KEGG   PATHWAY: pcad04145
Entry
pcad04145                   Pathway                                
Name
Phagosome - Physeter macrocephalus (sperm whale)
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
pcad04145  Phagosome
pcad04145

Other DBs
GO: 0045335
Organism
Physeter macrocephalus (sperm whale) [GN:pcad]
Gene
102973277  RAB5B; ras-related protein Rab-5B [KO:K07888]
102973323  [KO:K06259]
102973615  [KO:K08009]
102973627  ATP6V1C2; V-type proton ATPase subunit C 2 isoform X2 [KO:K02148]
102973745  [KO:K02152]
102973764  [KO:K06752]
102973944  [KO:K06752]
102974327  [KO:K08763]
102974359  [KO:K06259]
102974479  [KO:K06752]
102974731  STX12; syntaxin-12 [KO:K13813]
102974795  [KO:K10074]
102974923  [KO:K01365] [EC:3.4.22.15]
102974956  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 isoform X1 [KO:K10416]
102975170  PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 isoform X1 [KO:K00914] [EC:2.7.1.137]
102975289  ATP6V0A4; V-type proton ATPase 116 kDa subunit a 4 [KO:K02154]
102975405  [KO:K06259]
102975576  COMP; cartilage oligomeric matrix protein [KO:K04659]
102975630  TUBB3; tubulin beta-3 chain isoform X1 [KO:K07375]
102976000  ATP6V0A1; V-type proton ATPase 116 kDa subunit a 1 isoform X1 [KO:K02154]
102976012  [KO:K06752]
102976248  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
102976287  [KO:K06752]
102976342  TLR2; toll-like receptor 2 [KO:K10159]
102976617  SFTPD; pulmonary surfactant-associated protein D [KO:K10068]
102976852  [KO:K08057]
102976904  MBL2; mannose-binding protein C [KO:K03991]
102976905  RAB7A; ras-related protein Rab-7a [KO:K07897]
102977013  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase [KO:K00921] [EC:2.7.1.150]
102977227  THBS4; thrombospondin-4 [KO:K04659]
102977354  SFTPA1; pulmonary surfactant-associated protein A1 isoform X2 [KO:K10067]
102977382  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
102977795  ITGA2; integrin alpha-2 [KO:K06481]
102977860  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
102978040  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
102978546  [KO:K06752]
102978613  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit c [KO:K02155]
102978958  SEC61A1; protein transport protein Sec61 subunit alpha [KO:K10956]
102979195  [KO:K04392]
102979432  C3; complement C3 [KO:K03990]
102979493  TCIRG1; V-type proton ATPase 116 kDa subunit a 3 [KO:K02154]
102979734  TLR6; toll-like receptor 6 [KO:K10169]
102979785  CTSS; cathepsin S isoform X1 [KO:K01368] [EC:3.4.22.27]
102979827  THBS2; thrombospondin-2 isoform X1 [KO:K04659]
102979859  TUBB; tubulin beta chain [KO:K07375]
102979938  TUBAL3; tubulin alpha chain-like 3 [KO:K07374]
102980331  RILP; rab-interacting lysosomal protein isoform X1 [KO:K13883]
102980636  [KO:K07374]
102980786  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
102980851  ITGAV; integrin alpha-V [KO:K06487]
102980876  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
102981449  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
102981831  TUBB4B; tubulin beta-4B chain isoform X1 [KO:K07375]
102982078  MPO; myeloperoxidase [KO:K10789] [EC:1.11.2.2]
102982464  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
102982542  NCF1; neutrophil cytosol factor 1 isoform X2 [KO:K08011]
102982837  [KO:K07374]
102983046  ITGA5; integrin alpha-5 [KO:K06484]
102983076  TLR4; toll-like receptor 4 isoform X1 [KO:K10160]
102983124  EEA1; early endosome antigen 1 isoform X1 [KO:K12478]
102983789  ITGB2; integrin beta-2 [KO:K06464]
102983796  DYNC2H1; cytoplasmic dynein 2 heavy chain 1 [KO:K10414]
102983864  [KO:K12560]
102984093  CORO1A; coronin-1A [KO:K13882]
102984396  ATP6V1G2; V-type proton ATPase subunit G 2 isoform X1 [KO:K02152]
102984407  CANX; calnexin [KO:K08054]
102984481  RAB5A; ras-related protein Rab-5A isoform X1 [KO:K07887]
102984552  VAMP3; vesicle-associated membrane protein 3 [KO:K13505]
102984702  ITGB1; integrin beta-1 isoform X2 [KO:K05719]
102984856  [KO:K07375]
102984866  RAB5C; ras-related protein Rab-5C [KO:K07889]
102985147  TUBB2A; tubulin beta-2A chain isoform X2 [KO:K07375]
102985437  TFRC; transferrin receptor protein 1 isoform X1 [KO:K06503]
102985559  DYNC1I1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
102985837  [KO:K03661]
102985933  [KO:K06751]
102986688  TUBB1; tubulin beta-1 chain isoform X1 [KO:K07375]
102986739  THBS3; thrombospondin-3 isoform X1 [KO:K04659]
102986918  ATP6V0A2; V-type proton ATPase 116 kDa subunit a 2 isoform X3 [KO:K02154]
102987023  SEC61A2; protein transport protein Sec61 subunit alpha isoform X1 [KO:K10956]
102987030  NCF2; neutrophil cytosol factor 2 isoform X1 [KO:K08010]
102987067  DYNC1I2; cytoplasmic dynein 1 intermediate chain 2 isoform X1 [KO:K10415]
102987095  [KO:K06461]
102987448  ATP6V1E1; V-type proton ATPase subunit E 1 [KO:K02150]
102987503  TUBB4A; tubulin beta-4A chain isoform X1 [KO:K07375]
102987516  MSR1; macrophage scavenger receptor types I and II isoform X1 [KO:K06558]
102987712  COLEC11; collectin-11 [KO:K10066]
102987728  TUBA8; tubulin alpha-8 chain isoform X1 [KO:K07374]
102987961  C1R; complement C1r subcomponent isoform X1 [KO:K01330] [EC:3.4.21.41]
102988048  ACTG1; actin, cytoplasmic 2 [KO:K05692]
102988275  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X2 [KO:K06528]
102988303  DYNC1H1; cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
102988333  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
102988543  [KO:K01365] [EC:3.4.22.15]
102988587  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
102988621  MRC1; macrophage mannose receptor 1 [KO:K06560]
102988740  ITGB3; integrin beta-3 isoform X2 [KO:K06493]
102988905  [KO:K05692]
102989679  STX7; syntaxin-7 isoform X2 [KO:K08488]
102989820  ATP6V1E2; V-type proton ATPase subunit E 2 [KO:K02150]
102990276  RAC1; ras-related C3 botulinum toxin substrate 1 isoform X2 [KO:K04392]
102990434  SCARB1; scavenger receptor class B member 1 isoform X4 [KO:K13885]
102990526  CD14; monocyte differentiation antigen CD14 [KO:K04391]
102990877  [KO:K06463]
102990900  [KO:K07374]
102990956  [KO:K07374]
102991400  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1 [KO:K03661]
102991432  MRC2; C-type mannose receptor 2 [KO:K06560]
102991473  ATP6V0D1; V-type proton ATPase subunit d 1 isoform X1 [KO:K02146]
102991923  PLA2R1; secretory phospholipase A2 receptor isoform X1 [KO:K06560]
102991967  NOS1; nitric oxide synthase, brain [KO:K13240] [EC:1.14.13.39]
102992310  [KO:K07374]
102992584  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
102992683  RAB7B; ras-related protein Rab-7b isoform X3 [KO:K07898]
102992706  STX18; syntaxin-18 isoform X1 [KO:K08492]
102992942  [KO:K06752]
102993493  [KO:K21421] [EC:1.-.-.-]
102993572  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
102993603  CD209; CD209 antigen [KO:K06563]
102993663  HGS; hepatocyte growth factor-regulated tyrosine kinase substrate isoform X1 [KO:K12182]
102993692  NCF4; neutrophil cytosol factor 4 [KO:K08012]
102994182  SEC61G; protein transport protein Sec61 subunit gamma isoform X4 [KO:K07342]
102994322  [KO:K06752]
102994605  [KO:K06752]
102994748  ATP6V1F; V-type proton ATPase subunit F [KO:K02151]
102995043  MARCO; macrophage receptor MARCO [KO:K13884]
102995173  TAP1; antigen peptide transporter 1 [KO:K05653] [EC:7.4.2.14]
102995205  ITGB5; integrin beta-5 [KO:K06588]
102995354  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
102995420  THBS1; thrombospondin-1 [KO:K16857]
102995698  ATP6V0E2; V-type proton ATPase subunit e 2 [KO:K02153]
102995701  COLEC12; collectin-12 isoform X1 [KO:K10062]
102995730  TAP2; antigen peptide transporter 2 [KO:K05654] [EC:7.4.2.14]
102995815  ATP6V1B1; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
102996007  TUBB6; tubulin beta-6 chain [KO:K07375]
102996121  [KO:K10956]
102996148  CTSL; procathepsin L isoform X2 [KO:K01365] [EC:3.4.22.15]
102996245  [KO:K06751]
102996583  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
102996599  [KO:K02153]
102996910  CALR; calreticulin [KO:K08057]
102997022  [KO:K02152]
112062206  [KO:K02153]
112062393  [KO:K02153]
112062432  [KO:K06472]
112063645  [KO:K05692]
112064291  [KO:K06751]
112064292  [KO:K06751]
112064318  [KO:K06751]
112064711  [KO:K07374]
112065466  [KO:K07342]
112067146  [KO:K07374]
112067373  [KO:K01365] [EC:3.4.22.15]
129391776  [KO:K07342]
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
pcad04142  Lysosome
pcad04144  Endocytosis
pcad04610  Complement and coagulation cascades
pcad04612  Antigen processing and presentation
pcad04620  Toll-like receptor signaling pathway
pcad04666  Fc gamma R-mediated phagocytosis
KO pathway
ko04145   

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