KEGG   PATHWAY: ath04142
Entry
ath04142                    Pathway                                
Name
Lysosome - Arabidopsis thaliana (thale cress)
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
ath04142  Lysosome
ath04142

Other DBs
GO: 0005764
Organism
Arabidopsis thaliana (thale cress) [GN:ath]
Gene
AT1G02300  [KO:K01363] [EC:3.4.22.1]
AT1G02305  [KO:K01363] [EC:3.4.22.1]
AT1G05590  HEXO2; beta-hexosaminidase 2 [KO:K12373] [EC:3.2.1.52]
AT1G10730  [KO:K12393]
AT1G14700  PAP3; purple acid phosphatase 3 [KO:K14379] [EC:3.1.3.2]
AT1G15960  NRAMP6; NRAMP metal ion transporter 6 [KO:K21398]
AT1G19910  AVA-P2; ATPase, F0/V0 complex, subunit C protein [KO:K02155]
AT1G23900  GAMMA-ADAPTIN_1; gamma-adaptin 1 [KO:K12391]
AT1G25230  [KO:K14379] [EC:3.1.3.2]
AT1G31730  [KO:K12400]
AT1G42470  [KO:K12385]
AT1G47240  NRAMP2; NRAMP metal ion transporter 2 [KO:K21398]
AT1G48760  delta-ADR; delta-adaptin [KO:K12396]
AT1G56590  ZIP4; Clathrin adaptor complexes medium subunit family protein [KO:K12398]
AT1G60070  [KO:K12391]
AT1G60780  HAP13; Clathrin adaptor complexes medium subunit family protein [KO:K12393]
AT1G62710  BETA-VPE; beta vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT1G65590  HEXO3; beta-hexosaminidase 3 [KO:K12373] [EC:3.2.1.52]
AT1G67830  FXG1; alpha-fucosidase 1 [KO:K01206] [EC:3.2.1.51]
AT1G69100  [KO:K01379] [EC:3.4.23.5]
AT1G72990  BGAL17; beta-galactosidase 17 [KO:K12309] [EC:3.2.1.23]
AT1G75630  AVA-P4; vacuolar H+-pumping ATPase 16 kDa proteolipid subunit 4 [KO:K02155]
AT1G80830  NRAMP1; natural resistance-associated macrophage protein 1 [KO:K21398]
AT2G01880  PAP7; purple acid phosphatase 7 [KO:K14379] [EC:3.1.3.2]
AT2G01890  PAP8; purple acid phosphatase 8 [KO:K14379] [EC:3.1.3.2]
AT2G15230  LIP1; lipase 1 [KO:K01052] [EC:3.1.1.13]
AT2G16510  [KO:K02155]
AT2G17380  AP19; associated protein 19 [KO:K12394]
AT2G19790  [KO:K12403]
AT2G21410  VHA-A2; vacuolar proton ATPase A2 [KO:K02154]
AT2G21430  [KO:K01373] [EC:3.4.22.41]
AT2G23150  NRAMP3; natural resistance-associated macrophage protein 3 [KO:K21398]
AT2G25610  [KO:K03661]
AT2G25940  ALPHA-VPE; alpha-vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT2G28100  FUC1; alpha-L-fucosidase 1 [KO:K01206] [EC:3.2.1.51]
AT2G28520  VHA-A1; vacuolar proton ATPase A1 [KO:K02154]
AT2G46560  [KO:K24155]
AT3G08530  [KO:K04646]
AT3G11130  [KO:K04646]
AT3G17790  PAP17; purple acid phosphatase 17 [KO:K14379] [EC:3.1.3.2]
AT3G20210  DELTA-VPE; delta vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT3G28710  [KO:K02146]
AT3G28715  [KO:K02146]
AT3G42050  [KO:K02144]
AT3G45310  [KO:K01366] [EC:3.4.22.16]
AT3G50860  [KO:K12399]
AT3G51730  [KO:K12382]
AT3G52840  BGAL2; beta-galactosidase 2 [KO:K12309] [EC:3.2.1.23]
AT3G54940  [KO:K01373] [EC:3.4.22.41]
AT3G55260  HEXO1; beta-hexosaminidase 1 [KO:K12373] [EC:3.2.1.52]
AT3G55480  PAT2; protein affected trafficking 2 [KO:K12397]
AT3G60340  [KO:K01074] [EC:3.1.2.22]
AT4G01610  [KO:K01363] [EC:3.4.22.1]
AT4G11270  [KO:K24738]
AT4G11380  [KO:K12392]
AT4G16190  [KO:K01373] [EC:3.4.22.41]
AT4G17470  [KO:K01074] [EC:3.1.2.22]
AT4G17480  [KO:K01074] [EC:3.1.2.22]
AT4G17483  [KO:K01074] [EC:3.1.2.22]
AT4G18790  NRAMP5; NRAMP metal ion transporter family protein [KO:K21398]
AT4G22050  [KO:K01379] [EC:3.4.23.5]
AT4G23460  [KO:K12392]
AT4G24550  [KO:K12402]
AT4G32530  [KO:K03661]
AT4G32940  GAMMA-VPE; gamma vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT4G34720  AVA-P1; ATPase, F0/V0 complex, subunit C protein [KO:K02155]
AT4G35410  [KO:K12394]
AT4G38350  [KO:K12385]
AT4G38920  VHA-C3; vacuolar-type H[+]-ATPase C3 [KO:K02155]
AT4G39080  VHA-A3; vacuolar proton ATPase A3 [KO:K02154]
AT4G39090  RD19; Papain family cysteine protease [KO:K01373] [EC:3.4.22.41]
AT5G01800  [KO:K12382]
AT5G06260  [KO:K27947]
AT5G13190  GILP; GSH-induced LITAF domain protein [KO:K19363]
AT5G13690  CYL1; alpha-N-acetylglucosaminidase family / NAGLU family [KO:K01205] [EC:3.2.1.50]
AT5G40670  [KO:K12386]
AT5G47330  [KO:K01074] [EC:3.1.2.22]
AT5G47340  [KO:K01074] [EC:3.1.2.22]
AT5G47350  [KO:K01074] [EC:3.1.2.22]
AT5G60360  ALP; aleurain-like protease [KO:K01366] [EC:3.4.22.16]
AT5G61540  [KO:K01444] [EC:3.5.1.26]
AT5G67330  NRAMP4; natural resistance associated macrophage protein 4 [KO:K21398]
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
ath00511  Other glycan degradation
ath00531  Glycosaminoglycan degradation
ath04130  SNARE interactions in vesicular transport
ath04144  Endocytosis
KO pathway
ko04142   

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