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]
AT1G02630  [KO:K15014]
AT1G04750  VAMP721; vesicle-associated membrane protein 721 [KO:K08515]
AT1G04760  VAMP726; vesicle-associated membrane protein 726 [KO:K08515]
AT1G05590  HEXO2; beta-hexosaminidase 2 [KO:K12373] [EC:3.2.1.52]
AT1G08190  VPS41; vacuolar protein sorting 41 [KO:K20184]
AT1G10730  [KO:K12393]
AT1G12470  [KO:K20181]
AT1G12840  DET3; vacuolar ATP synthase subunit C (VATC) / V-ATPase C subunit / vacuolar proton pump C subunit (DET3) [KO:K02148]
AT1G13170  ORP1D; OSBP(oxysterol binding protein)-related protein 1D [KO:K20456]
AT1G14700  PAP3; purple acid phosphatase 3 [KO:K14379] [EC:3.1.3.2]
AT1G15960  NRAMP6; NRAMP metal ion transporter 6 [KO:K21398]
AT1G17340  [KO:K22913] [EC:3.1.3.-]
AT1G19910  AVA-P2; ATPase, F0/V0 complex, subunit C protein [KO:K02155]
AT1G20260  VAB3; ATPase, V1 complex, subunit B protein [KO:K02147]
AT1G22620  ATSAC1; Phosphoinositide phosphatase family protein [KO:K22913] [EC:3.1.3.-]
AT1G22740  RABG3B; RAB GTPase homolog G3B [KO:K07897]
AT1G23900  GAMMA-ADAPTIN_1; gamma-adaptin 1 [KO:K12391]
AT1G25230  [KO:K14379] [EC:3.1.3.2]
AT1G31730  [KO:K12400]
AT1G34260  FAB1D; FORMS APLOID AND BINUCLEATE CELLS 1A [KO:K00921] [EC:2.7.1.150]
AT1G42470  [KO:K12385]
AT1G47240  NRAMP2; NRAMP metal ion transporter 2 [KO:K21398]
AT1G47830  [KO:K11827]
AT1G48090  [KO:K19525]
AT1G48760  delta-ADR; delta-adaptin [KO:K12396]
AT1G49300  RABG3E; RAB GTPase homolog G3E [KO:K07897]
AT1G50030  TOR; target of rapamycin [KO:K07203] [EC:2.7.11.1]
AT1G52280  RABG3d; RAB GTPase homolog G3D [KO:K07897]
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]
AT1G61630  ENT7; equilibrative nucleoside transporter 7 [KO:K15014]
AT1G62200  PTR6; Major facilitator superfamily protein [KO:K14638]
AT1G62710  BETA-VPE; beta vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT1G64200  VHA-E3; vacuolar H+-ATPase subunit E isoform 3 [KO:K02150]
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]
AT1G70330  ENT1; equilibrative nucleotide transporter 1 [KO:K15014]
AT1G71010  FAB1C; FORMS APLOID AND BINUCLEATE CELLS 1C [KO:K00921] [EC:2.7.1.150]
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]
AT1G75850  VPS35B; VPS35 homolog B [KO:K18468]
AT1G76030  VAB1; ATPase, V1 complex, subunit B protein [KO:K02147]
AT1G78900  VHA-A; vacuolar ATP synthase subunit A [KO:K02145] [EC:7.1.2.2]
AT1G79190  [KO:K20403]
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]
AT2G02020  PTR4; Major facilitator superfamily protein [KO:K14638]
AT2G02040  PTR2; peptide transporter 2 [KO:K14638]
AT2G05170  VPS11; vacuolar protein sorting 11 [KO:K20179]
AT2G15230  LIP1; lipase 1 [KO:K01052] [EC:3.1.1.13]
AT2G16510  [KO:K02155]
AT2G17380  AP19; associated protein 19 [KO:K12394]
AT2G17790  VPS35A; vacuolar protein sorting-associated 35A-like protein [KO:K18468]
AT2G19790  [KO:K12403]
AT2G20790  [KO:K19023]
AT2G21410  VHA-A2; vacuolar proton ATPase A2 [KO:K02154]
AT2G21430  [KO:K01373] [EC:3.4.22.41]
AT2G21880  RAB7A; RAB GTPase homolog 7A [KO:K07897]
AT2G22040  LST8-2; Transducin/WD40 repeat-like superfamily protein [KO:K08266]
AT2G23150  NRAMP3; natural resistance-associated macrophage protein 3 [KO:K21398]
AT2G25340  VAMP712; vesicle-associated membrane protein 712 [KO:K08515]
AT2G25610  [KO:K03661]
AT2G25730  [KO:K19027]
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]
AT2G30330  BLOS1; GCN5L1 family protein [KO:K20185]
AT2G31020  ORP1A; OSBP(oxysterol binding protein)-related protein 1A [KO:K20456]
AT2G31030  ORP1B; OSBP(oxysterol binding protein)-related protein 1B [KO:K20456]
AT2G32670  VAMP725; vesicle-associated membrane protein 725 [KO:K08515]
AT2G33110  VAMP723; vesicle-associated membrane protein 723 [KO:K08515]
AT2G33120  SAR1; synaptobrevin-related protein 1 [KO:K08515]
AT2G38020  VCL1; vacuoleless1 (VCL1) [KO:K20180]
AT2G42005  [KO:K14209]
AT2G46560  [KO:K24155]
AT3G01390  VMA10; vacuolar membrane ATPase 10 [KO:K02152]
AT3G08530  [KO:K04646]
AT3G08560  VHA-E2; vacuolar H+-ATPase subunit E isoform 2 [KO:K02150]
AT3G08850  RAPTOR1; Regulatory-associated protein of TOR 1 [KO:K07204]
AT3G09300  ORP3B; OSBP(oxysterol binding protein)-related protein 3B [KO:K20456]
AT3G09990  [KO:K15014]
AT3G11130  [KO:K04646]
AT3G11900  ANT1; aromatic and neutral transporter 1 [KO:K14209]
AT3G14205  [KO:K22913] [EC:3.1.3.-]
AT3G14270  FAB1B; phosphatidylinositol-4-phosphate 5-kinase family protein [KO:K00921] [EC:2.7.1.150]
AT3G15160  [KO:K19025]
AT3G16100  RABG3c; RAB GTPase homolog G3C [KO:K07897]
AT3G17790  PAP17; purple acid phosphatase 17 [KO:K14379] [EC:3.1.3.2]
AT3G18140  LST8-1; Transducin/WD40 repeat-like superfamily protein [KO:K08266]
AT3G18820  RAB7B; RAB GTPase homolog G3F [KO:K07897]
AT3G19870  [KO:K19022]
AT3G20210  DELTA-VPE; delta vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT3G24890  VAMP728; vesicle-associated membrane protein 728 [KO:K08515]
AT3G27170  CLC-B; chloride channel B [KO:K05016]
AT3G28710  [KO:K02146]
AT3G28715  [KO:K02146]
AT3G29130  [KO:K20818]
AT3G42050  [KO:K02144]
AT3G43220  [KO:K22913] [EC:3.1.3.-]
AT3G45310  [KO:K01366] [EC:3.4.22.16]
AT3G47810  MAG1; Calcineurin-like metallo-phosphoesterase superfamily protein [KO:K18467]
AT3G48470  EMB2423; embryo defective 2423 [KO:K11137]
AT3G49860  ARLA1B; ADP-ribosylation factor-like A1B [KO:K07955]
AT3G49870  ARLA1C; ADP-ribosylation factor-like A1C [KO:K07955]
AT3G50860  [KO:K12399]
AT3G51310  VPS35C; VPS35 homolog C [KO:K18468]
AT3G51730  [KO:K12382]
AT3G54140  PTR1; peptide transporter 1 [KO:K14638]
AT3G54300  VAMP727; vesicle-associated membrane protein 727 [KO:K08515]
AT3G54860  ATVPS33; Sec1/munc18-like (SM) proteins superfamily [KO:K20182]
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]
AT3G58730  [KO:K02149]
AT3G60340  [KO:K01074] [EC:3.1.2.22]
AT4G01610  [KO:K01363] [EC:3.4.22.1]
AT4G02620  [KO:K02151]
AT4G05110  ENT6; equilibrative nucleoside transporter 6 [KO:K15014]
AT4G05120  FUR1; Major facilitator superfamily protein [KO:K15014]
AT4G05130  ENT4; equilibrative nucleoside transporter 4 [KO:K15014]
AT4G05140  [KO:K15014]
AT4G08180  ORP1C; OSBP(oxysterol binding protein)-related protein 1C [KO:K20456]
AT4G09720  RABG3A; RAB GTPase homolog G3A [KO:K07897]
AT4G11150  TUF; vacuolar ATP synthase subunit E1 [KO:K02150]
AT4G11270  [KO:K24738]
AT4G11380  [KO:K12392]
AT4G12460  ORP2B; OSBP(oxysterol binding protein)-related protein 2B [KO:K20456]
AT4G15780  VAMP724; vesicle-associated membrane protein 724 [KO:K08515]
AT4G16190  [KO:K01373] [EC:3.4.22.41]
AT4G17140  [KO:K19525]
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]
AT4G22540  ORP2A; OSBP(oxysterol binding protein)-related protein 2A [KO:K20456]
AT4G23460  [KO:K12392]
AT4G23710  VAG2; vacuolar ATP synthase subunit G2 [KO:K02152]
AT4G24550  [KO:K12402]
AT4G25950  VATG3; vacuolar ATP synthase G3 [KO:K02152]
AT4G26710  [KO:K02153]
AT4G27690  VPS26B; vacuolar protein sorting 26B [KO:K18466]
AT4G32150  VAMP711; vesicle-associated membrane protein 711 [KO:K08515]
AT4G32530  [KO:K03661]
AT4G32940  GAMMA-VPE; gamma vacuolar processing enzyme [KO:K01369] [EC:3.4.22.34]
AT4G33240  FAB1A; 1-phosphatidylinositol-3-phosphate 5-kinase FAB1A [KO:K00921] [EC:2.7.1.150]
AT4G34720  AVA-P1; ATPase, F0/V0 complex, subunit C protein [KO:K02155]
AT4G35410  [KO:K12394]
AT4G36630  EMB2754; Vacuolar sorting protein 39 [KO:K20183]
AT4G38250  [KO:K14209]
AT4G38350  [KO:K12385]
AT4G38510  VAB2; ATPase, V1 complex, subunit B protein [KO:K02147]
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]
AT4G39420  [KO:K19026]
AT5G01180  PTR5; peptide transporter 5 [KO:K14638]
AT5G01770  RAPTOR2; regulatory-associated protein of TOR 2 (RAPTOR2) [KO:K07204]
AT5G01800  [KO:K12382]
AT5G02100  UNE18; Oxysterol-binding family protein [KO:K20456]
AT5G06260  [KO:K27947]
AT5G07880  SNAP29; synaptosomal-associated protein SNAP25-like 29 [KO:K08509]
AT5G11150  VAMP713; vesicle-associated membrane protein 713 [KO:K08515]
AT5G13190  GILP; GSH-induced LITAF domain protein [KO:K19363]
AT5G13690  CYL1; alpha-N-acetylglucosaminidase family / NAGLU family [KO:K01205] [EC:3.2.1.50]
AT5G20840  [KO:K22913] [EC:3.1.3.-]
AT5G22360  VAMP714; vesicle-associated membrane protein 714 [KO:K08515]
AT5G22770  alpha-ADR; alpha-adaptin [KO:K11824]
AT5G22780  [KO:K11824]
AT5G26240  CLC-D; chloride channel D [KO:K05016]
AT5G33280  [KO:K05016]
AT5G37680  ARLA1A; ADP-ribosylation factor-like A1A [KO:K07955]
AT5G40670  [KO:K12386]
AT5G40890  CLC-A; chloride channel A [KO:K05016]
AT5G46630  [KO:K11826]
AT5G47330  [KO:K01074] [EC:3.1.2.22]
AT5G47340  [KO:K01074] [EC:3.1.2.22]
AT5G47350  [KO:K01074] [EC:3.1.2.22]
AT5G49550  BLOS2; biogenesis of lysosome organelles complex 1 subunit-like protein [KO:K16750]
AT5G49890  CLC-C; chloride channel C [KO:K05016]
AT5G53530  VPS26A; vacuolar protein sorting 26A [KO:K18466]
AT5G55290  [KO:K02153]
AT5G59420  ORP3C; OSBP(oxysterol binding protein)-related protein 3C [KO:K20456]
AT5G60360  ALP; aleurain-like protease [KO:K01366] [EC:3.4.22.16]
AT5G61540  [KO:K01444] [EC:3.5.1.26]
AT5G65990  [KO:K14209]
AT5G67330  NRAMP4; natural resistance associated macrophage protein 4 [KO:K21398]
AT5G67560  ARLA1D; ADP-ribosylation factor-like A1D [KO:K07955]
Compound
C00002  ATP
C00008  ADP
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 22:339-352 (2022)
DOI:10.1038/s41577-021-00626-8
Related
pathway
ath00511  Other glycan degradation
ath00531  Glycosaminoglycan degradation
ath04130  SNARE interactions in vesicular transport
ath04144  Endocytosis
ath04145  Phagosome
ath04620  Toll-like receptor signaling pathway
KO pathway
ko04142   

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