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Table 2 The actin-centered core of the phagocytosis machinery: components of actin filaments and proteins involved in filament remodelinga

From: The origins of phagocytosis and eukaryogenesis

Protein family; a representative (GI)

Detection in proteomic studies (number of species, out of 5 studied)

Role in phagocytosis

Domain architecture (with CDD IDs)band structural features (N-C)c

Range of orthologs in eukaryotes

Prokaryotic homologs

References

Actin

66826069

4 (except for Tetrahymena)

Actin filament rearrangement is the universal mechanical basis for phagosome formation

Actin (cd00012)

All eukaryotes

A group of Crenarchaeal-Korarchaeal proteins are the closest prokaryotic orthologs of actins; MreB, FtsA, ParM, MamK and their euryarchaeal homologs (Ta0583) are distant prokaryotic homologs (see main text for details).

[24, 74]

[113]

Actin-related protein 2/3 (ARP2/3) complex – 7 subunits

Actin-related protein 2 (ARP2) 4093161

1(Entamoeba)

Enables branching of actin filaments by providing new nucleation sites for G-actin. Arp2/3 complex is essential for apparently all known types of phagocytosis (not documented in Ciliata)

Actin (cd00012)

All eukaryotes except for Diplomonadida

Same as for actins

[44, 118]

Actin-related protein 3 (ARP3) 60467470

3 (except for Tetrahymena and Entamoeba)

 

Actin (cd00012)

All eukaryotes except for Diplomonadida

  

ARP complex(ARPC) protein 1

(p41-Arc)

66816255

2 (Drosophila and Entamoeba)

 

WD40 domain (cl02567)

All eukaryotes except for Diplomonadida and Chlorophyta

No orthologs but proteins containing WD40 domains are common in bacteria, particularly, those with complex signal transduction systems.

 

ARPC2

(p34-Arc) 60467975

0

 

p34-Arc (pfam04045)

All eukaryotes except for Diplomonadida and Apicomplexa

none

 

ARPC3

(p21-Arc)

50344884

1(Entamoeba)

 

p21-Arc (pfam04062)

All eukaryotes except for Diplomonadida and Apicomplexa

none

 

ARPC4

(p20-Arc) 115495705

2 (mouse and Entamoeba)

 

ARPC4 (pfam05856)

All eukaryotes except for Diplomonadida

None

 

ARPC5

(p16-Arc) 66806101

0

 

p16-Arc (pfam04699)

absent in Diplomonadida, Apicomplexa, Chlorophyta, Choanoflagellida, and Ciliophora

None

 

WASp (Wiskott-Aldrich syndrome protein) 10880935

0 Entamoeba proteome contained RickA protein, acting as WASp (167383163)

Actin assembly factor, activates the Arp2/3 complex

WH1-irregular superhelix

(proline-rich; cd01205)

WH1 is a derived plekstrin homology (PH) domain

Cdc42/Rac interactive binding (CRIB) motif (cd00132)

All animals and fungi, Monosiga, Dictyostelium, Entamoeba, ciliates, Trichomonas; missing in plants

None

PH-fold is, largely, specific to eukaryotes. Some pathogenic bacteria have proteins that mimics WASp: RickA (168824102, Rickettsia raoultii), ActA (58500210, Listeria seeligeri).

[73, 78, 79, 119]

WAVE1/SCAR1 66809177

1 (Drosophila)

Actin assembly factor, activates the Arp2/3 complex

WH1-unstructured

(proline-rich)

Paralog of WASp, diverged variant of WH1 domain

All animals and plants, Dictyostelium, Monosiga, Trichomonas

None

[83, 87, 89]

Profilin

730406

3 (except for Tetrahymena and Dictyostelium)

Regulator of actin polymerization, stoichiometric complex with actin, activator of WASP and SCAR (binds to their prolin-rich regions), lipid-binding

Profilin domain (cd00148)

All eukaryotes with the apparent exception of Diplomonadida

No orthologs.

Profilin-like fold found in PAS and GAF signaling domains that are common in bacteria, and Roadblock/LC7 domain that is present in bacteria and some archaea, and interacts with small GTPases

[8486, 88]

Formin 158518557

3 (except for Tetrahymena and Dictyostelium)

nucleates the formation of linear actin filaments

Globular -unstructured proline-rich -FH2 (formin homology)

Multiple paralogs, apparently, in all eukaryotes except for Diplomonadida

None

FH2 is a unique fold restricted to eukaryotes

[36, 82]

Cofilin/ADF 3182971

4 (except for Tetrahymena)

reversibly controls actin polymerization and depolymerization

Cofilin domain

cd00013, ADF, Actin depolymerisation factor/cofilin -like domains

Multiple paralogs, apparently, in all eukaryotes except for Diplomonadida

A homolog only in Streptomyces (112791749), probable HGT

[80]

Coronin

11023

2 (mouse and Dictyostelium)

associates with the Arp2p/Arp3p complex to regulate its activity

WD40 (cl02567)

Apparently, single orthologs in all eukaryotes except for Diplomonadida, green algae, plants

No orthologs but numerous WD40-domain proteins are present, primarily, in bacteria with complex signal transduction systems

[21, 81, 90]

alpha-actinin

60474969

3 (except for Tetrahymena and Dictyostelium). An actin cross-linker cortexillin (ctxA, 66804885) is found on Dictyostelium phagosome.

cross-links actin filaments; involved in membrane anchoring actin filaments.

CH-SPEC-EF-hands

(actin-binding domain composed of two calponin homology (CH) domains (cd00014); spectrin repeats (SPEC, cd00176); EF-hand, calcium-binding domain (cd00051)

Animals, fungi, amoebozoa, Monosiga, Trichomonas, oomycetes; in plants, green alga, Ciliata, Apicomplexa, Kinetoplastida, Diplomonada have other EF-hand family proteins

No orthologs or homologs with high similarity but many bacteria encode EF-hand-containing proteins (e.g., 148256632)

[91, 100, 103]

Filamin/ABP120

121115

3 (except for Tetrahymena and Dictyostelium). An actin cross-linker cortexillin (ctxA, 66804885) is found on Dictyostelium phagosome.

Cross-links actin filaments

Actin-binding domain composed of two CH domains (cd00014); Filamin/ABP280 repeats (cl02665)

Animals and amoebozoa; others eukaryotes have non-orthologous EF-hand family proteins;

plants have multiple CH domain proteins

None

[99, 103]

  1. aOnly proteins whose role in phagocytosis was characterized in detail are included.
  2. bThe domain identifier from the Conserved Domain Database [96] is given in parentheses.
  3. cThe domains are listed from the N-terminus to the C-terminus of the respective protein.