KEGG   PATHWAY: rtem04142
Entry
rtem04142                   Pathway                                
Name
Lysosome - Rana temporaria (common frog)
Description
Lysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than 40 hydrolases in an acidic environment (pH of about 5). After synthesis in the ER, lysosomal enzymes are decorated with mannose-6-phosphate residues, which are recognized by mannose-6-phosphate receptors in the trans-Golgi network. They are packaged into clathrin-coated vesicles and are transported to late endosomes. Substances for digestion are acquired by the lysosomes via a series of processes including endocytosis, phagocytosis, and autophagy.
Class
Cellular Processes; Transport and catabolism
Pathway map
rtem04142  Lysosome
rtem04142

Other DBs
GO: 0005764
Organism
Rana temporaria (common frog) [GN:rtem]
Gene
120909274  TCIRG1; V-type proton ATPase 116 kDa subunit a3 [KO:K02154]
120919045  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
120932747  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
120934673  ATP6V0A2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
120941258  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
120917631  V-type proton ATPase subunit d 1 [KO:K02146]
120940990  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
120931843  V-type proton ATPase subunit S1-like [KO:K03662]
120913928  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
120943367  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
120946149  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
120931336  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
120931958  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
120927038  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
120937292  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
120918572  lysosomal protective protein-like isoform X1 [KO:K13289] [EC:3.4.16.5]
120918573  lysosomal protective protein-like [KO:K13289] [EC:3.4.16.5]
120936191  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
120928963  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
120916518  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
120917294  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
120917295  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
120930385  cathepsin E-like [KO:K01382] [EC:3.4.23.34]
120927148  CTSE; cathepsin E isoform X1 [KO:K01382] [EC:3.4.23.34]
120917498  CTSF; cathepsin F [KO:K01373] [EC:3.4.22.41]
120909938  mast cell protease 1A-like [KO:K01319] [EC:3.4.21.20]
120921060  cathepsin K-like isoform X1 [KO:K01371] [EC:3.4.22.38]
120921061  cathepsin K-like [KO:K01371] [EC:3.4.22.38]
120931432  zingipain-2-like [KO:K01365] [EC:3.4.22.15]
120931433  zingipain-2-like [KO:K01365] [EC:3.4.22.15]
120931434  ervatamin-C-like [KO:K01365] [EC:3.4.22.15]
120931563  cathepsin S-like [KO:K01365] [EC:3.4.22.15]
120942021  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
120942037  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
120920237  CTSO; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
120920090  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
120920158  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
120920159  cathepsin S-like isoform X1 [KO:K01368] [EC:3.4.22.27]
120920357  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
120917542  cathepsin W-like isoform X1 [KO:K08569] [EC:3.4.22.-]
120917543  cathepsin W-like [KO:K08569] [EC:3.4.22.-]
120918214  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
120920961  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
120928863  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
120913078  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
120940460  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
120919155  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
120919333  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
120913975  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
120943521  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
120918258  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
120920305  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
120926640  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
120937387  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120926788  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120929744  beta-hexosaminidase subunit beta-like isoform X1 [KO:K12373] [EC:3.2.1.52]
120929770  HEXB; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
120918357  MANBA; beta-mannosidase isoform X1 [KO:K01192] [EC:3.2.1.25]
120933374  MAN2B1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
120913260  NEU1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
120931837  hyaluronidase-like [KO:K01197] [EC:3.2.1.35]
120944794  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
120944795  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
120944967  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
120944968  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
120944969  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
120944970  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
120931568  ARSA; arylsulfatase A isoform X1 [KO:K01134] [EC:3.1.6.8]
120929350  LOW QUALITY PROTEIN: arylsulfatase B-like [KO:K01135] [EC:3.1.6.12]
120934180  LOW QUALITY PROTEIN: arylsulfatase B-like [KO:K01135] [EC:3.1.6.12]
120918847  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
120917919  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
120932008  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
120913664  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
120919573  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
120947097  lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
120947099  putative lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
120917468  PLA2G15; LOW QUALITY PROTEIN: phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
120945979  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
120933354  DNASE2; deoxyribonuclease-2-alpha isoform X1 [KO:K01158] [EC:3.1.22.1]
120917139  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
120933339  ACP5; tartrate-resistant acid phosphatase type 5 isoform X1 [KO:K14379] [EC:3.1.3.2]
120928788  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
120921971  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
120921113  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
120908951  prosaposin isoform X1 [KO:K12382]
120932616  ganglioside GM2 activator-like [KO:K12383]
120932617  ganglioside GM2 activator-like [KO:K12383]
120932619  ganglioside GM2 activator-like [KO:K12383]
120913247  PPT2; lysosomal thioesterase PPT2 isoform X1 [KO:K01074] [EC:3.1.2.22]
120926781  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
120913753  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
120926387  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
120936796  LAMP3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
120929555  CD63; CD63 antigen [KO:K06497]
120944289  CD63 antigen-like [KO:K06497]
120916889  SCARB2; lysosome membrane protein 2 isoform X1 [KO:K12384]
120940925  NPC1; NPC intracellular cholesterol transporter 1 [KO:K12385]
120920710  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
120921993  NPC intracellular cholesterol transporter 2-like isoform X1 [KO:K13443]
120927749  CTNS; cystinosin isoform X1 [KO:K12386]
120937036  SLC17A5; sialin [KO:K12301]
120944222  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
120929429  SLC11A2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
120938008  lysosomal-associated transmembrane protein 5-like [KO:K12387]
120941407  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
120926947  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
120936301  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
120914035  ABCA2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
120934481  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
120937197  CD164; sialomucin core protein 24 [KO:K06546]
120933083  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
120927169  SORT1; sortilin [KO:K12388]
120943084  CLN3; battenin [KO:K12389]
120929694  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
120936946  major facilitator superfamily domain-containing protein 8-like [KO:K12307]
120918878  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
120910441  heparan-alpha-glucosaminide N-acetyltransferase-like [KO:K10532] [EC:2.3.1.78]
120914568  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
120944901  SUMF1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
120932134  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
120943436  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
120927614  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
120937585  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
120946927  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
120946948  CLTA; clathrin light chain A isoform X1 [KO:K04644]
120932179  CLTB; clathrin light chain B isoform X1 [KO:K04645]
120926765  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
120936292  CLTCL1; clathrin heavy chain 2 isoform X1 [KO:K04646]
120917937  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
120941127  AP1G2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
120939359  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
120913278  AP-1 complex subunit mu-1 [KO:K12393]
120933298  AP1M2; AP-1 complex subunit mu-2 [KO:K12393]
120933480  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
120936570  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
120913407  AP3D1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
120929397  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
120931450  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
120909047  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
120933162  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
120931216  AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
120931886  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
120931343  AP4E1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
120927036  AP4B1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
120933514  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
120921003  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
120919168  GGA3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
120945011  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
120933207  MCOLN1; mucolipin-1 [KO:K04992]
120943594  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X1 [KO:K19363]
120943596  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
Compound
C00002  ATP
C00008  ADP
C00159  D-Mannose
C00275  D-Mannose 6-phosphate
Reference
PMID:12628346
  Authors
Eskelinen EL, Tanaka Y, Saftig P
  Title
At the acidic edge: emerging functions for lysosomal membrane proteins.
  Journal
Trends Cell Biol 13:137-45 (2003)
DOI:10.1016/S0962-8924(03)00005-9
Reference
PMID:1883197
  Authors
Neufeld EF
  Title
Lysosomal storage diseases.
  Journal
Annu Rev Biochem 60:257-80 (1991)
DOI:10.1146/annurev.bi.60.070191.001353
Reference
PMID:2943218
  Authors
von Figura K, Hasilik A
  Title
Lysosomal enzymes and their receptors.
  Journal
Annu Rev Biochem 55:167-93 (1986)
DOI:10.1146/annurev.bi.55.070186.001123
Reference
PMID:15987739
  Authors
Janvier K, Bonifacino JS
  Title
Role of the endocytic machinery in the sorting of lysosome-associated membrane proteins.
  Journal
Mol Biol Cell 16:4231-42 (2005)
DOI:10.1091/mbc.E05-03-0213
Reference
PMID:18635948
  Authors
Vergarajauregui S, Puertollano R
  Title
Mucolipidosis type IV: the importance of functional lysosomes for efficient autophagy.
  Journal
Autophagy 4:832-4 (2008)
DOI:10.4161/auto.6567
Reference
PMID:34249946
  Authors
Jaskolka MC, Winkley SR, Kane PM
  Title
RAVE and Rabconnectin-3 Complexes as Signal Dependent Regulators of Organelle Acidification.
  Journal
Front Cell Dev Biol 9:698190 (2021)
DOI:10.3389/fcell.2021.698190
Reference
PMID:34646033
  Authors
Majdoul S, Compton AA
  Title
Lessons in self-defence: inhibition of virus entry by intrinsic immunity.
  Journal
Nat Rev Immunol 10.1038/s41577-021-00626-8 (2021)
DOI:10.1038/s41577-021-00626-8
Related
pathway
rtem00511  Other glycan degradation
rtem00531  Glycosaminoglycan degradation
rtem04130  SNARE interactions in vesicular transport
rtem04140  Autophagy - animal
rtem04144  Endocytosis
KO pathway
ko04142   
LinkDB

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