KEGG   PATHWAY: nnt04145
Entry
nnt04145                    Pathway                                
Name
Phagocytosis - Nestor notabilis (Kea)
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
nnt04145  Phagocytosis
nnt04145

Other DBs
GO: 0006909
Organism
Nestor notabilis (Kea) [GN:nnt]
Gene
104399045  VPS11; vacuolar protein sorting-associated protein 11 homolog [KO:K20179]
104399183  DCTN4; dynactin subunit 4 isoform X1 [KO:K10426]
104399203  CALR3; calreticulin-3 [KO:K08057]
104399255  [KO:K05398]
104399409  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
104399438  PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 [KO:K00914] [EC:2.7.1.137]
104399557  PIK3CB; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform isoform X1 [KO:K00922] [EC:2.7.1.153]
104399563  DCTN3; dynactin subunit 3 [KO:K10425]
104399570  ITGB5; integrin beta-5 [KO:K06588]
104399687  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
104399765  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
104399808  [KO:K27045]
104399828  [KO:K13504]
104399922  CANX; calnexin isoform X1 [KO:K08054]
104400010  ITGAV; integrin alpha-V [KO:K06487]
104400079  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104400125  STX18; syntaxin-18 [KO:K08492]
104400129  THBS1; thrombospondin-1 [KO:K16857]
104400314  STX12; syntaxin-12 [KO:K13813]
104400335  DYNLRB1; dynein light chain roadblock-type 1 [KO:K10419]
104400377  DYNC1LI1; cytoplasmic dynein 1 light intermediate chain 1 [KO:K10416]
104400382  MON1A; vacuolar fusion protein MON1 homolog A isoform X1 [KO:K20195]
104400412  CD36; platelet glycoprotein 4 isoform X1 [KO:K06259]
104400489  [KO:K13505]
104400510  [KO:K01365] [EC:3.4.22.15]
104400538  [KO:K05719]
104400723  DCTN6; dynactin subunit 6 [KO:K10428]
104400756  SNAP23; synaptosomal-associated protein 23 isoform X1 [KO:K08508]
104400760  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
104400769  RAB7A; ras-related protein Rab-7a [KO:K07897] [EC:3.6.5.2]
104400817  DYNLT1; dynein light chain Tctex-type 1 [KO:K10420]
104400851  [KO:K04392]
104400885  PIK3R4; phosphoinositide 3-kinase regulatory subunit 4 [KO:K08333] [EC:2.7.11.1]
104400940  RAB5A; ras-related protein Rab-5A isoform X1 [KO:K07887]
104401036  [KO:K05692]
104401058  [KO:K07374]
104401093  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
104401127  [KO:K10418]
104401143  [KO:K10418]
104401150  TLR2; toll-like receptor 2 [KO:K10159]
104401215  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
104401220  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
104401392  GABARAPL2; gamma-aminobutyric acid receptor-associated protein-like 2 [KO:K08341]
104401445  TIMD4; T-cell immunoglobulin and mucin domain-containing protein 4 [KO:K26936]
104401671  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
104401858  [KO:K10435]
104401879  HGS; hepatocyte growth factor-regulated tyrosine kinase substrate [KO:K12182]
104402183  [KO:K07374]
104402339  [KO:K07374]
104402369  VPS18; vacuolar protein sorting-associated protein 18 homolog [KO:K20181]
104402393  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
104402481  DYNC1LI2; cytoplasmic dynein 1 light intermediate chain 2 [KO:K10416]
104402619  BECN1; beclin-1 [KO:K08334]
104402868  [KO:K06563]
104403155  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
104403243  [KO:K07375]
104403482  [KO:K20174]
104403579  PIK3R3; phosphatidylinositol 3-kinase regulatory subunit gamma [KO:K02649]
104403655  RAB27A; ras-related protein Rab-27A [KO:K07885]
104403961  OSBPL2; oxysterol-binding protein-related protein 2 isoform X1 [KO:K20174]
104404236  [KO:K04659]
104404243  ACTR10; actin-related protein 10 [KO:K16576]
104404248  [KO:K21421] [EC:1.-.-.-]
104404308  SEC22B; vesicle-trafficking protein SEC22b [KO:K08517]
104404492  PIK3CD; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform [KO:K00922] [EC:2.7.1.153]
104404581  HVCN1; voltage-gated hydrogen channel 1 [KO:K22644]
104404829  NOS1; nitric oxide synthase, brain isoform X1 [KO:K13240] [EC:1.14.13.39]
104405064  THBS4; thrombospondin-4 [KO:K04659]
104405382  [KO:K13915] [EC:3.2.1.17]
104405561  ITGB2; integrin beta-2 [KO:K06464]
104405657  NCF1; neutrophil cytosol factor 1 [KO:K08011]
104405736  TUBB1; tubulin beta-1 chain isoform X1 [KO:K07375]
104405778  [KO:K05692]
104405840  ALPL; alkaline phosphatase, tissue-nonspecific isozyme [KO:K01077] [EC:3.1.3.1]
104405857  [KO:K10435]
104405963  TLR4; toll-like receptor 4 [KO:K10160]
104405987  [KO:K25374]
104406174  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
104406179  DYNC2LI1; cytoplasmic dynein 2 light intermediate chain 1 [KO:K10417]
104406385  [KO:K02146]
104406387  COLEC12; collectin-12 [KO:K10062]
104406422  KIAA0226; run domain Beclin-1 interacting and cysteine-rich containing protein [KO:K19330]
104406923  [KO:K06751]
104406940  PIKFYVE; 1-phosphatidylinositol 3-phosphate 5-kinase [KO:K00921] [EC:2.7.1.150]
104407103  MARCO; macrophage receptor MARCO [KO:K13884]
104407111  [KO:K10789] [EC:1.11.2.2]
104407185  VPS41; vacuolar protein sorting-associated protein 41 homolog isoform X1 [KO:K20184]
104407200  ALPI; intestinal-type alkaline phosphatase [KO:K01077] [EC:3.1.3.1]
104407202  [KO:K01077] [EC:3.1.3.1]
104407403  NCF4; neutrophil cytosol factor 4 [KO:K08012]
104407499  [KO:K16141]
104407536  NCF2; neutrophil cytosol factor 2 [KO:K08010]
104407705  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
104407921  DYNLT3; dynein light chain Tctex-type 3 [KO:K10420]
104408284  DNM1; dynamin-1 [KO:K01528] [EC:3.6.5.5]
104408311  [KO:K07374]
104408312  TUBAL3; tubulin alpha chain-like 3 [KO:K07374]
104408329  DCTN5; dynactin subunit 5 [KO:K10427]
104408395  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
104408510  PIK3CA; LOW QUALITY PROTEIN: phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform [KO:K00922] [EC:2.7.1.153]
104408622  MAP1LC3A; microtubule-associated proteins 1A/1B light chain 3A [KO:K10435]
104408748  STX7; syntaxin-7 [KO:K08488]
104408795  VPS39; vam6/Vps39-like protein [KO:K20183]
104408863  [KO:K21249]
104408884  COMP; cartilage oligomeric matrix protein [KO:K04659]
104408966  TUBB6; tubulin beta-6 chain [KO:K07375]
104409045  ATP6V1C1; V-type proton ATPase subunit C 1 isoform X1 [KO:K02148]
104409204  ATG5; autophagy protein 5 isoform X1 [KO:K08339]
104409358  THBS2; thrombospondin-2 [KO:K04659]
104409361  CTSS; cathepsin S isoform X1 [KO:K01368] [EC:3.4.22.27]
104409362  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
104409431  ATG16L1; autophagy-related protein 16-1 isoform X1 [KO:K17890]
104409470  COLEC11; collectin-11 isoform X1 [KO:K10066]
104409570  ATG7; ubiquitin-like modifier-activating enzyme ATG7 [KO:K08337]
104409589  CFTR; cystic fibrosis transmembrane conductance regulator [KO:K05031] [EC:5.6.1.6]
104409766  ATG4A; cysteine protease ATG4A [KO:K08342] [EC:3.4.22.-]
104409865  [KO:K10415]
104410000  RAB5C; ras-related protein Rab-5C isoform X1 [KO:K07889]
104410133  ATG3; ubiquitin-like-conjugating enzyme ATG3 [KO:K08343]
104410207  ATP6V1C2; V-type proton ATPase subunit C 2 [KO:K02148]
104410319  [KO:K10104]
104410325  ITGA2; integrin alpha-2 [KO:K06481]
104410515  DYNC1I2; cytoplasmic dynein 1 intermediate chain 2 isoform X1 [KO:K10415]
104410602  SEC61G; protein transport protein Sec61 subunit gamma [KO:K07342]
104410689  SCARB1; scavenger receptor class B member 1 [KO:K13885]
104410743  [KO:K10956]
104410804  RAB7B; ras-related protein Rab-7b [KO:K07898]
104410866  PIK3R1; phosphatidylinositol 3-kinase regulatory subunit alpha isoform X1 [KO:K02649]
104410905  ITGB3; integrin beta-3 [KO:K06493]
104410999  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
104411272  GAPVD1; GTPase-activating protein and VPS9 domain-containing protein 1 isoform X1 [KO:K27566]
104411289  EEA1; early endosome antigen 1 [KO:K12478]
104411307  VPS33A; vacuolar protein sorting-associated protein 33A [KO:K20182]
104411333  MRC1; macrophage mannose receptor 1 [KO:K06560]
104411334  [KO:K06560]
104411335  [KO:K06560]
104411336  [KO:K06560]
104411337  [KO:K06560]
104411346  [KO:K10067]
104411347  [KO:K10067]
104411348  [KO:K03991]
104411564  DYNC1H1; cytoplasmic dynein 1 heavy chain 1 [KO:K10413]
104411587  [KO:K10418]
104411865  [KO:K08341]
104411991  DYNLRB2; dynein light chain roadblock-type 2 [KO:K10419]
104412074  ATG4B; cysteine protease ATG4B [KO:K08342] [EC:3.4.22.-]
104412111  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
104412119  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104412147  MMP9; LOW QUALITY PROTEIN: matrix metalloproteinase-9 [KO:K01403] [EC:3.4.24.35]
104412189  ATP6V1E1; V-type proton ATPase subunit E 1 isoform X1 [KO:K02150]
104412202  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
104412405  RAC2; ras-related C3 botulinum toxin substrate 2 [KO:K07860]
104412504  DCTN2; LOW QUALITY PROTEIN: dynactin subunit 2 [KO:K10424]
104412605  ACTR1A; alpha-centractin [KO:K16575]
104412631  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
104412653  ATG4C; cysteine protease ATG4C [KO:K08342] [EC:3.4.22.-]
104412796  [KO:K23484]
104413100  [KO:K10435]
104413102  C3; complement C3 [KO:K03990]
104413119  OSBPL1A; oxysterol-binding protein-related protein 1 isoform X1 [KO:K20174]
104413180  [KO:K02649]
104413202  MRC2; C-type mannose receptor 2 [KO:K06560]
104413246  RILP; rab-interacting lysosomal protein [KO:K13883]
104413393  VAMP7; vesicle-associated membrane protein 7 isoform X1 [KO:K08515]
104413423  RABGEF1; rab5 GDP/GTP exchange factor isoform X1 [KO:K20131]
104413459  SYK; LOW QUALITY PROTEIN: tyrosine-protein kinase SYK [KO:K05855] [EC:2.7.10.2]
104413539  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104413593  DNM3; dynamin-3 [KO:K01528] [EC:3.6.5.5]
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
nnt04142  Lysosome biogenesis
nnt04144  Endocytosis
nnt04148  Efferocytosis
nnt04620  Toll-like receptor signaling pathway
KO pathway
ko04145   

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