KEGG   PATHWAY: tben04142
Entry
tben04142                   Pathway                                
Name
Lysosome - Trematomus bernacchii (emerald rockcod)
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
tben04142  Lysosome
tben04142

Other DBs
GO: 0005764
Organism
Trematomus bernacchii (emerald rockcod) [GN:tben]
Gene
117485505  tcirg1b; T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b isoform X1 [KO:K02154]
117496824  atp6v0a2b; V-type proton ATPase 116 kDa subunit a [KO:K02154]
117473353  V-type proton ATPase 116 kDa subunit a-like isoform X1 [KO:K02154]
117492546  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
117476674  atp6v0a2a; V-type proton ATPase 116 kDa subunit a [KO:K02154]
117488940  V-type proton ATPase subunit d 1-like [KO:K02146]
117471503  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
117482528  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
117483448  V-type proton ATPase subunit S1-like [KO:K03662]
117483453  atp6ap1a; V-type proton ATPase subunit S1 [KO:K03662]
117474046  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
117492194  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
117488365  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
117473228  LOW QUALITY PROTEIN: dmX-like protein 1 [KO:K24155]
117471434  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
117478877  LOW QUALITY PROTEIN: WD repeat-containing protein 7 [KO:K24738]
117486400  si:ch211-15d5.11; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
117493131  nuclear receptor coactivator 7 isoform X1 [KO:K25442]
117499321  ctsa; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
117471429  si:ch211-122f10.4; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
117492239  cathepsin B-like [KO:K01363] [EC:3.4.22.1]
117471404  ctsba; cathepsin B [KO:K01363] [EC:3.4.22.1]
117470315  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
117492389  napsa; napsin-A [KO:K01379] [EC:3.4.23.5]
117471499  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
117487117  nots; nothepsin [KO:K01382] [EC:3.4.23.34]
117475048  ctsf; cathepsin F isoform X1 [KO:K01373] [EC:3.4.22.41]
117491363  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
117471203  pro-cathepsin H-like [KO:K01366] [EC:3.4.22.16]
117478362  ctss1; cathepsin S, ortholog 1 [KO:K01371] [EC:3.4.22.38]
117494853  ctsk; cathepsin K [KO:K01371] [EC:3.4.22.38]
117473052  ctsla; cathepsin La [KO:K01365] [EC:3.4.22.15]
117496654  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
117496796  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
117495108  cts12; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
117491620  ctso; cathepsin O [KO:K01374] [EC:3.4.22.42]
117478363  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
117494842  cathepsin S-like isoform X1 [KO:K01368] [EC:3.4.22.27]
117489621  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
117500304  cathepsin Z [KO:K08568] [EC:3.4.18.1]
117481420  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
117485661  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
117488530  gla; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
117482283  glb1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
117492328  lysosomal alpha-glucosidase-like isoform X1 [KO:K12316] [EC:3.2.1.20]
117492329  lysosomal alpha-glucosidase-like isoform X1 [KO:K12316] [EC:3.2.1.20]
117492330  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
117482174  si:ch73-12o23.1; LOW QUALITY PROTEIN: lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
117480261  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
117473157  idua; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
117492290  alpha-N-acetylgalactosaminidase-like [KO:K01204] [EC:3.2.1.49]
117470771  alpha-N-acetylgalactosaminidase-like isoform X1 [KO:K01204] [EC:3.2.1.49]
117473487  naglu; alpha-N-acetylglucosaminidase isoform X1 [KO:K01205] [EC:3.2.1.50]
117486328  galcb; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
117469429  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
117478243  tissue alpha-L-fucosidase-like [KO:K01206] [EC:3.2.1.51]
117497130  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
117491637  hexa; beta-hexosaminidase subunit alpha isoform X1 [KO:K12373] [EC:3.2.1.52]
117476588  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
117493906  manba; LOW QUALITY PROTEIN: beta-mannosidase [KO:K01192] [EC:3.2.1.25]
117482041  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
117478179  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
117489911  hyal1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
117489961  hyal2a; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
117479730  hyal6; hyaluronoglucosaminidase 6 [KO:K01197] [EC:3.2.1.35]
117479738  hyaluronidase-4-like [KO:K01197] [EC:3.2.1.35]
117479739  hyaluronidase-5-like isoform X1 [KO:K01197] [EC:3.2.1.35]
117479744  hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
117494460  hyal3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
117494507  si:dkey-72l14.3; glyco_hydro_56 domain-containing protein [KO:K01197] [EC:3.2.1.35]
117483249  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
117489369  hyal2b; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
117491610  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
117476532  arsb; LOW QUALITY PROTEIN: arylsulfatase B [KO:K01135] [EC:3.1.6.12]
117473643  arsg; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
117471744  galns; N-acetylgalactosamine-6-sulfatase isoform X1 [KO:K01132] [EC:3.1.6.4]
117484985  gnsa; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
117476439  gnsb; glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b [KO:K01137] [EC:3.1.6.14]
117475064  ids; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
117474650  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
117472109  lipf; gastric triacylglycerol lipase [KO:K01052] [EC:3.1.1.13]
117491475  pla2g15; phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
117495551  deoxyribonuclease-2-alpha-like isoform X1 [KO:K01158] [EC:3.1.22.1]
117495552  deoxyribonuclease-2-beta-like [KO:K01158] [EC:3.1.22.1]
117468502  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
117498983  acp2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
117480750  acp5a; tartrate-resistant acid phosphatase type 5a isoform X1 [KO:K14379] [EC:3.1.3.2]
117498616  acp5b; LOW QUALITY PROTEIN: tartrate-resistant acid phosphatase type 5b [KO:K14379] [EC:3.1.3.2]
117481725  tartrate-resistant acid phosphatase type 5-like isoform X1 [KO:K14379] [EC:3.1.3.2]
117490319  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
117482345  asah1b; N-acylsphingosine amidohydrolase (acid ceramidase) 1b [KO:K12348] [EC:3.5.1.23]
117490793  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
117496820  sftpbb; surfactant protein Bb [KO:K12382]
117499445  psap; prosaposin isoform X1 [KO:K12382]
117476726  prosaposin-like [KO:K12382]
117469661  gm2a; ganglioside GM2 activator [KO:K12383]
117478371  ppt1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
117500493  lysosomal thioesterase PPT2-A-like [KO:K01074] [EC:3.1.2.22]
117477927  ppt2b; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
117489612  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
117481193  lamp1b; lysosome-associated membrane glycoprotein 1b [KO:K06528]
117471431  lamp1a; lysosome-associated membrane glycoprotein 1a isoform X1 [KO:K06528]
117495979  lysosome-associated membrane glycoprotein 3 [KO:K06562]
117482667  si:ch211-212k18.7; macrosialin [KO:K06501]
117473466  CD151 antigen-like [KO:K06497]
117487497  cd63; CD63 antigen [KO:K06497]
117472587  scarb2a; lysosome membrane protein 2a isoform X1 [KO:K12384]
117476381  lysosome membrane protein 2-like isoform X1 [KO:K12384]
117476814  scarb2c; LOW QUALITY PROTEIN: lysosome membrane protein 2c [KO:K12384]
117488764  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
117477308  NPC intracellular cholesterol transporter 2-like [KO:K13443]
117490964  ctns; cystinosin [KO:K12386]
117499611  slc17a5; sialin isoform X1 [KO:K12301]
117478092  si:ch1073-513e17.1; sialin [KO:K12301]
117489511  natural resistance-associated macrophage protein 2-like isoform X1 [KO:K21398]
117483445  natural resistance-associated macrophage protein 2-like [KO:K21398]
117492395  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
117470753  lysosomal-associated transmembrane protein 4B-like [KO:K12387]
117477572  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
117472732  abca2; ATP-binding cassette sub-family A member 2 [KO:K05642]
117484548  abcb9; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
117493267  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
117496847  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
117485095  si:dkey-159a18.1; sortilin [KO:K12388]
117486582  LOW QUALITY PROTEIN: sortilin-like [KO:K12388]
117494164  sort1b; sortilin 1b [KO:K12388]
117469289  cln3; LOW QUALITY PROTEIN: battenin [KO:K12389]
117481071  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
117496166  mfsd8l1; uncharacterized protein mfsd8l1 [KO:K12307]
117487865  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
117488279  mfsd8l2; major facilitator superfamily domain-containing protein 8 [KO:K12307]
117481695  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
117499567  si:dkey-192p21.6; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
117489540  sumf1; formylglycine-generating enzyme isoform X1 [KO:K13444] [EC:1.8.3.7]
117484858  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
117474079  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma isoform X1 [KO:K10087]
117496441  N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase-like [KO:K01125] [EC:3.1.4.45]
117496442  N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase-like isoform X1 [KO:K01125] [EC:3.1.4.45]
117475065  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
117480211  m6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
117474633  clta; clathrin light chain A isoform X1 [KO:K04644]
117475218  cltb; clathrin light chain B [KO:K04645]
117472776  cltcl1; clathrin heavy chain 1 isoform X1 [KO:K04646]
117469560  cltca; clathrin, heavy chain a (Hc) isoform X1 [KO:K04646]
117470149  clathrin heavy chain 1 isoform X1 [KO:K04646]
117488518  ap1g2; AP-1 complex subunit gamma-like 2 [KO:K12391]
117471226  ap1g1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
117496757  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
117495622  ap1m3; adaptor related protein complex 1 subunit mu 3 [KO:K12393]
117481638  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
117500296  ap1m1; AP-1 complex subunit mu-1 isoform X1 [KO:K12393]
117490075  ap1s1; AP-1 complex subunit sigma-1A [KO:K12394]
117488417  AP-1 complex subunit sigma-2-like isoform X1 [KO:K12394]
117471310  ap1s2; AP-1 complex subunit sigma-2 [KO:K12394]
117475910  ap1s3a; AP-1 complex subunit sigma-3a [KO:K12395]
117495617  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
117497201  AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
117476533  ap3b1a; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
117496955  ap3m2; LOW QUALITY PROTEIN: AP-3 complex subunit mu-2 [KO:K12398]
117499477  AP-3 complex subunit mu-1-like [KO:K12398]
117473079  ap3s1; AP-3 complex subunit sigma-1 [KO:K12399]
117496994  ap3s2; AP-3 complex subunit sigma-2 [KO:K12399]
117491901  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
117491154  ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
117469615  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
117475940  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
117480918  ADP-ribosylation factor-binding protein GGA1-like [KO:K12404]
117492254  gga3b; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
117492605  LOW QUALITY PROTEIN: ADP-ribosylation factor-binding protein GGA1-like [KO:K12404]
117482274  gga3a; ADP-ribosylation factor-binding protein GGA3a [KO:K12404]
117482312  ADP-ribosylation factor-binding protein GGA2-like [KO:K12404]
117479978  mucolipin-1-like isoform X1 [KO:K04992]
117482134  mucolipin-1-like [KO:K04992]
117474483  LITAF domain-containing protein-like [KO:K19363]
117492359  snrnp25; U11/U12 small nuclear ribonucleoprotein 25 kDa protein isoform X1 [KO:K19363]
117481957  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
117492955  cell death-inducing p53-target protein 1 homolog [KO:K19363]
117492958  LITAF domain-containing protein-like [KO:K19363]
117492965  LITAF domain-containing protein-like [KO:K19363]
117482166  si:dkeyp-75b4.8; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
117482340  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [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
tben00511  Other glycan degradation
tben00531  Glycosaminoglycan degradation
tben04130  SNARE interactions in vesicular transport
tben04140  Autophagy - animal
tben04144  Endocytosis
KO pathway
ko04142   
LinkDB

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