KEGG   PATHWAY: nni04145
Entry
nni04145                    Pathway                                
Name
Phagosome - Nipponia nippon (crested ibis)
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
nni04145  Phagosome
nni04145

Other DBs
GO: 0045335
Organism
Nipponia nippon (crested ibis) [GN:nni]
Gene
104008524  vesicle-associated membrane protein 3 [KO:K13505]
104009023  VAMP3; vesicle-associated membrane protein 3 [KO:K13505]
104015607  STX12; syntaxin-12 [KO:K13813]
104008835  STX7; syntaxin-7 [KO:K08488]
104016716  actin, cytoplasmic type 5 isoform X1 [KO:K05692]
104014277  ACTG1; actin, cytoplasmic 2 isoform X1 [KO:K05692]
104015100  ACTB; actin, cytoplasmic 1 isoform X1 [KO:K05692]
104018078  STX18; syntaxin-18 [KO:K08492]
104010450  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
104009142  class I histocompatibility antigen, F10 alpha chain-like [KO:K06751]
104019826  class II histocompatibility antigen, M alpha chain [KO:K06752]
104019829  class II histocompatibility antigen, M beta 1 chain-like [KO:K06752]
104017643  HLA class II histocompatibility antigen, DR alpha chain-like [KO:K06752]
104017648  class II histocompatibility antigen, B-L beta chain [KO:K06752]
104013901  RAB5A; ras-related protein Rab-5A isoform X1 [KO:K07887]
104017466  RAB5B; ras-related protein Rab-5B isoform X1 [KO:K07888]
104009874  RAB5C; ras-related protein Rab-5C isoform X1 [KO:K07889]
104011697  EEA1; early endosome antigen 1 [KO:K12478]
104015660  TFRC; transferrin receptor protein 1 [KO:K06503]
104018613  HGS; LOW QUALITY PROTEIN: hepatocyte growth factor-regulated tyrosine kinase substrate [KO:K12182]
104008620  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
104014444  V-type proton ATPase catalytic subunit A-like [KO:K02145] [EC:7.1.2.2]
104020958  ATP6V1B1; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
104016011  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
104016450  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
104013011  ATP6V1C2; V-type proton ATPase subunit C 2 [KO:K02148]
104020298  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
104020205  ATP6V1E1; V-type proton ATPase subunit E 1 isoform X1 [KO:K02150]
104008506  V-type proton ATPase subunit F-like [KO:K02151]
104020934  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
104022540  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
104019013  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
104021396  V-type proton ATPase subunit e 2 [KO:K02153]
104009877  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
104012376  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
104009033  V-type proton ATPase 116 kDa subunit a isoform 3-like [KO:K02154]
104019709  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 isoform X1 [KO:K02154]
104017441  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104022785  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
104019760  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
104011181  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
104015429  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104011823  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
104022657  RAB7A; ras-related protein Rab-7a isoform X1 [KO:K07897]
104013122  RAB7B; ras-related protein Rab-7b [KO:K07898]
104016730  RILP; rab-interacting lysosomal protein [KO:K13883]
104014544  DYNC1H1; LOW QUALITY PROTEIN: cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
104023066  DYNC2H1; cytoplasmic dynein 2 heavy chain 1 [KO:K10414]
104009997  DYNC1I2; cytoplasmic dynein 1 intermediate chain 2 isoform X1 [KO:K10415]
104012811  DYNC1I1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
104013286  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 [KO:K10416]
104013954  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
104020202  TUBA8; tubulin alpha-8 chain [KO:K07374]
104010483  TUBAL3; tubulin alpha chain-like 3 [KO:K07374]
104010484  tubulin alpha-3 chain-like [KO:K07374]
104015619  tubulin alpha-3 chain [KO:K07374]
104010053  tubulin alpha-1 chain isoform X1 [KO:K07374]
104010055  tubulin alpha-1B chain-like [KO:K07374]
104010056  LOW QUALITY PROTEIN: tubulin alpha-5 chain-like [KO:K07374]
104017935  tubulin alpha-2/alpha-4 chain-like [KO:K07374]
104011077  tubulin alpha-8 chain [KO:K07374]
104009564  TUBB1; tubulin beta-1 chain isoform X1 [KO:K07375]
104021837  tubulin beta-2 chain [KO:K07375]
104021839  tubulin beta-2 chain-like [KO:K07375]
104014478  tubulin beta-7 chain [KO:K07375]
104023623  TUBB3; tubulin beta-3 chain [KO:K07375]
104017658  TUBB6; tubulin beta-6 chain [KO:K07375]
104022259  TUBB4B; tubulin beta-4B chain [KO:K07375]
104019091  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
104019415  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104010224  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase [KO:K00921] [EC:2.7.1.150]
104014579  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
104010553  NOS1; nitric oxide synthase, brain [KO:K13240] [EC:1.14.13.39]
104012465  LPO; lactoperoxidase [KO:K10789] [EC:1.11.2.2]
104018797  LOW QUALITY PROTEIN: cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
104011755  CTSL; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
104014433  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
104014434  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
104014623  SEC61A2; protein transport protein Sec61 subunit alpha isoform 2 isoform X1 [KO:K10956]
104022671  SEC61A1; protein transport protein Sec61 subunit alpha isoform 1 [KO:K10956]
104018203  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
104010118  uncharacterized protein LOC104010118 [KO:K08057]
104018793  CALR3; calreticulin-3 [KO:K08057]
104018438  CANX; LOW QUALITY PROTEIN: calnexin [KO:K08054]
104009783  C1R; complement C1r subcomponent [KO:K01330] [EC:3.4.21.41]
104013641  ITGB2; integrin beta-2 [KO:K06464]
104014965  C3; complement C3 [KO:K03990]
104009155  COLEC11; collectin-11 isoform X1 [KO:K10066]
104018126  COLEC12; collectin-12 [KO:K10062]
104015425  SFTPD; LOW QUALITY PROTEIN: pulmonary surfactant-associated protein D [KO:K03991]
104015405  pulmonary surfactant-associated protein A-like [KO:K10067]
104015416  pulmonary surfactant-associated protein A-like [KO:K10067]
104015304  ITGAV; integrin alpha-V [KO:K06487]
104012504  ITGA2; integrin alpha-2 [KO:K06481]
104022255  ITGB1; integrin beta-1 [KO:K05719]
104009899  ITGB3; integrin beta-3 [KO:K06493]
104018787  ITGB5; integrin beta-5 [KO:K06588]
104020294  THBS1; thrombospondin-1 [KO:K16857]
104013690  COMP; cartilage oligomeric matrix protein [KO:K04659]
104017909  THBS2; thrombospondin-2 [KO:K04659]
104009111  THBS4; thrombospondin-4 [KO:K04659]
104020504  THBS3; thrombospondin-3 [KO:K04659]
104021229  TLR2; toll-like receptor 2 [KO:K10159]
104021230  toll-like receptor 2 type-2 [KO:K10159]
104008501  toll-like receptor 2 type-2 [KO:K10159]
104009810  toll-like receptor 1 [KO:K10169]
104022122  TLR4; toll-like receptor 4 [KO:K10160]
104022144  CD14; monocyte differentiation antigen CD14 [KO:K04391]
104013327  macrophage mannose receptor 1-like [KO:K06560]
104013329  macrophage mannose receptor 1-like [KO:K06560]
104013315  macrophage mannose receptor 1-like [KO:K06560]
104013316  macrophage mannose receptor 1-like [KO:K06560]
104013318  macrophage mannose receptor 1-like [KO:K06560]
104009953  MRC2; C-type mannose receptor 2 [KO:K06560]
104010045  PLA2R1; secretory phospholipase A2 receptor [KO:K06560]
104018398  hepatic lectin-like [KO:K06563]
104020973  SCARB1; scavenger receptor class B member 1 [KO:K13885]
104010749  CD36; platelet glycoprotein 4 isoform X1 [KO:K06259]
104023645  cytochrome b-245 light chain [KO:K08009]
104020081  cytochrome b-245 heavy chain [KO:K21421] [EC:1.-.-.-]
104015059  RAC1; ras-related C3 botulinum toxin substrate 1 [KO:K04392]
104016121  NCF1; neutrophil cytosol factor 1 [KO:K08011]
104011317  NCF2; neutrophil cytosol factor 2 [KO:K08010]
104021580  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
nni04142  Lysosome
nni04144  Endocytosis
nni04620  Toll-like receptor signaling pathway
KO pathway
ko04145   
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