KEGG   PATHWAY: msam04142
Entry
msam04142                   Pathway                                
Name
Lysosome - Micropterus salmoides (largemouth bass)
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
msam04142  Lysosome
msam04142

Other DBs
GO: 0005764
Organism
Micropterus salmoides (largemouth bass) [GN:msam]
Gene
119881860  [KO:K04646]
119882112  [KO:K19363]
119882210  [KO:K01368] [EC:3.4.22.27]
119882211  [KO:K01371] [EC:3.4.22.38]
119882707  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
119882720  ap1s3a; AP-1 complex subunit sigma-3a [KO:K12395]
119882772  [KO:K04646]
119883157  [KO:K04992]
119883763  [KO:K12388]
119884083  [KO:K12404]
119884416  lipf; gastric triacylglycerol lipase [KO:K01052] [EC:3.1.1.13]
119884542  cln5; ceroid-lipofuscinosis neuronal protein 5 homolog [KO:K12390]
119884562  [KO:K12404]
119885426  napsa; napsin-A [KO:K01379] [EC:3.4.23.5]
119885619  sumf1; formylglycine-generating enzyme isoform X1 [KO:K13444] [EC:1.8.3.7]
119885934  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
119886008  hyal2b; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
119886036  [KO:K21398]
119886135  ctsa; lysosomal protective protein isoform X1 [KO:K13289] [EC:3.4.16.5]
119886251  hyal2a; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
119886252  hyal1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
119886398  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
119886509  [KO:K12388]
119887973  [KO:K01204] [EC:3.2.1.49]
119888199  [KO:K19363]
119888202  ids; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
119888219  [KO:K19363]
119888553  ctso; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
119888623  gga3b; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
119888659  gm2a; ganglioside GM2 activator [KO:K12383]
119888667  cltb; clathrin light chain B isoform X1 [KO:K04645]
119888678  gla; alpha-galactosidase A isoform X1 [KO:K01189] [EC:3.2.1.22]
119888788  tcirg1b; LOW QUALITY PROTEIN: T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b [KO:K02154]
119888875  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
119888922  ctsf; cathepsin F [KO:K01373] [EC:3.4.22.41]
119888928  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
119889149  gaa; LOW QUALITY PROTEIN: lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
119889750  [KO:K12394]
119889837  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
119889855  ap3s2; AP-3 complex subunit sigma-2 [KO:K12399]
119889911  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
119889945  galns; N-acetylgalactosamine-6-sulfatase isoform X1 [KO:K01132] [EC:3.1.6.4]
119890085  [KO:K02146]
119890104  [KO:K13289] [EC:3.4.16.5]
119890122  lamp1a; lysosome-associated membrane glycoprotein 1a [KO:K06528]
119890271  [KO:K01379] [EC:3.4.23.5]
119890479  ctsba; cathepsin B [KO:K01363] [EC:3.4.22.1]
119890554  [KO:K01366] [EC:3.4.22.16]
119890600  [KO:K01379] [EC:3.4.23.5]
119890996  si:ch211-122f10.4; cathepsin A-like [KO:K13289] [EC:3.4.16.5]
119891186  [KO:K12398]
119891192  scarb2a; lysosome membrane protein 2a isoform X1 [KO:K12384]
119891297  cltcl1; clathrin heavy chain 1 isoform X1 [KO:K04646]
119891345  [KO:K12392]
119891395  sftpbb; surfactant protein Bb [KO:K12382]
119891423  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
119891575  [KO:K12398]
119891682  [KO:K24155]
119891714  [KO:K19363]
119891721  idua; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
119891821  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
119891902  ap3s1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
119892265  [KO:K01365] [EC:3.4.22.15]
119892266  [KO:K01365] [EC:3.4.22.15]
119892267  [KO:K01365] [EC:3.4.22.15]
119892268  [KO:K01365] [EC:3.4.22.15]
119892280  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
119892300  [KO:K02154]
119892849  [KO:K02146]
119893097  [KO:K01197] [EC:3.2.1.35]
119893120  meak7; MTOR-associated protein MEAK7 isoform X1 [KO:K27947]
119893176  hyal6; hyaluronoglucosaminidase 6 [KO:K01197] [EC:3.2.1.35]
119893187  hexa; beta-hexosaminidase subunit alpha isoform X1 [KO:K12373] [EC:3.2.1.52]
119893770  arsa; LOW QUALITY PROTEIN: arylsulfatase A [KO:K01134] [EC:3.1.6.8]
119893848  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
119893869  [KO:K12397]
119893881  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
119894110  [KO:K01197] [EC:3.2.1.35]
119894190  [KO:K01197] [EC:3.2.1.35]
119894208  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
119894920  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
119895273  nots; nothepsin [KO:K01382] [EC:3.4.23.34]
119895405  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
119895621  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
119896351  [KO:K12316] [EC:3.2.1.20]
119896430  cln3; battenin isoform X1 [KO:K12389]
119896737  [KO:K01052] [EC:3.1.1.13]
119896938  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase isoform X1 [KO:K01125] [EC:3.1.4.45]
119897014  ctsk; cathepsin K [KO:K01371] [EC:3.4.22.38]
119897015  ctss2.1; cathepsin S, ortholog2, tandem duplicate 1 isoform X1 [KO:K01368] [EC:3.4.22.27]
119897102  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
119897155  [KO:K01074] [EC:3.1.2.22]
119897464  m6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
119897566  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
119898066  [KO:K12387]
119898153  [KO:K01204] [EC:3.2.1.49]
119898586  man2b1; LOW QUALITY PROTEIN: lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
119898675  [KO:K19363]
119898677  [KO:K12404]
119898805  asah1b; N-acylsphingosine amidohydrolase (acid ceramidase) 1b isoform X1 [KO:K12348] [EC:3.5.1.23]
119898957  glb1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
119899121  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
119899189  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
119899258  gga3a; ADP-ribosylation factor-binding protein GGA3a isoform X1 [KO:K12404]
119899290  [KO:K04992]
119899372  clta; clathrin light chain A isoform X1 [KO:K04644]
119899535  [KO:K01565] [EC:3.10.1.1]
119899637  acp5a; tartrate-resistant acid phosphatase type 5a isoform X1 [KO:K14379] [EC:3.1.3.2]
119900100  [KO:K03662]
119900338  [KO:K06562]
119900388  ap1m3; adaptor related protein complex 1 subunit mu 3 [KO:K12393]
119900575  mfsd8l1; major facilitator superfamily domain-containing protein 8 [KO:K12307]
119900631  dnase2b; deoxyribonuclease-2-beta isoform X1 [KO:K01158] [EC:3.1.22.1]
119900635  [KO:K01158] [EC:3.1.22.1]
119900636  [KO:K01158] [EC:3.1.22.1]
119900763  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
119901049  cts12; procathepsin L [KO:K01365] [EC:3.4.22.15]
119901112  [KO:K12394]
119901310  [KO:K12386]
119901311  [KO:K12386]
119901733  [KO:K14410] [EC:3.1.3.2]
119901749  [KO:K14410] [EC:3.1.3.2]
119901806  [KO:K08568] [EC:3.4.18.1]
119901855  ap1m1; AP-1 complex subunit mu-1 [KO:K12393]
119901915  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
119901946  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
119901962  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
119902172  [KO:K12394]
119902328  mfsd8l2; major facilitator superfamily domain-containing protein 8 [KO:K12307]
119902505  ap1g2; AP-1 complex subunit gamma-like 2 [KO:K12391]
119904270  lamp1b; lysosome-associated membrane glycoprotein 1b [KO:K06528]
119905029  atp6ap1a; ATPase H+ transporting accessory protein 1a isoform X1 [KO:K03662]
119905058  [KO:K01158] [EC:3.1.22.1]
119905252  cd63; CD63 antigen [KO:K06497]
119905365  atp6ap1b; V-type proton ATPase subunit S1b [KO:K03662]
119905585  sort1b; sortilin 1b [KO:K12388]
119905714  hyal3; hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
119905727  si:dkey-72l14.3; glyco_hydro_56 domain-containing protein [KO:K01197] [EC:3.2.1.35]
119905769  [KO:K12401]
119906010  [KO:K21398]
119906458  [KO:K04644]
119906692  ctss1; cathepsin S, ortholog 1 isoform X1 [KO:K01368] [EC:3.4.22.27]
119906853  ppt2b; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
119907047  laptm4b; lysosomal-associated transmembrane protein 4B isoform X1 [KO:K12387]
119907152  si:ch1073-513e17.1; sialin [KO:K12301]
119907254  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
119907465  [KO:K01206] [EC:3.2.1.51]
119907847  ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
119908500  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
119908918  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
119909038  [KO:K01204] [EC:3.2.1.49]
119909163  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
119909576  [KO:K25442]
119909904  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
119909989  galcb; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
119910071  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
119910240  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
119910377  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
119910524  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
119910566  [KO:K13443]
119910934  ctsl.1; cathepsin L.1 isoform X1 [KO:K01365] [EC:3.4.22.15]
119911202  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
119911208  [KO:K25442]
119911252  [KO:K12316] [EC:3.2.1.20]
119911559  [KO:K19363]
119911800  ap1s1; AP-1 complex subunit sigma-1A [KO:K12394]
119911862  si:ch211-212k18.7; cell wall protein DAN4 [KO:K06501]
119913381  [KO:K19363]
119913448  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
119914170  [KO:K12382]
119914271  gnsb; glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b [KO:K01137] [EC:3.1.6.14]
119914294  ap3b1a; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
119914325  scarb2c; lysosome membrane protein 2c [KO:K12384]
119914376  [KO:K24738]
119914435  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
119914446  [KO:K12382]
119914678  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
119914862  [KO:K01158] [EC:3.1.22.1]
119915018  [KO:K12384]
119915019  atp6v0a2a; V-type proton ATPase 116 kDa subunit a2 isoform X1 [KO:K02154]
119915318  [KO:K19363]
119915528  [KO:K06497]
119915544  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma isoform X1 [KO:K10087]
119915949  [KO:K01052] [EC:3.1.1.13]
119916264  atp6v0a1b; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
119916363  naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
119916422  arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
119917091  [KO:K12382]
119917543  slc17a5; sialin [KO:K12301]
119917614  si:dkey-192p21.6; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
119917699  [KO:K12382]
119917715  ap3m1; AP-3 complex subunit mu-1 [KO:K12398]
119917805  [KO:K01565] [EC:3.10.1.1]
119917927  [KO:K01197] [EC:3.2.1.35]
119917979  gnptab; LOW QUALITY PROTEIN: N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
119918060  gnsa; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
119918168  [KO:K01158] [EC:3.1.22.1]
119918549  si:dkey-159a18.1; sortilin isoform X1 [KO:K12388]
119919308  [KO:K19363]
119919382  [KO:K12401]
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
msam00511  Other glycan degradation
msam00531  Glycosaminoglycan degradation
msam04130  SNARE interactions in vesicular transport
msam04140  Autophagy - animal
msam04144  Endocytosis
KO pathway
ko04142   

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