9.B.159 The Inclusion Membrane Protein (IncA) Family

The IncA family includes several proteins that are secreted via Type III Secretion Systems (TC# 3.A.6) in chlamydial species.  No member of this family has been identified with certainty outside of the Chlamydiae.  The proteins enterred into TCDB as IncA proteins usually have a 2 or 4 TMS topology but are in general not demonstrably homologous using TC BLAST.  They are very divergent in sequence, but they all belong to the IncA family of Pfam.  They may be related to mitochodrial Ca2+ uniporters and prokaryotic Mg2+ channels (TC# 1.A.77), and consequently, these IncA homologues may function as divalent cation channels (Lee et al. 2014). The N-terminal regions appear to be more similar than the remaining parts of the protein.  9.B.159.2.3 retrieves members of 7 sub-families including its own.

Inc proteins may assemble in the membrane of the inclusion (which separates the bacteria from the host cell cytoplasm) to form specific multi-molecular complexes (Gauliard et al. 2015).  IncA plays a critical role in both protecting the inclusion from lysosomal fusion and inducing the homotypic fusion of inclusions. Within IncA are two regions homologous to eukaryotic SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) domains referred to as SNARE-like domain 1 (SLD1) and SNARE-like domain 2 (SLD2). The functional core of IncA retains the ability to both inhibit SNARE-mediated fusion and promote the homotypic fusion of Chlamydia inclusions.This core region of 2 TMS proteins is composed almost entirely of α-helices and assembles into stable homodimers in solution (Ronzone et al. 2014).

Many intracellular bacteria, including Chlamydia, establish a parasitic membrane-bound organelle inside the host cell that is essential for the bacteria's survival. Chlamydia trachomatis forms inclusions that are decorated with poorly characterized membrane proteins known as Incs. The prototypical Inc, called IncA, enhances Chlamydia pathogenicity by promoting the homotypic fusion of inclusions and shares structural and functional similarity to eukaryotic SNAREs. Cingolani et al. 2019 presented the atomic structure of the cytoplasmic domain of IncA, which reveals a non-canonical four-helix bundle. Structure-based mutagenesis, molecular dynamics simulation, and functional cellular assays identified an intramolecular clamp that is essential for IncA-mediated homotypic membrane fusion during infection. Solithromycin (Sol) impedes homotypic fusion of Chlamydia-containing vacuoles and reduces secretion of the type III secretion (T3S) effector IncA (Gao et al. 2018).

VAMP3 and VAMP4 are eukaryotic SNARE proteins that mediate membrane fusion and are recruited to the inclusion to facilitate inclusion expansion (Bui et al. 2020). VAMPs 3 and 4 are probably recruited by Incs. In chlamydia-infected cells, five Incs temporally and transiently interact with VAMP3. Loss of incA or ct813 expression altered VAMP3 localization to the inclusion. Thus, these transient interactions likely contribute to the chlamydial developmental cycle (Bui et al. 2020).


 

References:

Bui, D.C., L.M. Jorgenson, S.P. Ouellette, and E.A. Rucks. (2020). EUKARYOTIC SNARE VAMP3 DYNAMICALLY INTERACTS WITH MULTIPLE CHLAMYDIAL INCLUSION MEMBRANE PROTEINS. Infect. Immun. [Epub: Ahead of Print]

Cingolani, G., M. McCauley, A. Lobley, A.J. Bryer, J. Wesolowski, D.L. Greco, R.K. Lokareddy, E. Ronzone, J.R. Perilla, and F. Paumet. (2019). Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA. Nat Commun 10: 2747.

Gao, L., Y. Wang, Z. Hua, E. Liu, and L. Shen. (2018). Potency of Solithromycin against Fast- and Slow-Growing Chlamydial Organisms. Antimicrob. Agents Chemother. 62:.

Gauliard, E., S.P. Ouellette, K.J. Rueden, and D. Ladant. (2015). Characterization of interactions between inclusion membrane proteins from Chlamydia trachomatis. Front Cell Infect Microbiol 5: 13.

Lee, A., A. Vastermark, and M.H. Saier, Jr. (2014). Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins. Microbiology 160: 1679-1689.

Ronzone, E., J. Wesolowski, L.D. Bauler, A. Bhardwaj, T. Hackstadt, and F. Paumet. (2014). An α-helical core encodes the dual functions of the chlamydial protein IncA. J. Biol. Chem. 289: 33469-33480.

Examples:

TC#NameOrganismal TypeExample
9.B.159.1.1

Inclusion membrane protein IncA of 585 aas and 4 TMSs in a 2 + 2 arrangement.

Chlamydiae

IncA of Chlamydia trachomatis

 
9.B.159.1.2

Uncharacterized protein of 516 aas and 4 TMSs in a 2 + 2 TMS arrangement.

UP of Chlamydia pecorum

 
9.B.159.1.3

Uncharacterized protein of 514 aas and 4 TMSs in a 2 + 2 TMS arrangement.

UP of Chlamydia pneumoniae

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.10.1

IncA homologue of 419 aas

Chlamydia

IncA homologue of Chlamydia pneumoniae

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.11.1

IncA homologue from Pfam of 252 aas.

Chlamyidiae

IncA homologue of Chlamydophila caviae

 
9.B.159.11.2

TMH family membrane protein of 187 aas and 2 TMSs.

TMH family protein of Chlamydia abortus

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.12.1

IncA of 264 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydia trachomatis

 
9.B.159.12.2

Uncharacterized protein of 215 aas and 2 TMSs.

UP of Chlamydia muridarum

 
Examples:

TC#NameOrganismal TypeExample
Examples:

TC#NameOrganismal TypeExample
Examples:

TC#NameOrganismal TypeExample
9.B.159.2.1

IncA protein of 215 aas and 2 TMSs

Chlamydiae

IncA of Chlamydia trachomatis

 
9.B.159.2.2

IncA of 129 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydia trachomatis

 
9.B.159.2.3

IncA of 210 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydia muridarum

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.3.1

IncA protein of 133 aas and 2 TMSs

Chlamydiae

IncA protein of Chlamydia trachomatis

 
9.B.159.3.2

Uncharacterized Inc homolog of 138 aas and 2 TMSs.

UP of Chlamydia muridarum

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.4.1

IncA protein from Pfam of 223 aas

Chlamyidiae

IncA homologue of Chlamydophila abortus

 
9.B.159.4.2

IncA of 258 aas and 2 TMSs

Chlamydiae

IncA of Chlamydia pecorum

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.5.1

IncA homologue of 238 aas

Chlamydia

IncA homologue of Chlamydia muridarum

 
9.B.159.5.2

IncA of 270 aas and 2 TMSs

Chlamidiae

IncA of Chlamydia trachomatis

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.6.1

IncA homologue from Pfam of 282 aas.

Chlamydiae

IncA homologue of Chlamydophila psittaci

 
9.B.159.6.2

IncA of 366 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydophila abortus

 
9.B.159.6.3

IncA of 397 aas and 2 TMSs

Chlamydiae

IncA of Chlamydia pneumoniae

 
9.B.159.6.4

IncA of 811 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydia pneumoniae (Chlamydophila pneumoniae)

 
9.B.159.6.5

IncA of 884 aas and 4 TMSs in a 2 + 2 arrangement where the two N-terminal repeats are very similar to each other.

Chlamydiae

IncA of Chlmaydia (Chlamydophila) pneumoniae

 
9.B.159.6.6

IncA of 223 aas and 2 TMSs

Chlamydiae

IncA of Chlamydia pneumophila

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.7.1

IncA homologue of 373 aas.

Chlamydiae

IncA homologue of Chlamydophila caviae

 
9.B.159.7.2

IncA of 257 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydophila abortus

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.8.1

IncA homologue of 372 aas

Chlamydiae

IncA homologue of Chlamydophila felis

 
9.B.159.8.2

Uncharacterized protein of 278 aas and 2 TMSs.

UP of Thermofilum sp. NZ13 (hot spring metagenome)

 
Examples:

TC#NameOrganismal TypeExample
9.B.159.9.1

IncA homologue of 372 aas

Chlamydiae

IncA homologue of Chlamydophila felis

 
9.B.159.9.2

IncA homologue of 355 aas

Chlamydiae

IncA homologue of Chlamydophila caviae

 
9.B.159.9.3

IncA of 328 aas and 2 TMSs.

Chlamydiae

IncA of Chlamydophila caviae

 
9.B.159.9.4

IncA of 856 aas and 2 N-terminal TMSs.

Chlamydiae

IncA of Chlamydophila felis