KEGG   PATHWAY: omc04145
Entry
omc04145                    Pathway                                
Name
Phagosome - Onychostoma macrolepis
Description
Phagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is formed when the specific receptors on the phagocyte surface recognize ligands on the particle surface. After formation, nascent phagosomes progressively acquire digestive characteristics. This maturation of phagosomes involves regulated interaction with the other membrane organelles, including recycling endosomes, late endosomes and lysosomes. The fusion of phagosomes and lysosomes releases toxic products that kill most bacteria and degrade them into fragments. However, some bacteria have strategies to escape the bactericidal mechanisms associated with phagocytosis and survive within host phagocytes.
Class
Cellular Processes; Transport and catabolism
Pathway map
omc04145  Phagosome
omc04145

Other DBs
GO: 0045335
Organism
Onychostoma macrolepis [GN:omc]
Gene
131548911  vamp3; vesicle-associated membrane protein 3 [KO:K13505]
131526198  stx12; syntaxin-12 [KO:K13813]
131521830  stx12l; syntaxin-12 isoform X1 [KO:K13813]
131527134  stx7l; syntaxin-7 [KO:K08488]
131549288  actb1; actin, cytoplasmic 1 [KO:K05692]
131537017  actb2; actin, cytoplasmic 2 [KO:K05692]
131536637  coro1a; coronin-1A [KO:K13882]
131553058  stx18; syntaxin-18 [KO:K08492]
131531945  sec22ba; vesicle-trafficking protein SEC22b-A [KO:K08517]
131545851  sec22bb; vesicle-trafficking protein SEC22b-B [KO:K08517]
131525181  LOW QUALITY PROTEIN: beta-2-microglobulin-like [KO:K06751]
131525666  H-2 class I histocompatibility antigen, K-D alpha chain-like [KO:K06751]
131525844  uncharacterized protein LOC131525844 [KO:K06751]
131526016  H-2 class I histocompatibility antigen, K-B alpha chain-like [KO:K06751]
131526027  H-2 class I histocompatibility antigen, Q9 alpha chain-like isoform X1 [KO:K06751]
131525544  HLA class II histocompatibility antigen, DP beta 1 chain-like [KO:K06752]
131536784  H-2 class II histocompatibility antigen, A-U alpha chain-like isoform X1 [KO:K06752]
131537595  H-2 class II histocompatibility antigen, A-U alpha chain-like [KO:K06752]
131545327  H-2 class II histocompatibility antigen, A-U alpha chain-like [KO:K06752]
131546079  LOW QUALITY PROTEIN: H-2 class II histocompatibility antigen, I-E beta chain-like [KO:K06752]
131546087  H-2 class II histocompatibility antigen, E-S beta chain-like [KO:K06752]
131546088  H-2 class II histocompatibility antigen, A-U alpha chain-like [KO:K06752]
131546203  H-2 class II histocompatibility antigen, E-S beta chain-like [KO:K06752]
131546204  mamu class II histocompatibility antigen, DR alpha chain-like [KO:K06752]
131522071  si:ch73-31d8.2; H-2 class II histocompatibility antigen, A-U alpha chain [KO:K06752]
131547276  H-2 class II histocompatibility antigen, A-D alpha chain-like [KO:K06752]
131547275  H-2 class II histocompatibility antigen, I-E beta chain-like [KO:K06752]
131525403  rab5aa; RAB5A, member RAS oncogene family, a [KO:K07887]
131522155  rab5ab; RAB5A, member RAS oncogene family, b [KO:K07887]
131547015  rab5b; ras-related protein Rab-5B [KO:K07888]
131537535  rab5c; ras-related protein Rab-5C [KO:K07889]
131524519  eea1; early endosome antigen 1 [KO:K12478]
131544716  pik3c3; phosphatidylinositol 3-kinase catalytic subunit type 3 isoform X1 [KO:K00914] [EC:2.7.1.137]
131531211  tfr1a; transferrin receptor 1a [KO:K06503]
131533384  tfr1b; transferrin receptor 1b [KO:K06503]
131537871  hgs; hepatocyte growth factor-regulated tyrosine kinase substrate isoform X1 [KO:K12182]
131541243  atp6v1aa; ATPase H+ transporting V1 subunit Aa [KO:K02145] [EC:7.1.2.2]
131533231  atp6v1ab; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
131523515  atp6v1ba; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
131547966  atp6v1b2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
131523518  atp6v1c2; V-type proton ATPase subunit C 1-B isoform X1 [KO:K02148]
131526359  atp6v1c1b; V-type proton ATPase subunit C 1-B isoform X1 [KO:K02148]
131522581  atp6v1c1a; V-type proton ATPase subunit C 1-A isoform X1 [KO:K02148]
131527065  atp6v1d; V-type proton ATPase subunit D [KO:K02149]
131534936  atp6v1e1a; V-type proton ATPase subunit E 1a [KO:K02150]
131527124  V-type proton ATPase subunit E 1-like [KO:K02150]
131539089  atp6v1e1b; V-type proton ATPase subunit E 1 [KO:K02150]
131539653  atp6v1f; V-type proton ATPase subunit F [KO:K02151]
131540069  atp6v1g1; V-type proton ATPase subunit G 1 [KO:K02152]
131530642  atpv0e2; ATPase H+ transporting V0 subunit e2 [KO:K02153]
131553238  atp6v0e1; V-type proton ATPase subunit e 1 [KO:K02153]
131541351  atp6v0a2b; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
131541663  tcirg1a; V-type proton ATPase 116 kDa subunit a 3 isoform X1 [KO:K02154]
131548484  atp6v0a2a; V-type proton ATPase 116 kDa subunit a 2 isoform X1 [KO:K02154]
131533269  atp6v0a1b; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
131533489  si:ch73-173p19.2; LOW QUALITY PROTEIN: V-type proton ATPase 116 kDa subunit a 1 [KO:K02154]
131536837  atp6v0a1a; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
131553335  tcirg1b; T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b [KO:K02154]
131545018  atp6v0d1; V-type proton ATPase subunit d 1 [KO:K02146]
131521527  atp6v1h; V-type proton ATPase subunit H isoform X1 [KO:K02144]
131533778  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
131538027  atp6v0ca; ATPase H+ transporting V0 subunit ca [KO:K02155]
131530640  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
131531830  atp6ap1b; V-type proton ATPase subunit S1b [KO:K03662]
131532087  atp6ap1a; ATPase H+ transporting accessory protein 1a [KO:K03662]
131548118  zgc:100918; ras-related protein rab7-like [KO:K07897]
131549076  rab7a; ras-related protein Rab-7a [KO:K07897]
131549951  si:dkey-13a21.4; ras-related protein rab7 isoform X1 [KO:K07897]
131545284  rab7b; ras-related protein Rab-7b [KO:K07897]
131520411  rilp; RILP-like protein 1 [KO:K13883]
131523421  dync1h1; LOW QUALITY PROTEIN: cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
131554401  dync2h1; dynein cytoplasmic 2 heavy chain 1 isoform X1 [KO:K10414]
131542194  dync1i2b; dynein, cytoplasmic 1, intermediate chain 2a isoform X1 [KO:K10415]
131525487  cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
131546865  dync1i2a; dynein, cytoplasmic 1, intermediate chain 2a isoform X1 [KO:K10415]
131522608  dync1i1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
131525987  dync1li1; cytoplasmic dynein 1 light intermediate chain 1 isoform X1 [KO:K10416]
131543932  dync1li2; cytoplasmic dynein 1 light intermediate chain 2 isoform X1 [KO:K10416]
131547889  tuba7l; LOW QUALITY PROTEIN: tubulin, alpha 7 like [KO:K07374]
131532222  tuba1c; tubulin alpha-1C chain [KO:K07374]
131532290  tuba1a; tubulin alpha-1A chain [KO:K07374]
131532291  tubulin alpha-1C chain [KO:K07374]
131548963  tubulin alpha-1B chain-like [KO:K07374]
131542213  tubulin alpha-1A chain-like [KO:K07374]
131542214  tuba8l4; tubulin, alpha 8 like 4 [KO:K07374]
131551752  tuba4l; LOW QUALITY PROTEIN: tubulin, alpha 4 like [KO:K07374]
131545288  tuba5; tubulin alpha 5 [KO:K07374]
131538389  tuba8l2; tubulin, alpha 8 like 2 [KO:K07374]
131547279  tubulin alpha chain-like [KO:K07374]
131547280  tubulin alpha-1D chain-like [KO:K07374]
131531569  tubb2; tubulin beta-2A chain [KO:K07375]
131541092  zgc:55461; beta-tubulin family protein [KO:K07375]
131542088  tubb1; tubulin beta-1 chain isoform X1 [KO:K07375]
131533657  tubb6; tubulin, beta 6 class V [KO:K07375]
131536235  zgc:65894; tubulin beta chain [KO:K07375]
131545478  tubb2b; tubulin beta-2b chain [KO:K07375]
131537952  tubb4bl; tubulin beta-4B chain isoform X1 [KO:K07375]
131553093  tubulin beta chain [KO:K07375]
131521522  tubb5; tubulin beta-5 chain isoform X1 [KO:K07375]
131539892  lamp1a; lysosome-associated membrane glycoprotein 1a isoform X1 [KO:K06528]
131546746  lamp1b; lysosome-associated membrane glycoprotein 1b [KO:K06528]
131547024  pikfyve; 1-phosphatidylinositol 3-phosphate 5-kinase isoform X1 [KO:K00921] [EC:2.7.1.150]
131522557  m6pr; cation-dependent mannose-6-phosphate receptor [KO:K10089]
131540926  nos1; nitric oxide synthase, brain [KO:K13240] [EC:1.14.13.39]
131530851  cts12; procathepsin L [KO:K01365] [EC:3.4.22.15]
131540608  ctsla; cathepsin La [KO:K01365] [EC:3.4.22.15]
131540902  ctsll; cathepsin L, like [KO:K01365] [EC:3.4.22.15]
131525527  ctss1; cathepsin S, ortholog 1 [KO:K01368] [EC:3.4.22.27]
131521518  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
131522036  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
131522320  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
131542904  sec61a1a; protein transport protein Sec61 subunit alpha-like 1 [KO:K10956]
131542929  sec61a1b; protein transport protein Sec61 subunit alpha-like 2 [KO:K10956]
131522492  sec61b; protein transport protein Sec61 subunit beta [KO:K09481]
131533054  sec61g; protein transport protein Sec61 subunit gamma [KO:K07342]
131521848  tap1; antigen peptide transporter 1 [KO:K05653] [EC:7.4.2.14]
131525174  tap2a; antigen peptide transporter 2a [KO:K05654] [EC:7.4.2.14]
131550522  tap2t; antigen peptide transporter 2 [KO:K05654] [EC:7.4.2.14]
131527657  calr3b; calreticulin 3b [KO:K08057]
131545427  calr; calreticulin [KO:K08057]
131530469  calr3a; calreticulin 3a [KO:K08057]
131552972  si:ch211-274f20.2; calnexin [KO:K08054]
131553406  canx; calnexin [KO:K08054]
131521205  complement C1r-A subcomponent-like [KO:K01330] [EC:3.4.21.41]
131551074  integrin alpha-X-like isoform X1 [KO:K06461]
131551511  LOW QUALITY PROTEIN: integrin alpha-M-like [KO:K06461]
131546453  itgb2; integrin beta-2 [KO:K06464]
131526119  complement C3-like [KO:K03990]
131545854  complement C3-like [KO:K03990]
131545870  complement C3-like [KO:K03990]
131545887  complement C3-like [KO:K03990]
131530188  complement C3-like [KO:K03990]
131523675  colec11; collectin-11 isoform X1 [KO:K10066]
131552399  collectin-12-like [KO:K10062]
131526856  mannose-binding protein C-like isoform X1 [KO:K03991]
131527186  LOW QUALITY PROTEIN: mannose-binding protein A-like [KO:K03991]
131528510  hbl4; LOW QUALITY PROTEIN: hexose-binding lectin 4 [KO:K03991]
131546705  itgav; integrin alpha-V isoform X1 [KO:K06487]
131548718  itga2.2; integrin alpha-2 [KO:K06481]
131532331  itga5; integrin alpha-5 [KO:K06484]
131533096  itgb1a; integrin beta-1a [KO:K05719]
131551560  integrin beta-1-like [KO:K05719]
131551400  itgb3b; integrin beta-3b [KO:K06493]
131536226  itgb3a; integrin beta-3a isoform X1 [KO:K06493]
131546618  itgb5; integrin beta-5 isoform X1 [KO:K06588]
131523347  thbs1a; thrombospondin-1 [KO:K16857]
131527248  thbs1b; thrombospondin-1 [KO:K16857]
131540492  thbs4a; thrombospondin-4a isoform X1 [KO:K04659]
131549197  comp; cartilage oligomeric matrix protein [KO:K04659]
131525542  thbs3b; thrombospondin-3b [KO:K04659]
131551393  thbs2b; thrombospondin-2 isoform X1 [KO:K04659]
131552636  thbs2a; thrombospondin-2 [KO:K04659]
131521246  thbs3a; thrombospondin-3a isoform X1 [KO:K04659]
131528683  thbs4b; thrombospondin-4-B [KO:K04659]
131549258  tlr2; toll-like receptor 2 [KO:K10159]
131521342  tlr18; toll-like receptor 18 isoform X1 [KO:K10159]
131539136  toll-like receptor 1 isoform X1 [KO:K10169]
131552009  toll-like receptor 4 isoform X1 [KO:K10160]
131552803  toll-like receptor 4 isoform X1 [KO:K10160]
131549154  pla2r1; secretory phospholipase A2 receptor isoform X1 [KO:K06560]
131543448  mrc1a; macrophage mannose receptor 1 isoform X1 [KO:K06560]
131536220  mrc2; C-type mannose receptor 2 isoform X1 [KO:K06560]
131552366  mrc1b; macrophage mannose receptor 1b [KO:K06560]
131528845  macrophage mannose receptor 1 [KO:K06560]
131546496  marco; macrophage receptor MARCO isoform X1 [KO:K13884]
131548682  scarb1; scavenger receptor class B member 1 isoform X1 [KO:K13885]
131539133  cd36; platelet glycoprotein 4 [KO:K06259]
131524748  cytochrome b-245 light chain [KO:K08009]
131549120  cytochrome b-245 heavy chain [KO:K21421] [EC:1.-.-.-]
131551015  rac1a; ras-related C3 botulinum toxin substrate 1 [KO:K04392]
131536680  rac1b; ras-related C3 botulinum toxin substrate 1b [KO:K04392]
131520971  ras-related C3 botulinum toxin substrate 1-like [KO:K04392]
131541015  ncf1; neutrophil cytosol factor 1 [KO:K08011]
131543538  ncf2; neutrophil cytosol factor 2 [KO:K08010]
131530232  ncf4; neutrophil cytosol factor 4 [KO:K08012]
Compound
C04549  1-Phosphatidyl-1D-myo-inositol 3-phosphate
Reference
PMID:15894272
  Authors
Stuart LM, Ezekowitz RA
  Title
Phagocytosis: elegant complexity.
  Journal
Immunity 22:539-50 (2005)
DOI:10.1016/j.immuni.2005.05.002
Reference
PMID:10684585
  Authors
Tjelle TE, Lovdal T, Berg T
  Title
Phagosome dynamics and function.
  Journal
Bioessays 22:255-63 (2000)
DOI:10.1002/(SICI)1521-1878(200003)22:3<255::AID-BIES7>3.0.CO;2-R
Reference
PMID:18492791
  Authors
Dupuy AG, Caron E
  Title
Integrin-dependent phagocytosis: spreading from microadhesion to new concepts.
  Journal
J Cell Sci 121:1773-83 (2008)
DOI:10.1242/jcs.018036
Reference
PMID:15036145
  Authors
Brumell JH, Grinstein S
  Title
Salmonella redirects phagosomal maturation.
  Journal
Curr Opin Microbiol 7:78-84 (2004)
DOI:10.1016/j.mib.2003.12.005
Reference
PMID:17245426
  Authors
Huynh KK, Eskelinen EL, Scott CC, Malevanets A, Saftig P, Grinstein S
  Title
LAMP proteins are required for fusion of lysosomes with phagosomes.
  Journal
EMBO J 26:313-24 (2007)
DOI:10.1038/sj.emboj.7601511
Reference
PMID:17637737
  Authors
Luzio JP, Pryor PR, Bright NA
  Title
Lysosomes: fusion and function.
  Journal
Nat Rev Mol Cell Biol 8:622-32 (2007)
DOI:10.1038/nrm2217
Reference
PMID:18513324
  Authors
Sumimoto H
  Title
Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species.
  Journal
FEBS J 275:3249-77 (2008)
DOI:10.1111/j.1742-4658.2008.06488.x
Related
pathway
omc04142  Lysosome
omc04144  Endocytosis
omc04620  Toll-like receptor signaling pathway
KO pathway
ko04145   
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