KEGG   PATHWAY: pswi04142
Entry
pswi04142                   Pathway                                
Name
Lysosome - Pseudoliparis swirei (Mariana hadal snailfish)
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
pswi04142  Lysosome
pswi04142

Other DBs
GO: 0005764
Organism
Pseudoliparis swirei (Mariana hadal snailfish) [GN:pswi]
Gene
130187924  [KO:K01125] [EC:3.1.4.45]
130187947  [KO:K01368] [EC:3.4.22.27]
130187951  ctsk; cathepsin K isoform X1 [KO:K01371] [EC:3.4.22.38]
130187957  [KO:K01125] [EC:3.1.4.45]
130188103  gga3b; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
130188192  cln3; battenin isoform X1 [KO:K12389]
130188239  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
130188439  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
130188505  [KO:K19363]
130188719  [KO:K19363]
130188833  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
130189095  gaa; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
130189150  [KO:K04992]
130189217  [KO:K12404]
130189240  [KO:K19363]
130189508  [KO:K04992]
130189664  glb1; beta-galactosidase isoform X1 [KO:K12309] [EC:3.2.1.23]
130189804  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
130189959  asah1b; acid ceramidase [KO:K12348] [EC:3.5.1.23]
130189995  sgsh; N-sulphoglucosamine sulphohydrolase isoform X1 [KO:K01565] [EC:3.10.1.1]
130190014  ap1m2; AP-1 complex subunit mu-2 isoform X1 [KO:K12393]
130190159  [KO:K12404]
130190336  clta; clathrin light chain A isoform X1 [KO:K04644]
130190361  [KO:K19363]
130190422  gga3a; ADP-ribosylation factor-binding protein GGA3a [KO:K12404]
130190449  [KO:K12404]
130190510  [KO:K19363]
130190612  si:dkeyp-75b4.8; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
130190718  acp5a; tartrate-resistant acid phosphatase type 5a isoform X1 [KO:K14379] [EC:3.1.3.2]
130190742  man2b1; lysosomal alpha-mannosidase isoform X1 [KO:K12311] [EC:3.2.1.24]
130191284  ap4m1; LOW QUALITY PROTEIN: AP-4 complex subunit mu-1 [KO:K12402]
130191511  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
130191599  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
130192270  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
130192341  ap1s2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
130192466  ppt2b; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
130192500  lamp1a; lysosome-associated membrane glycoprotein 1a [KO:K06528]
130192534  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
130192575  dmxl2; dmX-like protein 2 [KO:K24155]
130192671  [KO:K12399]
130192942  si:ch211-122f10.4; cathepsin A-like [KO:K13289] [EC:3.4.16.5]
130193025  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
130193034  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
130193076  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
130193169  ctsba; cathepsin B [KO:K01363] [EC:3.4.22.1]
130193417  lamp3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
130193432  ap1m3; adaptor related protein complex 1 subunit mu 3 [KO:K12393]
130193458  [KO:K01158] [EC:3.1.22.1]
130193487  cts12; procathepsin L [KO:K01365] [EC:3.4.22.15]
130193620  [KO:K04992]
130193762  mfsd8l1; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
130194197  si:ch1073-513e17.1; sialin isoform X1 [KO:K12301]
130194231  dnase2b; LOW QUALITY PROTEIN: deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
130194284  ctns; cystinosin isoform X1 [KO:K12386]
130194621  [KO:K12397]
130194906  [KO:K27947]
130194922  hyal6; LOW QUALITY PROTEIN: hyaluronoglucosaminidase 6 [KO:K01197] [EC:3.2.1.35]
130194923  [KO:K01197] [EC:3.2.1.35]
130195002  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
130195395  [KO:K01197] [EC:3.2.1.35]
130195607  ap4e1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
130195748  [KO:K01197] [EC:3.2.1.35]
130195831  hexa; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
130195938  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
130196116  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
130196161  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
130196167  [KO:K12305] [EC:3.6.1.6]
130196186  [KO:K24155]
130196384  cltcl1; clathrin heavy chain 1 isoform X1 [KO:K04646]
130196392  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
130196395  abca2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
130196433  sftpbb; surfactant protein Bb [KO:K12382]
130196455  scarb2a; lysosome membrane protein 2a isoform X1 [KO:K12384]
130196472  ctsla; cathepsin La isoform X1 [KO:K01365] [EC:3.4.22.15]
130196686  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
130197197  ap3m2; AP-3 complex subunit mu-2 [KO:K12398]
130197415  atp6v0a2b; V-type proton ATPase 116 kDa subunit a [KO:K02154]
130197756  ap1g2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
130197796  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
130197832  [KO:K08568] [EC:3.4.18.1]
130198408  [KO:K02146]
130198506  ap1m1; AP-1 complex subunit mu-1 isoform X1 [KO:K12393]
130198519  mfsd8l2; major facilitator superfamily domain-containing protein 8 [KO:K12307]
130198545  ap1s3b; AP-1 complex subunit sigma-3b isoform X1 [KO:K12394]
130199133  ap4b1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
130199150  sort1b; sortilin 1b [KO:K12388]
130199401  cd63; CD63 antigen [KO:K06497]
130199415  atp6ap1b; V-type proton ATPase subunit S1b [KO:K03662]
130199474  atp6ap1a; ATPase H+ transporting accessory protein 1a [KO:K03662]
130199645  [KO:K21398]
130199912  hyal3; LOW QUALITY PROTEIN: hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
130200307  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
130200376  nots; nothepsin [KO:K01382] [EC:3.4.23.34]
130200738  [KO:K01197] [EC:3.2.1.35]
130200766  si:dkey-159a18.1; sortilin isoform X1 [KO:K12388]
130200801  gnsa; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
130201056  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
130201251  ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
130201389  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
130201491  si:ch211-15d5.11; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
130201832  [KO:K13443]
130201958  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
130201975  ctsl.1; cathepsin L.1 [KO:K01365] [EC:3.4.22.15]
130202014  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
130202022  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
130202299  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
130202414  cd164; sialomucin core protein 24 [KO:K06546]
130202419  [KO:K01204] [EC:3.2.1.49]
130202452  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
130202468  [KO:K25442]
130203011  [KO:K01363] [EC:3.4.22.1]
130203231  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
130203277  [KO:K02154]
130203279  naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
130203428  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
130203740  [KO:K12381] [EC:3.1.6.-]
130203883  cln5; ceroid-lipofuscinosis neuronal protein 5 homolog [KO:K12390]
130204331  acp2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
130204400  [KO:K01052] [EC:3.1.1.13]
130204948  [KO:K12384]
130205159  [KO:K01137] [EC:3.1.6.14]
130205205  atp6v0a2a; V-type proton ATPase 116 kDa subunit a 2 isoform X1 [KO:K02154]
130205255  ap3b1a; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
130205302  [KO:K01206] [EC:3.2.1.51]
130205372  [KO:K01206] [EC:3.2.1.51]
130205375  [KO:K24738]
130205515  scarb2c; lysosome membrane protein 2c isoform X1 [KO:K12384]
130205561  lamp1b; lysosome-associated membrane glycoprotein 1b [KO:K06528]
130205665  [KO:K12382]
130205750  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
130206216  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
130206259  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
130206474  [KO:K01204] [EC:3.2.1.49]
130207010  [KO:K12382]
130207162  slc17a5; sialin [KO:K12301]
130207208  si:dkey-192p21.6; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
130207613  ap3m1; AP-3 complex subunit mu-1 isoform X1 [KO:K12398]
130207949  hyal2a; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
130207952  hyal1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
130208005  [KO:K21398]
130208610  sumf1; formylglycine-generating enzyme isoform X1 [KO:K13444] [EC:1.8.3.7]
130208647  hyal2b; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
130208862  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
130209063  ctsa; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
130209183  cltb; clathrin light chain B isoform X1 [KO:K04645]
130209380  gla; LOW QUALITY PROTEIN: alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
130209397  tcirg1b; T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b [KO:K02154]
130209553  [KO:K01373] [EC:3.4.22.41]
130209570  ids; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
130209680  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
130209774  ctso; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
130209785  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
130210458  [KO:K04646]
130211088  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
130211125  ap1s3a; AP-1 complex subunit sigma-3a isoform X1 [KO:K12395]
130211465  [KO:K06501]
130211479  cltca; clathrin, heavy chain a (Hc) [KO:K04646]
130211832  ap1s1; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
130211964  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
130212418  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
130212733  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
130212920  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
130213207  [KO:K01074] [EC:3.1.2.22]
130213474  m6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
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 22:339-352 (2022)
DOI:10.1038/s41577-021-00626-8
Related
pathway
pswi00511  Other glycan degradation
pswi00531  Glycosaminoglycan degradation
pswi04130  SNARE interactions in vesicular transport
pswi04140  Autophagy - animal
pswi04144  Endocytosis
KO pathway
ko04142   

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