KEGG   PATHWAY: osa04142
Entry
osa04142                    Pathway                                
Name
Lysosome - Oryza sativa japonica (Japanese rice)
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
osa04142  Lysosome
osa04142

Other DBs
GO: 0005764
Organism
Oryza sativa japonica (Japanese rice) [GN:osa]
Gene
107275667  [KO:K01052] [EC:3.1.1.13]
112936019  [KO:K01369] [EC:3.4.22.34]
136351272  [KO:K12382]
136355711  [KO:K01205] [EC:3.2.1.50]
4324036  [KO:K12396]
4324247  [KO:K12393]
4324331  [KO:K12400]
4324486  NRAMP4; metal transporter Nramp4 [KO:K21398]
4324550  [KO:K02155]
4324683  [KO:K01369] [EC:3.4.22.34]
4324914  [KO:K12373] [EC:3.2.1.52]
4325848  [KO:K24155]
4326400  [KO:K12397]
4327145  [KO:K12382]
4327412  [KO:K02154]
4327660  OsJ_02396; probable V-type proton ATPase subunit D [KO:K02146]
4327731  [KO:K03661]
4328200  Nrat1; metal transporter NRAT1 [KO:K21398]
4329339  [KO:K01373] [EC:3.4.22.41]
4329476  [KO:K19363]
4329623  [KO:K02155]
4330133  [KO:K01369] [EC:3.4.22.34]
4331060  [KO:K12391]
4331284  [KO:K01074] [EC:3.1.2.22]
4332012  NRAMP2; metal transporter Nramp2 [KO:K21398]
4332084  [KO:K12373] [EC:3.2.1.52]
4332139  [KO:K12399]
4332195  [KO:K14379] [EC:3.1.3.2]
4332270  [KO:K02154]
4332864  [KO:K12392]
4333420  [KO:K21398]
4334331  [KO:K12394]
4334539  [KO:K12394]
4335455  [KO:K01373] [EC:3.4.22.41]
4336523  Glup3; vacuolar-processing enzyme beta-isozyme 1 precursor [KO:K01369] [EC:3.4.22.34]
4336581  [KO:K01444] [EC:3.5.1.26]
4337563  [KO:K02155]
4337620  [KO:K12373] [EC:3.2.1.52]
4338648  [KO:K12398]
4338802  [KO:K12373] [EC:3.2.1.52]
4339457  OsJ_19375; beta-galactosidase 8 precursor [KO:K12309] [EC:3.2.1.23]
4339486  [KO:K12393]
4339804  [KO:K01369] [EC:3.4.22.34]
4340249  [KO:K12391]
4340922  [KO:K24738]
4342859  NRAMP5; metal transporter Nramp5 [KO:K21398]
4342862  Nramp1; metal transporter Nramp1 [KO:K21398]
4343231  [KO:K01373] [EC:3.4.22.41]
4343697  [KO:K12373] [EC:3.2.1.52]
4343931  [KO:K12402]
4345488  [KO:K12403]
4346120  [KO:K01052] [EC:3.1.1.13]
4346369  [KO:K01052] [EC:3.1.1.13]
4347180  [KO:K01366] [EC:3.4.22.16]
4347611  [KO:K01206] [EC:3.2.1.51]
4347989  [KO:K14379] [EC:3.1.3.2]
4348218  [KO:K02154]
4348463  [KO:K12403]
4349396  [KO:K01074] [EC:3.1.2.22]
4349546  [KO:K04646]
4349589  [KO:K12382]
4349890  VATP-P1; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
4351255  [KO:K04646]
4351549  [KO:K27947]
4351612  [KO:K02155]
4351977  [KO:K12386]
4352640  NRAMP6; metal transporter Nramp6 [KO:K21398]
9266367  [KO:K14379] [EC:3.1.3.2]
9266400  [KO:K12385]
9267024  [KO:K12382]
9267339  B1153E06.4; metal transporter Nramp3 [KO:K21398]
9267789  [KO:K01363] [EC:3.4.22.1]
9270735  [KO:K01205] [EC:3.2.1.50]
9272111  [KO:K02144]
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 22:339-352 (2022)
DOI:10.1038/s41577-021-00626-8
Related
pathway
osa00511  Other glycan degradation
osa00531  Glycosaminoglycan degradation
osa04130  SNARE interactions in vesicular transport
osa04144  Endocytosis
KO pathway
ko04142   

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