A genetic engineering approach to study the mode of assembly of the OmpF porin in the envelope of E coli

Computational prediction of extracellular loops of the Por39 outer membrane porin of Rhodospirillum rubrum suitable for epitope surface display

Outer membrane porins from Gram-negative bacteria are established vehicles for the production of vaccines. Typically, one or more of the extracellular loops of a porin are replaced by a peptide encoding a foreign epitope, and recombinant porin is then used as a vaccine. However, many host strains are potentially pathogenic, and also produce toxic lipopolysaccharide (LPS), both of which are undesirable for safety reasons. In contrast, the outer membrane porins from photosynthetic, purple bacteria have no known human pathology and produce only weakly toxic LPS. The purple bacterium Rhodospirillum rubrum is well-suited for large-scale biotechnology, and expresses a major porin, Por39, which is a candidate for a vaccine platform. Unfortunately, the atomic structure of Por39 could not be determined so far, and Por39 shows only a weak homology to other porins of known structure, making the assignment of external loops difficult. Here, we construct a knowledge-based model of Por39 using secondary structure constraints from both the low sequence homology to the 2POR porin from Rhodobacter capsulatus, for which the X-ray structure is known, as well as those obtained using secondary structure prediction packages. The secondary structure predictions were used to constrain a three-dimensional model created using the I-TASSER package. The modelling procedure was validated by predicting the structure of 2POR using the same strategy, but excluding the 2POR X-ray structure from the I-TASSER database. The final Por39 model allows three external loops to be defined precisely, and could also be used to obtain an initial model for the closely related Por41 using molecular modelling. These structures provide a good starting point for the insertion of epitopes with vaccine potential.

The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli

The lipoprotein Lpp is the most numerically abundant protein in Escherichia coli, has been investigated for over 40 years, and has served as the paradigmatic bacterial lipoprotein since its initial discovery. It exists in two distinct forms: a 'bound-form', which is covalently bound to the cell's peptidoglycan layer, and a 'free-form', which is not. Although it is known that the carboxyl-terminus of bound-form Lpp is located in the periplasm, the precise location of free-form Lpp has never been determined. For decades, it has been widely assumed that free-form Lpp is associated with bound-form. In this work, we show that the free and bound forms of Lpp are not largely associated with each other, but are found in distinct subcellular locations. Our results indicate that free-form Lpp spans the outer membrane and is surface-exposed, whereas bound-form Lpp resides in the periplasm. Thus, Lpp represents a novel example of a single lipoprotein that is able to occupy distinct subcellular locations, and challenges models in which the free and bound forms of Lpp are assumed to be associated with each other.

Membrane assembly of the Escherichia coli outer membrane protein OmpA: exploring sequence constraints on transmembrane beta-strands

The eight-stranded antiparallel beta-barrel domain of the OmpA protein from Escherichia coli serves as a paradigm for the study of membrane assembly of integral beta-structured membrane proteins. Previous studies have shown that neither the periplasmic turns nor the surface-exposed loops contain topogenic information. Consequently, the question of whether any structural constraint is imposed onto individual transmembrane beta-strands is now addressed. To this end, amino acid sequences of beta-strands 4, 6 and 8 were randomized. In vivo membrane assembly of mutant proteins was assayed and 288 variants were sequenced. Three parameters were found to be important for efficient membrane assembly. (i) At least four of five randomized residues with side-chains pointing towards the lipid bilayer must be hydrophobic and none of the three central residues must be charged. (ii) Side-chains pointing into the beta-barrel interior must not be enlarged too much, possibly because of packing constraints. (iii) Proline residues are, in general, hardly tolerated in the transmembrane beta-strands.

Specific regions of Escherichia coli OmpF protein involved in antigenic and colicin receptor sites and in stable trimerization

Four different mutations were obtained by selecting for resistance to colicin N and screening for continued production of the OmpF protein of Escherichia coli. Two of them also conferred resistance to colicin A. The substitutions C for R-168 (R168C) and E284K caused the loss of the E21 epitope, while the transition G285D altered the E18, E19, and E20 antigenic sites. The substitution G119D drastically affected the stability of the trimeric conformation.

Dynamics of the exposure of epitopes on OmpF, an outer membrane protein of Escherichia coli

The OmpF protein is the major outer membrane trimeric porin of Escherichia coli B. The exposure of several cell-surface-exposed epitopes, that are recognized by various monoclonal antibodies directed against the protein, is investigated. Kinetic analyses show that two epitopes (E18 and E19) appear early during the in-vivo assembly on the folded monomer, just after the removal of the signal peptide, and are conserved in the native trimer. The trimerization that immediately follows or occurs in conjunction with the folding of monomers exposes another antigenic site (E21) at the surface of metastable forms. The binding of nascent lipopolysaccharide promotes the conversion of the heat-modifiable intermediate to a stable trimer and ensures the exposure of E20, E1, E3, E4 and E7. Late epitopes, E1, E3, E4 and E7 are only detected in the outer membrane fraction. These results suggest that different steps induce the sequential exposure of native antigenic sites. The detection of these epitopes depends on conformational changes occurring during the OmpF insertion into the outer membrane.