KEGG   PATHWAY: tvc04142
Entry
tvc04142                    Pathway                                
Name
Lysosome - Tachysurus vachellii
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
tvc04142  Lysosome
tvc04142

Other DBs
GO: 0005764
Organism
Tachysurus vachellii [GN:tvc]
Gene
132854517  atp6v0a2b; V-type proton ATPase 116 kDa subunit a [KO:K02154]
132855502  tcirg1b; T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b [KO:K02154]
132860717  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
132863085  atp6v0a2a; V-type proton ATPase 116 kDa subunit a 2 isoform X1 [KO:K02154]
132840087  si:ch73-173p19.2; V-type proton ATPase 116 kDa subunit a 1 [KO:K02154]
132840396  atp6v0a1b; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
132838852  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
132848435  atp6v1h; V-type proton ATPase subunit H [KO:K02144]
132862699  atp6ap1a; ATPase H+ transporting accessory protein 1a [KO:K03662]
132862797  atp6ap1b; V-type proton ATPase subunit S1b [KO:K03662]
132861013  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
132845470  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
132848357  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
132851509  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
132853238  dmxl1; dmX-like protein 1 isoform X1 [KO:K24155]
132859725  WD repeat-containing protein 7 isoform X1 [KO:K24738]
132854474  nuclear receptor coactivator 7 isoform X1 [KO:K25442]
132851989  si:ch211-15d5.11; oxidation resistance protein 1 isoform X1 [KO:K25442]
132844619  ctsa; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
132852874  ctsba; cathepsin B isoform X1 [KO:K01363] [EC:3.4.22.1]
132858141  ctsc; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
132842540  napsa; napsin-A [KO:K01379] [EC:3.4.23.5]
132851295  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
132859039  nots; nothepsin [KO:K01382] [EC:3.4.23.34]
132856403  ctsf; cathepsin F [KO:K01373] [EC:3.4.22.41]
132839189  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
132845888  ctsk; cathepsin K [KO:K01371] [EC:3.4.22.38]
132854508  ctsla; cathepsin La [KO:K01365] [EC:3.4.22.15]
132851971  cathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852057  procathepsin L-like isoform X1 [KO:K01365] [EC:3.4.22.15]
132852060  procathepsin L-like isoform X1 [KO:K01365] [EC:3.4.22.15]
132852062  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852069  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852070  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852074  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852075  procathepsin L-like isoform X1 [KO:K01365] [EC:3.4.22.15]
132852097  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132852362  cts12; procathepsin L [KO:K01365] [EC:3.4.22.15]
132852486  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
132855601  ctso; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
132856753  ctss1; cathepsin S, ortholog 1 [KO:K01368] [EC:3.4.22.27]
132857241  cathepsin S-like isoform X1 [KO:K01368] [EC:3.4.22.27]
132857244  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
132857254  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
132857353  cathepsin S-like isoform X1 [KO:K01368] [EC:3.4.22.27]
132845887  ctss2.1; cathepsin S, ortholog2, tandem duplicate 1 [KO:K01368] [EC:3.4.22.27]
132862373  cathepsin Z [KO:K08568] [EC:3.4.18.1]
132844747  ctsz; cathepsin Z isoform X1 [KO:K08568] [EC:3.4.18.1]
132842056  legumain-like [KO:K01369] [EC:3.4.22.34]
132861760  legumain-like [KO:K01369] [EC:3.4.22.34]
132861776  legumain-like [KO:K01369] [EC:3.4.22.34]
132861792  legumain-like isoform X1 [KO:K01369] [EC:3.4.22.34]
132861808  legumain-like isoform X1 [KO:K01369] [EC:3.4.22.34]
132861868  legumain-like [KO:K01369] [EC:3.4.22.34]
132858771  legumain-like [KO:K01369] [EC:3.4.22.34]
132858801  legumain-like [KO:K01369] [EC:3.4.22.34]
132846831  lgmn; legumain [KO:K01369] [EC:3.4.22.34]
132852722  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
132841641  glb1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
132861172  gaa; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
132839233  gaa2; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
132845960  gba1; lysosomal acid glucosylceramidase isoform X1 [KO:K01201] [EC:3.2.1.45]
132855026  idua; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
132859198  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
132846380  naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
132843136  galca; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
132852945  galcb; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
132841312  gusb; beta-glucuronidase isoform X1 [KO:K01195] [EC:3.2.1.31]
132852364  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
132864206  fuca1.2; alpha-L-fucosidase 1, tandem duplicate 2 [KO:K01206] [EC:3.2.1.51]
132841307  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
132857065  hexa; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
132847159  manba; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
132838644  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
132842748  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
132837801  hyal2b; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
132844642  hyal2a; hyaluronidase-2 isoform X1 [KO:K01197] [EC:3.2.1.35]
132844643  hyal1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
132856943  spam1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
132857199  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
132857499  hyaluronidase-4-like isoform X1 [KO:K01197] [EC:3.2.1.35]
132853724  si:dkey-72l14.3; glyco_hydro_56 domain-containing protein [KO:K01197] [EC:3.2.1.35]
132853956  hyal3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
132851394  arsa; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
132860452  arylsulfatase B [KO:K01135] [EC:3.1.6.12]
132838751  arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
132838565  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
132863026  gnsb; glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b [KO:K01137] [EC:3.1.6.14]
132859158  gnsa; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
132856169  ids; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
132838836  sgsh; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
132839608  lipf; gastric triacylglycerol lipase isoform X1 [KO:K01052] [EC:3.1.1.13]
132855882  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
132840544  dnase2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
132853701  dnase2b; deoxyribonuclease-2-beta isoform X1 [KO:K01158] [EC:3.1.22.1]
132838515  acp2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
132845462  lysosomal acid phosphatase-like isoform X1 [KO:K14410] [EC:3.1.3.2]
132844075  acp5a; tartrate-resistant acid phosphatase type 5a [KO:K14379] [EC:3.1.3.2]
132845805  acp5b; tartrate-resistant acid phosphatase type 5b [KO:K14379] [EC:3.1.3.2]
132862961  smpd1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
132841993  asah1b; acid ceramidase [KO:K12348] [EC:3.5.1.23]
132856213  asah1a; N-acylsphingosine amidohydrolase (acid ceramidase) 1a [KO:K12348] [EC:3.5.1.23]
132856191  aga; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
132846719  zgc:153169; N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
132846983  psap; prosaposin isoform X1 [KO:K12382]
132856224  gm2a; ganglioside GM2 activator [KO:K12383]
132837444  ppt1; palmitoyl-protein thioesterase 1 isoform X1 [KO:K01074] [EC:3.1.2.22]
132857344  ppt2b; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
132858591  ppt2a.2; lysosomal thioesterase PPT2-A-like [KO:K01074] [EC:3.1.2.22]
132850028  lamp1b; lysosome-associated membrane glycoprotein 1b [KO:K06528]
132839164  lamp1a; lysosome-associated membrane glycoprotein 1a [KO:K06528]
132842231  lamp3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
132848526  cd68; macrosialin [KO:K06501]
132862055  cd63; CD63 antigen [KO:K06497]
132855362  scarb2a; lysosome membrane protein 2a isoform X1 [KO:K12384]
132859603  scarb2c; lysosome membrane protein 2c [KO:K12384]
132859627  scarb2b; lysosome membrane protein 2 [KO:K12384]
132844600  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
132852598  NPC intracellular cholesterol transporter 2-like [KO:K13443]
132852308  ctns; cystinosin [KO:K12386]
132837442  si:ch1073-513e17.1; sialin [KO:K12301]
132847376  slc17a5; sialin [KO:K12301]
132838146  slc11a2; natural resistance-associated macrophage protein 2 [KO:K21398]
132843072  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
132837525  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
132855174  abca2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
132855152  abcb9; ATP-binding cassette sub-family B member 9 [KO:K05656]
132854338  cd164; sialomucin core protein 24 [KO:K06546]
132853290  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
132837726  sort1a; sortilin [KO:K12388]
132858849  si:dkey-159a18.1; sortilin isoform X1 [KO:K12388]
132853674  sort1b; sortilin 1b [KO:K12388]
132860925  cln3; battenin isoform X1 [KO:K12389]
132850173  cln5; ceroid-lipofuscinosis neuronal protein 5 homolog [KO:K12390]
132847849  mfsd8l2; major facilitator superfamily domain-containing protein 8 [KO:K12307]
132842316  mfsd8l1; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
132862117  mfsd8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
132842030  hgsnat; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
132847386  si:dkey-192p21.6; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
132844134  sumf1; formylglycine-generating enzyme isoform X1 [KO:K13444] [EC:1.8.3.7]
132856718  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
132846424  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
132845654  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
132843091  igf2r; cation-independent mannose-6-phosphate receptor [KO:K06564]
132845858  m6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
132842026  clta; clathrin light chain A isoform X1 [KO:K04644]
132861377  cltb; clathrin light chain B [KO:K04645]
132858148  cltcb; clathrin, heavy chain b (Hc) [KO:K04646]
132858660  clathrin heavy chain 1-like [KO:K04646]
132848314  ap1g2; AP-1 complex subunit gamma-like 2 [KO:K12391]
132846440  ap1g1; AP-1 complex subunit gamma-1 [KO:K12391]
132854950  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
132844276  ap1m3; adaptor related protein complex 1 subunit mu 3 [KO:K12393]
132844874  ap1m2; AP-1 complex subunit mu-2 [KO:K12393]
132845170  ap1m1; AP-1 complex subunit mu-1 [KO:K12393]
132841786  ap1s2; AP-1 complex subunit sigma-2 [KO:K12394]
132848604  ap1s1; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
132861932  AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
132846822  ap1s3b; AP-1 complex subunit sigma-3b isoform X1 [KO:K12395]
132853198  ap3d1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
132857187  AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
132859600  ap3b1a; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
132855190  ap3m2; AP-3 complex subunit mu-2 [KO:K12398]
132847403  ap3m1; AP-3 complex subunit mu-1 [KO:K12398]
132855729  ap3s2; AP-3 complex subunit sigma-2 [KO:K12399]
132853480  ap3s1; AP-3 complex subunit sigma-1 [KO:K12399]
132856824  ap4e1; AP-4 complex subunit epsilon-1 [KO:K12400]
132862090  ap4b1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
132863571  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
132852785  ap4s1; AP-4 complex subunit sigma-1 isoform X1 [KO:K12403]
132842621  gga3b; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
132844856  gga1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
132839390  ADP-ribosylation factor-binding protein GGA2-like isoform X1 [KO:K12404]
132842635  mcoln1b; mucolipin-1b [KO:K04992]
132839167  mcoln1a; mucolipin-1a [KO:K04992]
132837609  litaf; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
132839543  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
132839546  cell death-inducing p53-target protein 1 homolog [KO:K19363]
132839548  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
132839602  si:dkeyp-75b4.8; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X1 [KO:K19363]
132864223  uncharacterized protein LOC132864223 isoform X1 [KO:K19363]
Compound
C00002  ATP
C00008  ADP
C00159  D-Mannose
C00275  D-Mannose 6-phosphate
Reference
  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
  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
  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
  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
  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
tvc00511  Other glycan degradation
tvc00531  Glycosaminoglycan degradation
tvc04130  SNARE interactions in vesicular transport
tvc04140  Autophagy - animal
tvc04144  Endocytosis
KO pathway
ko04142   
LinkDB

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