KEGG   PATHWAY: alim04142
Entry
alim04142                   Pathway                                
Name
Lysosome - Austrofundulus limnaeus (annual killifish)
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
alim04142  Lysosome
alim04142

Other DBs
GO: 0005764
Organism
Austrofundulus limnaeus (annual killifish) [GN:alim]
Gene
106528122  atp6v0a1; V-type proton ATPase 116 kDa subunit a isoform 1 isoform X1 [KO:K02154]
106532937  V-type proton ATPase 116 kDa subunit a isoform 1-like isoform X1 [KO:K02154]
106521672  atp6v0a2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
106517239  V-type proton ATPase 116 kDa subunit a isoform 3-like isoform X1 [KO:K02154]
106514499  V-type proton ATPase 116 kDa subunit a isoform 2-like [KO:K02154]
106526755  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
106534494  V-type proton ATPase subunit d 1-like [KO:K02146]
106524526  V-type proton ATPase subunit H [KO:K02144]
106535376  V-type proton ATPase subunit S1-like [KO:K03662]
106533687  V-type proton ATPase subunit S1-like [KO:K03662]
106516477  V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
106517404  V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
106532869  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
106513676  dmxl1; dmX-like protein 1 isoform X1 [KO:K24155]
106530931  dmxl2; dmX-like protein 2 [KO:K24155]
106536389  dmX-like protein 2 isoform X1 [KO:K24155]
106530893  wdr7; WD repeat-containing protein 7 [KO:K24738]
106516934  nuclear receptor coactivator 7-like isoform X1 [KO:K25442]
106522066  nuclear receptor coactivator 7-like [KO:K25442]
106531749  ctsa; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
106532157  lysosomal protective protein-like [KO:K13289] [EC:3.4.16.5]
106523671  ctsb; cathepsin B [KO:K01363] [EC:3.4.22.1]
106516844  cathepsin B-like [KO:K01363] [EC:3.4.22.1]
106517256  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
106520647  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
106537140  cathepsin D [KO:K01379] [EC:3.4.23.5]
106532654  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
106532841  cathepsin E-like isoform X1 [KO:K01382] [EC:3.4.23.34]
106528385  cathepsin L-like [KO:K01373] [EC:3.4.22.41]
106518961  cathepsin L-like [KO:K01373] [EC:3.4.22.41]
106514343  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
106518967  pro-cathepsin H-like [KO:K01366] [EC:3.4.22.16]
106524066  cathepsin K-like [KO:K01371] [EC:3.4.22.38]
106534848  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
106510770  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
106533257  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
106522442  cathepsin L1-like isoform X1 [KO:K01365] [EC:3.4.22.15]
106536424  ctso; cathepsin O [KO:K01374] [EC:3.4.22.42]
106518088  cathepsin L1-like [KO:K01368] [EC:3.4.22.27]
106524065  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
106513222  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
106533483  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
106520731  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
106520732  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
106525878  cathepsin Z-like [KO:K08568] [EC:3.4.18.1]
106533809  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
106521394  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
106514532  gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
106517036  glb1; beta-galactosidase isoform X1 [KO:K12309] [EC:3.2.1.23]
106518748  gaa; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
106522707  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
106531574  gba; glucosylceramidase [KO:K01201] [EC:3.2.1.45]
106529500  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
106520049  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
106518992  naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
106519976  galc; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
106525415  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
106532196  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
106532073  fuca1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
106510822  beta-hexosaminidase subunit beta-like [KO:K12373] [EC:3.2.1.52]
106514396  beta-hexosaminidase subunit alpha-like [KO:K12373] [EC:3.2.1.52]
106524290  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
106527227  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
106520830  sialidase-1-like [KO:K01186] [EC:3.2.1.18]
106520833  sialidase-1-like [KO:K01186] [EC:3.2.1.18]
106516188  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
106516190  hyal2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
106516068  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
106517222  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
106517223  hyaluronidase-4-like [KO:K01197] [EC:3.2.1.35]
106517224  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
106513082  hyaluronidase-3-like [KO:K01197] [EC:3.2.1.35]
106531729  hyaluronidase-2-like [KO:K01197] [EC:3.2.1.35]
106520311  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
106515071  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
106528799  arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
106535460  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
106513999  N-acetylgalactosamine-6-sulfatase-like [KO:K01132] [EC:3.1.6.4]
106526380  N-acetylglucosamine-6-sulfatase-like [KO:K01137] [EC:3.1.6.14]
106524433  gns; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
106533195  ids; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
106534568  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
106528199  lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
106520219  group XV phospholipase A2-like [KO:K06129] [EC:3.1.1.5]
106511353  dnase2b; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
106511383  deoxyribonuclease-2-alpha-like isoform X1 [KO:K01158] [EC:3.1.22.1]
106510744  deoxyribonuclease-2-alpha-like [KO:K01158] [EC:3.1.22.1]
106523070  deoxyribonuclease-2-alpha-like [KO:K01158] [EC:3.1.22.1]
106519161  acp2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
106526932  acp5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
106514117  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
106525838  asah1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
106513252  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform X1 [KO:K01444] [EC:3.5.1.26]
106523777  sftpb; pulmonary surfactant-associated protein B [KO:K12382]
106515929  psap; prosaposin isoform X1 [KO:K12382]
106514507  prosaposin-like [KO:K12382]
106533716  gm2a; ganglioside GM2 activator [KO:K12383]
106510754  ppt1; palmitoyl-protein thioesterase 1 isoform X1 [KO:K01074] [EC:3.1.2.22]
106532611  lysosomal thioesterase PPT2-like [KO:K01074] [EC:3.1.2.22]
106520838  ppt2; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
106514721  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
106519815  lysosome-associated membrane glycoprotein 1-like [KO:K06528]
106535921  lamp1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
106531480  hepatitis A virus cellular receptor 1-like [KO:K06562]
106526081  lysosome-associated membrane glycoprotein 3-like [KO:K06562]
106522966  cd63; CD63 antigen [KO:K06497]
106516943  CD63 antigen-like [KO:K06497]
106516233  scarb2; lysosome membrane protein 2 [KO:K12384]
106514528  lysosome membrane protein 2-like [KO:K12384]
106528928  lysosome membrane protein 2-like [KO:K12384]
106533041  npc1; Niemann-Pick C1 protein [KO:K12385]
106520665  npc2; epididymal secretory protein E1 [KO:K13443]
106523864  ctns; cystinosin [KO:K12386]
106534012  sialin-like isoform X1 [KO:K12301]
106533426  slc17a5; sialin [KO:K12301]
106533487  slc11a2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
106528361  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
106522624  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
106515854  lysosomal-associated transmembrane protein 4B-like [KO:K12387]
106521935  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
106518649  cd164; sialomucin core protein 24 [KO:K06546]
106520453  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
106513217  sort1; sortilin [KO:K12388]
106525759  sortilin-like [KO:K12388]
106514773  sortilin-like [KO:K12388]
106528999  cln3; battenin isoform X1 [KO:K12389]
106527135  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
106510830  major facilitator superfamily domain-containing protein 8-like [KO:K12307]
106537108  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
106530181  major facilitator superfamily domain-containing protein 8-like [KO:K12307]
106525611  heparan-alpha-glucosaminide N-acetyltransferase-like isoform X1 [KO:K10532] [EC:2.3.1.78]
106515196  heparan-alpha-glucosaminide N-acetyltransferase-like [KO:K10532] [EC:2.3.1.78]
106518060  sumf1; sulfatase-modifying factor 1 [KO:K13444] [EC:1.8.3.7]
106534107  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta-like [KO:K08239] [EC:2.7.8.17]
106534822  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
106524898  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
106536326  igf2r; LOW QUALITY PROTEIN: cation-independent mannose-6-phosphate receptor [KO:K06564]
106520488  m6pr; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
106528333  clta; clathrin light chain A isoform X1 [KO:K04644]
106515995  cltb; clathrin light chain B isoform X1 [KO:K04645]
106519921  clathrin heavy chain 1-like isoform X1 [KO:K04646]
106525909  clathrin heavy chain 1 [KO:K04646]
106536646  clathrin heavy chain 1-like [KO:K04646]
106531554  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
106514954  AP-1 complex subunit gamma-1-like [KO:K12391]
106521667  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
106515243  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
106528254  AP-1 complex subunit mu-1-like [KO:K12393]
106516870  AP-1 complex subunit mu-1 [KO:K12393]
106532077  AP-1 complex subunit sigma-2-like [KO:K12394]
106512429  ap1s2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
106526973  ap1s1; AP-1 complex subunit sigma-1A [KO:K12394]
106528171  AP-1 complex subunit sigma-1A-like isoform X1 [KO:K12394]
106521557  ap3d1; AP-3 complex subunit delta-1 [KO:K12396]
106515064  ap3b1; AP-3 complex subunit beta-1 [KO:K12397]
106534641  AP-3 complex subunit beta-1-like [KO:K12397]
106526402  AP-3 complex subunit beta-2-like isoform X1 [KO:K12397]
106524727  ap3m2; AP-3 complex subunit mu-2 [KO:K12398]
106520512  AP-3 complex subunit mu-1-like isoform X1 [KO:K12398]
106522531  ap3s2; AP-3 complex subunit sigma-2 [KO:K12399]
106513670  ap3s1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
106521144  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
106523020  ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
106533650  ap4m1; AP-4 complex subunit mu-1 isoform X1 [KO:K12402]
106534273  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
106522068  gga3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
106535604  ADP-ribosylation factor-binding protein GGA1-like isoform X1 [KO:K12404]
106536600  ADP-ribosylation factor-binding protein GGA3-like [KO:K12404]
106533452  ADP-ribosylation factor-binding protein GGA1-like [KO:K12404]
106536667  ADP-ribosylation factor-binding protein GGA3-like [KO:K12404]
106522712  gga2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
106515287  mucolipin-1-like [KO:K04992]
106517836  mucolipin-1-like isoform X1 [KO:K04992]
106532305  litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
106520401  cell death-inducing p53-target protein 1 homolog [KO:K19363]
106519673  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
106528739  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
106531792  cell death-inducing p53-target protein 1 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
alim00511  Other glycan degradation
alim00531  Glycosaminoglycan degradation
alim04130  SNARE interactions in vesicular transport
alim04140  Autophagy - animal
alim04144  Endocytosis
KO pathway
ko04142   
LinkDB

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