KEGG   PATHWAY: pop04144
Entry
pop04144                    Pathway                                
Name
Endocytosis - Populus trichocarpa (black cottonwood)
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
pop04144  Endocytosis
pop04144

Other DBs
GO: 0006897
Organism
Populus trichocarpa (black cottonwood) [GN:pop]
Gene
7495115  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
7473006  phosphatidylinositol 4-phosphate 5-kinase 8 [KO:K00889] [EC:2.7.1.68]
7460243  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
7469129  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
7492747  phosphatidylinositol 4-phosphate 5-kinase 10 [KO:K00889] [EC:2.7.1.68]
7484083  phosphatidylinositol 4-phosphate 5-kinase 1 isoform X1 [KO:K00889] [EC:2.7.1.68]
7464101  phosphatidylinositol 4-phosphate 5-kinase 4 [KO:K00889] [EC:2.7.1.68]
18097778  phosphatidylinositol 4-phosphate 5-kinase 1 [KO:K00889] [EC:2.7.1.68]
18100123  phosphatidylinositol 4-phosphate 5-kinase 9 isoform X1 [KO:K00889] [EC:2.7.1.68]
7476843  phosphatidylinositol 4-phosphate 5-kinase 6 [KO:K00889] [EC:2.7.1.68]
18096626  phosphatidylinositol 4-phosphate 5-kinase 7-like isoform X1 [KO:K00889] [EC:2.7.1.68]
7490921  phospholipase D beta 1 [KO:K01115] [EC:3.1.4.4]
7494030  phospholipase D beta 2 [KO:K01115] [EC:3.1.4.4]
7477219  phospholipase D zeta 1 isoform X2 [KO:K01115] [EC:3.1.4.4]
7468635  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
7496922  phospholipase D gamma 1 [KO:K01115] [EC:3.1.4.4]
18096711  phospholipase D alpha 1 isoform X1 [KO:K01115] [EC:3.1.4.4]
18096739  phospholipase D alpha 4 [KO:K01115] [EC:3.1.4.4]
7470100  phospholipase D alpha 1 isoform X1 [KO:K01115] [EC:3.1.4.4]
7478921  phospholipase D zeta 1 [KO:K01115] [EC:3.1.4.4]
7468855  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
7496896  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
7480751  phospholipase D delta isoform X1 [KO:K01115] [EC:3.1.4.4]
7483104  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
18101895  phospholipase D zeta 1 isoform X1 [KO:K01115] [EC:3.1.4.4]
7485622  phospholipase D delta isoform X1 [KO:K01115] [EC:3.1.4.4]
7475119  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
18096593  dynamin-2A [KO:K01528] [EC:3.6.5.5]
18098358  dynamin-2A isoform X1 [KO:K01528] [EC:3.6.5.5]
18108411  dynamin-2A [KO:K01528] [EC:3.6.5.5]
7474422  clathrin heavy chain 1 isoform X2 [KO:K04646]
7487811  clathrin heavy chain 1 [KO:K04646]
7494511  clathrin heavy chain 1 [KO:K04646]
7454854  clathrin heavy chain 1 [KO:K04646]
7474927  AP-2 complex subunit alpha-1 [KO:K11824]
18098001  AP-2 complex subunit alpha-1 isoform X2 [KO:K11824]
18096961  AP-2 complex subunit mu [KO:K11826]
18094182  AP-2 complex subunit mu isoform X1 [KO:K11826]
7479681  AP-2 complex subunit sigma [KO:K11827]
7477670  AP-2 complex subunit sigma [KO:K11827]
7481537  uncharacterized protein LOC7481537 [KO:K12471]
7467547  uncharacterized protein LOC7467547 [KO:K12471]
7485707  uncharacterized protein LOC7485707 [KO:K12471]
7468494  clathrin interactor EPSIN 2 isoform X1 [KO:K12471]
7470725  clathrin interactor EPSIN 1 [KO:K12471]
7489913  clathrin interactor EPSIN 2 [KO:K12471]
18103744  uncharacterized protein LOC18103744 isoform X1 [KO:K12472]
7480465  actin cytoskeleton-regulatory complex protein PAN1 isoform X2 [KO:K12472]
7494253  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic [KO:K19366]
7470395  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic [KO:K19366]
18099170  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic [KO:K19366]
7456250  actin-related protein 2 isoform X2 [KO:K17260]
7480945  actin-related protein 3 [KO:K18584]
7460730  actin-related protein 3 [KO:K18584]
7466293  actin-related protein 2/3 complex subunit 1A isoform X1 [KO:K05757]
7491454  actin-related protein 2/3 complex subunit 2A isoform X1 [KO:K05758]
7459984  actin-related protein 2/3 complex subunit 2B [KO:K05758]
7481228  actin-related protein 2/3 complex subunit 2A isoform X2 [KO:K05758]
7473474  actin-related protein 2/3 complex subunit 2B isoform X1 [KO:K05758]
18111075  actin-related protein 2/3 complex subunit 3 [KO:K05756]
18099910  actin-related protein 2/3 complex subunit 3 isoform X2 [KO:K05756]
18107079  actin-related protein 2/3 complex subunit 4 isoform X1 [KO:K05755]
7453909  actin-related protein 2/3 complex subunit 5A [KO:K05754]
18105042  actin-related protein 2/3 complex subunit 5A [KO:K05754]
18094241  heat shock 70 kDa protein [KO:K03283]
7493237  heat shock 70 kDa protein [KO:K03283]
7458152  heat shock 70 kDa protein 4 [KO:K03283]
7469823  heat shock cognate 70 kDa protein 2 isoform X1 [KO:K03283]
7469825  LOW QUALITY PROTEIN: heat shock cognate 70 kDa protein 2 [KO:K03283]
18111154  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
7469820  heat shock cognate 70 kDa protein 2 [KO:K03283]
18102722  heat shock cognate 70 kDa protein 2 [KO:K03283]
18102723  heat shock cognate 70 kDa protein 2 [KO:K03283]
18094242  heat shock 70 kDa protein [KO:K03283]
18098323  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
7481732  F-actin-capping protein subunit alpha [KO:K10364]
18098669  F-actin-capping protein subunit alpha [KO:K10364]
7464787  probable F-actin-capping protein subunit beta isoform X1 [KO:K10365]
18095280  vacuolar protein sorting-associated protein 29 [KO:K18467]
7483595  vacuolar protein sorting-associated protein 29 [KO:K18467]
7488176  vacuolar protein sorting-associated protein 26A [KO:K18466]
7487240  vacuolar protein sorting-associated protein 26B [KO:K18466]
18107896  vacuolar protein sorting-associated protein 26B isoform X1 [KO:K18466]
18094945  vacuolar protein sorting-associated protein 26A [KO:K18466]
7485605  vacuolar protein sorting-associated protein 35B isoform X1 [KO:K18468]
7496914  vacuolar protein sorting-associated protein 35B isoform X1 [KO:K18468]
18099161  vacuolar protein sorting-associated protein 35A [KO:K18468]
7482259  AMSH-like ubiquitin thioesterase 3 isoform X1 [KO:K11866] [EC:3.4.19.12]
7492397  AMSH-like ubiquitin thioesterase 2 isoform X1 [KO:K11866] [EC:3.4.19.12]
7453881  AMSH-like ubiquitin thioesterase 1 [KO:K11866] [EC:3.4.19.12]
7475065  ras-related protein Rab7 [KO:K07897]
7464034  ras-related protein Rab7 [KO:K07897]
7483525  ras-related protein Rab7 [KO:K07897]
7464784  ras-related protein Rab7 [KO:K07897]
7468752  ras-related protein Rab7 [KO:K07897]
7469986  ras-related protein Rab7 [KO:K07897]
7486342  ras-related protein Rab7 isoform X2 [KO:K07897]
7462811  protein ELC-like [KO:K12183]
7480662  protein ELC [KO:K12183]
7455791  protein ELC-like [KO:K12183]
7494341  vacuolar protein sorting-associated protein 28 homolog 1 [KO:K12184]
7495265  vacuolar protein sorting-associated protein 28 homolog 1 [KO:K12184]
7486508  vacuolar protein-sorting-associated protein 37 homolog 1 [KO:K12185]
18100103  vacuolar protein-sorting-associated protein 37 homolog 1 [KO:K12185]
18095958  vacuolar protein sorting-associated protein 22 homolog 1 [KO:K12188]
7491585  vacuolar protein sorting-associated protein 36 [KO:K12190]
18094111  vacuolar protein sorting-associated protein 25 [KO:K12189]
7466761  vacuolar protein sorting-associated protein 20 homolog 2 [KO:K12195]
7466867  vacuolar protein sorting-associated protein 20 homolog 2 [KO:K12195]
18100390  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
18107661  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
7494932  vacuolar protein sorting-associated protein 24 homolog 1 isoform X1 [KO:K12193]
18098242  vacuolar protein sorting-associated protein 24 homolog 1 [KO:K12193]
7490692  vacuolar protein sorting-associated protein 2 homolog 2 [KO:K12191]
7478111  vacuolar protein sorting-associated protein 2 homolog 1 [KO:K12191]
18107704  vacuolar protein sorting-associated protein 2 homolog 1 [KO:K12191]
7471955  vacuolar protein sorting-associated protein 2 homolog 3 [KO:K12192]
7476932  vacuolar protein sorting-associated protein 2 homolog 3-like isoform X1 [KO:K12192]
7481450  uncharacterized protein LOC7481450 isoform X1 [KO:K15053]
7477176  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 isoform X1 [KO:K12196]
7496229  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 isoform X1 [KO:K12196]
7466822  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 isoform X1 [KO:K12196]
18109637  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 isoform X1 [KO:K12196]
7495316  protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5 [KO:K12199]
7478182  ESCRT-related protein CHMP1B [KO:K12197]
7475124  ESCRT-related protein CHMP1B [KO:K12197]
127905509  ESCRT-related protein CHMP1B [KO:K12197]
7490888  vacuolar protein sorting-associated protein 60.1 [KO:K12198]
7469518  vacuolar protein sorting-associated protein 60.1 [KO:K12198]
7475548  vacuolar-sorting protein BRO1 [KO:K12200]
7488385  vacuolar-sorting protein BRO1 [KO:K12200]
7479225  uncharacterized protein LOC7479225 isoform X1 [KO:K19367]
18094399  uncharacterized protein LOC18094399 isoform X1 [KO:K19367]
7467568  sorting nexin 1 [KO:K17917]
7492244  sorting nexin 1 [KO:K17917]
7483517  ras-related protein RHN1 [KO:K07889]
7485415  EH domain-containing protein 1 [KO:K12483]
7478702  EH domain-containing protein 1 [KO:K12483]
7466414  vacuolar protein sorting-associated protein 45 homolog [KO:K12479]
7492449  vacuolar protein sorting-associated protein 45 homolog [KO:K12479]
7458596  ras-related protein RABE1c [KO:K07901]
7488135  ras-related protein RABE1c [KO:K07901]
7465129  ras-related protein RABE1c [KO:K07901]
7469805  ras-related protein RABE1c [KO:K07901]
7480096  ras-related protein RABA4d [KO:K07904]
7489919  ras-related protein RABA5d [KO:K07904]
7457414  ras-related protein RABA3 [KO:K07904]
7455195  ras-related protein Rab11D isoform X1 [KO:K07904]
7476322  ras-related protein RABA1d [KO:K07904]
7489179  ras-related protein Rab11C [KO:K07904]
7463818  ras-related protein RABA1d [KO:K07904]
7486792  ras-related protein RABA3 [KO:K07904]
18111135  ras-related protein RABA2a [KO:K07904]
7487989  ras-related protein Rab2BV [KO:K07904]
18099860  ras-related protein RABA4d [KO:K07904]
7455818  ras-related protein RABA5a [KO:K07904]
7483994  ras-related protein RABA4d [KO:K07904]
18106002  ras-related protein Rab11C [KO:K07904]
7468492  ras-related protein RABA5d [KO:K07904]
7490362  ras-related protein Rab2BV [KO:K07904]
18098340  LOW QUALITY PROTEIN: ras-related protein RABA2a [KO:K07904]
7466795  ras-related protein Rab11D [KO:K07904]
7463689  ras-related protein RABA5a [KO:K07904]
112323346  ras-related protein RABA1f [KO:K07904]
7494608  ras-related protein RABA1f [KO:K07904]
18104558  ras-related protein RABA1f [KO:K07904]
7487009  probable ADP-ribosylation factor GTPase-activating protein AGD11 [KO:K12486]
7485584  ADP-ribosylation factor GTPase-activating protein AGD5 isoform X1 [KO:K12486]
18097185  probable ADP-ribosylation factor GTPase-activating protein AGD11 isoform X1 [KO:K12486]
7462363  ADP-ribosylation factor GTPase-activating protein AGD5 [KO:K12486]
7454035  probable ADP-ribosylation factor GTPase-activating protein AGD15 isoform X1 [KO:K12486]
18103294  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
18095647  ADP-ribosylation factor GTPase-activating protein AGD5 [KO:K12486]
18097461  ADP-ribosylation factor GTPase-activating protein AGD5 isoform X1 [KO:K12486]
7487566  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
127903892  probable ADP-ribosylation factor GTPase-activating protein AGD11 isoform X1 [KO:K12486]
7496532  ADP-ribosylation factor GTPase-activating protein AGD3 [KO:K12489]
7491430  ADP-ribosylation factor GTPase-activating protein AGD3 isoform X1 [KO:K12489]
7456644  ADP-ribosylation factor GTPase-activating protein AGD1 [KO:K12489]
7454918  probable ADP-ribosylation factor GTPase-activating protein AGD6 [KO:K12492]
18106269  probable ADP-ribosylation factor GTPase-activating protein AGD6 [KO:K12492]
18096976  probable ADP-ribosylation factor GTPase-activating protein AGD8 isoform X1 [KO:K12493]
18094163  probable ADP-ribosylation factor GTPase-activating protein AGD8 [KO:K12493]
7464867  brefeldin A-inhibited guanine nucleotide-exchange protein 2 [KO:K18442]
7494008  brefeldin A-inhibited guanine nucleotide-exchange protein 2 isoform X1 [KO:K18442]
18098172  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform X1 [KO:K18442]
7463353  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform X1 [KO:K18442]
18107297  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
7458753  ARF guanine-nucleotide exchange factor GNL2 [KO:K18443]
18107296  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
7492062  ADP-ribosylation factor 2 [KO:K07937]
7481423  ADP-ribosylation factor [KO:K07937]
7476402  ADP-ribosylation factor 1 [KO:K07937]
7498230  ADP-ribosylation factor 1 [KO:K07937]
7495198  ADP-ribosylation factor [KO:K07937]
7478883  LOW QUALITY PROTEIN: ADP-ribosylation factor [KO:K07937]
18098508  ADP-ribosylation factor isoform X3 [KO:K07937]
7465227  ADP-ribosylation factor isoform X2 [KO:K07937]
7490060  ADP-ribosylation factor 2 [KO:K07937]
7485865  ADP-ribosylation factor 1 [KO:K07937]
112325621  uncharacterized protein LOC112325621 [KO:K07937]
7494400  uncharacterized protein LOC7494400 [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
pop04070  Phosphatidylinositol signaling system
pop04130  SNARE interactions in vesicular transport
KO pathway
ko04144   
LinkDB

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