1.B.21 The OmpG Porin (OmpG) Family

The OmpG family consists of two distantly related functionally characterized E. coli proteins, OmpG and OmpL. The OmpG channel appears to be much larger than the E. coli OmpC or OmpF channels (estimated limited diameter of about 2 nm) (Fajardo et al., 1998). The channel lacks solute specificity, and a folding model suggests a 16-stranded β-barrel porin lacking the large external loop, L3, that constricts the pores in other porins. However, Liang and Tamm (2007) found a 14-stranded β-barrel based on NMR analyses. OmpG has been reconstituted in planar bilayers where it exhibits uniform sized channels. Results suggested that OmpG forms a monomeric rather than the usual trimeric porin (Conlan et al., 2000).  The pH-gating conformations of the beta-barrel have been solved. When the pH changes from neutral to acidic, the flexible extracellular loop L6 folds into and closes the OmpG pore (Damaghi et al. 2010).

Voltage-induced closure occurred in a single step, and channel block by Gd3+ lacked cooperativity seen with trimeric porin OmpF. Incorporation of OmpG into lipid membranes revealing protein-lipid interactions and β-barrel orientation, as sudied by Anbazhagan et al. (2008). OmpG has been intensively studied using physical approaches, providing data on its possible structure and biogenesis (Damaghi et al., 2010; Korkmaz-Ozkan et al., 2010). Refolding pathways of the sequential β-hairpins and kinetics of OmpG folding have been reported (Damaghi et al., 2011).

OmpL has been purified and reconstituted. It allowed diffusion of small solutes including sugars (Dartigalongue et al., 2000). Contrary to an earlier report, it does not influence Dsb-mediated redox potential in the periplasm (Sardesai et al., 2003). The OmpG family is related to the Cyclodextrin Porin (CDP; 1.B.26) and the Oligogalacturonate Porin (KdgM; 1.B.35) families (Condemine et al., 2005). 

β-barrel porins have potential as nanosensors for single-molecule detection. However, they have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. By replacing beta1-beta6 strands of the protein OmpF that lack these motifs with beta1-beta6 strands of OmpG enriched with these motifs and computational verification of increased stability of its transmembrane region, Lin et al. 2017 engineered a novel porin called OmpGF. OmpGF forms a monomer with a stable transmembrane region. It can refold in vitro with a predominant beta-sheet structure, as confirmed by circular dichroism. Evidence of OmpGF membrane insertion was provided by intrinsic tryptophan fluorescence spectroscopy, and its pore-forming property was determined by a dye-leakage assay. Single-channel conductance measurements confirmed that OmpGF function as a monomer and exhibits increased conductance relative to OmpG or OmpF (Lin et al. 2017).

OmpG of E. coli is a robust, monomeric, transmembrane β-barrel without ion selectivity. Kahlstatt et al. 2018 presented a photocaged diethylaminocoumarin (DEACM) hybrid of OmpG. Blockage of the pore by DEACM was confirmed by measuring the reduced conductivity. An optimal effect was obtained when two bulky butyl-substituted coumarin cages were attached on the inside of the pore. Irradiation at 385 nm removed the photocages, leading to a restoration of channel conductivity (Kahlstatt et al. 2018).



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

 

References:

Anbazhagan, V., J. Qu, J.H. Kleinschmidt, and D. Marsh. (2008). Incorporation of outer membrane protein OmpG in lipid membranes: protein-lipid interactions and β-barrel orientation. Biochemistry 47: 6189-6198.

Condemine, G., C. Berrier, J. Plumbridge, and A. Ghazi. (2005). Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli. J. Bacteriol. 187: 1959-1965.

Conlan, S., Y. Zhang, S. Cheley, and H. Bayley. (2000). Biochemical and biophysical characterization of OmpG: A monomeric porin. Biochemistry 39: 11845-11854.

Damaghi, M., C. Bippes, S. Köster, O. Yildiz, S.A. Mari, W. Kühlbrandt, and D.J. Muller. (2010). pH-dependent interactions guide the folding and gate the transmembrane pore of the β-barrel membrane protein OmpG. J. Mol. Biol. 397: 878-882.

Damaghi, M., K.T. Sapra, S. Köster, &.#.2.1.4.;. Yildiz, W. Kühlbrandt, and D.J. Muller. (2010). Dual energy landscape: the functional state of the β-barrel outer membrane protein G molds its unfolding energy landscape. Proteomics 10: 4151-4162.

Damaghi, M., S. Köster, C.A. Bippes, O. Yildiz, and D.J. Müller. (2011). One β hairpin follows the other: exploring refolding pathways and kinetics of the transmembrane β-barrel protein OmpG. Angew Chem Int Ed Engl 50: 7422-7424.

Dartigalongue, C., H. Nikaido, and S. Raina. (2000). Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox poential in periplasmic space via OmpL porin. EMBO J. 19: 5980-5988.

Fajardo, D.A., J. Cheung, C. Ito, E. Sugawara, H. Nikaido, and R. Misra. (1998). Biochemistry and regulation of a novel Escherichia coli K-12 porin protein, OmpG, which produces unusually large channels. J. Bacteriol. 180: 4452-4459.

Freeman, T.C., Jr, S.J. Landry, and W.C. Wimley. (2011). The prediction and characterization of YshA, an unknown outer-membrane protein from Salmonella typhimurium. Biochim. Biophys. Acta. 1808: 287-297.

Grosse, W., G. Psakis, B. Mertins, P. Reiss, D. Windisch, F. Brademann, J. Bürck, A. Ulrich, U. Koert, and L.O. Essen. (2014). Structure-based engineering of a minimal porin reveals loop-independent channel closure. Biochemistry 53: 4826-4838.

Kahlstatt, J., , P. Reiß, , T. Halbritter, , L.O. Essen, , U. Koert, , and A. Heckel,. (2018). A light-triggered transmembrane porin. Chem Commun (Camb) 54: 9623-9626.

Korkmaz, F., K. van Pee, and &.#.2.1.4.;. Yildiz. (2015). IR-spectroscopic characterization of an elongated OmpG mutant. Arch Biochem Biophys 576: 73-79.

Korkmaz-Ozkan, F., S. Köster, W. Kühlbrandt, W. Mäntele, and O. Yildiz. (2010). Correlation between the OmpG secondary structure and its pH-dependent alterations monitored by FTIR. J. Mol. Biol. 401: 56-67.

Köster, S., K. van Pee, and &.#.2.1.4.;. Yildiz. (2015). Purification, Refolding, and Crystallization of the Outer Membrane Protein OmpG from Escherichia coli. Methods Enzymol 557: 149-166.

Liang, B., and L.K. Tamm. (2007). Structure of outer membrane protein G by solution NMR spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 104: 16140-16145.

Lin, M., G. Zhang, M. Fahie, L.K. Morgan, M. Chen, T.A. Keiderling, L.J. Kenney, and J. Liang. (2017). Engineering a novel porin OmpGF via strand replacement from computational analysis of sequence motif. Biochim. Biophys. Acta. [Epub: Ahead of Print]

Mari, S.A., S. Köster, C.A. Bippes, O. Yildiz, W. Kühlbrandt, and D.J. Muller. (2010). pH-induced conformational change of the β-barrel-forming protein OmpG reconstituted into native E. coli lipids. J. Mol. Biol. 396: 610-616.

Perez-Rathke, A., M.A. Fahie, C. Chisholm, J. Liang, and M. Chen. (2018). Mechanism of OmpG pH-Dependent Gating from Loop Ensemble and Single Channel Studies. J. Am. Chem. Soc. 140: 1105-1115.

Retel, J.S., A.J. Nieuwkoop, M. Hiller, V.A. Higman, E. Barbet-Massin, J. Stanek, L.B. Andreas, W.T. Franks, B.J. van Rossum, K.R. Vinothkumar, L. Handel, G.G. de Palma, B. Bardiaux, G. Pintacuda, L. Emsley, W. Kühlbrandt, and H. Oschkinat. (2017). Structure of outer membrane protein G in lipid bilayers. Nat Commun 8: 2073.

Sardesai, A.A., P. Genevaux, F. Schwager, D. Ang, and C. Georgopoulos. (2003). The OmpL porin does not modulate redox potential in the periplasmic space of Escherichia coli. EMBO J. 22: 1461-1466.

Shevchik, V.E. and N. Hugouvieux-Cotte-Pattat. (2003). PaeX, a second pectin acetylesterase of Erwinia chrysanthemi 3937. J. Bacteriol. 185: 3091-3100.

Utsunomia, C., C. Hori, K. Matsumoto, and S. Taguchi. (2017). Investigation of the Escherichia coli membrane transporters involved in the secretion of d-lactate-based oligomers by loss-of-function screening. J Biosci Bioeng 124: 635-640.

Examples:

TC#NameOrganismal TypeExample
1.B.21.1.1

Non-specific, 14 β-stranded monomeric OmpG porin (Conlan et al. 2000). pH-induced conformational changes of OmpG have been studied after reconstitution in native E. coli lipids (Mari et al., 2010).  Encoded by a gene in a gene cluster also encoding an ABC sugar uptake system (TC# 3.A.1.1.46), a glucosyl hydrolase and two oxidoreductases.  Therefore it's phsiological function may be glucoside uptake. At neutral/high pH, the channel is open and permeable to substrates of size up to 900Da. At acidic pH, loop L6 folds across the channel and blocks the pore. The channel blockage at acidic pH appears to be triggered by the protonation of a histidine pair on neighboring β-strands, which repel one another, resulting in the rearrangement of loop L6 and channel closure (Köster et al. 2015).  Crystallization and analysis by electron microscopy and X-ray crystallography revealed the fundamental mechanisms essential for the channel activity.  A 28 aa extension has been added to the 14 β-TMS barrel to make a 16 β-TMS barrel with normal activity and stability but differing pH sensitivity (Korkmaz et al. 2015). A minimized OmpG porin of only 220 aas still exhibits gating, but it was 5-fold less frequent than in native OmpG. The residual gating of the minimal pore is independent of L6 rearrangements and involves narrowing of the ion conductance pathway, most probably driven by global stretching-flexing deformations of the membrane-embedded β-barrel (Grosse et al. 2014).  pH-dependent gating is controlled by an electrostatic interaction network formed between the gating loop and charged residues in the lumen (Perez-Rathke et al. 2018). 3-d structures of the protein in lipid bilayers have been solved (Retel et al. 2017). OmpG may provide a route for D-lactate/D-3-hydroxybutyrate oligo-ester secretion (Utsunomia et al. 2017).

Proteobacteria

OmpG of E. coli

 
1.B.21.1.2

Putative porin

Fusobacteria

Putative porin of Fusobacterium mortiferum

 
1.B.21.1.3

Uncharacterized protein of 355 aas

Fusobacteria

UP of Sebaldella termitidis

 
Examples:

TC#NameOrganismal TypeExample
1.B.21.2.1

Putative porin

γ-Proteobacteria

Putative porin of E. coli

 
1.B.21.2.2

Putative porin of 361 aas

Proteobacteria

Putative porin of Providencia burhodogranariea

 
Examples:

TC#NameOrganismal TypeExample
1.B.21.3.1

Putative porin

Proteobacteria

Putative porin of Vibrio sinaloensis

 
1.B.21.3.2

Putative porin

γ-Proteobacteria

Putative porin of Vibrio harveyi

 
1.B.21.3.3

Putative porin

γ-Proteobacteria

Putative porin of Vibrio parahaemolyticus

 
Examples:

TC#NameOrganismal TypeExample