KEGG   PATHWAY: dre04142
Entry
dre04142                    Pathway                                
Name
Lysosome - Danio rerio (zebrafish)
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
dre04142  Lysosome
dre04142

Other DBs
GO: 0005764
Organism
Danio rerio (zebrafish) [GN:dre]
Gene
324307  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform 1a [KO:K02154]
553691  atp6v0a1b; V-type proton ATPase 116 kDa subunit a isoform 1b [KO:K02154]
406342  tcirg1b; T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b [KO:K02154]
100003139  tcirg1a; V-type proton ATPase 116 kDa subunit a [KO:K02154]
561469  atp6v0a2a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
561117  atp6v0a2b; V-type proton ATPase 116 kDa subunit a isoform 2b [KO:K02154]
100332691  si:ch73-173p19.2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
322811  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
286779  atp6v1h; V-type proton ATPase subunit H isoform 1 [KO:K02144]
195824  atp6ap1b; V-type proton ATPase subunit S1b [KO:K03662]
100004566  atp6ap1a; ATPase H+ transporting accessory protein 1a precursor [KO:K03662]
192336  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
325402  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
321724  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
100333625  dmX-like protein 1 [KO:K24155]
378958  dmxl2; dmX-like protein 2 [KO:K24155]
572502  wdr7; WD repeat-containing protein 7 [KO:K24738]
569262  nuclear receptor coactivator 7-like isoform X2 [KO:K25442]
559575  si:ch211-15d5.11; oxidation resistance protein 1-like isoform X1 [KO:K25442]
792966  si:ch211-122f10.4; cathepsin A-like precursor [KO:K13289] [EC:3.4.16.5]
321818  ctsa; lysosomal protective protein precursor [KO:K13289] [EC:3.4.16.5]
406645  ctsba; cathepsin B precursor [KO:K01363] [EC:3.4.22.1]
569298  ctsbb; cathepsin Bb precursor [KO:K01363] [EC:3.4.22.1]
368704  ctsc; dipeptidyl peptidase 1 precursor [KO:K01275] [EC:3.4.14.1]
65225  ctsd; cathepsin D precursor [KO:K01379] [EC:3.4.23.5]
336746  napsa; napsin-A precursor [KO:K01379] [EC:3.4.23.5]
114367  nots; nothepsin [KO:K01382] [EC:3.4.23.34]
565588  ctsf; cathepsin F precursor [KO:K01373] [EC:3.4.22.41]
324818  ctsh; pro-cathepsin H precursor [KO:K01366] [EC:3.4.22.16]
550475  ctsk; cathepsin K precursor [KO:K01371] [EC:3.4.22.38]
321453  ctsla; cathepsin La precursor [KO:K01365] [EC:3.4.22.15]
30443  ctslb; cathepsin Lb precursor [KO:K01365] [EC:3.4.22.15]
567046  cts12; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
100537591  zgc:174154; uncharacterized protein LOC100537591 precursor [KO:K01365] [EC:3.4.22.15]
436641  ctsl.1; cathepsin L.1 precursor [KO:K01365] [EC:3.4.22.15]
563390  si:dkey-26g8.5; uncharacterized protein LOC563390 precursor [KO:K01365] [EC:3.4.22.15]
100001785  si:dkey-239j18.3; cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
567623  zgc:174153; uncharacterized protein LOC567623 precursor [KO:K01365] [EC:3.4.22.15]
569326  zgc:174855; uncharacterized protein LOC569326 precursor [KO:K01365] [EC:3.4.22.15]
321853  si:dkey-239j18.2; uncharacterized protein LOC321853 precursor [KO:K01365] [EC:3.4.22.15]
567333  ctso; cathepsin O isoform X2 [KO:K01374] [EC:3.4.22.42]
554157  ctss2.1; cathepsin S, ortholog2, tandem duplicate 1 precursor [KO:K01368] [EC:3.4.22.27]
337572  ctss2.2; cathepsin S, ortholog 2, tandem duplicate 2 precursor [KO:K01368] [EC:3.4.22.27]
393398  ctss1; cathepsin S, ortholog 1 [KO:K01368] [EC:3.4.22.27]
450022  ctsz; cathepsin Z precursor [KO:K08568] [EC:3.4.18.1]
100333521  cathepsin Z-like isoform X1 [KO:K08568] [EC:3.4.18.1]
406625  lgmn; legumain precursor [KO:K01369] [EC:3.4.22.34]
100005175  legumain-like [KO:K01369] [EC:3.4.22.34]
100005356  uncharacterized protein LOC100005356 [KO:K01369] [EC:3.4.22.34]
100005220  legumain-like [KO:K01369] [EC:3.4.22.34]
100005266  legumain-like [KO:K01369] [EC:3.4.22.34]
100005129  legumain-like [KO:K01369] [EC:3.4.22.34]
569153  legumain [KO:K01369] [EC:3.4.22.34]
798347  tpp1; tripeptidyl-peptidase 1 precursor [KO:K01279] [EC:3.4.14.9]
450083  gla; alpha-galactosidase A precursor [KO:K01189] [EC:3.2.1.22]
548343  glb1; beta-galactosidase precursor [KO:K12309] [EC:3.2.1.23]
100002366  gaa; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
100332784  si:ch73-12o23.1; lysosomal alpha-glucosidase isoform X2 [KO:K12316] [EC:3.2.1.20]
559072  gba; glucosylceramidase [KO:K01201] [EC:3.2.1.45]
567720  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
560778  naga; alpha-N-acetylgalactosaminidase precursor [KO:K01204] [EC:3.2.1.49]
560126  naglu; alpha-N-acetylglucosaminidase isoform X2 [KO:K01205] [EC:3.2.1.50]
406385  galcb; galactocerebrosidase precursor [KO:K01202] [EC:3.2.1.46]
449649  galca; galactocerebrosidase precursor [KO:K01202] [EC:3.2.1.46]
571441  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
335494  fuca1.1; alpha-L-fucosidase 1, tandem duplicate 1 precursor [KO:K01206] [EC:3.2.1.51]
445487  fuca2; plasma alpha-L-fucosidase precursor [KO:K01206] [EC:3.2.1.51]
445165  fuca1.2; alpha-L-fucosidase 1, tandem duplicate 2 precursor [KO:K01206] [EC:3.2.1.51]
323613  hexb; beta-hexosaminidase subunit beta isoform 1 precursor [KO:K12373] [EC:3.2.1.52]
550460  hexa; beta-hexosaminidase subunit alpha precursor [KO:K12373] [EC:3.2.1.52]
393128  manba; beta-mannosidase precursor [KO:K01192] [EC:3.2.1.25]
541519  man2b1; lysosomal alpha-mannosidase precursor [KO:K12311] [EC:3.2.1.24]
559850  neu1; sialidase-1 precursor [KO:K01186] [EC:3.2.1.18]
567869  hyal2a; hyaluronidase-2-like isoform X2 [KO:K01197] [EC:3.2.1.35]
559228  hyal2b; hyaluronidase-2 isoform X2 [KO:K01197] [EC:3.2.1.35]
100004557  hyal3; hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
791189  hyal6; hyaluronoglucosaminidase 6 precursor [KO:K01197] [EC:3.2.1.35]
664772  hyal1; hyaluronidase-1 precursor [KO:K01197] [EC:3.2.1.35]
108181664  hyaluronidase-4-like [KO:K01197] [EC:3.2.1.35]
562480  si:dkey-72l14.3; Glyco_hydro_56 domain-containing protein [KO:K01197] [EC:3.2.1.35]
791203  spam1; hyaluronidase PH-20 precursor [KO:K01197] [EC:3.2.1.35]
541416  arsa; arylsulfatase A precursor [KO:K01134] [EC:3.1.6.8]
100538007  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
564790  arsg; arylsulfatase G precursor [KO:K12381] [EC:3.1.6.-]
103910035  arylsulfatase G-like [KO:K12381] [EC:3.1.6.-]
791159  galns; N-acetylgalactosamine-6-sulfatase precursor [KO:K01132] [EC:3.1.6.4]
566506  gnsa; N-acetylglucosamine-6-sulfatase precursor [KO:K01137] [EC:3.1.6.14]
327635  gnsb; glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b precursor [KO:K01137] [EC:3.1.6.14]
559959  ids; iduronate 2-sulfatase precursor [KO:K01136] [EC:3.1.6.13]
563849  sgsh; N-sulphoglucosamine sulphohydrolase precursor [KO:K01565] [EC:3.10.1.1]
406713  lipf; gastric triacylglycerol lipase precursor [KO:K01052] [EC:3.1.1.13]
335008  pla2g15; group XV phospholipase A2 precursor [KO:K06129] [EC:3.1.1.5]
100000399  dnase2; deoxyribonuclease-2-alpha precursor [KO:K01158] [EC:3.1.22.1]
562996  dnase2b; deoxyribonuclease-2-beta isoform X2 [KO:K01158] [EC:3.1.22.1]
503759  acp2; lysosomal acid phosphatase precursor [KO:K14410] [EC:3.1.3.2]
406801  acp5a; tartrate-resistant acid phosphatase type 5a precursor [KO:K14379] [EC:3.1.3.2]
436725  acp5b; tartrate-resistant acid phosphatase type 5b precursor [KO:K14379] [EC:3.1.3.2]
556700  smpd1; sphingomyelin phosphodiesterase precursor [KO:K12350] [EC:3.1.4.12]
393549  asah1b; acid ceramidase precursor [KO:K12348] [EC:3.5.1.23]
450068  asah1a; N-acylsphingosine amidohydrolase (acid ceramidase) 1a precursor [KO:K12348] [EC:3.5.1.23]
566517  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase precursor [KO:K01444] [EC:3.5.1.26]
767799  zgc:153169; uncharacterized protein LOC767799 [KO:K01444] [EC:3.5.1.26]
140811  psap; prosaposin isoform 2 precursor [KO:K12382]
550529  gm2a; ganglioside GM2 activator precursor [KO:K12383]
406648  ppt1; palmitoyl-protein thioesterase 1 precursor [KO:K01074] [EC:3.1.2.22]
393135  ppt2a.2; Lysosomal thioesterase PPT2-A-like precursor [KO:K01074] [EC:3.1.2.22]
393657  ppt2a.1; lysosomal thioesterase PPT2a.1 precursor [KO:K01074] [EC:3.1.2.22]
405845  ppt2a.4; uncharacterized protein LOC405845 precursor [KO:K01074] [EC:3.1.2.22]
100126133  ppt2b; lysosomal thioesterase PPT2 precursor [KO:K01074] [EC:3.1.2.22]
406830  ppt2a.3; uncharacterized protein LOC406830 precursor [KO:K01074] [EC:3.1.2.22]
324985  lamp1a; lysosome-associated membrane glycoprotein 1a precursor [KO:K06528]
563328  lamp1b; lysosome-associated membrane glycoprotein 1b precursor [KO:K06528]
100003043  lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
100000085  si:ch211-212k18.7; macrosialin [KO:K06501]
321461  cd63; CD63 antigen [KO:K06497]
192340  scarb2a; lysosome membrane protein 2a [KO:K12384]
337532  scarb2c; lysosome membrane protein 2c [KO:K12384]
564077  scarb2b; lysosome membrane protein 2 [KO:K12384]
553330  npc1; NPC intracellular cholesterol transporter 1 precursor [KO:K12385]
282673  npc2.1; NPC intracellular cholesterol transporter 2 precursor [KO:K13443]
565099  npc2.2; Epididymal secretory protein E1-like precursor [KO:K13443]
553594  ctns; cystinosin precursor [KO:K12386]
767760  slc17a5; sialin [KO:K12301]
571066  si:ch1073-513e17.1; sialin isoform X1 [KO:K12301]
678623  slc11a2; natural resistance-associated macrophage protein 2 [KO:K21398]
100003844  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
368911  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
100006090  abca2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
570148  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
555639  cd164; sialomucin core protein 24 precursor [KO:K06546]
436692  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
406511  sort1a; sortilin precursor [KO:K12388]
560593  si:dkey-159a18.1; sortilin isoform X1 [KO:K12388]
799153  sort1b; sortilin 1b precursor [KO:K12388]
492340  cln3; battenin [KO:K12389]
569407  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
564731  major facilitator superfamily domain-containing protein 8-like [KO:K12307]
564342  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
565645  si:ch211-38m6.6; major facilitator superfamily domain-containing protein 8 [KO:K12307]
565246  si:dkey-192p21.6; uncharacterized protein LOC565246 precursor [KO:K10532] [EC:2.3.1.78]
100329505  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
553423  sumf1; formylglycine-generating enzyme precursor [KO:K13444] [EC:1.8.3.7]
553365  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
415147  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma precursor [KO:K10087]
569719  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase precursor [KO:K01125] [EC:3.1.4.45]
557061  igf2r; cation-independent mannose-6-phosphate receptor precursor [KO:K06564]
406486  m6pr; cation-dependent mannose-6-phosphate receptor precursor [KO:K10089]
406318  clta; clathrin light chain A [KO:K04644]
100329879  cltb; clathrin light chain B isoform X1 [KO:K04645]
323579  cltca; clathrin, heavy chain a (Hc) [KO:K04646]
503600  cltcb; clathrin, heavy chain b (Hc) [KO:K04646]
100330183  cltcl1; clathrin heavy chain 1 [KO:K04646]
324466  ap1g1; AP-1 complex subunit gamma-1 [KO:K12391]
100007877  ap1g2; AP-1 complex subunit gamma-like 2 [KO:K12391]
562166  ap1b1; AP-1 complex subunit beta-1 [KO:K12392]
403021  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
445244  ap1m3; adaptor related protein complex 1 subunit mu 3 [KO:K12393]
100330411  ap1m1; AP-1 complex subunit mu-1 [KO:K12393]
327237  ap1s2; AP-1 complex subunit sigma-2 [KO:K12394]
393279  ap1s1; AP-1 complex subunit sigma-1A isoform 1 [KO:K12394]
337771  zgc:162858; uncharacterized protein LOC337771 [KO:K12394]
447897  ap1s3b; AP-1 complex subunit sigma-3b [KO:K12395]
550415  ap1s3a; AP-1 complex subunit sigma-3a [KO:K12395]
563359  ap3d1; AP-3 complex subunit delta-1 [KO:K12396]
100000165  ap3b2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
563316  ap3b1; AP-3 complex subunit beta-1 [KO:K12397]
266798  ap3m1; AP-3 complex subunit mu-1 [KO:K12398]
415244  ap3m2; AP-3 complex subunit mu-2 [KO:K12398]
436812  ap3s2; AP-3 complex subunit sigma-2 [KO:K12399]
449791  ap3s1; AP-3 complex subunit sigma-1 [KO:K12399]
570467  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
393309  ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
436945  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
368852  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
492643  gga3a; ADP-ribosylation factor-binding protein GGA3a [KO:K12404]
798361  gga1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
100334661  si:ch73-157i16.3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
795916  mcoln1b; mucolipin-1b [KO:K04992]
406689  mcoln1a; mucolipin-1a [KO:K04992]
103911283  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
431731  litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
559480  si:ch211-202h22.9; uncharacterized protein LOC559480 [KO:K19363]
796031  si:dkeyp-75b4.8; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
559550  si:ch211-202h22.8; Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog-like [KO:K19363]
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
dre00511  Other glycan degradation
dre00531  Glycosaminoglycan degradation
dre04130  SNARE interactions in vesicular transport
dre04140  Autophagy - animal
dre04144  Endocytosis
KO pathway
ko04142   
LinkDB

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