KEGG   PATHWAY: ccw04145
Entry
ccw04145                    Pathway                                
Name
Phagocytosis - Corvus cornix (hooded crow)
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
ccw04145  Phagocytosis
ccw04145

Other DBs
GO: 0006909
Organism
Corvus cornix (hooded crow) [GN:ccw]
Gene
104683128  SNAP23; synaptosomal-associated protein 23 [KO:K08508]
104683283  RAB7A; ras-related protein Rab-7a [KO:K07897] [EC:3.6.5.2]
104683428  MON1A; LOW QUALITY PROTEIN: vacuolar fusion protein MON1 homolog A [KO:K20195]
104683473  SEC61A1; LOW QUALITY PROTEIN: protein transport protein Sec61 subunit alpha [KO:K10956]
104683676  ATG16L1; autophagy-related protein 16-1 isoform X2 [KO:K17890]
104683786  DYNLRB1; dynein light chain roadblock-type 1 [KO:K10419]
104683787  MAP1LC3A; microtubule-associated proteins 1A/1B light chain 3A [KO:K10435]
104683858  [KO:K11140] [EC:3.4.11.2]
104683864  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
104684021  RAB27A; ras-related protein Rab-27A [KO:K07885]
104684025  THBS1; thrombospondin-1 [KO:K16857]
104684330  THBS2; thrombospondin-2 isoform X2 [KO:K04659]
104684642  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
104684732  DCTN5; dynactin subunit 5 [KO:K10427]
104684799  ACTB; actin, cytoplasmic 1 [KO:K05692]
104684849  CCZ1; vacuolar fusion protein CCZ1 homolog [KO:K27045]
104684856  RAC1; ras-related C3 botulinum toxin substrate 1 isoform X1 [KO:K04392]
104685440  ATP6V1C2; V-type proton ATPase subunit C 2 isoform X1 [KO:K02148]
104685461  COLEC11; collectin-11 isoform X1 [KO:K10066]
104685680  DYNC2LI1; cytoplasmic dynein 2 light intermediate chain 1 isoform X3 [KO:K10417]
104685816  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
104686217  [KO:K21421] [EC:1.-.-.-]
104686219  DYNLT3; dynein light chain Tctex-type 3 [KO:K10420]
104686321  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104686529  ITGB1; integrin beta-1 isoform X1 [KO:K05719]
104686556  DCTN3; dynactin subunit 3 [KO:K10425]
104686657  ITGA2; integrin alpha-2 isoform X1 [KO:K06481]
104686712  PIK3R1; phosphatidylinositol 3-kinase regulatory subunit alpha isoform X1 [KO:K02649]
104686818  [KO:K03662]
104686891  CD36; platelet glycoprotein 4 [KO:K06259]
104687098  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
104687159  UVRAG; UV radiation resistance-associated gene protein isoform X3 [KO:K21249]
104687201  ATG3; ubiquitin-like-conjugating enzyme ATG3 [KO:K08343]
104687268  TUBB6; tubulin beta-6 chain [KO:K07375]
104687317  OSBPL1A; oxysterol-binding protein-related protein 1 isoform X1 [KO:K20174]
104687354  COLEC12; collectin-12 [KO:K10062]
104687406  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 [KO:K10416]
104687625  TUBB1; tubulin beta-1 chain isoform X1 [KO:K07375]
104687639  OSBPL2; oxysterol-binding protein-related protein 2 [KO:K20174]
104687728  MMP9; matrix metalloproteinase-9 [KO:K01403] [EC:3.4.24.35]
104687838  [KO:K25374]
104687846  [KO:K25374]
104687942  RUBCN; LOW QUALITY PROTEIN: run domain Beclin-1-interacting and cysteine-rich domain-containing protein [KO:K19330]
104688020  PIK3CA; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform [KO:K00922] [EC:2.7.1.153]
104688131  [KO:K01077] [EC:3.1.3.1]
104688132  [KO:K01077] [EC:3.1.3.1]
104688184  [KO:K07374]
104688225  [KO:K07375]
104688233  VPS39; vam6/Vps39-like protein isoform X1 [KO:K20183]
104688244  TLR4; toll-like receptor 4 [KO:K10160]
104688249  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
104688395  GAPVD1; GTPase-activating protein and VPS9 domain-containing protein 1 isoform X1 [KO:K27566]
104688445  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
104688460  DNM1; dynamin-1 isoform X1 [KO:K01528] [EC:3.6.5.5]
104688542  [KO:K10418]
104688543  [KO:K10418]
104688681  HVCN1; voltage-gated hydrogen channel 1 [KO:K22644]
104688729  ATP6V0A2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
104688736  SCARB1; scavenger receptor class B member 1 isoform X1 [KO:K13885]
104688828  VPS33A; vacuolar protein sorting-associated protein 33A [KO:K20182]
104688833  DYNC1H1; cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
104688898  VPS41; vacuolar protein sorting-associated protein 41 homolog isoform X3 [KO:K20184]
104688920  SEC61G; protein transport protein Sec61 subunit gamma [KO:K07342]
104688978  ACTR10; actin-related protein 10 [KO:K16576]
104689019  PIK3R4; phosphoinositide 3-kinase regulatory subunit 4 isoform X1 [KO:K08333] [EC:2.7.11.1]
104689064  RAB5A; ras-related protein Rab-5A [KO:K07887]
104689211  [KO:K06560]
104689212  [KO:K06560]
104689213  [KO:K06560]
104689214  [KO:K06560]
104689215  [KO:K06560]
104689291  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
104689331  DYNC1I1; cytoplasmic dynein 1 intermediate chain 1 isoform X1 [KO:K10415]
104689503  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
104689569  DCTN4; dynactin subunit 4 isoform X1 [KO:K10426]
104689588  CANX; calnexin [KO:K08054]
104689725  SYK; tyrosine-protein kinase SYK isoform X1 [KO:K05855] [EC:2.7.10.2]
104689821  DYNLT1; dynein light chain Tctex-type 1 [KO:K10420]
104690111  DYNC2H1; cytoplasmic dynein 2 heavy chain 1 isoform X1 [KO:K10414]
104690216  [KO:K10067]
104690217  SFTPD; pulmonary surfactant-associated protein D [KO:K10067]
104690270  M6PR; LOW QUALITY PROTEIN: cation-dependent mannose-6-phosphate receptor [KO:K10089]
104690391  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
104690495  ATG12; ubiquitin-like protein ATG12 [KO:K08336]
104690588  STX7; syntaxin-7 [KO:K08488]
104690679  [KO:K10169]
104690680  [KO:K05398]
104690908  STX18; syntaxin-18 [KO:K08492]
104690978  DYNLL2; dynein light chain 2, cytoplasmic isoform X1 [KO:K10418]
104691078  RABGEF1; rab5 GDP/GTP exchange factor isoform X1 [KO:K20131]
104691212  [KO:K13883]
104691594  VAMP7; vesicle-associated membrane protein 7 [KO:K08515]
104691757  ATG5; autophagy protein 5 isoform X5 [KO:K08339]
104691774  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104691915  MAP1LC3B; microtubule-associated proteins 1A/1B light chain 3B [KO:K10435]
104691940  TUBB3; tubulin beta-3 chain [KO:K07375]
104691966  GABARAPL2; gamma-aminobutyric acid receptor-associated protein-like 2 [KO:K08341]
104692009  CTSL; procathepsin L [KO:K01365] [EC:3.4.22.15]
104692160  VPS11; vacuolar protein sorting-associated protein 11 homolog [KO:K20179]
104692248  ATP6V1E1; V-type proton ATPase subunit E 1 [KO:K02150]
104692253  TUBA8; tubulin alpha-8 chain [KO:K07374]
104692360  RAB7B; ras-related protein Rab-7b isoform X1 [KO:K07898]
104692444  LYZ; lysozyme C [KO:K13915] [EC:3.2.1.17]
104692452  [KO:K07374]
104692504  [KO:K04011]
104692705  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
104692772  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
104693012  TCIRG1; V-type proton ATPase 116 kDa subunit a3 [KO:K02154]
104693039  PIK3CB; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform isoform X1 [KO:K00922] [EC:2.7.1.153]
104693042  [KO:K13504]
104693270  VAMP3; vesicle-associated membrane protein 3 [KO:K13505]
104693336  PIK3CD; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform [KO:K00922] [EC:2.7.1.153]
104693619  NCF2; neutrophil cytosol factor 2 isoform X4 [KO:K08010]
104693720  ITGAV; integrin alpha-V [KO:K06487]
104693795  MAP1LC3C; microtubule-associated proteins 1A/1B light chain 3C [KO:K10435]
104693820  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase isoform X4 [KO:K00921] [EC:2.7.1.150]
104693881  DYNC1I2; cytoplasmic dynein 1 intermediate chain 2 isoform X1 [KO:K10415]
104693936  PLA2R1; secretory phospholipase A2 receptor isoform X2 [KO:K06560]
104693949  [KO:K07374]
104694025  ITGB5; integrin beta-5 [KO:K06588]
104694053  MARCO; macrophage receptor MARCO isoform X2 [KO:K13884]
104694434  LAMP2; LOW QUALITY PROTEIN: lysosome-associated membrane glycoprotein 2 [KO:K06528]
104694482  ATG4A; cysteine protease ATG4A isoform X2 [KO:K08342] [EC:3.4.22.-]
104694503  SEC61A2; protein transport protein Sec61 subunit alpha isoform X2 [KO:K10956]
104694819  PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 isoform X1 [KO:K00914] [EC:2.7.1.137]
104694843  ATP6V1B2; LOW QUALITY PROTEIN: V-type proton ATPase subunit B, brain isoform [KO:K02147]
104695038  NOS1; nitric oxide synthase, brain isoform X1 [KO:K13240] [EC:1.14.13.39]
104695141  ATG4C; cysteine protease ATG4C [KO:K08342] [EC:3.4.22.-]
104695234  [KO:K02649]
104695263  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104695413  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
104695448  DNM3; dynamin-3 isoform X1 [KO:K01528] [EC:3.6.5.5]
104695601  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
104695637  ACTR1A; alpha-centractin [KO:K16575]
104695692  THBS4; thrombospondin-4 [KO:K04659]
104695749  ATG7; ubiquitin-like modifier-activating enzyme ATG7 isoform X2 [KO:K08337]
104695773  NCF1; neutrophil cytosol factor 1 isoform X1 [KO:K08011]
104695782  [KO:K10789] [EC:1.11.2.2]
104695807  [KO:K10789] [EC:1.11.2.2]
104695968  TUBAL3; tubulin alpha chain-like 3 [KO:K07374]
104696137  GABARAPL1; gamma-aminobutyric acid receptor-associated protein-like 1 [KO:K08341]
104696215  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
104696285  NCF4; neutrophil cytosol factor 4 isoform X2 [KO:K08012]
104696295  RAC2; ras-related C3 botulinum toxin substrate 2 [KO:K07860]
104696453  EEA1; early endosome antigen 1 isoform X1 [KO:K12478]
104696748  ATG4B; cysteine protease ATG4B [KO:K08342] [EC:3.4.22.-]
104696836  DCTN6; dynactin subunit 6 [KO:K10428]
104696872  CTSB; LOW QUALITY PROTEIN: cathepsin B [KO:K01363] [EC:3.4.22.1]
104696977  PIK3R2; phosphatidylinositol 3-kinase regulatory subunit beta [KO:K02649]
104696999  [KO:K01319] [EC:3.4.21.20]
104697168  TLR2; toll-like receptor 2 [KO:K10159]
104697387  [KO:K04659]
104697759  RAB5C; ras-related protein Rab-5C [KO:K07889]
104697763  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
104697768  BECN1; beclin-1 isoform X1 [KO:K08334]
104697786  [KO:K01319] [EC:3.4.21.20]
104697907  [KO:K02153]
104698230  HGS; hepatocyte growth factor-regulated tyrosine kinase substrate isoform X1 [KO:K12182]
104698247  ITGB2; integrin beta-2 [KO:K06464]
104698338  VPS18; vacuolar protein sorting-associated protein 18 homolog [KO:K20181]
104698445  CFTR; cystic fibrosis transmembrane conductance regulator [KO:K05031] [EC:5.6.1.6]
104698488  MRC2; C-type mannose receptor 2 isoform X1 [KO:K06560]
104698490  ITGB3; integrin beta-3 isoform X1 [KO:K06493]
104698589  ALPL; alkaline phosphatase, tissue-nonspecific isozyme isoform X1 [KO:K01077] [EC:3.1.3.1]
109144626  [KO:K26936]
120409612  [KO:K10159]
120409623  TUBB4B; tubulin beta-4B chain [KO:K07375]
120409897  ALB; albumin [KO:K16141]
120410287  [KO:K07374]
120410609  [KO:K08009]
120410965  ACTG1; LOW QUALITY PROTEIN: actin, cytoplasmic 2 [KO:K05692]
120411068  [KO:K25374]
120411927  ATP6V1F; V-type proton ATPase subunit F [KO:K02151]
120412065  [KO:K05653] [EC:7.4.2.14]
120412070  [KO:K05654] [EC:7.4.2.14]
120412174  [KO:K06752]
120412176  [KO:K06751]
120412238  DNM2; dynamin-2 isoform X1 [KO:K23484]
120412241  ATG4D; cysteine protease ATG4D [KO:K08342] [EC:3.4.22.-]
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
Reference
PMID:40590685
  Authors
Depierre M, Pompili C, Niedergang F
  Title
Phagocytosis at a glance.
  Journal
J Cell Sci 138:368455 (2025)
DOI:10.1242/jcs.263833
Reference
PMID:32854338
  Authors
Lee HJ, Woo Y, Hahn TW, Jung YM, Jung YJ
  Title
Formation and Maturation of the Phagosome: A Key Mechanism in Innate Immunity against Intracellular Bacterial Infection.
  Journal
Microorganisms 8:microorganisms8091298 (2020)
DOI:10.3390/microorganisms8091298
Reference
PMID:30787029
  Authors
Heckmann BL, Green DR
  Title
LC3-associated phagocytosis at a glance.
  Journal
J Cell Sci 132:132/5/jcs222984 (2019)
DOI:10.1242/jcs.222984
Reference
PMID:36014984
  Authors
Yuan J, Zhang Q, Chen S, Yan M, Yue L
  Title
LC3-Associated Phagocytosis in Bacterial Infection.
  Journal
Pathogens 11:pathogens11080863 (2022)
DOI:10.3390/pathogens11080863
Reference
PMID:36288309
  Authors
Pena-Martinez C, Rickman AD, Heckmann BL
  Title
Beyond autophagy: LC3-associated phagocytosis and endocytosis.
  Journal
Sci Adv 8:eabn1702 (2022)
DOI:10.1126/sciadv.abn1702
Reference
PMID:33683814
  Authors
Othman A, Sekheri M, Filep JG
  Title
Roles of neutrophil granule proteins in orchestrating inflammation and immunity.
  Journal
FEBS J 289:3932-3953 (2022)
DOI:10.1111/febs.15803
Reference
PMID:29515456
  Authors
Rosales C
  Title
Neutrophil: A Cell with Many Roles in Inflammation or Several Cell Types?
  Journal
Front Physiol 9:113 (2018)
DOI:10.3389/fphys.2018.00113
Reference
PMID:36440666
  Authors
Naish E, Wood AJ, Stewart AP, Routledge M, Morris AC, Chilvers ER, Lodge KM
  Title
The formation and function of the neutrophil phagosome.
  Journal
Immunol Rev 314:158-180 (2023)
DOI:10.1111/imr.13173
Reference
PMID:39674879
  Authors
Skubitz KM
  Title
The role of CEACAMs in neutrophil function.
  Journal
Eur J Clin Invest 54 Suppl 2:e14349 (2024)
DOI:10.1111/eci.14349
Reference
PMID:25703560
  Authors
Weiss G, Schaible UE
  Title
Macrophage defense mechanisms against intracellular bacteria.
  Journal
Immunol Rev 264:182-203 (2015)
DOI:10.1111/imr.12266
Reference
PMID:36804685
  Authors
Cruz FM, Chan A, Rock KL
  Title
Pathways of MHC I cross-presentation of exogenous antigens.
  Journal
Semin Immunol 66:101729 (2023)
DOI:10.1016/j.smim.2023.101729
Related
pathway
ccw04142  Lysosome biogenesis
ccw04144  Endocytosis
ccw04148  Efferocytosis
ccw04620  Toll-like receptor signaling pathway
KO pathway
ko04145   

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