KEGG   PATHWAY: dpub04145
Entry
dpub04145                   Pathway                                
Name
Phagosome - Dryobates pubescens (Downy woodpecker)
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
dpub04145  Phagosome
dpub04145

Other DBs
GO: 0045335
Organism
Dryobates pubescens (Downy woodpecker) [GN:dpub]
Gene
104309947  VAMP3; vesicle-associated membrane protein 3 [KO:K13505]
104310063  STX12; syntaxin-12 [KO:K13813]
104305559  STX7; syntaxin-7 [KO:K08488]
104297951  ACTG1; LOW QUALITY PROTEIN: actin, cytoplasmic 2 [KO:K05692]
104310186  actin, cytoplasmic type 5 isoform X1 [KO:K05692]
104297045  ACTB; actin, cytoplasmic 1 isoform X1 [KO:K05692]
104303587  STX18; syntaxin-18 [KO:K08492]
104298214  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
104299202  class II histocompatibility antigen, B-L beta chain-like [KO:K06752]
104301057  class II histocompatibility antigen, B-L beta chain-like [KO:K06752]
104297183  RLA class II histocompatibility antigen, DP alpha-1 chain-like [KO:K06752]
104297185  class II histocompatibility antigen, B-L beta chain-like [KO:K06752]
104306885  SLA class II histocompatibility antigen, DQ haplotype C beta chain-like [KO:K06752]
104303103  RAB5A; ras-related protein Rab-5A isoform X1 [KO:K07887]
104309568  RAB5C; ras-related protein Rab-5C [KO:K07889]
104305190  EEA1; LOW QUALITY PROTEIN: early endosome antigen 1 [KO:K12478]
104301021  PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 [KO:K00914] [EC:2.7.1.137]
104302943  TFRC; transferrin receptor protein 1 [KO:K06503]
104297979  HGS; hepatocyte growth factor-regulated tyrosine kinase substrate [KO:K12182]
104302909  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
104296801  V-type proton ATPase catalytic subunit A-like [KO:K02145] [EC:7.1.2.2]
104308695  ATP6V1B1; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
104306033  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
104298141  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
104299654  ATP6V1C2; V-type proton ATPase subunit C 2 [KO:K02148]
104297283  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
104304690  ATP6V1E1; V-type proton ATPase subunit E 1 isoform X1 [KO:K02150]
104300046  ATP6V1F; V-type proton ATPase subunit F [KO:K02151]
104303675  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
104306149  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
104304012  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
104307070  V-type proton ATPase subunit e 2 [KO:K02153]
104308370  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
104299806  TCIRG1; V-type proton ATPase 116 kDa subunit a isoform 3 [KO:K02154]
104309597  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
104296552  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
104304643  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104309199  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
104303098  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
104301557  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104296483  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
104308814  RAB7A; ras-related protein Rab-7a isoform X1 [KO:K07897]
104304770  RAB7B; ras-related protein Rab-7b [KO:K07898]
104302827  RILP; rab-interacting lysosomal protein [KO:K13883]
104304634  DYNC1H1; cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
104296913  DYNC2H1; cytoplasmic dynein 2 heavy chain 1 [KO:K10414]
104304729  DYNC1I2; LOW QUALITY PROTEIN: cytoplasmic dynein 1 intermediate chain 2 [KO:K10415]
104306568  DYNC1I1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
104298321  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
104300832  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 [KO:K10416]
104304551  tubulin alpha-3 chain [KO:K07374]
104300006  TUBAL3; tubulin alpha chain-like 3 isoform X1 [KO:K07374]
104304687  TUBA8; tubulin alpha-8 chain isoform X1 [KO:K07374]
104309733  tubulin alpha-4A chain-like [KO:K07374]
104309734  tubulin alpha-5 chain [KO:K07374]
104300063  tubulin alpha chain-like [KO:K07374]
104300161  tubulin alpha-8 chain [KO:K07374]
104302640  TUBB1; tubulin beta-1 chain isoform X1 [KO:K07375]
104303198  tubulin beta-2 chain-like [KO:K07375]
104303199  LOW QUALITY PROTEIN: tubulin beta-2 chain-like [KO:K07375]
104303768  tubulin beta-3 chain isoform X1 [KO:K07375]
104303818  tubulin beta chain-like [KO:K07375]
104308697  TUBB6; tubulin beta-6 chain [KO:K07375]
104296979  tubulin beta chain [KO:K07375]
104298651  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104301192  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
104298935  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase [KO:K00921] [EC:2.7.1.150]
104306893  M6PR; LOW QUALITY PROTEIN: cation-dependent mannose-6-phosphate receptor [KO:K10089]
104308456  NOS1; nitric oxide synthase, brain isoform X1 [KO:K13240] [EC:1.14.13.39]
104300255  MPO; myeloperoxidase [KO:K10789] [EC:1.11.2.2]
104298792  cathepsin L1 [KO:K01365] [EC:3.4.22.15]
104300452  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
104308818  SEC61A1; protein transport protein Sec61 subunit alpha isoform 1 isoform X1 [KO:K10956]
104300076  SEC61A2; protein transport protein Sec61 subunit alpha isoform 2 [KO:K10956]
104306077  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
104298254  SEC61G; protein transport protein Sec61 subunit gamma [KO:K07342]
104309951  CANX; LOW QUALITY PROTEIN: calnexin [KO:K08054]
104299509  complement C1r subcomponent-like [KO:K01330] [EC:3.4.21.41]
104300208  ITGB2; integrin beta-2 [KO:K06464]
104301663  COLEC11; collectin-11 isoform X1 [KO:K10066]
104307752  COLEC12; collectin-12 [KO:K10062]
104298834  LOW QUALITY PROTEIN: mannose-binding protein C-like [KO:K03991]
104307870  pulmonary surfactant-associated protein A-like [KO:K10067]
104298833  pulmonary surfactant-associated protein A-like [KO:K10067]
104299256  ITGAV; LOW QUALITY PROTEIN: integrin alpha-V [KO:K06487]
104304335  ITGA2; integrin alpha-2 [KO:K06481]
104297059  ITGB1; integrin beta-1 [KO:K05719]
104309227  ITGB3; integrin beta-3 [KO:K06493]
104303722  ITGB5; integrin beta-5 [KO:K06588]
104306853  THBS1; LOW QUALITY PROTEIN: thrombospondin-1 [KO:K16857]
104309463  THBS4; thrombospondin-4 [KO:K04659]
104305470  THBS2; thrombospondin-2 [KO:K04659]
104310268  THBS3; thrombospondin-3 [KO:K04659]
104300738  COMP; cartilage oligomeric matrix protein [KO:K04659]
104298307  TLR2; toll-like receptor 2 [KO:K10159]
104298317  toll-like receptor 2 type-2 [KO:K10159]
104296729  toll-like receptor 6 [KO:K10169]
104306136  TLR4; toll-like receptor 4 [KO:K10160]
104302607  MRC1; macrophage mannose receptor 1 [KO:K06560]
104302610  macrophage mannose receptor 1-like [KO:K06560]
104309242  MRC2; C-type mannose receptor 2 [KO:K06560]
104309783  PLA2R1; LOW QUALITY PROTEIN: secretory phospholipase A2 receptor [KO:K06560]
104310165  macrophage mannose receptor 1-like [KO:K06560]
104310166  macrophage mannose receptor 1-like [KO:K06560]
104310167  macrophage mannose receptor 1-like [KO:K06560]
104308462  SCARB1; scavenger receptor class B member 1 [KO:K13885]
104299822  CD36; platelet glycoprotein 4 [KO:K06259]
104303781  cytochrome b-245 light chain [KO:K08009]
104303526  cytochrome b-245 heavy chain [KO:K21421] [EC:1.-.-.-]
104299652  RAC1; ras-related C3 botulinum toxin substrate 1 [KO:K04392]
104300239  NCF1; neutrophil cytosol factor 1 [KO:K08011]
104308005  NCF2; neutrophil cytosol factor 2 [KO:K08010]
104302048  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
dpub04142  Lysosome
dpub04144  Endocytosis
dpub04620  Toll-like receptor signaling pathway
KO pathway
ko04145   
LinkDB

DBGET integrated database retrieval system