1.B.17 The Outer Membrane Factor (OMF) Family

Proteins of the OMF family (Li et al., 2001; Wong et al., 2001) function in conjunction with a primary cytoplasmic membrane transporter of the MFS (TC #2.A.1) (Pao et al., 1998), the ABC superfamily (TC #3.A.1) (Saurin et al., 1999), the RND superfamily (TC #2.A.6) (Tseng et al., 1999) and the PET family (TC #9.B.4) (Harley and Saier, 2000) as well as a membrane fusion protein (MFP; TC #8.A.1) (Dinh et al., 1994). The complex thus formed allows transport (export) of various solutes (heavy metal cations; drugs, oligosaccharides, proteins, etc.) across the two envelopes of the Gram-negative bacterial cell envelope in a single energy-coupled step. The OMF proteins probably form homotrimeric 12 stranded β-barrel-type pores in the outer membrane through which the solutes pumped out of the cytoplasm or cytoplasmic membrane pass in response to the energy-coupled export process catalyzed by the cytoplasmic membrane permease. In one case, the complex of primary transporter, MFP and OMF forms transiently in response to substrate binding (Létoffé et al., 1996). In another case involving AcrA (RND superfamily 8.A.1.6.1) and TolC (1.B.17.1.1), the interaction appears to be substrate independent (Husain et al., 2004).

The Serratia marcescens hemophore is secreted by a type I secretion system consisting of three proteins: a membrane ABC protein, an adaptor protein, and the TolC-like outer membrane factor (Cescau et al., 2007). Assembly of these proteins is induced by substrate binding to the ABC protein. A hemophore mutant lacking the last 14 C-terminal amino acids is not secreted but rather interacts with the ABC protein and promotes a stable multiprotein complex. Strains expressing the transporter and the mutant protein are sensitive to detergents (sodium dodecyl sulfate [SDS]). TolC is trapped in the transporter, jammed by the truncated substrate, and therefore is not present at sufficient concentrations to allow the efflux pumps to expel detergents. Using an SDS sensitivity assay, the hemophore proved to interact with the ABC protein via two nonoverlapping sites. The C-terminal peptide, which functions as an intramolecular signal sequence in the complete substrate, may have intermolecular activity and trigger complex dissociation (Cescau et al., 2007).

The crystal structure of E. coli TolC has been solved to 2.1 Å resolution (Koronakis et al., 1997, 2000), and the VceC homologue of Vibrio cholerae has been solved to 1.8 Å resolution (Federici et al., 2005). Three TolC protomers form a continuous, solvent-accessible conduit, a channel tunnel over 140 Å long that spans both the outer membrane (as 12 β-strands, 4 each per protomer) and the periplasmic space (as 12 α-helices, 6 continuous, 6 discontinuous, 4 each protomer). The α-helices are continuous with the β-strands. The periplasmic end of the tunnel is sealed by sets of coiled helices that might untwist upon contact with the primary permease to open the channel (Andersen et al., 2001; Koronakis et al., 2001). 3-d structures of sequential open states in a symmetrical opening transition of the TolC of E. coli exit duct have been identified (Pei et al., 2011).

The OMFs exhibit a preudosymmetrical structure due to the presence of two internally duplicated segments. Thus, the outer membrane β-barrel is assembled from the three protomers with each one contributing 4 β-strands. Each strand is between 10 and 13 residues long. The strands both curve and twist, yielding a superhelical structure, but the channel is wide open and fully accessible to solvent. The possibility of channel closure due to conformational mobility has not been excluded (Koronakis et al., 2000). The results clearly suggest that the OMF (and not the MFP) is largely responsible for the formation of both the trans-outer membrane and trans-periplasmic channels. The roles played by the MFP have yet to be determined.

OMF family members are found in most classes of proteobacteria in cyanobacteria, spirochetes, and in species of Deinococcus, Aquafex and Porphyromonas. The proteins are of 347-541 aas in length and are exported to the outer membrane via the general secretory pathway (GSP) TC#3.A.5.

A two-receptor model for colicin E1 (ColE1) translocation across the outer membrane of Escherichia coli has been proposed (Masi et al., 2007). ColE1 initially binds to the vitamin B12 receptor BtuB and then translocates through the TolC channel-tunnel, presumably in a mostly unfolded state. In the early events in the import of ColE1, cleavage of colicin requires the presence of the receptor BtuB and the protease OmpT, but not that of TolC. Strains expressing OmpT cleaved ColE1 at K84 and K95 in the N-terminal translocation domain, leading to the removal of the TolQA box, which is essential for ColE1's cytotoxicity. Thus, OmpT degrades colicin at the cell surface to protect sensitive E. coli cells. Secondary binding of ColE1 to TolC depends on primary binding to BtuB, and alterations to residues in the TolC channel can interfere with the translocation of ColE1 but not binding of ColE1 to TolC (Masi et al., 2007).



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

 

References:

Andersen, C., C. Hughes and V. Koronakis (2001). Protein export and drug efflux through bacterial channel-tunnels. Curr. Opin. Cell Biol. 13: 412-416.

Bhat, S., X. Zhu, R.P. Patel, R. Orlando, and L.J. Shimkets. (2011). Identification and localization of Myxococcus xanthus porins and lipoproteins. PLoS One 6: e27475.

Binet, R., S. Létoffé, J.M. Ghigo, P. Delepelaire and C. Wandersman (1997). Protein secretion by Gram-negative bacterial ABC exporters–a review. Gene 192: 7-11.

Bleuel, C., C. Grosse, N. Taudte, J. Scherer, D. Wesenberg, G.J. Krauss, D.H. Nies, and G. Grass. (2005). TolC is involved in enterobactin efflux across the outer membrane of Escherichia coli. J. Bacteriol. 187: 6701-6707.

Cescau, S., L. Debarbieux, and C.J. Wandersman. (2007). Probing the in vivo dynamics of type I protein secretion complex association through sensitivity to detergents. Bacteriol. 189: 1496-1504.

Cosme, A.M., A. Becker, M.R. Santos, L.A. Sharypova, P.M. Santos, and L.M. Moreira. (2008). The outer membrane protein TolC from Sinorhizobium meliloti affects protein secretion, polysaccharide biosynthesis, antimicrobial resistance, and symbiosis. Mol. Plant Microbe Interact. 21: 947-957.

Crosby, J.A. and S.C. Kachlany. (2007). TdeA, a TolC-like protein required for toxin and drug export in Aggregatibacter (Actinobacillus) actinomycetemcomitans. Gene 388: 83-92.

Dinh, T., I.T. Paulsen and M.H. Saier, Jr. (1994). A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of Gram-negative bacteria. J. Bacteriol. 176: 3825-3831.

Federici, L., D. Du, F. Walas, H. Matsumura, J. Fernandez-Recio, K.S. McKeegan, M.I. Borges-Walmsley, B.F. Luisi, and A.R. Walmsley. (2005). The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 Å resolution. J. Biol. Chem. 280: 15307-15314.

Gimmestad M., M. Steigedal, H. Ertesvag, S. Moreno, B.E. Christensen, G. Espin, and S. Valla. (2006). Identification and characterization of an Azotobacter vinelandii Type I secretion system responsible for export of the AlgE-Type Mannuronan C-5-Epimerase. J. of Bacteriol. 188(15):5551-5560.

Guan, H.H., M. Yoshimura, P. Chuankhayan, C.C. Lin, N.C. Chen, M.C. Yang, A. Ismail, H.K. Fun, and C.J. Chen. (2015). Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism. Sci Rep 5: 16441.

Gupta, A., K. Matsui, J.-F. Lo and S. Silver (1999). Molecular basis for resistance to silver cations in Salmonella. Nature Med. 5: 183-188.

Hahn, A., M. Stevanovic, O. Mirus, and E. Schleiff. (2012). The TolC-like protein HgdD of the cyanobacterium Anabaena sp. PCC 7120 is involved in secondary metabolite export and antibiotic resistance. J. Biol. Chem. 287: 41126-41138.

Harley, K.T. and M.H. Saier, Jr. (2000). A novel ubiquitous family of putative efflux transporters. J. Mol. Microbiol. Biotechnol. 2: 195-198.

Hernández-Mendoza, A., N. Nava, O. Santana, C. Abreu-Goodger, A. Tovar, and C. Quinto. (2007). Diminished redundancy of outer membrane factor proteins in rhizobiales: a nodT homolog is essential for free-living Rhizobium etli. J. Mol. Microbiol. Biotechnol. 13: 22-34.

Husain, F., M. Humbard, and R. Misra. (2004). Interaction between the TolC and AcrA proteins of a multidrug efflux system of Escherichia coli. J. Bacteriol. 186: 8533-8536.

Koronakis, V., A. Sharff, E. Koronakis, B. Luisi, and C. Hughes. (2000). Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405: 914-919.

Koronakis, V., C. Andersen and C. Hughes (2001). Channel-tunnels. Curr. Opin. Struct. Biol. 11: 403-407.

Koronakis, V., J. Li, E. Koronakis and K. Stauffer (1997). Structure of TolC, the outer membrane component of the bacterial type I efflux system, derived from two-dimensional crystals. Mol. Microbiol. 23: 617-626.

Lei HT., Bolla JR., Bishop NR., Su CC. and Yu EW. (2014). Crystal structures of CusC review conformational changes accompanying folding and transmembrane channel formation. J Mol Biol. 426(2):403-11.

Létoffé, S., P. Delepelaire and C. Wandersman (1996). Protein secretion in Gram-negative bacteria: assembly of the three components of ABC protein-mediated exporters is ordered and promoted by substrate binding. EMBO J. 15: 5804-5811.

Li, X.Z. and K. Poole (2001). Mutational analysis of the OprM outer membrane component of the MexA-MexB-OprM multidrug efflux system of Pseudomonas aeruginosa. J. Bacteriol. 183: 12-27.

Masi, M., P. Vuong, M. Humbard, K. Malone, and R. Misra. (2007). Initial steps of colicin E1 import across the outer membrane of Escherichia coli. J. Bacteriol. 189: 2667-2676.

Munson, G.P., D.L. Lam, F.W. Outten and T.V. O'Halloran (2000). Identification of a copper-responsive two-component system on the chromosome of Escherichia coli K-12. J. Bacteriol. 182: 5864-5871.

Paulsen, I.T., J.H. Park, P.S. Choi and M.H. Saier, Jr. (1997). A family of Gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from Gram-negative bacteria. FEMS Microbiol. Lett. 156: 1-8.

Paulsen, I.T., M.H. Brown and R.A. Skurray (1996). Proton-dependent multidrug efflux systems. Microbiol. Revs. 60: 575-608.

Pei, X.Y., P. Hinchliffe, M.F. Symmons, E. Koronakis, R. Benz, C. Hughes, and V. Koronakis. (2011). Structures of sequential open states in a symmetrical opening transition of the TolC exit duct. Proc. Natl. Acad. Sci. USA 108: 2112-2117.

Polleichtner, G., C. Anderson. (2006). The channel-tunnel HI1462 of Haemophilus influenzae reveals differences to Escherichia coli TolC. Microbiology 152: 1639-1647.

Sulavik, M.C., C. Houseweart, C. Cramer, N. Jiwani, N. Murgolo, J. Greene, B. DiDomenico, K.J. Shaw, G.H. Miller, R. Hare, and G. Shimer. (2001). Antibiotic susceptibility profiles of Escherichia coli strains lacking multidrug efflux pump genes. Antimicrob. Agents Chemother. 45: 1126-1136.

Tseng, T.-T., K.S. Gratwick, J. Kollman, D. Park, D.H. Nies, A. Goffeau and M.H. Saier, Jr. (1999). The RND permease superfamily: an ancient, ubiquitous and diverse familly that includes human disease and development proteins. J. Mol. Microbiol. Biotechnol. 1: 107-125.

Wong, K.K., F.S. Brinkman, R.S. Benz and R.E. Hancock (2001). Evaluation of a structural model of Pseudomonas aeruginosa outer membrane protein OprM, an efflux component involved in intrinsic antibiotic resistance. J. Bacteriol. 183: 367-374.

Examples:

TC#NameOrganismal TypeExample
1.B.17.1.1

TolC outer membrane exporter of hemolysin, drugs, siderophores such as enterobactin, etc. (Bleuel et al., 2005). The 3-d structure is available (PDB#1EK9). The three monomers form a continuous channel, and each monomer contributes 4 β-strands to the 12 stranded β-barrel (Koronakis et al. 2000). The Salmonella enterica subspecies Typhi homologue is the ST50 antigen (G4C2H4) used in tests for typhoid fever, and a 2.98 Å resolution structure revealed a trimer that forms an alpha-helical tunnel and a beta-barrel transmembrane channel traversing the periplasmic space and outer membrane, respectively (Guan et al. 2015).

Gram-negative bacteria

TolC of E. coli

 
1.B.17.1.2PrtF outer membrane exporter of proteases Gram-negative bacteria PrtF of Erwinia chrysanthemi
 
1.B.17.1.3

The OMF, EexF (functions with ABC exporter, EexD (TC# 3.A.1.110.10) and MFP EexE (TC# 8.A.1.3.3)) (Gimmestad et al., 2006).

Gram-negative bacteria

EexF of Azotobacter vinelandii (C1DS86)

 
1.B.17.1.4TolC of Sinorhizobium meliloti (affects secretion of proteins, polysaccharide, and multiple drugs (Cosme et al., 2008))

Gram-negative bacteria

TolC of Sinorhizobium meliloti (Q92Q38)

 
1.B.17.1.5

Putative outer membrane factor of 420 aas

Chlamydiae

Outer membrane factor of Parachlamydia acanthamoebae

 
1.B.17.1.6

Uncharacterized protein of 425 aas with an N-terminal TMS.

UP of Bdellovibrio exovorus

 
1.B.17.1.7

Outer membrane protein of 462 aas and 1 N-terminal TMS

OMP of Bdellovibrio bacteriovorus

 
Examples:

TC#NameOrganismal TypeExample
1.B.17.2.1

CnrC outer membrane exporter of Ni2+ and Co2+.  Functions with TC# 2.A.6.1.1 and 8.A.1.2.1.

Gram-negative bacteria

CnrC of Alcaligenes eutrophus

 
1.B.17.2.10

Putative ABC-type glycolipid export outer membrane factor, HgdD, of 483 aas (Hahn et al., 2012).

Cyanobacteria

HgdD of Thermosynechococcus sp. NK55a.

 
1.B.17.2.11

Uncharacterized OMF protein of 485 aas and 1 N-terminlal TMS.

UP of Bdellovibrio bacteriovorus

 
1.B.17.2.2

CzcC outer membrane exporter of Co2+, Cd2+, Zn2+.  Functions with CzcAB (2.A.6.1.2).

Gram-negative bacteria

CzcC of Alcaligenes eutrophus

 
1.B.17.2.3CyaE outer membrane exporter of cyclolysin Gram-negative bacteria CyaE of Bordetella pertussis
 
1.B.17.2.4

Outer membrane efflux protein of the OEP or OMF family

Proteobacteria

OEP of Myxococcus xanthus

 
1.B.17.2.5

Outer membrane efflux protein

Firmicute with outer membrane

Outer membrane efflux protein of Selenomonas sputigena

 
1.B.17.2.6

Outer membrane efflux porin, Oep

Proteobacteria

Oep of Myxococcus xanthus

 
1.B.17.2.7

Outer membrane efflux porin, Oep (OMF family)

Proteobacteria

Oep of Myxococcus xanthus

 
1.B.17.2.8

Outer membrane efflux porin (Bhat et al. 2011).

Proteobacteria

Oep of Myxococcus xanthus

 
1.B.17.2.9

Outer membrane efflux protein, Oep

Proteobacteria

Oep of Myxococcus xanthus

 
Examples:

TC#NameOrganismal TypeExample
1.B.17.3.1NodT2 outer membrane exporter of lipooligosaccharides Gram-negative bacteria NodT2 of Rhizobium leguminosarum
 
1.B.17.3.10

Outer membrane factor of 478 aas, MdtQ (YohG). Involved in resistance to puromycin, acriflavin and tetraphenylarsonium chloride (Sulavik et al. 2001).

Proteobacteria

MdtQ of E. coli

 
1.B.17.3.11

TolC-like outer membrane factor protein, TdeA of 457 aas, required for leukotoxin and drug export (Crosby and Kachlany 2007).  Functions with the MFP, LtxD (TC# 8.A.1.3.4) and the ABC exporter (TC# 3.A.1.109.8).

TdeA of Aggregatibacter (Actinobacillus; Haemophilus) actinomycetemcomitans

 
1.B.17.3.12

The OMR, SilC, of 490 aas. Francisella tularensis, the causative agent of tularemia, contains three paralogs of OMRs, two, termed as TolC and FtlC, are important for tularemia pathogenesis. The third OM protein SilC, is homologous to the silver cation efflux protein of other bacteria. SilC is encoded in an operon encoding an Emr-type multi-drug efflux pump of F. tularensis. A ΔsilC mutant exhibited increased sensitivity towards antibiotics, oxidants and silver as well as diminished intramacrophage growth and attenuated virulence in mice.

SilC of Francisella tularensis

 
1.B.17.3.2FusA outer membrane exporter of fusaric acid Gram-negative bacteria FusA of Burkholderia cepacia
 
1.B.17.3.3OpcM outer membrane exporter of multiple drugs Gram-negative bacteria OpcM of Burkholderia cepacia
 
1.B.17.3.4SilC outer membrane exporter of silver ion, Ag+ Gram-negative bacteria SilC of Salmonella typhimurium
 
1.B.17.3.5

CusC outer membrane exporter of copper ion, Cu+, and silver ion Ag+.  The crystal structure of CusC is known (Lei et al. 2013) providing evidnce concerning the folding mechanism giving rise to the channel.

Gram-negative bacteria

CusC (YlcB) of E. coli

 
1.B.17.3.6VceC outer membrane exporter of drugs (Federici et al., 2005)

Gram-negative bacteria

VceC of Vibrio cholerae (A6XV56)

 
1.B.17.3.7HI1462 outer membrane, low conductance, anion-selective exporter (selectivity is due to an arginine residue at the tunnel entrance). (Polleichtner and Anderson, 2006)Gram-negative bacteriaHI1462 of Haemophilus influenzae (P45217)
 
1.B.17.3.8

Chromosomal NodTch (orthologous to 1.B.17.3.1) (478 aas) required for cell survival (Hernandez-Mendoza et al., 2007).

Gram-negative bacteria

NodTch of Rhizobium etli (B3PY75)

 
1.B.17.3.9

MdtP (acts with MdtO (TC# 2.A.85.6.1) and MdtN (TC# 8.A.1.1.3)) (Sulavik et al., 2001).

Gram-negative bacteria

MdtP of E. coli (P32714)

 
Examples:

TC#NameOrganismal TypeExample
1.B.17.4.1

Outer membrane factor of 459 aas.  May function with an ABC exporter (A0LKG3/A0LKG4) and a membrane fusion protein (A0LKG1) (based on genomic context).

Aquificae

OMF of Syntrophobacter fumaroxidans