KEGG   PATHWAY: oda04145
Entry
oda04145                    Pathway                                
Name
Phagosome - Oryx dammah (scimitar-horned oryx)
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
oda04145  Phagosome
oda04145

Other DBs
GO: 0045335
Organism
Oryx dammah (scimitar-horned oryx) [GN:oda]
Gene
120880163  VAMP3; vesicle-associated membrane protein 3 [KO:K13505]
120855149  STX12; syntaxin-12 [KO:K13813]
120863031  STX7; syntaxin-7 [KO:K08488]
120856263  ACTB; actin, cytoplasmic 1 [KO:K05692]
120873725  actin, cytoplasmic 1-like [KO:K05692]
120866873  ACTG1; actin, cytoplasmic 2 [KO:K05692]
120876870  CORO1A; coronin-1A [KO:K13882]
120862223  STX18; syntaxin-18 isoform X1 [KO:K08492]
120852196  vesicle-trafficking protein SEC22b-like [KO:K08517]
120855991  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
120859564  BOLA class I histocompatibility antigen, alpha chain BL3-7-like [KO:K06751]
120860566  BOLA class I histocompatibility antigen, alpha chain BL3-7-like [KO:K06751]
120870505  BOLA class I histocompatibility antigen, alpha chain BL3-7-like isoform X1 [KO:K06751]
120870511  BOLA class I histocompatibility antigen, alpha chain BL3-7-like isoform X1 [KO:K06751]
120870513  BOLA class I histocompatibility antigen, alpha chain BL3-7-like isoform X1 [KO:K06751]
120864527  H-2 class I histocompatibility antigen, Q10 alpha chain-like [KO:K06751]
120859624  BOLA class I histocompatibility antigen, alpha chain BL3-7-like [KO:K06752]
120860003  BOLA class I histocompatibility antigen, alpha chain BL3-7-like [KO:K06752]
120860570  SLA class II histocompatibility antigen, DQ haplotype D alpha chain-like [KO:K06752]
120869766  DLA class II histocompatibility antigen, DR-1 beta chain-like [KO:K06752]
120869857  HLA class II histocompatibility antigen, DM alpha chain [KO:K06752]
120869858  HLA class II histocompatibility antigen, DO alpha chain-like [KO:K06752]
120869859  HLA class II histocompatibility antigen, DM beta chain [KO:K06752]
120869865  HLA class II histocompatibility antigen, DO beta chain isoform X1 [KO:K06752]
120869866  rano class II histocompatibility antigen, A beta chain-like [KO:K06752]
120869867  SLA class II histocompatibility antigen, DQ haplotype D alpha chain-like [KO:K06752]
120869868  DLA class II histocompatibility antigen, DR-1 beta chain-like [KO:K06752]
120870613  mamu class II histocompatibility antigen, DR alpha chain [KO:K06752]
120870614  DLA class II histocompatibility antigen, DR-1 beta chain-like [KO:K06752]
120870615  DLA class II histocompatibility antigen, DR-1 beta chain-like [KO:K06752]
120870618  boLa class II histocompatibility antigen, DQB*0101 beta chain isoform X1 [KO:K06752]
120870619  SLA class II histocompatibility antigen, DQ haplotype D alpha chain-like [KO:K06752]
120870620  HLA class II histocompatibility antigen, DQ alpha 2 chain-like [KO:K06752]
120870621  boLa class II histocompatibility antigen, DQB*0101 beta chain-like [KO:K06752]
120880188  RAB5A; ras-related protein Rab-5A isoform X1 [KO:K07887]
120857425  RAB5B; ras-related protein Rab-5B [KO:K07888]
120867130  RAB5C; ras-related protein Rab-5C [KO:K07889]
120858384  EEA1; early endosome antigen 1 [KO:K12478]
120880908  PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 [KO:K00914] [EC:2.7.1.137]
120870094  TFRC; transferrin receptor protein 1 [KO:K06503]
120866860  HGS; hepatocyte growth factor-regulated tyrosine kinase substrate isoform X1 [KO:K12182]
120851553  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
120862991  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
120851292  ATP6V1B1; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
120878970  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
120851868  ATP6V1C2; V-type proton ATPase subunit C 2 isoform X1 [KO:K02148]
120882142  LOW QUALITY PROTEIN: V-type proton ATPase subunit D-like [KO:K02149]
120852802  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
120851738  ATP6V1E2; V-type proton ATPase subunit E 2 [KO:K02150]
120857833  ATP6V1E1; V-type proton ATPase subunit E 1 [KO:K02150]
120877331  ATP6V1F; V-type proton ATPase subunit F [KO:K02151]
120879888  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
120861754  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
120870533  ATP6V1G2; V-type proton ATPase subunit G 2 [KO:K02152]
120864324  V-type proton ATPase subunit G 1 [KO:K02152]
120877925  ATP6V0E2; V-type proton ATPase subunit e 2 [KO:K02153]
120879667  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
120877631  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
120874794  TCIRG1; V-type proton ATPase 116 kDa subunit a3 isoform X1 [KO:K02154]
120871019  ATP6V0A2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
120867069  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
120878524  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
120872737  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
120878573  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
120873700  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
120856270  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
120881819  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
120868064  RAB7A; ras-related protein Rab-7a [KO:K07897]
120862523  LOW QUALITY PROTEIN: ras-related protein Rab-7a-like [KO:K07897]
120879946  RAB7B; ras-related protein Rab-7b [KO:K07898]
120861229  ras-related protein Rab-7b-like [KO:K07898]
120858100  ras-related protein Rab-7b-like [KO:K07898]
120866226  rab-interacting lysosomal protein [KO:K13883]
120875163  DYNC1H1; cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
120876145  DYNC2H1; cytoplasmic dynein 2 heavy chain 1 isoform X1 [KO:K10414]
120877972  DYNC1I1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
120854919  DYNC1I2; cytoplasmic dynein 1 intermediate chain 2 isoform X1 [KO:K10415]
120867867  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
120872789  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 [KO:K10416]
120851630  tubulin alpha-1A chain-like [KO:K07374]
120859882  tubulin alpha-1C chain-like [KO:K07374]
120861269  tubulin alpha-1A chain isoform X1 [KO:K07374]
120861271  tubulin alpha-1C chain isoform X1 [KO:K07374]
120869479  TUBAL3; tubulin alpha chain-like 3 [KO:K07374]
120854340  tubulin alpha-1A chain-like [KO:K07374]
120854341  tubulin alpha-4A chain [KO:K07374]
120871336  tubulin alpha-3 chain [KO:K07374]
120871340  tubulin alpha-3 chain-like [KO:K07374]
120857825  TUBA8; tubulin alpha-8 chain [KO:K07374]
120858186  tubulin alpha-1B chain [KO:K07374]
120858187  tubulin alpha-1A chain isoform X1 [KO:K07374]
120858188  tubulin alpha-1C chain-like isoform X1 [KO:K07374]
120881051  TUBB6; tubulin beta-6 chain [KO:K07375]
120852227  tubulin beta chain [KO:K07375]
120869383  TUBB1; tubulin beta-1 chain [KO:K07375]
120869964  tubulin beta-2A chain [KO:K07375]
120869965  tubulin beta-2B chain [KO:K07375]
120870506  TUBB; tubulin beta chain [KO:K07375]
120864876  TUBB4A; tubulin beta-4A chain [KO:K07375]
120873331  tubulin beta-3 chain [KO:K07375]
120883256  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
120881514  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
120854549  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase [KO:K00921] [EC:2.7.1.150]
120858794  M6PR; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
120871573  NOS1; nitric oxide synthase, brain [KO:K13240] [EC:1.14.13.39]
120866469  MPO; myeloperoxidase [KO:K10789] [EC:1.11.2.2]
120867201  procathepsin L [KO:K01365] [EC:3.4.22.15]
120866989  CTSL; procathepsin L [KO:K01365] [EC:3.4.22.15]
120855927  CTSS; cathepsin S [KO:K01368] [EC:3.4.22.27]
120868053  SEC61A1; protein transport protein Sec61 subunit alpha [KO:K10956]
120869269  SEC61A2; protein transport protein Sec61 subunit alpha [KO:K10956]
120858873  protein transport protein Sec61 subunit beta-like [KO:K09481]
120862803  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
120867900  SEC61G; protein transport protein Sec61 subunit gamma [KO:K07342]
120869861  TAP1; antigen peptide transporter 1 [KO:K05653] [EC:7.4.2.14]
120869864  TAP2; antigen peptide transporter 2 [KO:K05654] [EC:7.4.2.14]
120864041  CALR; calreticulin [KO:K08057]
120864350  CANX; calnexin [KO:K08054]
120871903  FCAR; immunoglobulin alpha Fc receptor [KO:K06513]
120855951  FCGR1A; high affinity immunoglobulin gamma Fc receptor I [KO:K06498]
120855416  low affinity immunoglobulin gamma Fc region receptor II-like [KO:K12560]
120858754  C1R; complement C1r subcomponent isoform X1 [KO:K01330] [EC:3.4.21.41]
120877745  ITGAM; integrin alpha-M [KO:K06461]
120881345  ITGB2; integrin beta-2 [KO:K06464]
120860432  LOW QUALITY PROTEIN: complement C3-like [KO:K03990]
120860434  complement C3 [KO:K03990]
120864328  COLEC11; collectin-11 [KO:K10066]
120881115  COLEC12; collectin-12 [KO:K10062]
120865357  mannose-binding protein A-like [KO:K03991]
120873767  MBL2; mannose-binding protein C [KO:K03991]
120865355  pulmonary surfactant-associated protein A isoform X1 [KO:K10067]
120859171  collectin-43-like [KO:K10068]
120859172  collectin-43-like [KO:K10068]
120865352  collectin-46-like [KO:K10068]
120865356  pulmonary surfactant-associated protein D [KO:K10068]
120854008  ITGAV; integrin alpha-V isoform X1 [KO:K06487]
120879297  ITGA2; integrin alpha-2 [KO:K06481]
120858295  ITGA5; integrin alpha-5 [KO:K06484]
120869236  ITGB1; integrin beta-1 isoform X1 [KO:K05719]
120866975  ITGB3; integrin beta-3 [KO:K06493]
120870547  ITGB5; integrin beta-5 [KO:K06588]
120853227  THBS1; thrombospondin-1 isoform X1 [KO:K16857]
120852568  THBS4; thrombospondin-4 [KO:K04659]
120863007  THBS2; thrombospondin-2 [KO:K04659]
120855725  THBS3; thrombospondin-3 [KO:K04659]
120864272  cartilage oligomeric matrix protein [KO:K04659]
120871484  TLR2; toll-like receptor 2 [KO:K10159]
120862036  TLR6; toll-like receptor 6 isoform X1 [KO:K10169]
120864691  TLR4; toll-like receptor 4 isoform X1 [KO:K10160]
120863565  CD14; monocyte differentiation antigen CD14 [KO:K04391]
120869036  MRC1; macrophage mannose receptor 1 [KO:K06560]
120854840  PLA2R1; secretory phospholipase A2 receptor [KO:K06560]
120866960  MRC2; C-type mannose receptor 2 [KO:K06560]
120863899  CD209; CD209 antigen [KO:K06563]
120858820  CLEC7A; C-type lectin domain family 7 member A isoform X1 [KO:K10074]
120865789  MSR1; macrophage scavenger receptor types I and II isoform X1 [KO:K06558]
120854733  MARCO; macrophage receptor MARCO isoform X1 [KO:K13884]
120858802  OLR1; oxidized low-density lipoprotein receptor 1 [KO:K08763]
120871011  SCARB1; scavenger receptor class B member 1 isoform X1 [KO:K13885]
120878121  platelet glycoprotein 4-like [KO:K06259]
120878122  LOW QUALITY PROTEIN: platelet glycoprotein 4-like [KO:K06259]
120878123  platelet glycoprotein 4 [KO:K06259]
120872959  cytochrome b-245 light chain isoform X1 [KO:K08009]
120882340  cytochrome b-245 heavy chain [KO:K21421] [EC:1.-.-.-]
120856144  RAC1; ras-related C3 botulinum toxin substrate 1 [KO:K04392]
120878158  NCF1; neutrophil cytosol factor 1 [KO:K08011]
120880475  NCF2; neutrophil cytosol factor 2 isoform X1 [KO:K08010]
120861194  neutrophil cytosol factor 4 [KO:K08012]
120858568  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
oda04142  Lysosome
oda04144  Endocytosis
oda04610  Complement and coagulation cascades
oda04612  Antigen processing and presentation
oda04620  Toll-like receptor signaling pathway
oda04666  Fc gamma R-mediated phagocytosis
KO pathway
ko04145   
LinkDB

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