KEGG   PATHWAY: xhe04142
Entry
xhe04142                    Pathway                                
Name
Lysosome - Xiphophorus hellerii (green swordtail)
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
xhe04142  Lysosome
xhe04142

Other DBs
GO: 0005764
Organism
Xiphophorus hellerii (green swordtail) [GN:xhe]
Gene
116707783  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
116707827  ap3b2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
116708410  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
116708543  meak7; MTOR-associated protein MEAK7 isoform X1 [KO:K27947]
116708644  [KO:K01279] [EC:3.4.14.9]
116708757  npc2; NPC intracellular cholesterol transporter 2 [KO:K13443]
116708815  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
116708863  lgmn; legumain isoform X1 [KO:K01369] [EC:3.4.22.34]
116708979  [KO:K01279] [EC:3.4.14.9]
116709008  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
116709209  [KO:K25442]
116709385  galc; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
116709663  [KO:K01197] [EC:3.2.1.35]
116709760  [KO:K01197] [EC:3.2.1.35]
116709844  [KO:K01197] [EC:3.2.1.35]
116710199  [KO:K01197] [EC:3.2.1.35]
116710392  [KO:K01197] [EC:3.2.1.35]
116710478  [KO:K12388]
116710545  [KO:K12373] [EC:3.2.1.52]
116710614  [KO:K21398]
116710619  [KO:K01197] [EC:3.2.1.35]
116710678  sumf1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
116710825  [KO:K13289] [EC:3.4.16.5]
116710874  [KO:K01197] [EC:3.2.1.35]
116710875  [KO:K01197] [EC:3.2.1.35]
116710933  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
116711119  [KO:K01197] [EC:3.2.1.35]
116712640  [KO:K10532] [EC:2.3.1.78]
116713073  psap; prosaposin isoform X1 [KO:K12382]
116713106  slc17a5; sialin [KO:K12301]
116713214  [KO:K12398]
116713951  [KO:K01373] [EC:3.4.22.41]
116714148  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
116714351  cltb; clathrin light chain B isoform X1 [KO:K04645]
116714471  m6pr; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
116714642  ctso; cathepsin O [KO:K01374] [EC:3.4.22.42]
116714683  gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
116714705  [KO:K08568] [EC:3.4.18.1]
116714765  cd63; CD63 antigen [KO:K06497]
116714772  [KO:K02154]
116714780  ids; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
116714797  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
116714799  gm2a; ganglioside GM2 activator [KO:K12383]
116715814  acp2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
116716394  [KO:K12387]
116716974  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
116717363  [KO:K01368] [EC:3.4.22.27]
116717364  [KO:K01371] [EC:3.4.22.38]
116717417  [KO:K01074] [EC:3.1.2.22]
116717475  [KO:K03662]
116717527  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
116717803  [KO:K12387]
116717823  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
116718068  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
116718092  [KO:K21398]
116718196  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
116718242  lamp1; lysosome-associated membrane glycoprotein 1 isoform X1 [KO:K06528]
116718269  [KO:K02146]
116718549  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
116718562  [KO:K12399]
116718667  [KO:K12394]
116718743  [KO:K01363] [EC:3.4.22.1]
116718862  [KO:K13289] [EC:3.4.16.5]
116719271  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
116719500  [KO:K19363]
116719553  asah1; LOW QUALITY PROTEIN: acid ceramidase [KO:K12348] [EC:3.5.1.23]
116719616  acp5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
116719702  [KO:K12316] [EC:3.2.1.20]
116719896  clta; clathrin light chain A isoform X1 [KO:K04644]
116719922  [KO:K01158] [EC:3.1.22.1]
116719941  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
116720019  [KO:K04992]
116720056  [KO:K12309] [EC:3.2.1.23]
116720306  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
116720317  [KO:K19363]
116720330  [KO:K10532] [EC:2.3.1.78]
116720340  gga3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
116720465  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
116720499  [KO:K12404]
116720619  [KO:K12404]
116720671  [KO:K19363]
116721234  [KO:K12394]
116721327  [KO:K08568] [EC:3.4.18.1]
116721591  [KO:K12307]
116721592  [KO:K01197] [EC:3.2.1.35]
116721808  [KO:K12391]
116721824  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
116721848  atp6v1h; LOW QUALITY PROTEIN: V-type proton ATPase subunit H [KO:K02144]
116721857  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
116722048  [KO:K12393]
116722305  [KO:K03662]
116722681  [KO:K06528]
116723694  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
116724080  [KO:K01137] [EC:3.1.6.14]
116724097  scarb2; lysosome membrane protein 2 isoform X1 [KO:K12384]
116724172  wdr7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
116724191  ap4b1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
116724398  [KO:K12384]
116724791  [KO:K02154]
116724800  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
116724957  [KO:K12382]
116724961  ap3b1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
116725045  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
116725233  [KO:K01365] [EC:3.4.22.15]
116725316  [KO:K12307]
116725425  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
116725607  [KO:K01158] [EC:3.1.22.1]
116725608  [KO:K01158] [EC:3.1.22.1]
116725676  lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
116725841  [KO:K12393]
116726053  ctns; cystinosin isoform X1 [KO:K12386]
116726314  [KO:K12388]
116726335  [KO:K12394]
116726751  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
116726858  [KO:K02154]
116726966  naglu; alpha-N-acetylglucosaminidase isoform X1 [KO:K01205] [EC:3.2.1.50]
116727023  [KO:K06497]
116727051  arsg; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
116727065  [KO:K02155]
116727300  [KO:K01052] [EC:3.1.1.13]
116727610  litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
116727823  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
116727937  ap4m1; AP-4 complex subunit mu-1 isoform X1 [KO:K12402]
116727980  [KO:K04646]
116728596  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
116729097  [KO:K04646]
116729158  abca2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
116729292  ctsl; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
116729493  [KO:K12384]
116729803  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
116730030  atp6v0a2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
116730105  [KO:K01365] [EC:3.4.22.15]
116730172  [KO:K12398]
116730184  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
116730210  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
116730225  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
116730343  [KO:K12382]
116730396  dmxl1; dmX-like protein 1 isoform X1 [KO:K24155]
116730445  ap3s1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
116730670  [KO:K12387]
116730764  ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
116730861  fuca1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
116731400  [KO:K12301]
116731540  ppt2; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
116731587  [KO:K01368] [EC:3.4.22.27]
116731588  [KO:K01371] [EC:3.4.22.38]
116731929  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
116732736  mfsd8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
116732776  [KO:K06501]
116732858  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
116733150  [KO:K12387]
116733266  [KO:K12394]
116733466  arsa; LOW QUALITY PROTEIN: arylsulfatase A [KO:K01134] [EC:3.1.6.8]
116733744  [KO:K01363] [EC:3.4.22.1]
116733862  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
116734214  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
116734473  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
116734498  [KO:K25442]
116734632  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
116734704  [KO:K06129] [EC:3.1.1.5]
116734818  [KO:K02155]
116734987  [KO:K19363]
116734988  [KO:K19363]
116734989  [KO:K19363]
116735110  [KO:K01379] [EC:3.4.23.5]
116735194  snrnp25; U11/U12 small nuclear ribonucleoprotein 25 kDa protein isoform X1 [KO:K19363]
116735348  [KO:K12404]
116735523  cln3; battenin isoform X1 [KO:K12389]
116735558  gaa; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
116735638  [KO:K04992]
116735753  [KO:K02154]
116736217  ap4e1; LOW QUALITY PROTEIN: AP-4 complex subunit epsilon-1 [KO:K12400]
116736477  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
116736891  [KO:K12388]
116737075  [KO:K01382] [EC:3.4.23.34]
116737168  gns; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
116737206  ap1s3; AP-1 complex subunit sigma-3 [KO:K12395]
116737363  [KO:K04646]
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
xhe00511  Other glycan degradation
xhe00531  Glycosaminoglycan degradation
xhe04130  SNARE interactions in vesicular transport
xhe04140  Autophagy - animal
xhe04144  Endocytosis
KO pathway
ko04142   

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