ENTRY       sly04144                    Pathway
NAME        Endocytosis - Solanum lycopersicum (tomato)
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 sly04144  Endocytosis
DBLINKS     GO: 0006897
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101254537  phosphatidylinositol 4-phosphate 5-kinase 8 isoform X1 [KO:K00889] [EC:2.7.1.68]
            101265480  phosphatidylinositol 4-phosphate 5-kinase 6-like [KO:K00889] [EC:2.7.1.68]
            101255328  phosphatidylinositol 4-phosphate 5-kinase 9 [KO:K00889] [EC:2.7.1.68]
            101249317  phosphatidylinositol 4-phosphate 5-kinase 6-like [KO:K00889] [EC:2.7.1.68]
            101244630  phosphatidylinositol 4-phosphate 5-kinase 6-like [KO:K00889] [EC:2.7.1.68]
            101246219  phosphatidylinositol 4-phosphate 5-kinase 6-like [KO:K00889] [EC:2.7.1.68]
            101250943  phosphatidylinositol 4-phosphate 5-kinase 9-like isoform X1 [KO:K00889] [EC:2.7.1.68]
            101253180  phosphatidylinositol 4-phosphate 5-kinase 1-like [KO:K00889] [EC:2.7.1.68]
            101251739  phosphatidylinositol 4-phosphate 5-kinase 2 [KO:K00889] [EC:2.7.1.68]
            101265364  phospholipase D zeta 1 isoform X1 [KO:K01115] [EC:3.1.4.4]
            101260675  phospholipase D delta-like [KO:K01115] [EC:3.1.4.4]
            101245304  LOW QUALITY PROTEIN: phospholipase D zeta 1 [KO:K01115] [EC:3.1.4.4]
            101246303  phospholipase D delta [KO:K01115] [EC:3.1.4.4]
            101244067  phospholipase D alpha 4 [KO:K01115] [EC:3.1.4.4]
            101248969  phospholipase D delta-like [KO:K01115] [EC:3.1.4.4]
            101249590  phospholipase D gamma 1-like [KO:K01115] [EC:3.1.4.4]
            101253987  phospholipase D alpha 1 [KO:K01115] [EC:3.1.4.4]
            101256058  phospholipase D delta-like [KO:K01115] [EC:3.1.4.4]
            101257989  TPLD; phospholipase D alpha [KO:K01115] [EC:3.1.4.4]
            101264185  phospholipase D alpha 1-like [KO:K01115] [EC:3.1.4.4]
            101264680  phospholipase D delta-like [KO:K01115] [EC:3.1.4.4]
            544251  PLDa2; phospholipase PLDa2 [KO:K01115] [EC:3.1.4.4]
            543821  PLDb2; phospholipase PLDb2 [KO:K01115] [EC:3.1.4.4]
            543819  PLDa1; phospholipase PLDa1 [KO:K01115] [EC:3.1.4.4]
            544181  PLDb1; phospholipase PLDb1 [KO:K01115] [EC:3.1.4.4]
            101256548  dynamin-2A-like [KO:K01528] [EC:3.6.5.5]
            101258496  dynamin-2A [KO:K01528] [EC:3.6.5.5]
            101250125  clathrin heavy chain 1 [KO:K04646]
            101259158  clathrin heavy chain 1 [KO:K04646]
            101259922  clathrin heavy chain 1 [KO:K04646]
            101245025  LOW QUALITY PROTEIN: AP-2 complex subunit alpha-1-like [KO:K11824]
            101246147  AP-2 complex subunit alpha-1-like [KO:K11824]
            101255715  CAC; AP-2 complex subunit mu [KO:K11826]
            101267903  AP-2 complex subunit mu isoform X2 [KO:K11826]
            101261916  AP-2 complex subunit sigma [KO:K11827]
            101249218  clathrin interactor 1-like [KO:K12471]
            101265874  clathrin interactor 1 isoform X1 [KO:K12471]
            101255632  clathrin interactor EPSIN 2 isoform X2 [KO:K12471]
            101253169  clathrin interactor EPSIN 2 [KO:K12471]
            101254453  clathrin interactor EPSIN 1 [KO:K12471]
            101253053  epsin-3 [KO:K12471]
            101268015  clathrin interactor EPSIN 1 [KO:K12471]
            101253573  epidermal growth factor receptor substrate 15-like 1 [KO:K12472]
            101261917  intersectin-2 [KO:K12472]
            101261088  actin cytoskeleton-regulatory complex protein PAN1 [KO:K12472]
            101263355  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic isoform X1 [KO:K19366]
            101263663  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic-like [KO:K19366]
            101253155  protein EARLY-RESPONSIVE TO DEHYDRATION 7, chloroplastic-like [KO:K19366]
            109119895  uncharacterized protein LOC109119895 isoform X1 [KO:K23612]
            101263559  actin-related protein 2 [KO:K17260]
            101252768  actin-related protein 3 [KO:K18584]
            101250599  actin-related protein 3 [KO:K18584]
            101245162  actin-related protein 2/3 complex subunit 1A [KO:K05757]
            101261659  actin-related protein 2/3 complex subunit 2B isoform X1 [KO:K05758]
            101263574  actin-related protein 2/3 complex subunit 2A isoform X1 [KO:K05758]
            101260446  actin-related protein 2/3 complex subunit 3 [KO:K05756]
            101260916  actin-related protein 2/3 complex subunit 4 isoform X2 [KO:K05755]
            101261066  actin-related protein 2/3 complex subunit 5A [KO:K05754]
            101265681  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
            100134914  HSP70; heat shock protein 70 [KO:K03283]
            100736433  Hsc70.1; heat shock cognate 70 kDa protein 1 [KO:K03283]
            101055596  hsc70.3; heat shock protein 70-3 [KO:K03283]
            101247772  Hsc70.2; heat shock cognate 70 kDa protein 2 [KO:K03283]
            101248309  heat shock 70 kDa protein-like [KO:K03283]
            101247151  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101254866  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101255164  heat shock cognate 70 kDa protein [KO:K03283]
            101255185  heat shock 70 kDa protein 5 [KO:K03283]
            101255140  F-actin-capping protein subunit alpha [KO:K10364]
            101246178  F-actin-capping protein subunit alpha isoform X1 [KO:K10364]
            101256266  probable F-actin-capping protein subunit beta [KO:K10365]
            101249720  vacuolar protein sorting-associated protein 29 [KO:K18467]
            101247715  vacuolar protein sorting-associated protein 26A isoform 1 [KO:K18466]
            101265987  vacuolar protein sorting-associated protein 35A [KO:K18468]
            101243768  vacuolar protein sorting-associated protein 35A-like isoform X1 [KO:K18468]
            101249253  vacuolar protein sorting-associated protein 35B isoform X1 [KO:K18468]
            101258096  AMSH-like ubiquitin thioesterase 3 [KO:K11866] [EC:3.4.19.12]
            101266109  AMSH-like ubiquitin thioesterase 1 [KO:K11866] [EC:3.4.19.12]
            101254684  LOW QUALITY PROTEIN: AMSH-like ubiquitin thioesterase 2 [KO:K11866] [EC:3.4.19.12]
            101263553  ras-related protein RABG3f [KO:K07897]
            101261599  ras-related protein Rab7 [KO:K07897]
            101257955  ras-related protein Rab7 [KO:K07897]
            101258647  ras-related protein Rab7-like [KO:K07897]
            101266551  protein ELC [KO:K12183]
            101267950  protein ELC-like [KO:K12183]
            101266865  protein ELC-like [KO:K12183]
            101258121  vacuolar protein sorting-associated protein 28 homolog 2 isoform X1 [KO:K12184]
            101255562  vacuolar protein sorting-associated protein 28 homolog 2-like [KO:K12184]
            101266470  vacuolar protein-sorting-associated protein 37 homolog 1 [KO:K12185]
            101261084  vacuolar protein-sorting-associated protein 37 homolog 1 [KO:K12185]
            101266271  vacuolar protein sorting-associated protein 22 homolog 1 [KO:K12188]
            101251515  vacuolar protein sorting-associated protein 36 [KO:K12190]
            101265760  vacuolar protein sorting-associated protein 25 [KO:K12189]
            101250100  vacuolar protein sorting-associated protein 20 homolog 2 [KO:K12195]
            101264627  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
            101248169  vacuolar protein sorting-associated protein 32 homolog 2-like [KO:K12194]
            101268300  vacuolar protein sorting-associated protein 32 homolog 2 [KO:K12194]
            101259117  vacuolar protein sorting-associated protein 24 homolog 1-like [KO:K12193]
            101268191  vacuolar protein sorting-associated protein 24 homolog 1 [KO:K12193]
            104645908  vacuolar protein sorting-associated protein 2 homolog 2 [KO:K12191]
            101247586  SNF7 family protein [KO:K12191]
            101266227  vacuolar protein sorting-associated protein 2 homolog 3 [KO:K12192]
            101259667  charged multivesicular body protein 7 isoform X1 [KO:K15053]
            101256349  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 [KO:K12196]
            101246490  SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1-like protein [KO:K12196]
            101256646  protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 [KO:K12196]
            101264233  lyst-Interacting Protein5-like protein [KO:K12199]
            101247200  ESCRT-related protein CHMP1A [KO:K12197]
            101260829  ESCRT-related protein CHMP1A [KO:K12197]
            101248200  vacuolar protein sorting-associated protein 60.2 [KO:K12198]
            101259697  vacuolar protein sorting-associated protein 60.1 [KO:K12198]
            101245450  vacuolar-sorting protein BRO1-like [KO:K12200]
            101261621  vacuolar-sorting protein BRO1 [KO:K12200]
            101266058  maspardin [KO:K19367]
            101246655  LOW QUALITY PROTEIN: sorting nexin 1 [KO:K17917]
            101261973  ras-related protein RHN1 isoform X1 [KO:K07889]
            101265393  ras-related protein RHN1 [KO:K07889]
            101245117  ras-related protein RABF1 [KO:K07889]
            101252439  EH domain-containing protein 1-like isoform X1 [KO:K12483]
            101262894  EH domain-containing protein 1-like [KO:K12483]
            101250563  EH domain-containing protein 1-like [KO:K12483]
            101266049  EH domain-containing protein 1 isoform X1 [KO:K12483]
            101264116  vacuolar protein sorting-associated protein 45 homolog isoform X1 [KO:K12479]
            101264577  ras-related protein RABE1c [KO:K07901]
            101267153  ras-related protein RABE1a isoform X1 [KO:K07901]
            543575  ER43; ethylene-responsive small GTP-binding protein [KO:K07901]
            544288  ypt2; GTP-binding protein [KO:K07901]
            101250995  LOW QUALITY PROTEIN: ras-related protein RABE1c [KO:K07901]
            101263852  ras-related protein RABA2a [KO:K07904]
            101264460  ras-related protein RGP1 [KO:K07904]
            101259980  ras-related protein RABA3 [KO:K07904]
            101254053  ras-related protein RABA1d [KO:K07904]
            101254361  ras-related protein RABA1f [KO:K07904]
            101250669  ras-related protein RABA4d-like [KO:K07904]
            101258042  ras-related protein RABA2b-like [KO:K07904]
            101248300  ras-related protein RABA5a [KO:K07904]
            101258315  ras-related protein RABA4d-like [KO:K07904]
            101251092  ras-related protein RABA2b-like [KO:K07904]
            101247904  ras-related protein Rab11D [KO:K07904]
            101261857  ras-related protein RABA5e [KO:K07904]
            101250639  ras-related protein RABA2a [KO:K07904]
            543749  Rab11a; Rab11 GTPase [KO:K07904]
            101260785  ras-related protein Rab11D [KO:K07904]
            101259801  ras-related protein RABA5a [KO:K07904]
            101268402  ras-related protein Rab11A [KO:K07904]
            101256357  ras-related protein RABA1f [KO:K07904]
            101260347  ras-related protein Rab2BV [KO:K07904]
            101257485  ras-related protein RABA1f [KO:K07904]
            101258682  kinesin-like protein KIN-UB [KO:K10396]
            101267752  ADP-ribosylation factor GTPase-activating protein AGD12 [KO:K12486]
            101263379  ADP-ribosylation factor GTPase-activating protein AGD5 isoform X1 [KO:K12486]
            101258838  probable ADP-ribosylation factor GTPase-activating protein AGD15 [KO:K12486]
            101245592  ADP-ribosylation factor GTPase-activating protein AGD5-like [KO:K12486]
            101244017  probable ADP-ribosylation factor GTPase-activating protein AGD5 isoform 1 [KO:K12486]
            101266053  probable ADP-ribosylation factor GTPase-activating protein AGD11 [KO:K12486]
            101251466  ADP-ribosylation factor GTPase-activating protein AGD2-like isoform X1 [KO:K12489]
            104647411  ADP-ribosylation factor GTPase-activating protein AGD3 isoform X1 [KO:K12489]
            101246911  ADP-ribosylation factor GTPase-activating protein AGD3-like [KO:K12489]
            101263690  LOW QUALITY PROTEIN: ADP-ribosylation factor GTPase-activating protein AGD7 [KO:K12492]
            101251611  probable ADP-ribosylation factor GTPase-activating protein AGD6 [KO:K12492]
            101260680  probable ADP-ribosylation factor GTPase-activating protein AGD6 [KO:K12492]
            101244022  probable ADP-ribosylation factor GTPase-activating protein AGD9 [KO:K12493]
            101261344  probable ADP-ribosylation factor GTPase-activating protein AGD9 [KO:K12493]
            101254941  brefeldin A-inhibited guanine nucleotide-exchange protein 2-like [KO:K18442]
            101260383  brefeldin A-inhibited guanine nucleotide-exchange protein 1 [KO:K18442]
            101259044  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
            101249543  ARF guanine-nucleotide exchange factor GNOM-like [KO:K18443]
            101265108  ARF guanine-nucleotide exchange factor GNL2 [KO:K18443]
            101246883  LOW QUALITY PROTEIN: ARF guanine-nucleotide exchange factor GNOM-like [KO:K18443]
            101248166  ARF guanine-nucleotide exchange factor GNOM [KO:K18443]
            101250243  ADP-ribosylation factor 2 [KO:K07937]
            101249410  ADP-ribosylation factor 1 [KO:K07937]
            104644826  ADP-ribosylation factor 1 [KO:K07937]
            101248063  ADP-ribosylation factor 2-B-like [KO:K07937]
            101247318  ADP-ribosylation factor 2 [KO:K07937]
            101260126  ADP-ribosylation factor isoform X1 [KO:K07937]
            101246230  ADP-ribosylation factor 2 isoform X2 [KO:K07937]
            101264106  ADP-ribosylation factor 1-like 2 [KO:K07937]
            101261925  ADP-ribosylation factor 1-like 2 [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
REL_PATHWAY sly04070  Phosphatidylinositol signaling system
            sly04130  SNARE interactions in vesicular transport
KO_PATHWAY  ko04144
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