KEGG   PATHWAY: nfu04142
Entry
nfu04142                    Pathway                                
Name
Lysosome - Nothobranchius furzeri (turquoise 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
nfu04142  Lysosome
nfu04142

Other DBs
GO: 0005764
Organism
Nothobranchius furzeri (turquoise killifish) [GN:nfu]
Gene
107372361  [KO:K12399]
107372418  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
107372713  scarb2; lysosome membrane protein 2 [KO:K12384]
107372931  sftpb; pulmonary surfactant-associated protein B isoform X1 [KO:K12382]
107373005  [KO:K02154]
107373323  asah1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
107373363  [KO:K13289] [EC:3.4.16.5]
107373460  [KO:K01202] [EC:3.2.1.46]
107374141  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
107374275  [KO:K02154]
107374276  cltb; clathrin light chain B isoform X1 [KO:K04645]
107374545  ap1s1; AP-1 complex subunit sigma-1A [KO:K12394]
107374597  [KO:K01202] [EC:3.2.1.46]
107374842  ap3b1; AP-3 complex subunit beta-1 [KO:K12397]
107374848  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
107374957  hexb; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
107375039  [KO:K19363]
107375040  [KO:K01319] [EC:3.4.21.20]
107375088  wdr7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
107375296  glb1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
107375333  [KO:K19363]
107375363  [KO:K10532] [EC:2.3.1.78]
107375600  [KO:K12398]
107375771  psap; prosaposin isoform X1 [KO:K12382]
107375891  slc17a5; sialin [KO:K12301]
107375989  tcirg1; V-type proton ATPase 116 kDa subunit a isoform 3 [KO:K02154]
107376303  [KO:K12404]
107376365  [KO:K01379] [EC:3.4.23.5]
107376530  gaa; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
107376618  [KO:K19363]
107376678  [KO:K02155]
107377463  [KO:K25442]
107377539  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
107377587  ctsb; cathepsin B [KO:K01363] [EC:3.4.22.1]
107377663  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
107377699  gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
107377842  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
107377987  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
107378045  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
107378389  [KO:K19363]
107378446  atp6v0a1; V-type proton ATPase 116 kDa subunit a isoform 1 isoform X1 [KO:K02154]
107378860  [KO:K12387]
107379079  [KO:K01074] [EC:3.1.2.22]
107379154  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
107379223  [KO:K01368] [EC:3.4.22.27]
107379225  [KO:K01371] [EC:3.4.22.38]
107379282  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
107379426  m6pr; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
107379589  gba; glucosylceramidase isoform X1 [KO:K01201] [EC:3.2.1.45]
107379734  ctso; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
107379833  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
107380452  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
107380680  [KO:K04646]
107380746  gm2a; ganglioside GM2 activator [KO:K12383]
107380787  ap1s3; AP-1 complex subunit sigma-3 [KO:K12395]
107380829  ap3b2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
107381025  acp2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
107381170  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
107381178  [KO:K01363] [EC:3.4.22.1]
107381272  [KO:K01373] [EC:3.4.22.41]
107381336  [KO:K13289] [EC:3.4.16.5]
107381365  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
107381631  lamp1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
107381706  ap1s2; AP-1 complex subunit sigma-2 [KO:K12394]
107381714  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
107382031  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
107382058  [KO:K01379] [EC:3.4.23.5]
107382187  [KO:K08568] [EC:3.4.18.1]
107382299  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
107382335  gga3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
107382349  [KO:K04992]
107382373  ids; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
107382500  gns; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
107383333  [KO:K01206] [EC:3.2.1.51]
107383534  [KO:K08568] [EC:3.4.18.1]
107383604  ap1m1; AP-1 complex subunit mu-1 [KO:K12393]
107383790  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
107383817  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
107383834  npc1; Niemann-Pick C1 protein [KO:K12385]
107384030  [KO:K12394]
107384051  sumf1; sulfatase-modifying factor 1 [KO:K13444] [EC:1.8.3.7]
107384239  [KO:K12391]
107384475  [KO:K12307]
107384873  ctsa; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
107385134  [KO:K01197] [EC:3.2.1.35]
107385227  [KO:K01197] [EC:3.2.1.35]
107385228  hyal2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
107385578  [KO:K12388]
107385674  slc11a2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
107385676  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
107385764  [KO:K12388]
107386108  [KO:K01365] [EC:3.4.22.15]
107386109  [KO:K01365] [EC:3.4.22.15]
107386129  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
107386359  cltc; clathrin heavy chain 1 isoform X1 [KO:K04646]
107386969  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
107387048  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
107387170  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
107387317  ctns; cystinosin isoform X1 [KO:K12386]
107387496  [KO:K01052] [EC:3.1.1.13]
107387581  [KO:K01382] [EC:3.4.23.34]
107388029  atp6v0c; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
107388037  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
107388191  arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
107388519  hexa; LOW QUALITY PROTEIN: beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
107388567  [KO:K19363]
107388637  ap4e1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
107388794  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
107388896  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
107389057  [KO:K12316] [EC:3.2.1.20]
107389092  [KO:K12404]
107389201  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
107389304  tldc1; TLD domain-containing protein 1 [KO:K27947]
107389501  [KO:K01197] [EC:3.2.1.35]
107389502  [KO:K01197] [EC:3.2.1.35]
107389503  [KO:K01197] [EC:3.2.1.35]
107389735  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
107389812  [KO:K06528]
107390381  cd63; CD63 antigen [KO:K06497]
107390461  [KO:K03662]
107390535  atp6ap1; V-type proton ATPase subunit S1 [KO:K03662]
107390589  [KO:K01197] [EC:3.2.1.35]
107390663  [KO:K01197] [EC:3.2.1.35]
107390796  sort1; sortilin [KO:K12388]
107390942  clta; clathrin light chain A isoform X1 [KO:K04644]
107391285  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
107391431  [KO:K19363]
107391542  ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
107391599  cln3; battenin [KO:K12389]
107391750  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
107391875  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
107391909  ap4s1; AP-4 complex subunit sigma-1 isoform X1 [KO:K12403]
107391960  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
107392036  [KO:K01365] [EC:3.4.22.15]
107392187  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
107392206  [KO:K01365] [EC:3.4.22.15]
107392244  [KO:K25442]
107392300  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
107392385  npc2; epididymal secretory protein E1 isoform X1 [KO:K13443]
107392629  lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
107392715  [KO:K01158] [EC:3.1.22.1]
107392716  [KO:K01158] [EC:3.1.22.1]
107392755  [KO:K12307]
107392906  [KO:K12404]
107392936  [KO:K12393]
107393090  acp5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
107393181  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
107393378  [KO:K01365] [EC:3.4.22.15]
107393483  abcb9; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
107393528  [KO:K12398]
107393559  idua; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
107393774  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
107394150  dmxl1; dmX-like protein 1 [KO:K24155]
107394153  ap3s1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
107394193  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
107394195  atp6v0a2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
107394216  [KO:K12382]
107394263  [KO:K04646]
107394344  [KO:K12384]
107394512  [KO:K01186] [EC:3.2.1.18]
107394513  [KO:K01186] [EC:3.2.1.18]
107394534  [KO:K01074] [EC:3.1.2.22]
107394690  [KO:K01368] [EC:3.4.22.27]
107394696  [KO:K12387]
107394935  [KO:K12301]
107395254  [KO:K12384]
107395441  ppt1; palmitoyl-protein thioesterase 1 isoform X1 [KO:K01074] [EC:3.1.2.22]
107395870  [KO:K01137] [EC:3.1.6.14]
107396045  [KO:K12394]
107396843  mcoln1; mucolipin-1 isoform X1 [KO:K04992]
107396991  naglu; alpha-N-acetylglucosaminidase isoform X1 [KO:K01205] [EC:3.2.1.50]
107397321  [KO:K02155]
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
nfu00511  Other glycan degradation
nfu00531  Glycosaminoglycan degradation
nfu04130  SNARE interactions in vesicular transport
nfu04140  Autophagy - animal
nfu04144  Endocytosis
KO pathway
ko04142   

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