KEGG   PATHWAY: iti04142
Entry
iti04142                    Pathway                                
Name
Lysosome - Ictidomys tridecemlineatus (thirteen-lined ground squirrel)
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
iti04142  Lysosome
iti04142

Other DBs
GO: 0005764
Organism
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) [GN:iti]
Gene
101954290  Gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma isoform X2 [KO:K10087]
101954375  [KO:K12398]
101954573  Man2b1; lysosomal alpha-mannosidase isoform X1 [KO:K12311] [EC:3.2.1.24]
101954584  Lamp1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
101954652  Entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
101954653  Ctse; cathepsin E [KO:K01382] [EC:3.4.23.34]
101954755  Sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
101954780  Fuca1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
101954930  Lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
101955112  Cd68; macrosialin [KO:K06501]
101955236  Sort1; sortilin [KO:K12388]
101955344  Neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
101955400  [KO:K12395]
101955465  Npc2; NPC intracellular cholesterol transporter 2 isoform X1 [KO:K13443]
101955819  Dmxl2; dmX-like protein 2 isoform X8 [KO:K24155]
101955969  Aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform X2 [KO:K01444] [EC:3.5.1.26]
101956007  Galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
101956784  Cltcl1; clathrin heavy chain 2 isoform X1 [KO:K04646]
101957027  Wdr7; WD repeat-containing protein 7 isoform X3 [KO:K24738]
101957258  Ctso; cathepsin O [KO:K01374] [EC:3.4.22.42]
101957706  [KO:K02155]
101957956  Atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
101958027  Fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
101958151  Psapl1; proactivator polypeptide-like 1 [KO:K12382]
101958199  Ap1s1; AP-1 complex subunit sigma-1A [KO:K12394]
101958215  Gga3; ADP-ribosylation factor-binding protein GGA3 isoform X5 [KO:K12404]
101958227  Gm2a; ganglioside GM2 activator [KO:K12383]
101958545  Ap3m2; AP-3 complex subunit mu-2 isoform X3 [KO:K12398]
101958649  Cltc; clathrin heavy chain 1 isoform X4 [KO:K04646]
101958656  Ap4s1; AP-4 complex subunit sigma-1 isoform X1 [KO:K12403]
101958787  Slc11a1; natural resistance-associated macrophage protein 1 isoform X1 [KO:K12347]
101958956  Nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase isoform X3 [KO:K01125] [EC:3.1.4.45]
101959049  Clta; clathrin light chain A isoform X1 [KO:K04644]
101959078  Cltb; clathrin light chain B isoform X2 [KO:K04645]
101959337  Slc11a2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
101959357  Ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
101959382  Naga; alpha-N-acetylgalactosaminidase isoform X1 [KO:K01204] [EC:3.2.1.49]
101959528  Arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
101959587  Ap3b2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
101959930  [KO:K06546]
101959956  [KO:K01319] [EC:3.4.21.20]
101960045  Hexa; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
101960349  M6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
101960451  Smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
101960702  [KO:K01052] [EC:3.1.1.13]
101960805  Dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
101960876  Hexb; LOW QUALITY PROTEIN: beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
101960918  Atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit isoform X1 [KO:K03661]
101961359  Hgsnat; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
101961768  Glb1; beta-galactosidase isoform X2 [KO:K12309] [EC:3.2.1.23]
101961995  Ids; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
101962327  Meak7; MTOR-associated protein MEAK7 [KO:K27947]
101962498  Sumf1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
101962624  Ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
101962907  Atp6v0c; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
101963076  Ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
101963338  Npc1; NPC intracellular cholesterol transporter 1 isoform X2 [KO:K12385]
101963442  Ctsw; cathepsin W isoform X2 [KO:K08569] [EC:3.4.22.-]
101963465  Scarb2; lysosome membrane protein 2 [KO:K12384]
101963895  Atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
101964165  Ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
101964183  Cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
101964491  Ap1s2; AP-1 complex subunit sigma-2 isoform X3 [KO:K12394]
101965171  Tcirg1; V-type proton ATPase 116 kDa subunit a3 isoform X2 [KO:K02154]
101965184  Ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
101965319  Galc; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
101965360  Atp6v0a4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
101965437  Ap3m1; AP-3 complex subunit mu-1 [KO:K12398]
101965501  Ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
101965513  Igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
101965548  Asah1; acid ceramidase isoform X1 [KO:K12348] [EC:3.5.1.23]
101965663  Mfsd8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
101965681  Pla2g15; phospholipase A2 group XV isoform X1 [KO:K06129] [EC:3.1.1.5]
101966028  Manba; LOW QUALITY PROTEIN: beta-mannosidase [KO:K01192] [EC:3.2.1.25]
101966097  Tpp1; tripeptidyl-peptidase 1 isoform X1 [KO:K01279] [EC:3.4.14.9]
101966160  Dnase2b; deoxyribonuclease-2-beta isoform X1 [KO:K01158] [EC:3.1.22.1]
101966278  Lgmn; legumain [KO:K01369] [EC:3.4.22.34]
101966467  Ap1m2; AP-1 complex subunit mu-2 isoform X1 [KO:K12393]
101967068  Gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
101967092  Cln3; battenin isoform X1 [KO:K12389]
101967163  Atp6v0a1; V-type proton ATPase 116 kDa subunit a1 isoform X5 [KO:K02154]
101967271  Laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
101967452  Naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
101967685  Gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
101967815  [KO:K01074] [EC:3.1.2.22]
101968945  [KO:K01365] [EC:3.4.22.15]
101969718  Ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
101969737  [KO:K01365] [EC:3.4.22.15]
101969771  Ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
101969884  Ap3b1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
101970007  Ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
101970175  Cd164; sialomucin core protein 24 [KO:K06546]
101970358  Ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
101970741  Ctsa; LOW QUALITY PROTEIN: lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
101970770  Hyal4; hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
101970981  Ap1g2; LOW QUALITY PROTEIN: AP-1 complex subunit gamma-like 2 [KO:K12391]
101971197  Gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
101971329  Arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
101971514  Atp6v0a2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
101972107  Gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
101972193  Gga1; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
101972715  Ctsl; procathepsin L [KO:K01365] [EC:3.4.22.15]
101973412  Ap3s2; AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
101974043  Laptm5; lysosomal-associated transmembrane protein 5 [KO:K12387]
101974122  Arsa; arylsulfatase A isoform X4 [KO:K01134] [EC:3.1.6.8]
101974132  Laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
101974489  Gns; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
101974506  Cd63; CD63 antigen [KO:K06497]
101974806  Dmxl1; dmX-like protein 1 isoform X4 [KO:K24155]
101974863  Ap1m1; AP-1 complex subunit mu-1 isoform X2 [KO:K12393]
101975318  Hyal3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
101975433  Ncoa7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
101975781  Hyal1; hyaluronidase-1 isoform X2 [KO:K01197] [EC:3.2.1.35]
101975880  Litafd; LITAF domain-containing protein isoform X1 [KO:K19363]
101976004  Abca2; ATP-binding cassette sub-family A member 2 [KO:K05642]
101976055  Hyal2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
101976099  Ctns; cystinosin isoform X1 [KO:K12386]
101976367  Ctsf; cathepsin F [KO:K01373] [EC:3.4.22.41]
101976566  Spam1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
101976627  [KO:K12382]
101976648  Ctss; cathepsin S [KO:K01368] [EC:3.4.22.27]
101976844  [KO:K01197] [EC:3.2.1.35]
101976923  Ctsk; cathepsin K isoform X4 [KO:K01371] [EC:3.4.22.38]
101976968  Atp6ap1; V-type proton ATPase subunit S1 [KO:K03662]
101977015  Abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
101977016  Acp2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
101977058  Ap3s1; AP-3 complex subunit sigma-1 isoform X3 [KO:K12399]
101977176  Gga2; ADP-ribosylation factor-binding protein GGA2 isoform X1 [KO:K12404]
101977343  Lamp2; lysosome-associated membrane glycoprotein 2 isoform X2 [KO:K06528]
101977432  Napsa; napsin-A [KO:K08565] [EC:3.4.23.-]
101977464  Atp6v0d2; V-type proton ATPase subunit d 2 [KO:K02146]
101977836  Litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
101978251  Ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
101978312  Gaa; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
101978346  Idua; alpha-L-iduronidase isoform X4 [KO:K01217] [EC:3.2.1.76]
101978424  Acp5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
101978569  [KO:K12387]
106145109  Mcoln1; mucolipin-1 [KO:K04992]
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
iti00511  Other glycan degradation
iti00531  Glycosaminoglycan degradation
iti04130  SNARE interactions in vesicular transport
iti04140  Autophagy - animal
iti04144  Endocytosis
KO pathway
ko04142   

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