KEGG   PATHWAY: osa04144
Entry
osa04144                    Pathway                                
Name
Endocytosis - Oryza sativa japonica (Japanese rice) (RefSeq)
Description
Endocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins entering through clathrin-dependent endocytosis (CDE) have sequences in their cytoplasmic domains that bind to the APs (adaptor-related protein complexes) and enable their rapid removal from the PM. In addition to APs and clathrin, there are numerous accessory proteins including dynamin. Depending on the various proteins that enter the endosome membrane, these cargoes are sorted to distinct destinations. Some cargoes, such as nutrient receptors, are recycled back to the PM. Ubiquitylated membrane proteins, such as activated growth-factor receptors, are sorted into intraluminal vesicles and eventually end up in the lysosome lumen via multivesicular endosomes (MVEs). There are distinct mechanisms of clathrin-independent endocytosis (CIE) depending upon the cargo and the cell type.
Class
Cellular Processes; Transport and catabolism
Pathway map
osa04144  Endocytosis
osa04144

Other DBs
GO: 0006897
Organism
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
Gene
4333853  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
4333833  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
4344166  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
4351470  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
9267438  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
4331188  phosphatidylinositol 4-phosphate 5-kinase 9 [KO:K00889] [EC:2.7.1.68]
4349758  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
9269628  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
4332323  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
4349161  phospholipase D gamma 1 [KO:K01115] [EC:3.1.4.4]
4341467  phospholipase D alpha 2-like [KO:K01115] [EC:3.1.4.4]
4341468  phospholipase D alpha 2-like [KO:K01115] [EC:3.1.4.4]
4327647  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
4337942  phospholipase D alpha 1-like [KO:K01115] [EC:3.1.4.4]
4341469  phospholipase D alpha 2 [KO:K01115] [EC:3.1.4.4]
4331421  phospholipase D beta 1 [KO:K01115] [EC:3.1.4.4]
4347745  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
4347089  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
4342872  phospholipase D delta isoform X1 [KO:K01115] [EC:3.1.4.4]
107277488  phospholipase D zeta 1-like isoform X1 [KO:K01115] [EC:3.1.4.4]
9272440  phospholipase D zeta 1 isoform X1 [KO:K01115] [EC:3.1.4.4]
4333024  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
4334732  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
4345514  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
9266665  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
4330669  dynamin-2A [KO:K01528] [EC:3.6.5.5]
4340644  dynamin-2B [KO:K01528] [EC:3.6.5.5]
4345610  dynamin-2A [KO:K01528] [EC:3.6.5.5]
4349546  clathrin heavy chain 1 [KO:K04646]
4351255  clathrin heavy chain 2 [KO:K04646]
4331370  AP-2 complex subunit alpha-2 [KO:K11824]
4330379  AP-2 complex subunit mu [KO:K11826]
4351755  AP-2 complex subunit sigma [KO:K11827]
9268417  clathrin interactor EPSIN 2 [KO:K12471]
4327195  clathrin interactor EPSIN 1 isoform X1 [KO:K12471]
4336871  clathrin interactor EPSIN 1 [KO:K12471]
4346362  epsin-3 [KO:K12471]
4342079  uncharacterized protein LOC4342079 [KO:K19366]
4332215  uncharacterized protein LOC4332215 [KO:K19366]
4345402  actin-related protein 2 [KO:K17260]
4329867  actin-related protein 3 isoform X2 [KO:K18584]
4344577  actin-related protein 3 [KO:K18584]
4331146  actin-related protein 2/3 complex subunit 1B [KO:K05757]
4336383  actin-related protein 2/3 complex subunit 2B isoform X1 [KO:K05758]
4324174  actin-related protein 2/3 complex subunit 2A [KO:K05758]
4328824  actin-related protein 2/3 complex subunit 3 [KO:K05756]
4334780  actin-related protein 2/3 complex subunit 4 [KO:K05755]
4350726  actin-related protein 2/3 complex subunit 5A [KO:K05754]
4339012  probable mediator of RNA polymerase II transcription subunit 37c [KO:K03283]
4351208  heat shock cognate 70 kDa protein 2 [KO:K03283]
4351875  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
4327388  probable mediator of RNA polymerase II transcription subunit 37c [KO:K03283]
4332413  heat shock cognate 70 kDa protein 2 [KO:K03283]
4332420  heat shock cognate 70 kDa protein [KO:K03283]
4334598  heat shock cognate 70 kDa protein 2 [KO:K03283]
4332416  heat shock cognate 70 kDa protein [KO:K03283]
9271426  heat shock cognate 70 kDa protein [KO:K03283]
4349971  heat shock cognate 70 kDa protein [KO:K03283]
4349972  heat shock cognate 70 kDa protein [KO:K03283]
4338354  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
107275844  heat shock cognate 70 kDa protein-like [KO:K03283]
107279546  heat shock cognate 70 kDa protein-like [KO:K03283]
4340043  WASH complex subunit 7 isoform X1 [KO:K18465]
4335713  WASH complex subunit strumpellin homolog isoform X1 [KO:K18464]
4335425  uncharacterized protein LOC4335425 [KO:K18463]
4343018  F-actin-capping protein subunit alpha [KO:K10364]
4332978  probable F-actin-capping protein subunit beta isoform X1 [KO:K10365]
4328954  vacuolar protein sorting-associated protein 29 [KO:K18467]
4350961  vacuolar protein sorting-associated protein 26A [KO:K18466]
4352271  vacuolar protein sorting-associated protein 26A [KO:K18466]
4334459  vacuolar protein sorting-associated protein 35B [KO:K18468]
4326798  AMSH-like ubiquitin thioesterase 3 [KO:K11866] [EC:3.4.19.12]
4324542  AMSH-like ubiquitin thioesterase 3 [KO:K11866] [EC:3.4.19.12]
4327852  AMSH-like ubiquitin thioesterase 2 isoform X1 [KO:K11866] [EC:3.4.19.12]
4339322  ras-related protein Rab7 [KO:K07897]
4325946  ras-related protein Rab7 [KO:K07897]
4339450  ras-related protein Rab7 [KO:K07897]
4327180  ras-related protein Rab7 [KO:K07897]
4331267  protein ELC-like [KO:K12183]
4327840  vacuolar protein sorting-associated protein 28 homolog 1 [KO:K12184]
4331873  vacuolar protein-sorting-associated protein 37 homolog 1 isoform X1 [KO:K12185]
4333290  vacuolar protein-sorting-associated protein 37 homolog 1 isoform X1 [KO:K12185]
9269587  vacuolar protein sorting-associated protein 22 homolog 1 isoform X1 [KO:K12188]
107276137  vacuolar protein sorting-associated protein 22 homolog 1-like [KO:K12188]
4327592  vacuolar protein sorting-associated protein 36 [KO:K12190]
4327163  vacuolar protein sorting-associated protein 25 [KO:K12189]
4329866  vacuolar protein sorting-associated protein 20 homolog 2 [KO:K12195]
4349637  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
4351360  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
4341494  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
4346566  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
4343270  vacuolar protein sorting-associated protein 32 homolog 1 [KO:K12194]
4331337  vacuolar protein sorting-associated protein 24 homolog 1 [KO:K12193]
4343227  vacuolar protein sorting-associated protein 24 homolog 1 isoform X1 [KO:K12193]
4342791  vacuolar protein sorting-associated protein 2 homolog 1 [KO:K12191]
4333538  vacuolar protein sorting-associated protein 2 homolog 2 [KO:K12191]
4351205  vacuolar protein sorting-associated protein 2 homolog 1 [KO:K12191]
4348891  vacuolar protein sorting-associated protein 2 homolog 3 [KO:K12192]
4327915  uncharacterized protein LOC4327915 [KO:K15053]
4325480  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 [KO:K12196]
4328374  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 [KO:K12196]
107275709  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1-like [KO:K12196]
4340850  protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5 [KO:K12199]
4341638  ESCRT-related protein CHMP1 [KO:K12197]
4337536  charged multivesicular body protein 5 [KO:K12198]
9266052  charged multivesicular body protein 5 [KO:K12198]
4348999  ALG-2 interacting protein X [KO:K12200]
4330097  ALG-2 interacting protein X [KO:K12200]
4348183  maspardin isoform X1 [KO:K19367]
4324745  sorting nexin 1 [KO:K17917]
4352862  ras-related protein RABF2a [KO:K07889]
4328363  EH domain-containing protein 1 [KO:K12483]
4341894  EH domain-containing protein 1 [KO:K12483]
4337342  EH domain-containing protein 1 [KO:K12483]
4329228  vacuolar protein sorting-associated protein 45 homolog [KO:K12479]
4339021  ras-related protein RABE1c isoform X1 [KO:K07901]
4342644  ras-related protein RABE1d [KO:K07901]
4334590  ras-related protein RABE1c [KO:K07901]
4342802  ras-related protein RABE1c [KO:K07901]
4337555  ras-related protein RABA2a [KO:K07904]
4334746  ras-related protein RABA2a [KO:K07904]
4348493  ras-related protein Rab11D [KO:K07904]
4344016  ras-related protein RABA5a [KO:K07904]
4341266  ras-related protein RIC2 [KO:K07904]
4346744  ras-related protein RABA1f [KO:K07904]
4346614  ras-related protein RGP1 [KO:K07904]
4339324  ras-related protein RIC2-like [KO:K07904]
4334619  ras-related protein Rab11C [KO:K07904]
4338288  ras-related protein RGP2 [KO:K07904]
4346088  ras-related protein RABA5c [KO:K07904]
4324623  ras-related protein RIC2-like [KO:K07904]
4347642  ras-related protein RABA3 [KO:K07904]
4324856  ras-related protein Rab2BV [KO:K07904]
4342063  ras-related protein RABA3 [KO:K07904]
4339623  ras-related protein RABA1f [KO:K07904]
4343612  probable ADP-ribosylation factor GTPase-activating protein AGD5 [KO:K12486]
4325738  probable ADP-ribosylation factor GTPase-activating protein AGD11 [KO:K12486]
4338640  probable ADP-ribosylation factor GTPase-activating protein AGD11 [KO:K12486]
4328629  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
4330565  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
9271389  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
4346168  ADP-ribosylation factor GTPase-activating protein AGD3 [KO:K12489]
4347541  ADP-ribosylation factor GTPase-activating protein AGD3 [KO:K12489]
4330061  ADP-ribosylation factor GTPase-activating protein AGD2 [KO:K12489]
4332427  probable ADP-ribosylation factor GTPase-activating protein AGD6 [KO:K12492]
4334823  probable ADP-ribosylation factor GTPase-activating protein AGD9 [KO:K12493]
4349482  probable ADP-ribosylation factor GTPase-activating protein AGD8 [KO:K12493]
4332241  brefeldin A-inhibited guanine nucleotide-exchange protein 2 [KO:K18442]
4328595  brefeldin A-inhibited guanine nucleotide-exchange protein 1 [KO:K18442]
4341555  brefeldin A-inhibited guanine nucleotide-exchange protein 1 [KO:K18442]
4329190  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
4334954  ARF guanine-nucleotide exchange factor GNL2 [KO:K18443]
9271296  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
4339157  ADP-ribosylation factor 2 [KO:K07937]
4326208  ADP-ribosylation factor 2-like isoform X1 [KO:K07937]
4327591  ADP-ribosylation factor 1 [KO:K07937]
4342746  ADP-ribosylation factor 1 [KO:K07937]
4334545  ADP-ribosylation factor 1-like [KO:K07937]
107276116  ADP-ribosylation factor 1-like [KO:K07937]
4328177  ADP-ribosylation factor [KO:K07937]
4330422  ADP-ribosylation factor [KO:K07937]
4342745  ADP-ribosylation factor 1 [KO:K07937]
4349518  ADP-ribosylation factor isoform X1 [KO:K07937]
Compound
C00035  GDP
C00044  GTP
C04549  1-Phosphatidyl-1D-myo-inositol 3-phosphate
C04637  1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate
C05981  Phosphatidylinositol-3,4,5-trisphosphate
C11556  1-Phosphatidyl-1D-myo-inositol 3,5-bisphosphate
Reference
PMID:19007773
  Authors
Acconcia F, Sigismund S, Polo S
  Title
Ubiquitin in trafficking: the network at work.
  Journal
Exp Cell Res 315:1610-8 (2009)
DOI:10.1016/j.yexcr.2008.10.014
Reference
PMID:18647649
  Authors
Donaldson JG, Porat-Shliom N, Cohen LA
  Title
Clathrin-independent endocytosis: a unique platform for cell signaling and PM remodeling.
  Journal
Cell Signal 21:1-6 (2009)
DOI:10.1016/j.cellsig.2008.06.020
Reference
PMID:15261671
  Authors
Sorkin A
  Title
Cargo recognition during clathrin-mediated endocytosis: a team effort.
  Journal
Curr Opin Cell Biol 16:392-9 (2004)
DOI:10.1016/j.ceb.2004.06.001
Reference
PMID:19325624
  Authors
Raiborg C, Stenmark H
  Title
The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins.
  Journal
Nature 458:445-52 (2009)
DOI:10.1038/nature07961
Reference
PMID:20110990
  Authors
Scita G, Di Fiore PP
  Title
The endocytic matrix.
  Journal
Nature 463:464-73 (2010)
DOI:10.1038/nature08910
Reference
PMID:15687999
  Authors
Le Roy C, Wrana JL
  Title
Clathrin- and non-clathrin-mediated endocytic regulation of cell signalling.
  Journal
Nat Rev Mol Cell Biol 6:112-26 (2005)
DOI:10.1038/nrm1571
Reference
PMID:19924646
  Authors
Jovic M, Sharma M, Rahajeng J, Caplan S
  Title
The early endosome: a busy sorting station for proteins at the crossroads.
  Journal
Histol Histopathol 25:99-112 (2010)
DOI:10.14670/HH-25.99
Reference
PMID:16203612
  Authors
Pietiainen VM, Marjomaki V, Heino J, Hyypia T
  Title
Viral entry, lipid rafts and caveosomes.
  Journal
Ann Med 37:394-403 (2005)
DOI:10.1080/07853890510011976
Reference
PMID:19696797
  Authors
Grant BD, Donaldson JG
  Title
Pathways and mechanisms of endocytic recycling.
  Journal
Nat Rev Mol Cell Biol 10:597-608 (2009)
DOI:10.1038/nrm2755
Reference
PMID:22193161
  Authors
Cullen PJ, Korswagen HC
  Title
Sorting nexins provide diversity for retromer-dependent trafficking events.
  Journal
Nat Cell Biol 14:29-37 (2012)
DOI:10.1038/ncb2374
Related
pathway
osa04070  Phosphatidylinositol signaling system
osa04130  SNARE interactions in vesicular transport
KO pathway
ko04144   
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