KEGG   PATHWAY: xco04142
Entry
xco04142                    Pathway                                
Name
Lysosome - Xiphophorus couchianus (Monterrey platyfish)
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
xco04142  Lysosome
xco04142

Other DBs
GO: 0005764
Organism
Xiphophorus couchianus (Monterrey platyfish) [GN:xco]
Gene
114149974  V-type proton ATPase 116 kDa subunit a-like [KO:K02154]
114160259  atp6v0a1; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
114139538  V-type proton ATPase 116 kDa subunit a-like [KO:K02154]
114154869  atp6v0a2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
114150880  V-type proton ATPase 116 kDa subunit a-like isoform X1 [KO:K02154]
114142797  V-type proton ATPase subunit d 1 [KO:K02146]
114146751  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
114140292  atp6ap1; V-type proton ATPase subunit S1 [KO:K03662]
114140367  V-type proton ATPase subunit S1-like [KO:K03662]
114159520  V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
114156501  V-type proton ATPase 16 kDa proteolipid subunit-like [KO:K02155]
114146791  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
114154571  dmxl1; dmX-like protein 1 isoform X1 [KO:K24155]
114142482  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
114149621  wdr7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
114158525  nuclear receptor coactivator 7-like isoform X1 [KO:K25442]
114134688  nuclear receptor coactivator 7-like isoform X1 [KO:K25442]
114135284  ctsa; lysosomal protective protein isoform X1 [KO:K13289] [EC:3.4.16.5]
114142723  lysosomal protective protein-like [KO:K13289] [EC:3.4.16.5]
114143461  cathepsin B-like [KO:K01363] [EC:3.4.22.1]
114158275  cathepsin B-like [KO:K01363] [EC:3.4.22.1]
114133233  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
114142967  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
114159781  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
114160681  cathepsin E-like [KO:K01382] [EC:3.4.23.34]
114139016  cathepsin F-like isoform X1 [KO:K01373] [EC:3.4.22.41]
114159939  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
114142267  cathepsin K-like [KO:K01371] [EC:3.4.22.38]
114150480  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
114154740  ctsl; cathepsin L1 isoform X1 [KO:K01365] [EC:3.4.22.15]
114134492  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
114139560  ctso; cathepsin O [KO:K01374] [EC:3.4.22.42]
114156396  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
114142240  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
114147224  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
114138823  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
114136290  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
114134070  lgmn; legumain isoform X1 [KO:K01369] [EC:3.4.22.34]
114134419  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
114139456  gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
114144461  beta-galactosidase-like [KO:K12309] [EC:3.2.1.23]
114144344  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
114160012  gaa; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
114141690  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
114154579  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
114159062  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
114150688  naglu; alpha-N-acetylglucosaminidase isoform X1 [KO:K01205] [EC:3.2.1.50]
114134259  galc; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
114152576  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
114155708  fuca1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
114134053  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
114152585  beta-hexosaminidase subunit alpha-like [KO:K12373] [EC:3.2.1.52]
114149579  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
114134593  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
114145277  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
114156354  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
114154338  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114149323  hyaluronidase-3-like [KO:K01197] [EC:3.2.1.35]
114143524  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
114135144  hyal1; hyaluronidase-1 isoform X1 [KO:K01197] [EC:3.2.1.35]
114135145  hyaluronidase-1-like isoform X1 [KO:K01197] [EC:3.2.1.35]
114135147  hyaluronidase-1-like isoform X1 [KO:K01197] [EC:3.2.1.35]
114135148  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114135149  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114135150  hyal2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
114135788  hyaluronidase-1-like isoform X1 [KO:K01197] [EC:3.2.1.35]
114135789  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114135790  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114142534  hyaluronidase-like [KO:K01197] [EC:3.2.1.35]
114135882  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
114143797  hyaluronidase-4-like [KO:K01197] [EC:3.2.1.35]
114157974  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
114149560  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
114150964  arsg; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
114142561  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
114149340  N-acetylglucosamine-6-sulfatase-like [KO:K01137] [EC:3.1.6.14]
114161155  gns; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
114139558  ids; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
114144623  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
114150600  lipa; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
114133873  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
114150832  deoxyribonuclease-2-beta-like [KO:K01158] [EC:3.1.22.1]
114150833  deoxyribonuclease-2-alpha-like [KO:K01158] [EC:3.1.22.1]
114145165  deoxyribonuclease-2-beta-like isoform X1 [KO:K01158] [EC:3.1.22.1]
114141519  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
114140438  acp2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
114144211  acp5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
114152745  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
114144122  asah1; LOW QUALITY PROTEIN: acid ceramidase [KO:K12348] [EC:3.5.1.23]
114139533  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
114155189  prosaposin-like [KO:K12382]
114137480  psap; prosaposin isoform X1 [KO:K12382]
114150089  prosaposin-like [KO:K12382]
114139626  gm2a; ganglioside GM2 activator [KO:K12383]
114141548  lysosomal thioesterase PPT2-A-like [KO:K01074] [EC:3.1.2.22]
114156111  ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
114156141  ppt2; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
114148546  lysosome-associated membrane glycoprotein 1-like [KO:K06528]
114143297  lamp1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
114138879  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
114150561  lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
114157520  macrosialin-like isoform X1 [KO:K06501]
114151793  CD63 antigen-like [KO:K06497]
114140857  cd63; CD63 antigen [KO:K06497]
114149331  lysosome membrane protein 2-like isoform X1 [KO:K12384]
114153998  lysosome membrane protein 2-like isoform X1 [KO:K12384]
114149218  lysosome membrane protein 2-like [KO:K12384]
114146689  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
114134829  npc2; NPC intracellular cholesterol transporter 2 [KO:K13443]
114151442  ctns; cystinosin isoform X1 [KO:K12386]
114137782  slc17a5; sialin [KO:K12301]
114155995  sialin-like [KO:K12301]
114141140  natural resistance-associated macrophage protein 2-like isoform X1 [KO:K21398]
114136286  natural resistance-associated macrophage protein 2-like isoform X1 [KO:K21398]
114145570  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
114158679  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
114156545  lysosomal-associated transmembrane protein 4B-like [KO:K12387]
114155167  abca2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
114154309  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
114158401  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
114155002  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
114160999  sortilin-like isoform X1 [KO:K12388]
114135539  sortilin-like [KO:K12388]
114141662  sortilin-like [KO:K12388]
114147612  cln3; battenin isoform X1 [KO:K12389]
114148937  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
114150488  uncharacterized protein LOC114150488 isoform X1 [KO:K12307]
114157558  mfsd8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
114146904  major facilitator superfamily domain-containing protein 8-like [KO:K12307]
114137570  heparan-alpha-glucosaminide N-acetyltransferase-like isoform X1 [KO:K10532] [EC:2.3.1.78]
114144330  heparan-alpha-glucosaminide N-acetyltransferase-like [KO:K10532] [EC:2.3.1.78]
114135763  sumf1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
114160852  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
114158732  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
114142028  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
114158495  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
114139365  m6pr; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
114144699  clta; clathrin light chain A isoform X1 [KO:K04644]
114139294  cltb; clathrin light chain B isoform X1 [KO:K04645]
114152738  clathrin heavy chain 1-like isoform X1 [KO:K04646]
114154072  cltcl1; clathrin heavy chain 2 isoform X1 [KO:K04646]
114161568  clathrin heavy chain 1 isoform X1 [KO:K04646]
114146722  AP-1 complex subunit gamma-1-like [KO:K12391]
114143009  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
114154556  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
114145327  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
114151324  AP-1 complex subunit mu-1-like [KO:K12393]
114146887  ap1m1; AP-1 complex subunit mu-1 [KO:K12393]
114157931  AP-1 complex subunit sigma-1A [KO:K12394]
114143328  AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
114150678  AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
114146175  AP-1 complex subunit sigma-1A-like isoform X1 [KO:K12394]
114133470  ap1s3; AP-1 complex subunit sigma-3 [KO:K12395]
114150753  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
114149493  ap3b1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
114151309  ap3b2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
114155015  AP-3 complex subunit mu-2 [KO:K12398]
114137925  AP-3 complex subunit mu-1-like [KO:K12398]
114142940  AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
114154743  ap3s1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
114159671  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
114148151  ap4b1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
114153592  ap4m1; AP-4 complex subunit mu-1 isoform X1 [KO:K12402]
114155717  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
114145190  ADP-ribosylation factor-binding protein GGA3-like isoform X1 [KO:K12404]
114144530  ADP-ribosylation factor-binding protein GGA1-like isoform X1 [KO:K12404]
114159891  ADP-ribosylation factor-binding protein GGA1-like isoform X1 [KO:K12404]
114145028  gga3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
114145463  mucolipin-1-like isoform X1 [KO:K04992]
114148262  mcoln1; mucolipin-1 isoform X1 [KO:K04992]
114159957  uncharacterized protein LOC114159957 isoform X1 [KO:K19363]
114145517  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
114154744  litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
114159739  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X1 [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
xco00511  Other glycan degradation
xco00531  Glycosaminoglycan degradation
xco04130  SNARE interactions in vesicular transport
xco04140  Autophagy - animal
xco04144  Endocytosis
KO pathway
ko04142   
LinkDB

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