1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family

The Secretin family consists of a group of Gram-negative bacterial outer membrane proteins that form multimeric pores through which macromolecules, usually proteins, but also filamentous phage can be secreted (Bitter et al., 1998; Cornelis et al., 1998; Hu et al., 1998; Korotkov et al. 2011). These proteins form homomultimeric ring structures, with large central pores (inner diameters of ~5 nm). The pores are plugged, and consequently conductance through secretin pores is minimal. Two secretins, PilQ of Neisseria meningitidis, and PulD of Klebsiella oxytoca are dodecamers with 12 or 14 identical subunits arranged in a ring (Collins et al., 2001, 2003; Linderoth et al., 1997). Secretin phylogeny has been studied by Nguyen et al. (2000) and Clock et al. (2008).  At least some secretins are constitutively in a partially open state (Disconzi et al. 2014).

Secretins are large proteins (420-750 amino acyl residues) consisting of two domains: an N-terminal periplasmic domain (the first 280 residues of XcpQ) and a C-terminal 'homology' domain that is embedded in the outer membrane (residues 283-568 in XcpQ). The C-terminal 'homology' domains of secretins are exclusively responsible for channel formation (Brok et al., 1999) but also includes the central disc and the plug (Chami et al., 2005). The C-domain penetrates both the peptidoglycan on the periplasmic side and the lipopolysaccharide and capsule layers on the cell surface (Chami et al., 2005). A C-terminal S-domain interacts with pilotin, a protein that facilitates secretin targeting to the outer membrane. Secretin subunits, containing multiple domains, interact with numerous other proteins, including secretion-system partner proteins and exoproteins. Features common to all secretins include a cylindrical arrangement of 12-15 subunits, a large periplasmic vestibule with a wide opening at one end and a periplasmic gate at the other (Korotkov et al., 2011).

Secretins function in type II protein secretion (TC #3.5; McLaughlin et al. 2012) (e.g., PulD of Klebsiella oxytoca), type III protein secretion (TC #3.6) (e.g., the hypersensitivity response secretin (HrpH) of Pseudomonas syringiae and the invasion protein secretin (InvG) of Salmonella typhimurium), competence (competence protein E (ComE) of Haemophilus influenzae), fimbrial protein export and assembly (e.g., the fimbrial assembly protein (PilQ) of Pseudomonas aeruginosa), phage assembly (e.g., the gene IV protein of bacteriophage f1), and filamentous phage secretion (Linderoth et al., 1997; Martinez et al., 1998; Nguyen et al., 2000). In Vibrio cholerae, the secretin of the type III secretion system, EpsD, which exports cholera toxin, also exports the filamentous phage, CTXQ, the genome of which encodes cholera toxin (Davis et al., 2000; Marciano et al., 1999). Filamentous phage are secreted and assembled with coat proteins simultaneously. The enteropathogenic E. coli secretin, BfpB, exports pilin subunits and several EPEC proteins, and renders cells sensitive to the antibiotic, vancomycin (Schmidt et al., 2001). Secretins are also found in TC Family 9.A.47 (The Tight Adherens (Pilus) Biogenesis Apparatus)). 

The PilQ DNA competence secretin complex (3.A.11.1.3) is 15 nm wide and 34 nm long and consists of a stable 'cone' and 'cup' five ring structure with a large central channel (Burkhardt et al., 2011). The individual rings are formed by conserved domains of alternating α-helices and β-sheets. The PilQ complex spans the entire cell periphery of T. thermophilus, consistent with the hypothesis that PilQ accommodates a PilA4 comprising pseudopilus, mediating DNA transport across the outer membrane and periplasmic space in a single-step process (Burkhardt et al., 2011).



This family belongs to the Outer Membrane Pore-forming Protein (OMPP) Superfamily I.

 

References:

Assalkhou, R., S. Balasingham, R.F. Collins, S.A. Frye, T. Davidsen, A.V. Benam, M. Bjørås, J.P. Derrick, and T. Tønjum. (2007). The outer membrane secretin PilQ from Neisseria meningitidis binds DNA. Microbiology 153: 1593-1603.

Bitter, W., M. Koster, M. Latijnhouwers, H. de Cock, and J. Tommassen. (1998). Formation of oligomeric rings by XcpQ and PilQ, which are involved in protein transport across the outer membrane of Pseudomonas aeruginosa. Mol. Microbiol. 27: 209-219.

Brok, R., P. Van Gelder, M. Winterhalter, U. Ziese, A.J. Koster, H. de Cock, M. Koster, J. Tommassen, and W. Bitter. (1999). The C-terminal domain of the Pseudomonas secretin XcpQ forms oligomeric rings with pore activity. J. Mol. Biol. 294: 1169-1179.

Chami, M., Guilvout, I., Gregorini, M., Remigy, H.W., Muller, S.A., Valerio, M., Engel, A., Pugsley, A.P., and Bayan, N. (2005). Structural insights into the secretin PulD and its trypsin-resistant core. J. Biol. Chem. 280: 37732-37741.

Clock, S.A., P.J. Planet, B.A. Perez, and D.H. Figurski. (2008). Outer membrane components of the Tad (tight adherence) secreton of Aggregatibacter actinomycetemcomitans. J. Bacteriol. 190: 980-990.

Collins, R.F., L. Davidsen, J.P. Derrick, R.C. Ford, and T. Tønjum. (2001). Analysis of the PilQ secretin from Neisseria meningitidis by transmission electron microscopy reveals a dodecameric quaternary structure. J. Bacteriol. 183: 3825-3832.

Collins, R.F., R.C. Ford, A. Kitmitto, R.O. Olsen, T. Tønjum, and J.P. Derrick. (2003). Three-dimensional structure of the Neisseria meningitidis secretin PilQ determined from negative-stain transmission electron microscopy. J. Bacteriol. 185: 2611-2617.

Cornelis, G.R., A. Boland, A.P. Boyd, C. Geuijen, M. Iriarte, C. Neyt, M.-P. Sory, and I. Stainier. (1998). The virulence plasmid of Yersinia, an antihost genome. Microbiol. Mol. Biol. Rev. 62: 1315-1352.

Davis, B.M., E.H. Lawson, M. Sandkvist, A. Ali, S. Sozhamannan, and M. Waldor. (2000). Convergence of the secretory pathways for cholera toxin and the filamentous phage, CTXφ. Science 288: 333-335.

Disconzi, E., I. Guilvout, M. Chami, M. Masi, G.H. Huysmans, A.P. Pugsley, and N. Bayan. (2014). Bacterial secretins form constitutively open pores akin to general porins. J. Bacteriol. 196: 121-128.

Hu, N.-T., M.-N. Hung, D.C. Chen, and R.-T. Tsai. (1998). Insertion mutagenesis of XpsD, an outer-membrane protein involved in extracellular protein secretion in Xanthomonas campestris pv. campestris. Microbiology 144: 1479-1486.

Korotkov, K.V., J.R. Delarosa, and W.G. Hol. (2013). A dodecameric ring-like structure of the N0 domain of the type II secretin from enterotoxigenic Escherichia coli. J Struct Biol 183: 354-362.

Korotkov, K.V., T. Gonen, and W.G. Hol. (2011). Secretins: dynamic channels for protein transport across membranes. Trends. Biochem. Sci. 36: 433-443.

Lieberman, J.A., C.D. Petro, S. Thomas, A. Yang, and M.S. Donnenberg. (2015). Type IV Pilus Secretins Have Extracellular C Termini. MBio 6:.

Linderoth, N.A., M.N. Simon, and M. Russel. (1997). The filamentous phage pIV multimer visualized by scanning transmission electron microscopy. Science. 278: 1635-1638.

Marciano, D.K., M. Russel, and S.M. Simon. (1999). An aqueous channel for filamentous phage export. Science 284: 1516-1519.

Martínez, A., P. Ostrovsky, and D.N. Nunn. (1998). Identification of an additional member of the secretin superfamily of proteins in Pseudomonas aeruginosa that is able to function in type II protein secretion. Mol. Microbiol. 28: 1235-1246.

McLaughlin, L.S., R.J. Haft, and K.T. Forest. (2012). Structural insights into the Type II secretion nanomachine. Curr. Opin. Struct. Biol. 22: 208-216.

Nguyen, L., I.T. Paulsen, J. Tchieu, C.J. Hueck, and M.H. Saier, Jr. (2000). Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnol. 2: 125-144.

Schmidt, S.A., D. Bieber, S.W. Ramer, J. Hwang, C.-Y. Wu, and G. Schoolnik. (2001). Structure-function analysis of BfpB, a secretin-like protein encoded by the bundle-forming-pilus operon of enteropathogenic Escherichia coli. J. Bacteriol. 183: 4848-4859.

Sun, D., X. Zhang, L. Wang, M. Prudhomme, Z. Xie, B. Martin, and J.P. Claverys. (2009). Transforming DNA uptake gene orthologs do not mediate spontaneous plasmid transformation in Escherichia coli. J. Bacteriol. 191: 713-719.

Tarry, M., M. Jääskeläinen, A. Paino, H. Tuominen, R. Ihalin, and M. Högbom. (2011). The extra-membranous domains of the competence protein HofQ show DNA binding, flexibility and a shared fold with type I KH domains. J. Mol. Biol. 409: 642-653.

Thanassi, D.G. (2002). Ushers and secretins: channels for the section of folded proteins across the bacterial outer membrane. J. Mol. Micobiol. Biotechnol. 4: 11-20.

Trindade, M.B., V. Job, C. Contreras-Martel, V. Pelicic, and A. Dessen. (2008). Structure of a widely conserved type IV pilus biogenesis factor that affects the stability of secretin multimers. J. Mol. Biol. 378: 1031-1039.

Tønjum, T., D.A. Caugant, S.A. Dunham, and M. Koomey. (1998). Structure and function of repetitive sequence elements associated with a highly polymorphic domain of the Neisseria meningitidis PilQ protein. Mol. Microbiol. 29: 111-124.

Wall, D., P.E. Kolenbrander, and D. Kaiser. (1999). The Myxococcus xanthus pilQ (sglA) gene encodes a secretin homolog required for type IV pilus biogenesis, social motility, and development. J. Bacteriol. 181: 24-33.

Yan, Z., M. Yin, D. Xu, Y. Zhu, and X. Li. (2017). Structural insights into the secretin translocation channel in the type II secretion system. Nat Struct Mol Biol 24: 177-183.

Examples:

TC#NameOrganismal TypeExample
1.B.22.1.1

PulD protein secretin.  Involved in protein secretion via the Type II MTB system (TC# 3.A.15).  PulD allows the efflux of small fluorescent molecules with a permeation cutoff similar to that of general porins and is constitutively open (Disconzi et al. 2014).

Gram-negative bacteria

PulD of Klebsiella oxytoca

 
1.B.22.1.2XcpQ secretin protein Gram-negative bacteria XcpQ of Pseudomonas aeruginosa
 
1.B.22.1.3

The dodecameric secretin, GspD of 650 aas.  The 3-d structure is known (PDB 5WQ8) (Korotkov et al. 2013).  It reveals a double β-barrel channel with about 60 β-strands in each barrel (Yan et al. 2017).

GspD of E. coli

 
Examples:

TC#NameOrganismal TypeExample
1.B.22.2.1PilQ fimbrial subunit secretin Gram-negative bacteria PilQ of Pseudomonas aeruginosa
 
1.B.22.2.2

The Type IV pilus biogenesis/competence secretin precursor, PilQ (may serve as a pore for (1) pilus export, (2) DNA uptake, (3) heme uptake, (4) antimicrobial uptake (Tønjum et al., 1998); Binds DNA (Assalkhou et al., 2007); Structure known to 12 Å resolution (Collins et al., 2004) The pilus biogenesis factor, PilW (ABX73034) facilitates formation and/or stability of secretin (PilQ) multimers. The 3-D structure of PilW is known (Trindade et al., 2008).

Gram-negative bacteria

PilQ of Neisseria meningitidis (Q9ZHF3)

 
1.B.22.2.3

Fimbrial usher, HofQ of 760 aas

Chlamydiae

HofQ of Chlamydia trachomatis

 
1.B.22.2.4

The secretin, PilQ (SglA) of 901 aas, required for pilus biogenesis, social motility and development of fruiting bodies (Wall et al. 1999).

Proteobacteria

PilQ of Myxococcus xanthus

 
Examples:

TC#NameOrganismal TypeExample
1.B.22.3.1HrpH hypersensitivity response secretin Gram-negative bacteria HrpH of Pseudomonas syringae
 
1.B.22.3.2InvG invasion protein secretin Gram-negative bacteria InvG of Salmonella typhimurium
 
1.B.22.3.3YscC secretin Gram-negative bacteria YscC of Yersinia enterocolitica
 
Examples:

TC#NameOrganismal TypeExample
1.B.22.4.1ComE competence protein secretin Gram-negative bacteria ComE of Haemophilus influenzae
 
1.B.22.4.2

HofQ, may facilitate double stranded DNA uptake in E. coli (Sun et al., 2009).

Gram-negative Bacteria

HofQ of E. coli (Q1R5P6)

 
1.B.22.4.3

HofQ competence protein, the outer membrane DNA translocase (Tarry et al., 2011). The 2.3Å structures of the extramembraneous domains are known (Tarry et al., 2011).

Bacteria

HofQ of Aggregatibacter actinomycetemcomitans (C6ALC5)

 
Examples:

TC#NameOrganismal TypeExample
1.B.22.5.1Gene IV protein secretin Gram-negative bacteria Gene IV protein of bacteriophage f1
 
1.B.22.5.2

Putative pilus assembly transmembrane protein of 509 aas, PilQ.

PilQ of Bdellovibrio bacteriovorus

 
Examples:

TC#NameOrganismal TypeExample
1.B.22.6.1NolW secretin Gram-negative bacteria NolW of Rhizobium spp.
 
Examples:

TC#NameOrganismal TypeExample
1.B.22.7.1

Bundle-forming pilus-B (BfpB) secretin (catalyzes export of pilins and EPEC proteins; uptake of vancomycin). (BfpB complex formation requires BfpG, 113 aas; gbBAA84839).  While the N-terminus is periplasmic, the C-terminus is extracelllular. BfpB may form a beta barrel with 16 transmembrane beta strands with a C-terminal segment passing through the center of each monomer (Lieberman et al. 2015).

Proteobacteria

BfpB of enteropathogenic E. coli