin domain-containing protein DSK2b-like [KO:K04523]
            101255157  ubiquitin domain-containing protein DSK2b isoform X2 [KO:K04523]
            101265008  ubiquitin domain-containing protein DSK2b [KO:K04523]
            100736452  putative peptide:N-glycanase [KO:K01456] [EC:3.5.1.52]
            101258019  ataxin-3 homolog [KO:K11863] [EC:3.4.22.-]
            101267369  probable ubiquitin conjugation factor E4 [KO:K10597] [EC:2.3.2.27]
            101246209  eIF-2-alpha kinase GCN2 isoform X1 [KO:K16196] [EC:2.7.11.1]
            101257451  eukaryotic translation initiation factor 2 alpha subunit family protein [KO:K03237]
            101247955  subtilisin-like protease SBT6.1 isoform X1 [KO:K08653] [EC:3.4.21.112]
            101252708  membrane-bound transcription factor site-2 protease homolog isoform X1 [KO:K07765] [EC:3.4.24.85]
            101254520  membrane-bound transcription factor site-2 protease homolog isoform X4 [KO:K07765] [EC:3.4.24.85]
            101262583  serine/threonine-protein kinase/endoribonuclease IRE1a isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
            101263702  serine/threonine-protein kinase/endoribonuclease IRE1b-like isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
            101257809  probable E3 ubiquitin ligase SUD1 isoform X1 [KO:K10661] [EC:2.3.2.27]
            101266615  ubiquitin-conjugating enzyme E2 32 [KO:K10578] [EC:2.3.2.23]
            543683  ubiquitin conjugating enzyme 2 [KO:K04554] [EC:2.3.2.23]
            101248401  ubiquitin-conjugating enzyme E2 34 isoform X1 [KO:K04554] [EC:2.3.2.23]
            101256619  ubiquitin-conjugating enzyme E2 7 [KO:K10575] [EC:2.3.2.23]
            101262710  ubiquitin-conjugating enzyme E2 7 [KO:K10575] [EC:2.3.2.23]
            101262418  ubiquitin-conjugating enzyme E2 7 isoform X1 [KO:K10575] [EC:2.3.2.23]
            101262721  ubiquitin-conjugating enzyme E2 7 [KO:K10575] [EC:2.3.2.23]
            101257051  ERAD-associated E3 ubiquitin-protein ligase HRD1B [KO:K10601] [EC:2.3.2.27]
            101262220  ERAD-associated E3 ubiquitin-protein ligase HRD1B isoform X1 [KO:K10601] [EC:2.3.2.27]
            101256837  E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
            101250440  uncharacterized protein LOC101250440 [KO:K10666] [EC:2.3.2.27]
            101262966  RING finger protein 5-like [KO:K10666] [EC:2.3.2.27]
            101247183  E3 ubiquitin-protein ligase RMA1H1 [KO:K10666] [EC:2.3.2.27]
            101263175  E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
            101255151  LOW QUALITY PROTEIN: uncharacterized protein LOC101255151 [KO:K10666] [EC:2.3.2.27]
            101243642  E3 ubiquitin-protein ligase RMA3-like [KO:K10666] [EC:2.3.2.27]
            101262152  E3 ubiquitin-protein ligase RMA1H1 [KO:K10666] [EC:2.3.2.27]
            101262459  E3 ubiquitin-protein ligase RMA1H1 [KO:K10666] [EC:2.3.2.27]
            101267944  RING finger protein 5 isoform X1 [KO:K10666] [EC:2.3.2.27]
            101253976  E3 ubiquitin-protein ligase RMA1H1-like [KO:K10666] [EC:2.3.2.27]
            101248949  E3 ubiquitin-protein ligase RMA3 isoform X1 [KO:K10666] [EC:2.3.2.27]
            101248399  uncharacterized protein LOC101248399 [KO:K10666] [EC:2.3.2.27]
            101264841  E3 ubiquitin-protein ligase RMA1H1 [KO:K10666] [EC:2.3.2.27]
            101254012  E3 ubiquitin-protein ligase RMA3-like [KO:K10666] [EC:2.3.2.27]
            101243872  ERAD-associated E3 ubiquitin-protein ligase component HRD3A [KO:K14026]
            101247432  E3 ubiquitin protein ligase RIN2 isoform X2 [KO:K10636] [EC:2.3.2.36]
            101254909  E3 ubiquitin-protein ligase CHIP [KO:K09561] [EC:2.3.2.27]
            101250739  ubiquitin-conjugating enzyme E2 28 [KO:K06689] [EC:2.3.2.23]
            100303774  UBC; ubiquitin conjugating enzyme E2 [KO:K06689] [EC:2.3.2.23]
            101265051  ubiquitin-conjugating enzyme E2 10 [KO:K06689] [EC:2.3.2.23]
            101260872  ubiquitin-conjugating enzyme E2 28 [KO:K06689] [EC:2.3.2.23]
            101264951  ubiquitin-conjugating enzyme E2 28 [KO:K06689] [EC:2.3.2.23]
            101249890  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            101259644  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
            101249757  cullin-1 [KO:K03347]
            101255260  SSK2; SKP1-like protein 11-like [KO:K03094]
            101255553  SSK3; SKP1-like protein 11-like [KO:K03094]
            101268040  SKP1-like protein 1A [KO:K03094]
            101256470  SKP1-like protein 1B [KO:K03094]
            101246871  SKP1-like protein 1B [KO:K03094]
            101246572  SKP1-like protein 1B [KO:K03094]
            101264381  SKP1-like protein 11 [KO:K03094]
            101244826  SKP1-like protein 11 [KO:K03094]
            101246287  SKP1-like protein 1B [KO:K03094]
            101243954  SKP1-like protein 1A [KO:K03094]
            101256150  SKP1-like protein 1 [KO:K03094]
            101268328  SKP1; S-phase kinase-associated protein 1 [KO:K03094]
            101250894  SKP1-like protein 1B [KO:K03094]
            101251188  SKP1-like protein 11 [KO:K03094]
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
REL_PATHWAY sly00510  N-Glycan biosynthesis
            sly03050  Proteasome
            sly03060  Protein export
KO_PATHWAY  ko04141
///
