KEGG   PATHWAY: tgu04142
Entry
tgu04142                    Pathway                                
Name
Lysosome - Taeniopygia guttata (zebra finch)
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
tgu04142  Lysosome
tgu04142

Other DBs
GO: 0005764
Organism
Taeniopygia guttata (zebra finch) [GN:tgu]
Gene
100221499  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
100231607  TCIRG1; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
100229310  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform X6 [KO:K02154]
100218036  ATP6V0A2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
100222039  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
100227657  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
100220186  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
100225098  ATP6AP1; V-type proton ATPase subunit S1 isoform X1 [KO:K03662]
100221539  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
100190528  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
100232458  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
100232254  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
116806851  WD repeat-containing protein 7-like [KO:K24738]
100232465  WD repeat-containing protein 7 isoform X1 [KO:K24738]
100221439  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
100220062  CTSA; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
100190482  CTSB; cathepsin B precursor [KO:K01363] [EC:3.4.22.1]
100230748  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
100232592  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
100228499  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
100218931  cathepsin E [KO:K01382] [EC:3.4.23.34]
100225270  mast cell protease 1A [KO:K01319] [EC:3.4.21.20]
115496729  CTSH; pro-cathepsin H isoform X1 [KO:K01366] [EC:3.4.22.16]
101233119  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
100232421  CTSL; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
100226165  cathepsin L1-like isoform X1 [KO:K01365] [EC:3.4.22.15]
100224161  CTSO; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
100223082  CTSS; cathepsin S isoform X2 [KO:K01368] [EC:3.4.22.27]
100225523  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
100220965  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
100232321  TPP1; tripeptidyl-peptidase 1 isoform X1 [KO:K01279] [EC:3.4.14.9]
100218534  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
100226450  GLB1; beta-galactosidase isoform X1 [KO:K12309] [EC:3.2.1.23]
100227842  GAA; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
100226089  lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
100227578  lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
115498471  lysosomal acid glucosylceramidase-like [KO:K01201] [EC:3.2.1.45]
115498459  lysosomal acid glucosylceramidase-like [KO:K01201] [EC:3.2.1.45]
100231378  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
100229129  NAGA; LOW QUALITY PROTEIN: alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
100232350  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
100224899  GALC; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
100222352  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
100227568  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
100228048  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
100225163  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
100228061  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
100218699  MANBA; beta-mannosidase isoform X1 [KO:K01192] [EC:3.2.1.25]
100229824  SPAM1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
100224131  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
100228780  hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
100219184  hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
100227026  HYAL4; LOW QUALITY PROTEIN: hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
100222466  HYAL3; hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
115492587  ARSA; arylsulfatase A isoform X1 [KO:K01134] [EC:3.1.6.8]
100228383  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
100232718  ARSG; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
100222785  GALNS; N-acetylgalactosamine-6-sulfatase isoform X5 [KO:K01132] [EC:3.1.6.4]
100228596  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
100231299  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
100230664  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
100219865  putative lysosomal acid lipase/cholesteryl ester hydrolase isoform X1 [KO:K01052] [EC:3.1.1.13]
115495738  lipase member K-like [KO:K01052] [EC:3.1.1.13]
100219000  lysosomal acid lipase/cholesteryl ester hydrolase-like isoform X2 [KO:K01052] [EC:3.1.1.13]
100228608  lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
100228600  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
100231880  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
100224806  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
115491698  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
100221728  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
100223185  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
100231883  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
100223534  PSAP; prosaposin isoform X1 [KO:K12382]
100220618  prosaposin isoform X1 [KO:K12382]
100229991  GM2A; ganglioside GM2 activator [KO:K12383]
100190233  PPT1; palmitoyl-protein thioesterase 1 precursor [KO:K01074] [EC:3.1.2.22]
100219894  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
100218047  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
101233525  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
100190617  SCARB2; lysosome membrane protein 2 [KO:K12384]
100230708  NPC1; NPC intracellular cholesterol transporter 1 isoform X1 [KO:K12385]
100225420  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
100223329  CTNS; cystinosin [KO:K12386]
100223041  SLC17A5; sialin [KO:K12301]
100229331  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
115491394  natural resistance-associated macrophage protein 2 [KO:K21398]
100223064  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
100190407  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
100231461  LAPTM5; lysosomal-associated transmembrane protein 5 isoform X2 [KO:K12387]
100231140  ABCA2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
100218961  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
101233597  CD164; sialomucin core protein 24 isoform X1 [KO:K06546]
100227643  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
100220546  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
100228690  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
100228309  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
100231956  SUMF1; formylglycine-generating enzyme isoform X1 [KO:K13444] [EC:1.8.3.7]
100225345  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
100190673  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
100217812  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
100232425  IGF2R; cation-independent mannose-6-phosphate receptor isoform X1 [KO:K06564]
100225036  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
100190164  CLTA; clathrin light chain A [KO:K04644]
100218543  CLTB; clathrin light chain B isoform X1 [KO:K04645]
100228172  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
100228504  CLTCL1; clathrin heavy chain 2 isoform X4 [KO:K04646]
100217944  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
100232032  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
100227179  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
115491761  AP1M2; AP-1 complex subunit mu-2 [KO:K12393]
100229865  AP1S2; AP-1 complex subunit sigma-2 isoform X2 [KO:K12394]
115492730  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
100221442  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
100228101  AP3D1; AP-3 complex subunit delta-1 isoform X2 [KO:K12396]
100226392  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
100225464  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
100228948  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
100230902  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
100190508  AP3S2; AP-3 complex subunit sigma-2 [KO:K12399]
100223838  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
100218760  AP4E1; AP-4 complex subunit epsilon-1 [KO:K12400]
100218221  AP4B1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
100221043  AP4S1; AP-4 complex subunit sigma-1 isoform X1 [KO:K12403]
100223427  GGA1; ADP-ribosylation factor-binding protein GGA1 isoform X2 [KO:K12404]
100217744  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
100228476  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
105760771  MCOLN1; mucolipin-1 isoform X1 [KO:K04992]
100225426  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [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
tgu00511  Other glycan degradation
tgu00531  Glycosaminoglycan degradation
tgu04130  SNARE interactions in vesicular transport
tgu04140  Autophagy - animal
tgu04144  Endocytosis
KO pathway
ko04142   

  All links  
Genome (1)   
   KEGG GENOME (1)   
Gene (128)   
   KEGG GENES (128)   
All databases (129)   

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