KEGG   PATHWAY: lav04142
Entry
lav04142                    Pathway                                
Name
Lysosome - Loxodonta africana (African savanna elephant)
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
lav04142  Lysosome
lav04142

Other DBs
GO: 0005764
Organism
Loxodonta africana (African savanna elephant) [GN:lav]
Gene
100653590  CLN3; battenin [KO:K12389]
100653816  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
100654302  AP4S1; AP-4 complex subunit sigma-1 isoform X1 [KO:K12403]
100654462  CLTCL1; LOW QUALITY PROTEIN: clathrin heavy chain 2 [KO:K04646]
100654642  [KO:K01319] [EC:3.4.21.20]
100654939  GLA; alpha-galactosidase A isoform X1 [KO:K01189] [EC:3.2.1.22]
100655060  CLTA; clathrin light chain A isoform X1 [KO:K04644]
100655466  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
100655658  CLTC; clathrin heavy chain 1 [KO:K04646]
100655776  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
100655840  AP1M1; AP-1 complex subunit mu-1 isoform X1 [KO:K12393]
100655898  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
100656094  NAPSA; napsin-A [KO:K08565] [EC:3.4.23.-]
100656171  AP4M1; AP-4 complex subunit mu-1 isoform X2 [KO:K12402]
100656526  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X5 [KO:K12404]
100656844  WDR7; LOW QUALITY PROTEIN: WD repeat-containing protein 7 [KO:K24738]
100657160  DNASE2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
100657188  NAGA; alpha-N-acetylgalactosaminidase isoform X1 [KO:K01204] [EC:3.2.1.49]
100657280  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
100657433  AP4B1; LOW QUALITY PROTEIN: AP-4 complex subunit beta-1 [KO:K12401]
100657453  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
100657934  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
100657939  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
100657977  SLC17A5; sialin [KO:K12301]
100658119  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
100658130  GBA; glucosylceramidase [KO:K01201] [EC:3.2.1.45]
100658396  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
100658416  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
100658478  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
100658494  ASAH1; acid ceramidase isoform X1 [KO:K12348] [EC:3.5.1.23]
100658599  PLA2G15; group XV phospholipase A2 isoform X1 [KO:K06129] [EC:3.1.1.5]
100658667  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
100658867  MAN2B1; LOW QUALITY PROTEIN: lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
100658885  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
100658992  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
100659348  LAMP3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
100659459  GAA; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
100659487  DMXL1; dmX-like protein 1 isoform X2 [KO:K24155]
100659488  NEU1; sialidase-1 isoform X1 [KO:K01186] [EC:3.2.1.18]
100659563  NAGPA; LOW QUALITY PROTEIN: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
100659660  CTSW; cathepsin W [KO:K08569] [EC:3.4.22.-]
100660500  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X2 [KO:K06528]
100661108  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
100661254  SUMF1; sulfatase-modifying factor 1 isoform X2 [KO:K13444] [EC:1.8.3.7]
100661361  HEXA; beta-hexosaminidase subunit alpha isoform X2 [KO:K12373] [EC:3.2.1.52]
100661420  [KO:K01365] [EC:3.4.22.15]
100661493  FUCA2; plasma alpha-L-fucosidase isoform X1 [KO:K01206] [EC:3.2.1.51]
100661612  HYAL4; hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
100661689  SLC11A2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
100661872  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
100661926  SCARB2; lysosome membrane protein 2 [KO:K12384]
100661949  ATP6V0A2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
100661985  [KO:K01365] [EC:3.4.22.15]
100662087  NPC1; Niemann-Pick C1 protein isoform X1 [KO:K12385]
100662095  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
100662248  [KO:K12396]
100662324  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
100662496  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
100662574  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
100662591  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
100663037  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
100663159  CD68; macrosialin isoform X1 [KO:K06501]
100663356  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
100663561  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
100663650  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
100663899  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
100664107  GUSB; beta-glucuronidase isoform X1 [KO:K01195] [EC:3.2.1.31]
100664301  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
100664362  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
100664567  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
100664730  AP3B1; LOW QUALITY PROTEIN: AP-3 complex subunit beta-1 [KO:K12397]
100664931  SORT1; sortilin [KO:K12388]
100664975  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
100665041  CTSA; LOW QUALITY PROTEIN: lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
100665585  [KO:K01365] [EC:3.4.22.15]
100665589  ARSB; arylsulfatase B isoform X1 [KO:K01135] [EC:3.1.6.12]
100665656  [KO:K01074] [EC:3.1.2.22]
100665997  AP1G1; AP-1 complex subunit gamma-1 isoform X3 [KO:K12391]
100666004  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
100666040  CD63; CD63 antigen [KO:K06497]
100666333  ABCA2; LOW QUALITY PROTEIN: ATP-binding cassette sub-family A member 2 [KO:K05642]
100666542  TPP1; LOW QUALITY PROTEIN: tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
100666611  GNS; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
100666725  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
100666917  AP3M1; AP-3 complex subunit mu-1 isoform X1 [KO:K12398]
100667060  TCIRG1; V-type proton ATPase 116 kDa subunit a [KO:K02154]
100667382  [KO:K01365] [EC:3.4.22.15]
100667446  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
100667479  SPAM1; LOW QUALITY PROTEIN: hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
100667671  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
100667702  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
100668172  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
100668341  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
100668454  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
100668758  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
100668824  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
100668861  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
100668883  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
100668951  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
100669026  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
100669128  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
100669142  AP4E1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
100669188  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
100669368  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
100669471  HYAL1; hyaluronidase-1 isoform X2 [KO:K01197] [EC:3.2.1.35]
100669517  MCOLN1; mucolipin-1 isoform X10 [KO:K04992]
100669721  GM2A; ganglioside GM2 activator [KO:K12383]
100669845  MFSD8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
100669881  CTNS; cystinosin [KO:K12386]
100669993  DMXL2; LOW QUALITY PROTEIN: dmX-like protein 2 [KO:K24155]
100670350  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform X4 [KO:K02154]
100670478  CLTB; LOW QUALITY PROTEIN: clathrin light chain B [KO:K04645]
100670940  AP1G2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
100671099  AP1M2; LOW QUALITY PROTEIN: AP-1 complex subunit mu-2 [KO:K12393]
100671106  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
100671121  TLDC1; TLD domain-containing protein 1 [KO:K27947]
100671375  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
100672606  NPC2; epididymal secretory protein E1 [KO:K13443]
100672731  NAGLU; alpha-N-acetylglucosaminidase isoform X2 [KO:K01205] [EC:3.2.1.50]
100673211  AP1S1; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
100673950  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
100673972  AP3S2; AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
100674232  CTSS; cathepsin S isoform X2 [KO:K01368] [EC:3.4.22.27]
100674440  ACP2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
100674514  PSAP; prosaposin isoform X1 [KO:K12382]
100674554  GGA2; ADP-ribosylation factor-binding protein GGA2 isoform X1 [KO:K12404]
100675570  MANBA; beta-mannosidase isoform X1 [KO:K01192] [EC:3.2.1.25]
100676352  [KO:K13289] [EC:3.4.16.5]
100676360  CTSC; dipeptidyl peptidase 1 isoform X1 [KO:K01275] [EC:3.4.14.1]
100676928  CTSF; cathepsin F [KO:K01373] [EC:3.4.22.41]
100677047  SLC11A1; natural resistance-associated macrophage protein 1 isoform X7 [KO:K12347]
100677484  ATP6V0D1; V-type proton ATPase subunit d 1 isoform X2 [KO:K02146]
104846959  CD164; sialomucin core protein 24 [KO:K06546]
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
lav00511  Other glycan degradation
lav00531  Glycosaminoglycan degradation
lav04130  SNARE interactions in vesicular transport
lav04140  Autophagy - animal
lav04144  Endocytosis
KO pathway
ko04142   

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