OmpA protein of Escherichia coli outer membrane occurs in open and closed channel forms

OprF functions as a latch to direct Outer Membrane Vesicle release in Pseudomonas aeruginosa

Bacterial Outer Membrane Vesicles (OMVs) contribute to virulence, competition, immune avoidance and communication. This has led to great interest in how they are formed. To date, investigation has focused almost exclusively on what controls the initiation of OMV biogenesis. Regardless of the mechanism of initiation, all species face a similar challenge before an OMV can be released: How does the OM detach from the underlying peptidoglycan (PG) in regions that will ultimately bulge and then vesiculate? The OmpA family of OM proteins (OprF in P. aeruginosa) is widely conserved and unusually abundant in OMVs across species considering their major role in PG attachment. OmpA homologs also have the interesting ability to adopt both PG-bound (two-domain) and PG-released (one-domain) conformations. Using targeted deletion of the PG-binding domain we showed that loss of cell wall association, and not general membrane destabilization, is responsible for hypervesiculation in OprF-modified strains. We therefore propose that OprF functions as a 'latch', capable of releasing PG in regions destined to become OMVs. To test this hypothesis, we developed a protocol to assess OprF conformation in live cells and purified OMVs. While >90% of OprF proteins exist in the two-domain conformation in the OM of cells, we show that the majority of OprF in OMVs is present in the one-domain conformation. With this work, we take some of the first steps in characterizing late-stage OMV biogenesis and identify a family of proteins whose critical role can be explained by their unique ability to fold into two distinct conformations.

Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution

Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.

Roles of OmpA in Type III Secretion System-Mediated Virulence of Enterohemorrhagic Escherichia coli

Outer membrane proteins are commonly produced by gram-negative bacteria, and they have diverse functions. A subgroup of proteins, which includes OmpA, OmpW and OmpX, is often involved in bacterial pathogenesis. Here we show that OmpA, rather than OmpW or OmpX, contributes to the virulence of enterohemorrhagic Escherichia coli (EHEC) through its type III secretion system (T3SS). Deletion of ompA decreased secretion of the T3SS proteins EspA and EspB; however, the expression level of the LEE genes that encode a set of T3SS proteins did not decrease. The ompA mutant had less abilities to form A/E lesions in host epithelial cells and lyse human red blood cells than the parent strain. Moreover, the virulence of an ompA mutant of Citrobacter rodentium (traditionally used to estimate T3SS-associated virulence in mice) was attenuated. Mice infected with the ompA mutant survived longer than those infected with the parent strain. Furthermore, mice infected with ompA developed symptoms of diarrhea more slowly than mice infected with the parent strain. Altogether, these results suggest that OmpA sustains the activity of the T3SS and is required for optimal virulence in EHEC. This work expands the roles of outer membrane proteins in bacterial pathogenesis.

Triclosan at environmental concentrations can enhance the spread of extracellular antibiotic resistance genes through transformation

The dissemination of antibiotic resistance mediated by horizontal transfer of antibiotic resistance genes (ARGs) is exacerbating the global antibiotic crisis. Currently, little is known about whether non-antibiotic, anti-microbial (NAAM) chemicals are associated with the dissemination of ARGs in the environment. In this study, we aimed to evaluate whether a ubiquitous NAAM chemical, triclosan (TCS), is able to promote the transformation of plasmid-borne antibiotic resistance genes (ARGs). By using the plasmid pUC19 carrying ampicillin resistance genes as the extracellular ARG and a model microorganism Escherichia coli DH5ɑ as the recipient, we found that TCS at environmentally detected concentrations (0.2 μg/L to 20 μg/L) significantly enhanced the transformation of plasmid-borne ARGs into E. coli DH5ɑ for up to 1.4-fold. The combination of phenotypic experiments, genome-wide RNA sequencing and proteomic analyses revealed that TCS exposure stimulated the reactive oxygen species (ROS) production for 1.3- to 1.5-fold, induced bacterial membrane damage and up-regulated the translation of outer membrane porin. Moreover, general secretion system Sec (1.4-fold), twin arginine translocation system Tat (1.2-fold) and type IV pilus secretion systems (2.5-fold) were enhanced by TCS, which might contribute to the DNA searching/capture by pilus. Together, TCS might increase the transformation frequency of ARGs into E. coli DH5ɑ by ROS over-production, damaging cell membrane barrier, mediating the pilus capture of plasmid and the translocation of plasmid via cell membrane channels. This study reports that TCS could accelerate the transformation of extracellular ARGs to competent bacteria at environmentally relevant concentrations. The findings advance our understanding of the fate of ARGs in ecosystems and call for risk assessments of NAAM chemicals on disseminating antibiotic resistance.

Pushing beyond the Envelope: the Potential Roles of OprF in Pseudomonas aeruginosa Biofilm Formation and Pathogenicity

The ability of Pseudomonas aeruginosa to form biofilms, which are communities of cells encased in a self-produced extracellular matrix, protects the cells from antibiotics and the host immune response. While some biofilm matrix components, such as exopolysaccharides and extracellular DNA, are relatively well characterized, the extracellular matrix proteins remain understudied. Multiple proteomic analyses of the P. aeruginosa soluble biofilm matrix and outer membrane vesicles, which are a component of the matrix, have identified OprF as an abundant matrix protein. To date, the few reports on the effects of oprF mutations on biofilm formation are conflicting, and little is known about the potential role of OprF in the biofilm matrix. The majority of OprF studies focus on the protein as a cell-associated porin. As a component of the outer membrane, OprF assumes dual conformations and is involved in solute transport, as well as cell envelope integrity. Here, we review the current literature on OprF in P. aeruginosa, discussing how the structure and function of the cell-associated and matrix-associated protein may affect biofilm formation and pathogenesis in order to inform future research on this understudied matrix protein.

HldE Is Important for Virulence Phenotypes in Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrheal illness in third world countries and it especially affects children and travelers visiting these regions. ETEC causes disease by adhering tightly to the epithelial cells in a concerted effort by adhesins, flagella, and other virulence-factors. When attached ETEC secretes toxins targeting the small intestine host-cells, which ultimately leads to osmotic diarrhea. HldE is a bifunctional protein that catalyzes the nucleotide-activated heptose precursors used in the biosynthesis of lipopolysaccharide (LPS) and in post-translational protein glycosylation. Both mechanisms have been linked to ETEC virulence: Lipopolysaccharide (LPS) is a major component of the bacterial outer membrane and is needed for transport of heat-labile toxins to the host cells, and ETEC glycoproteins have been shown to play an important role for bacterial adhesion to host epithelia. Here, we report that HldE plays an important role for ETEC virulence. Deletion of hldE resulted in markedly reduced binding to the human intestinal cells due to reduced expression of colonization factor CFA/I on the bacterial surface. Deletion of hldE also affected ETEC motility in a flagella-dependent fashion. Expression of both colonization factors and flagella was inhibited at the level of transcription. In addition, the hldE mutant displayed altered growth, increased biofilm formation and clumping in minimal growth medium. Investigation of an orthogonal LPS-deficient mutant combined with mass spectrometric analysis of protein glycosylation indicated that HldE exerts its role on ETEC virulence both through protein glycosylation and correct LPS configuration. These results place HldE as an attractive target for the development of future antimicrobial therapeutics.

Structure, function and regulation of Pseudomonas aeruginosa porins

Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.

A Novel Regulatory Cascade Involving BluR, YcgZ, and Lon Controls the Expression of Escherichia coli OmpF Porin

In Escherichia coli, OmpF is an important outer membrane protein, which serves as a passive diffusion pore for small compounds including nutrients, antibiotics, and toxic compounds. OmpF expression responds to environmental changes such as temperature, osmolarity, nutrients availability, and toxic compounds via complex regulatory pathways involving transcriptional and post-transcriptional regulation. Our study identified a new regulatory cascade that controls the expression of OmpF porin. This pathway involves BluR, a transcriptional regulator repressing the expression of the ycgZ-ymgABC operon. We showed that BluR was responsible for the temperature-dependent regulation of the ycgZ-ymgABC operon. Furthermore, our results showed that independent expression of YcgZ led to a decreased activity of the ompF promoter, while YmgA, YmgB, and YmgC expression had no effect. We also determined that YcgZ accumulates in the absence of the Lon protease. Thus, mutation in bluR leads to de-repression of ycgZ-ymgABC transcription. With a second mutation in lon, YcgZ protein accumulates to reach levels that do not allow increased expression of OmpF under growth conditions that usually would, i.e., low temperature. With BluR responding to blue-light and temperature, this study sheds a new light on novel signals able to regulate OmpF porin.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075

The nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital-acquired infections worldwide and is a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. Here, to gain insight on A. baumannii antibiotic resistance mechanisms, we analyse the protein interaction network of a multidrug-resistant A. baumannii clinical strain (AB5075). Using in vivo chemical cross-linking and mass spectrometry, we identify 2,068 non-redundant cross-linked peptide pairs containing 245 intra- and 398 inter-molecular interactions. Outer membrane proteins OmpA and YiaD, and carbapenemase Oxa-23 are hubs of the identified interaction network. Eighteen novel interactors of Oxa-23 are identified. Interactions of Oxa-23 with outer membrane porins OmpA and CarO are verified with co-immunoprecipitation analysis. Furthermore, transposon mutagenesis of oxa-23 or interactors of Oxa-23 demonstrates changes in meropenem or imipenem sensitivity in strain AB5075. These results provide a view of porin-localized antibiotic inactivation and increase understanding of bacterial antibiotic resistance mechanisms.

Structural Basis for Recombinatorial Permissiveness in the Generation of Anaplasma marginale Msp2 Antigenic Variants

Sequential expression of outer membrane protein antigenic variants is an evolutionarily convergent mechanism used by bacterial pathogens to escape host immune clearance and establish persistent infection. Variants must be sufficiently structurally distinct to escape existing immune effectors yet retain the core structural elements required for localization and function within the outer membrane. We examined this balance using Anaplasma marginale, which generates antigenic variants in the outer membrane protein Msp2 using gene conversion. The overwhelming majority of Msp2 variants expressed during long-term persistent infection are mosaics, derived by recombination of oligonucleotide segments from multiple alleles to form unique hypervariable regions (HVR). As a result, the mosaics are not under long-term selective pressure to encode a functional protein; consequently, we hypothesized that the Msp2 HVR is structurally permissive for mosaic expression. Using an integrated approach of predictive modeling with determination of the native Msp2 protein structure and function, we demonstrate that structured elements, most notably, β-sheets, are significantly concentrated in the highly conserved N- and C-terminal domains. In contrast, the HVR is overwhelmingly a random coil, with the structured α-helices and β-sheets being confined to the genomically defined structural tethers that separate the antigenically variable microdomains. This structure is supported by the surface exposure of the HVR microdomains and the slow diffusion-type porin function in native Msp2. Importantly, the predominance of the random coil provides plasticity for the formation of functional HVR mosaics and realization of the full potential of segmental gene conversion to dramatically expand the variant repertoire.

Living with Stress: A Lesson from the Enteric Pathogen Salmonella enterica

The ability to sense and respond to the environment is essential for the survival of all living organisms. Bacterial pathogens such as Salmonella enterica are of particular interest due to their ability to sense and adapt to the diverse range of conditions they encounter, both in vivo and in environmental reservoirs. During this cycling from host to non-host environments, Salmonella encounter a variety of environmental insults ranging from temperature fluctuations, nutrient availability and changes in osmolarity, to the presence of antimicrobial peptides and reactive oxygen/nitrogen species. Such fluctuating conditions impact on various areas of bacterial physiology including virulence, growth and antimicrobial resistance. A key component of the success of any bacterial pathogen is the ability to recognize and mount a suitable response to the discrete chemical and physical stresses elicited by the host. Such responses occur through a coordinated and complex programme of gene expression and protein activity, involving a range of transcriptional regulators, sigma factors and two component regulatory systems. This review briefly outlines the various stresses encountered throughout the Salmonella life cycle and the repertoire of regulatory responses with which Salmonella counters. In particular, how these Gram-negative bacteria are able to alleviate disruption in periplasmic envelope homeostasis through a group of stress responses, known collectively as the Envelope Stress Responses, alongside the mechanisms used to overcome nitrosative stress, will be examined in more detail.

In situ structural studies of Anabaena sensory rhodopsin in the E. coli membrane

Magic-angle spinning nuclear magnetic resonance is well suited for the study of membrane proteins in the nativelike lipid environment. However, the natural cellular membrane is invariably more complex than the proteoliposomes most often used for solid-state NMR (SSNMR) studies, and differences may affect the structure and dynamics of the proteins under examination. In this work we use SSNMR and other biochemical and biophysical methods to probe the structure of a seven-transmembrane helical photoreceptor, Anabaena sensory rhodopsin (ASR), prepared in the Escherichia coli inner membrane, and compare it to that in a bilayer formed by DMPC/DMPA lipids. We find that ASR is organized into trimers in both environments but forms two-dimensional crystal lattices of different symmetries. It favors hexagonal packing in liposomes, but may form a square lattice in the E. coli membrane. To examine possible changes in structure site-specifically, we perform two- and three-dimensional SSNMR experiments and analyze the differences in chemical shifts and peak intensities. Overall, this analysis reveals that the structure of ASR is largely conserved in the inner membrane of E. coli, with many of the important structural features of rhodopsins previously observed in ASR in proteoliposomes being preserved. Small, site-specific perturbations in protein structure that occur as a result of the membrane changes indicate that the protein can subtly adapt to its environment without large structural rearrangement.

Influence of heat-labile serum components in the presence of OmpA on the outer membrane of Salmonella gallinarum

Salmonella gallinarum is the causative agent of fowl typhoid. Being a Gram-negative bacteria, its outer membrane proteins (OMP) can be regulated by different microenvironments. S. gallinarum was cultured under the following conditions: nutrient broth (NB), NB supplemented with serum from specific pathogen-free birds (NBS) and NB with serum incubated at 56 °C prior to incubation with the bacteria (NBSD); OMP were subsequently extracted. Several changes were observed in the apparent expression of OMP, mainly a decrease in an OMP with a size of 30 kDa, approximately, under the NBS condition. In contrast, the same event was not observed in NB and NBSD when using one- and two-dimensional polyacrylamide gels (SDS-PAGE). Using the OMP with a size of 30 kDa, approximately, as antigen in indirect ELISA, we were able to differentiate serum from healthy and vaccinated birds, as well as birds infected with S. gallinarum and S. enteritidis. The amino-terminal of this protein was sequenced, showing 100 % identity with OmpA of S. typhimurium. Subsequently, we designed primers to amplify the gene by PCR. The partial sequence of the amplified gene showed 100 % identity with OmpA of S. gallinarum. (1) Heat-labile serum components influence the presence of OmpA in the OM of S. gallinarum; (2) by the way of ELISA, OmpA allows to specifically differentiate healthy from diseased birds.

Flux theory for Poisson distributed pores with Gaussian permeability

The mean of the solute flux through membrane pores depends on the random distribution and permeability of the pores. Mathematical models including such randomness factors make it possible to obtain statistical parameters for pore characterization. Here, assuming that pores follow a Poisson distribution in the lipid phase and that their permeabilities follow a Gaussian distribution, a mathematical model for solute dynamics is obtained by applying a general result from a previous work regarding any number of different kinds of randomly distributed pores. The new proposed theory is studied using experimental parameters obtained elsewhere, and a method for finding the mean single pore flux rate from liposome flux assays is suggested. This method is useful for pores without requiring studies by patch-clamp in single cells or single-channel recordings. However, it does not apply in the case of ion-selective channels, in which a more complex flux law combining the concentration and electrical gradient is required.

Adaptive Immune Responses during Salmonella Infection

The interaction betweenSalmonella and its host is complex and dynamic: the host mounts an immune defense against the pathogen, which in turn acts to reduce, evade, or exploit these responses to successfully colonize the host. Although the exact mechanisms mediating protective immunity are poorly understood, it is known that T cells are a critical component of immunity to Salmonella infection, and a robust T-cell response is required for both clearance of primary infection and resistance to subsequent challenge. B-cell functions, including but not limited to antibody production, are also required for generation of protective immunity. Additionally, interactions among host cells are essential. For example, antigen-presenting cells (including B cells) express cytokines that participate in CD4+ T cell activation and differentiation. Differentiated CD4+ T cells secrete cytokines that have both autocrine and paracrine functions, including recruitment and activation of phagocytes, and stimulation of B cell isotype class switching and affinity maturation. Multiple bacterium-directed mechanisms, including altered antigen expression and bioavailability and interference with antigen-presenting cell activation and function, combine to modify Salmonella's "pathogenic signature" in order to minimize its susceptibility to host immune surveillance. Therefore, a more complete understanding of adaptive immune responses may provide insights into pathogenic bacterial functions. Continued identification of adaptive immune targets will guide rational vaccine development, provide insights into host functions required to resist Salmonella infection, and correspondingly provide valuable reagents for defining the critical pathogenic capabilities of Salmonella that contribute to their success in causing acute and chronic infections.

Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade

Since genome analysis did not allow unambiguous reconstruction of transport, catabolism, and substrate-specific regulation for several important carbohydrates in Phaeobacter inhibens DSM 17395, proteomic and metabolomic analyses of N-acetylglucosamine-, mannitol-, sucrose-, glucose-, and xylose-grown cells were carried out to close this knowledge gap. These carbohydrates can pass through the outer membrane via porins identified in the outer membrane fraction. For transport across the cytoplasmic membrane, carbohydrate-specific ABC transport systems were identified. Their coding genes mostly colocalize with the respective "catabolic" and "regulatory" genes. The degradation of N-acetylglucosamine proceeds via N-acetylglucosamine-6-phosphate and glucosamine-6-phosphate directly to fructose-6-phosphate; two of the three enzymes involved were newly predicted and identified. Mannitol is catabolized via fructose, sucrose via fructose and glucose, glucose via glucose-6-phosphate, and xylose via xylulose-5-phosphate. Of the 30 proteins predicted to be involved in uptake, regulation, and degradation, 28 were identified by proteomics and 19 were assigned to their respective functions for the first time. The peripheral degradation pathways feed into the Entner-Doudoroff (ED) pathway, which is connected to the lower branch of the Embden-Meyerhof-Parnas (EMP) pathway. The enzyme constituents of these pathways displayed higher abundances in P. inhibens DSM 17395 cells grown with any of the five carbohydrates tested than in succinate-grown cells. Conversely, gluconeogenesis is turned on during succinate utilization. While tricarboxylic acid (TCA) cycle proteins remained mainly unchanged, the abundance profiles of their metabolites reflected the differing growth rates achieved with the different substrates tested. Homologs of the 74 genes involved in the reconstructed catabolic pathways and central metabolism are present in various Roseobacter clade members.

Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN

We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP.

Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii

Outer membrane (OM) β-barrel proteins composed of 12-18 β-strands mediate cellular entry of small molecules in Gram-negative bacteria. Small OM proteins with barrels of 10 strands or less are not known to transport small molecules. CarO (carbapenem-associated outer membrane protein) from Acinetobacter baumannii is a small OM protein that has been implicated in the uptake of ornithine and carbapenem antibiotics. Here we report crystal structures of three isoforms of CarO. The structures are very similar and show a monomeric eight-stranded barrel lacking an open channel. CarO has a substantial extracellular domain resembling a glove that contains all the divergent residues between the different isoforms. Liposome swelling experiments demonstrate that full-length CarO and a "loop-less" truncation mutant mediate small-molecule uptake at low levels but that they are unlikely to mediate passage of carbapenem antibiotics. These results are confirmed by biased molecular dynamics simulations that allowed us to quantitatively model the transport of selected small molecules.

The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition

Gram-negative bacteria such as Escherichia coli are surrounded by two membranes with a thin peptidoglycan (PG)-layer located in between them in the periplasmic space. The outer membrane protein A (OmpA) is a 325-residue protein and it is the major protein component of the outer membrane of E. coli. Previous structure determinations have focused on the N-terminal fragment (residues 1-171) of OmpA, which forms an eight stranded transmembrane β-barrel in the outer membrane. Consequently it was suggested that OmpA is composed of two independently folded domains in which the N-terminal β-barrel traverses the outer membrane and the C-terminal domain (residues 180-325) adopts a folded structure in the periplasmic space. However, some reports have proposed that full-length OmpA can instead refold in a temperature dependent manner into a single domain forming a larger transmembrane pore. Here, we have determined the NMR solution structure of the C-terminal periplasmic domain of E. coli OmpA (OmpA(180-325)). Our structure reveals that the C-terminal domain folds independently into a stable globular structure that is homologous to the previously reported PG-associated domain of Neisseria meningitides RmpM. Our results lend credence to the two domain structure model and a PG-binding function for OmpA, and we could indeed localize the PG-binding site on the protein through NMR chemical shift perturbation experiments. On the other hand, we found no evidence for binding of OmpA(180-325) with the TonB protein. In addition, we have also expressed and purified full-length OmpA (OmpA(1-325)) to study the structure of the full-length protein in micelles and nanodiscs by NMR spectroscopy. In both membrane mimetic environments, the recombinant OmpA maintains its two domain structure that is connected through a flexible linker. A series of temperature-dependent HSQC experiments and relaxation dispersion NMR experiments detected structural destabilization in the bulge region of the periplasmic domain of OmpA above physiological temperatures, which may induce dimerization and play a role in triggering the previously reported larger pore formation.

Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA

The transmembrane domain of the outer membrane protein A (OmpA) from Escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. However, full-length OmpA resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. Here we use site-directed mutagenesis and mass spectrometry of different constructs of OmpA, released in the gas phase from detergent micelles, to define the minimal region encompassing the C-terminal dimer interface. Combining knowledge of the location of the dimeric interface with molecular modeling and ion mobility data allows us to propose a low-resolution model for the full-length OmpA dimer. Our model of the dimer is in remarkable agreement with experimental ion mobility data, with none of the unfolding or collapse observed for full-length monomeric OmpA, implying that dimer formation stabilizes the overall structure and prevents collapse of the flexible linker that connects the two domains.

Fluxes theory in experiments with random distributed channels on vesicles

When channels are randomly distributed in a population of vesicles, disregarding the number of channels per vesicle, these channels follow a Poisson distribution. This has been verified in many cases, determining the average of channels per vesicle. However, to determine kinetic parameters in population studies, a mathematical expression for the mean flux of solute through channels per vesicle is necessary. Hence, here, this mean flux is calculated, assuming Poisson distributed channels in a population of vesicle. Moreover, this result has been generalized to any number of different kinds of channels (i.e., channels with different permeabilities). These results, useful for in vitro experiments with mixed both channels and vesicles, can be supplemented with those from other techniques, in order to understanding how the nature of the lipid membrane affects kinetic parameters of channel.

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains

Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE) technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

The role of short-chain conjugated poly-(R)-3-hydroxybutyrate (cPHB) in protein folding

Poly-(R)-3-hydroxybutyrate (PHB), a linear polymer of R-3-hydroxybutyrate (R-3HB), is a fundamental constituent of biological cells. Certain prokaryotes accumulate PHB of very high molecular weight (10,000 to >1,000,000 residues), which is segregated within granular deposits in the cytoplasm; however, all prokaryotes and all eukaryotes synthesize PHB of medium-chain length (~100-200 residues) which resides within lipid bilayers or lipid vesicles, and PHB of short-chain length (<12 residues) which is conjugated to proteins (cPHB), primarily proteins in membranes and organelles. The physical properties of cPHB indicate it plays important roles in the targeting and folding of cPHB-proteins. Here we review the occurrence, physical properties and molecular characteristics of cPHB, and discuss its influence on the folding and structure of outer membrane protein A (OmpA) of Escherichia coli.

Block and boost DNA transfer: opposite roles of OmpA in natural and artificial transformation of Escherichia coli

Our previous work established that DNA is naturally transferable on agar plates through a new transformation system which is regulated by the stationary phase master regulator RpoS in Escherichia coli. In this transformation system, neither additional Ca²⁺ nor heat shock is required. Instead, transformation is stimulated by agar. The membrane protein OmpA, a gated pore permeable to ions and larger solutes, serves as a receptor for DNA transfer during bacteriophage infection and conjugation. However, it remains unknown how DNA transfers across membranes and whether OmpA is involved in transformation of E. coli. Here, we explored potential roles of OmpA in natural and chemical transformation of E. coli. We observed that ompA inactivation significantly improved natural transformation on agar plates, indicating that OmpA blocks DNA transfer. Transformation promotion by ompA inactivation also occurred on soft plates, indicating that OmpA blocks DNA transfer independent of agar. By contrast, compared with the wild-type strain, chemical transformation of the ompA mutant was lower, indicating that OmpA has a role in DNA transfer. Inactivation of ompA also reduced chemical transformation in solution containing less Ca²⁺ or with a shortened time for heat shock, suggesting that the promotion effect of OmpA on DNA transfer does not solely rely on Ca²⁺ or heat shock. We conclude that OmpA plays opposite roles in natural and chemical transformation: it blocks DNA uptake on agar plates but promotes DNA transfer in the liquid Ca²⁺ solution. Considering that no single factor was identified to reverse the function of OmpA, we propose that multiple factors may cooperate in the functional reversal of OmpA during natural and artificial transformation of E. coli. Finally, we observed that ompA transcription was not affected by the expression of RpoS, excluding the possibility that RpoS regulates DNA transfer by suppressing ompA transcription.

Eicosapentaenoic acid facilitates the folding of an outer membrane protein of the psychrotrophic bacterium, Shewanella livingstonensis Ac10

Polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), are found in various cold-adapted microorganisms. We previously demonstrated that EPA-containing phospholipids (EPA-PLs) synthesized by the psychrotrophic bacterium Shewanella livingstonensis Ac10 support cell division, membrane biogenesis, and the production of membrane proteins at low temperatures. In this article, we demonstrate the effects of EPA-PLs on the folding and conformational transition of Omp74, a major outer membrane cold-inducible protein in this bacterium. Omp74 from an EPA-less mutant migrated differently from that of the parent strain on SDS-polyacrylamide gel, suggesting that EPA-PLs affect the conformation of Omp74 in vivo. To examine the effects of EPA-PLs on Omp74 protein folding, in vitro refolding of recombinant Omp74 was carried out with liposomes composed of 1,2-dipalmitoleoyl-sn-glycero-3-phosphoglycerol and 1,2-dipalmitoleoyl-sn-glycero-3-phosphoethanolamine (1:1 molar ratio) with or without EPA-PLs as guest lipids. SDS-PAGE analysis of liposome-reconstituted Omp74 revealed more rapid folding in the presence of EPA-PLs. CD spectroscopy of Omp74 folding kinetics at 4 °C showed that EPA-PLs accelerated β-sheet formation. These results suggest that EPA-PLs act as chemical chaperones, accelerating membrane insertion and secondary structure formation of Omp74 at low temperatures.

OmpA is the principal nonspecific slow porin of Acinetobacter baumannii

Acinetobacter species show high levels of intrinsic resistance to many antibiotics. The major protein species in the outer membrane of Acinetobacter baumannii does not belong to the high-permeability trimeric porin family, which includes Escherichia coli OmpF/OmpC, and instead is a close homolog of E. coli OmpA and Pseudomonas aeruginosa OprF. We characterized the pore-forming function of this OmpA homolog, OmpA(Ab), by a reconstitution assay. OmpA(Ab) produced very low pore-forming activity, about 70-fold lower than that of OmpF and an activity similar to that of E. coli OmpA and P. aeruginosa OprF. The pore size of the OmpA(Ab) channel was similar to that of OprF, i.e., about 2 nm in diameter. The low permeability of OmpA(Ab) is not due to the inactivation of this protein during purification, because the permeability of the whole A. baumannii outer membrane was also very low. Furthermore, the outer membrane permeability to cephalothin and cephaloridine, measured in intact cells, was about 100-fold lower than that of E. coli K-12. The permeability of cephalothin and cephaloridine in A. baumannii was decreased 2- to 3-fold when the ompA(Ab) gene was deleted. These results show that OmpA(Ab) is the major nonspecific channel in A. baumannii. The low permeability of this porin, together with the presence of constitutive β-lactamases and multidrug efflux pumps, such as AdeABC and AdeIJK, appears to be essential for the high levels of intrinsic resistance to a number of antibiotics.

Insights into the structure and assembly of Escherichia coli outer membrane protein A

Outer membrane protein A (OmpA) of Escherichia coli is a paradigm for the biogenesis of outer membrane proteins; however, the structure and assembly of OmpA have remained controversial. A review of studies to date supports the hypothesis that native OmpA is a single-domain large pore, while a two-domain narrow-pore structure is a folding intermediate or minor conformer. The in vitro refolding of OmpA to the large-pore conformation requires isolation of the protein from outer membranes with retention of an intact disulfide bond followed by sufficient incubation in lipids at temperatures of ≥ 26 °C to overcome the high energy of activation for refolding. The in vivo maturation of the protein involves covalent modification of serines in the eighth β-barrel of the N-terminal domain by oligo-(R)-3-hydroxybutyrates as the protein is escorted across the cytoplasm by SecB for post-translational secretion across the secretory translocase in the inner membrane. After cleavage of the signal sequence, protein chaperones, such as Skp, DegP and SurA, guide OmpA across the periplasm to the β-barrel assembly machinery (BAM) complex in the outer membrane. During this passage, a disulfide bond is formed between C290 and C302 by DsbA, and the hydrophobicity of segments of the C-terminal domain, which are destined for incorporation as β-barrels in the outer membrane bilayer, is increased by covalent attachment of oligo-(R)-3-hydroxybutyrates. With the aid of the BAM complex, OmpA is then assembled into the outer membrane as a single-domain large pore.

Alternative folding pathways of the major porin OprF of Pseudomonas aeruginosa

OprF is the major porin of Pseudomonas aeruginosa and allows very slow, nonspecific, diffusion of solutes. The low permeability of this porin channel is a major factor that enhances other types of resistance mechanisms and often creates strong multidrug resistance in this nosocomial pathogen. We have previously shown that the low permeability is caused by the folding of OprF into two conformers: a majority, two-domain closed-channel conformer containing the N-terminal transmembrane β-barrel and the C-terminal periplasmic, globular domain; and a minority, one-domain open-channel conformer comprising < 5% of the protein population. Our analysis of the bifurcate folding pathway using site-directed mutagenesis showed that slowing down the folding of the two-domain conformer increases the fraction of the open, one-domain conformer. Use of outer membrane protein assembly machinery mutants showed that the absence of the Skp chaperone led to an increased proportion of open conformers. As many environmental pathogens causing nosocomial infections appear to have outer membrane protein (OmpA)/OprF homologs as the major porin, efforts to understand the low permeability of these 'slow porins' are important in our fight against these organisms.

OmpA-like protein influences cell shape and adhesive activity of Tannerella forsythia

Tannerella forsythia, a gram-negative fusiform rod, is implicated in several types of oral anaerobic infections. Most gram-negative bacteria have OmpA-like proteins that are homologous to the OmpA protein in Escherichia coli. We identified an OmpA-like protein in T. forsythia encoded by the tf1331 gene as one of the major proteins by mass spectrometric analysis. Two-dimensional, diagonal electrophoresis showed that the OmpA-like protein formed a dimeric or trimeric structure via intermolecular disulfide bonds. A biotin labeling experiment revealed that a portion of the protein was exposed on the cell surface, even though T. forsythia possesses an S-layer at the outermost cell surface. Using a tf1331-deletion mutant, we showed that the OmpA-like protein affected cell morphology. The length of the mutant cell was reduced almost by half. Cell swelling was observed in more than 40% of the mutant cells. Moreover, the mutant exhibited decreased adhesion to fibronectin, retarded autoaggregation, and reduced cell surface hydrophobicity. These results suggest that the OmpA-like protein in T. forsythia plays an important role in cellular integrity and adhesive function.

Characterization of an OmpA-like outer membrane protein of the acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans

An OmpA family protein (FopA) previously reported as one of the major outer membrane proteins of an acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans was characterized with emphasis on the modification by heat and the interaction with peptidoglycan. A 30-kDa band corresponding to the FopA protein was detected in outer membrane proteins extracted at 75°C or heated to 100°C for 10 min prior to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). However, the band was not detected in outer membrane proteins extracted at ≤40°C and without boiling prior to electrophoresis. By Western blot analysis using the polyclonal antibody against the recombinant FopA, FopA was detected as bands with apparent molecular masses of 30 and 90 kDa, suggesting that FopA existed as an oligomeric form in the outer membrane of A. ferrooxidans. Although the fopA gene with a sequence encoding the signal peptide was successfully expressed in the outer membrane of Escherichia coli, the recombinant FopA existed as a monomer in the outer membrane of E. coli. FopA was detected in peptidoglycan-associated proteins from A. ferrooxidans. The recombinant FopA also showed the peptidoglycan-binding activity.

Expression of the ompATb operon accelerates ammonia secretion and adaptation of Mycobacterium tuberculosis to acidic environments

Homeostasis of intracellular pH is a trait critical for survival of Mycobacterium tuberculosis in macrophages. However, mechanisms by which M. tuberculosis adapts to acidic environments are poorly understood. In this study, we analysed the physiological functions of OmpATb, a surface-accessible protein of M. tuberculosis. OmpATb did not complement the permeability defects of a Mycobacterium smegmatis porin mutant to glucose, serine and glycerol, in contrast to the porin MspA. Uptake rates of these solutes were unchanged in an ompATb operon mutant of M. tuberculosis indicating that OmpATb is not a general porin. Chemical analysis of low-pH culture filtrates showed that the proteins encoded by the ompATb operon are involved in generating a rapid ammonia burst, which neutralized medium pH and preceded exponential growth of M. tuberculosis. Addition of ammonia accelerated growth of the ompATb operon mutant demonstrating that ammonia secretion is indeed a mechanism by which M. tuberculosis neutralizes acidic environments. Infection experiments revealed that the ompATb operon was not required for full virulence in mice suggesting that M. tuberculosis has multiple mechanisms of resisting phagosomal acidification. Taken together, these results show that the ompATb operon is necessary for rapid ammonia secretion and adaptation of M. tuberculosis to acidic environments in vitro but not in mice.

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.

Factors affecting the folding of Pseudomonas aeruginosa OprF porin into the one-domain open conformer

Pseudomonas aeruginosa OprF is a largely monomeric outer membrane protein that allows the slow, nonspecific transmembrane diffusion of solutes. This protein folds into two different conformers, with the majority conformer folding into a two-domain conformation that has no porin activity and the minority conformer into a one-domain conformation with high porin activity and presumably consisting of a large β barrel. We examined the factors that control the divergent folding pathways of OprF. OprF contains four Cys residues in the linker region connecting the N-terminal β-barrel domain and the C-terminal globular domain in the majority conformer. Prevention of disulfide bond formation either by expression of OprF in an Escherichia coli dsbA strain grown with dithiothreitol or by replacement of all Cys residues with serine (CS OprF) increased the specific pore-forming activity of OprF significantly. Replacement of Phe160 with Ile at the end of the β-barrel termination signal as well as replacement of Lys164 in the linker region with Gly, Cys, or Glu increased porin activity 2-fold. Improving a potential β-barrel termination signal in the periplasmic domain by replacement of Asp211 with asparagine also increased porin activity. The porin activity could be improved about 5-fold by the combination of these replacements. OprF mutants with higher porin activity were shown to contain more one-domain conformers by surface labeling of the A312C residue in intact cells, as this residue is located in the periplasmic domain in the two-domain conformers. Finally, when the OprF protein was expressed in an E. coli strain lacking the periplasmic chaperone Skp, the CS OprF protein exhibited increased pore-forming activity.

High intrinsic levels of resistance to many antimicrobial agents, seen in Gram-negative bacterial species such as Pseudomonas aeruginosa and Acinetobacter species, are largely due to the extremely low permeability of their major porin OprF and OmpA. Because this low permeability is caused by the fact that these proteins mostly fold into a two-domain conformer without pores, knowledge as to what conditions increase the production of the pore-forming minority conformer may lead to dramatic improvements in the treatment of infections by these bacteria. We have found several factors that increase the proportion of the pore-forming conformer up to 5-fold. Although these studies were done with Escherichia coli, they may serve as the starting point for the design of strategies for improvement of antimicrobial therapy for these difficult-to-treat pathogens, some strains of which have now attained the “pan-resistant” status.

Oligo-(R)-3-hydroxybutyrate modification of sorting signal enables pore formation by Escherichia coli OmpA

The outer membrane protein A (OmpA) of Escherichia coli is a well-known model for protein targeting and protein folding. Wild-type OmpA, isolated either from cytoplasmic inclusion bodies or from outer membranes, forms narrow pores of approximately 80 pS in planar lipid bilayers at room temperature. The pores are well structured with narrow conductance range when OmpA is isolated using lithium dodecyl sulfate (LDS) or RapiGest surfactant but display irregular conductance when OmpA is isolated with urea or guanidine hydrochloride. Previous studies have shown that serine residues S163 and S167 of the sorting signal of OmpA (residues 163-169), i.e., the essential sequence for outer membrane incorporation, are covalently modified by oligomers of (R)-3-hydroxybutyrate (cOHB). Here we find that single-mutants S163 and S167 of OmpA, which still contain cOHB on one serine of the sorting signal, form narrow pores in planar lipid bilayers at room temperature with lower and more irregular conductance than wild-type OmpA, whereas double mutants S163:S167 and S163:V166 of OmpA, with no cOHB on the sorting signal, are unable to form stable pores in planar lipid bilayers. Our results indicate that modification of serines in the sorting signal of OmpA by cOHB in the cytoplasm enables OmpA to incorporate into lipid bilayers at room temperature as a narrow pore. They further suggest that cOHB modification may be an important factor in protein targeting and protein folding.

Fast-time scale dynamics of outer membrane protein A by extended model-free analysis of NMR relaxation data

In order to better understand the dynamics of an integral membrane protein, backbone amide (15)N NMR dynamics measurements of the beta-barrel membrane protein OmpA have been performed at three magnetic fields. A total of nine relaxation data sets were globally analyzed using an extended model-free formalism. The diffusion tensor was found to be prolate axially symmetric with an axial ratio of 5.75, indicating a possible rotation of the protein within the micelle. The generalized order parameters gradually decreased from the mid-plane towards the two ends of the barrel, counteracting the dynamic gradient of the lipids in a matching bilayer, and were dramatically reduced in the extracellular loops. Large-scale internal motions on the ns time scale indicate that entire loops most likely undergo concerted ("sea anemone"-like) motions emanating from their anchoring points on the barrel. The case of OmpA in DPC micelles also illustrates inherent limitations of analyzing the data with even the most sophisticated current models of the model-free formalism. It is likely that conformational exchange processes on the ms-mus also play a role in describing the motions of some residues, but their analysis did not produce unique results that could be independently verified.

Characteristics of Bacteroides fragilis lacking the major outer membrane protein, OmpA

OmpA1 is the major outer membrane protein of the Gram-negative anaerobic pathogen Bacteroides fragilis. We identified three additional conserved ompA homologues (ompA2-ompA4) and three less homologous ompA-like genes (ompAs 5, 6 and 7) in B. fragilis. We constructed an ompA1 disruption mutant in B. fragilis 638R (WAL6 OmegaompA1) using insertion-mediated mutagenesis. WAL6 OmegaompA1 formed much smaller colonies and had smaller, rounder forms on Gram stain analysis than the parental strain or other unrelated disruption mutants. SDS-PAGE and Western blot analysis (with anti-OmpA1 IgY) of the OMP patterns of WAL6 OmegaompA1 grown in both high- and low-salt media did not reveal any other OmpA proteins even under osmotic stress. An ompA1 deletant (WAL186DeltaompA1) was constructed using a two-step double-crossover technique, and an ompA 'reinsertant', WAL360+ompA1, was constructed by reinserting the ompA gene into WAL186DeltaompA1. WAL186DeltaompA1 was significantly more sensitive to exposure to SDS, high salt and oxygen than the parental (WAL108) or reinsertant (WAL360+ompA1) strain. No significant change was seen in MICs of a variety of antimicrobials for either WAL6 OmegaompA1 or WAL186DeltaompA1 compared to WAL108. RT-PCR revealed that all of the ompA genes are transcribed in the parental strain and in the disruption mutant, but, as expected, ompA1 is not transcribed in WAL186DeltaompA1. Unexpectedly, ompA4 is also not transcribed in WAL186DeltaompA1. A predicted structure indicated that among the four OmpA homologues, the barrel portion is more conserved than the loops, except for specific conserved patches on loop 1 and loop 3. The presence of multiple copies of such similar genes in one organism would suggest a critical role for this protein in B. fragilis.

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

The N-terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight-stranded antiparallel beta-barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the crystal structure of the homologous protein OmpA of Escherichia coli. A number of molecular dynamics simulations have been carried out for the homology modeled structure of OprF in an explicit molecular model for the rough lipopolysaccharide (LPS) outer membrane of P. aeruginosa. The structural stability of the outer membrane model as a result of the strong electrostatic interactions compared with simple lipid bilayers is restricting both the conformational flexibility and the lateral diffusion of the porin in the membrane. Constricting side-chain interactions within the pore are similar to those found in reported simulations of the protein in a solvated lipid bilayer membrane. Because of the strong interactions between the loop regions of OprF and functional groups in the saccharide core of the LPS, the entrance to the channel from the extracellular space is widened compared with the lipid bilayer simulations in which the loops are extruding in the solvent. The specific electrostatic signature of the LPS membrane, which results in a net intrinsic dipole across the membrane, is found to be altered by the presence of OprF, resulting in a small electrically positive patch at the position of the channel.

Innate immune response in rainbow trout (Oncorhynchus mykiss) against primary and secondary infections with Yersinia ruckeri O1

Response mechanisms in teleosts against bacterial pathogens have been widely studied following injection procedures applying preparations of killed bacteria. In contrast, investigations on immune reactions in fish which have survived a primary infection and subsequently have been challenged are few or lacking. However, knowledge on these factors during infection and re-infection could provide the basis for development of improved vaccines. The innate immune response in rainbow trout (Oncorhynchus mykiss) against Yersinia ruckeri O1 has been studied following a primary intra-peritoneal injection with 5 x 10(5) CFU Y. ruckeri, and after bacterial clearance a secondary infection 35 days later. The number of pathogens in the liver was measured with a Y. ruckeri specific 16S ribosomal RNA quantitative real-time RT-PCR (q-PCR) during the course of infection. The bacterial counts peaked on day 3 during the primary infection and were significantly lower during the re-infection. Re-challenged fish showed a highly increased survival when compared to the naïve fish receiving a primary infection indicating development of adaptive immunity in the fish against this bacterial pathogen. We investigated the gene expression of innate immune factors in the liver during infections in order to elucidate molecules involved in survival of hosts before adaptive immunity was mounted. Transcription of mRNA was measured in liver samples taken 8 h, 1, 3, 7, 14 and 28 d post-infection using q-PCR. The investigation focused on genes encoding toll-like receptor 5 (TLR5), the pro-inflammatory cytokines IL-1beta, IL-6 and TNF-alpha, the acute phase proteins (APPs) serum amyloid protein a (SAA), trout C polysaccharide binding protein, a CRP/SAP like pentraxin, precerebellin, transferrin, hepcidin and finally the complement factors C3, C5 and factor B. Infection elicited significantly increased gene expression of all the cytokines (IL-6 > 1000-fold), some acute phase proteins (SAA > 3000-fold) and down-regulation of complement factors (C3, C5 and factor B). SAA expression was significantly earlier activated during the re-infection when compared to the primary infection. The pattern of gene activation suggested that the innate response was based on pathogen binding to toll-like receptors, production of cytokines and subsequent release of APPs. In general, both the innate immune response and the amount of Y. ruckeri measured in the liver during the re-infection was much lower compared to the first infection, probably reflecting development of adaptive immunity.

Characterization of membrane protein reconstitution in LUVs of different lipid composition by fluorescence anisotropy

A major requirement to perform structural studies with membrane proteins is not only to define efficient reconstitution protocols, that assure a high incorporation degree in preformed liposomes, but also a protein directionality and topology that mimics its in vivo conditions. For this kind of studies, protein reconstitution in membranes systems via a detergent-mediated pathway is usually successfully adopted, since detergents are generally used in the initial isolation and purification of membrane proteins. In this study we report the reconstitution of OmpF in preformed DMPC and E. coli liposomes using two different techniques for detergent removal: (1) exclusion chromatography and (2) incubation with detergent-adsorbing beads. The incorporation degree was determined by bicinchoninic acid assay and fluorescence anisotropy was used to determine OmpF effect on the structural order of membrane lipids. These results show that protein insertion in membranes depends both on the technique used to remove detergent and on the lipids used to prepare the liposomes. Furthermore, it is possible to state that although the insertion is directly related to the size distributions of proteoliposomes, it could be efficiently recognized by steady-state fluorescence anisotropy. This technique, more popular among cell biologists, can be a very practical and straightforward alternative to DLS to confirm membrane protein insertion.

Cloning and molecular characterization of outer membrane protein A (ompA) gene from Mycobacterium bovis

The ompA gene, 981 bp in size and identified in the Mycobacterium bovis genome, was cloned and sequenced. Predicted amino acid sequences showed a protein of molecular weight 33.5 kDa with an isoelectric point of 7.28 and an OmpA conserved domain at the carboxy terminal with signal sequence at the N-terminal. Homology search showed complete homology with the Mycobacterium tuberculosis ompA gene with varying degree of homology with omp genes of other bacteria, so it was predicted that it may act like porin. The ompA gene of M. bovis was expressed in the pProEX HTb expression vector. Recombinant protein OmpA, was purified by using a nickel affinity column. The expressed recombinant OmpA (32 kDa) was confirmed by western blot with Ni-NTA horseradish peroxidase (HRP) conjugate and with specific antiserum raised in rabbits. The effect of low pH (pH 6.0, 5.5 and 5) on the transcription of the ompA gene in M. bovis using real-time PCR showed that there was an increase in transcription of ompA in M. bovis cultured at low pH (maximum at pH 5.5).

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.

An outer membrane protein A (ompA) homologue from the photosynthetic purple sulfur bacterium Allochromatium vinosum

A 991 bp DNA fragment, consisting of a 225 amino acid reading frame homologous to outer membrane protein coding ompA gene, was cloned from a purple sulfur bacterium Allochromatium vinosum. The homology analysis revealed up to 51% similarity to other bacterial species. The absence of branching within diazotrophs or other taxonomically related groups shows the structural importance of the protein regardless of the metabolism and evolution of the species.

Genes under positive selection in Escherichia coli

We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.

Sorting signal of Escherichia coli OmpA is modified by oligo-(R)-3-hydroxybutyrate

Escherichia coli outer membrane protein A (OmpA) is a well-established model for the study of membrane assembly. Previous studies have shown that the essential sequence for outer membrane localization, known as the sorting signal, is contained in a segment of the eighth beta-strand, residues 163-171. Sequential digestion of OmpA, purified from outer membranes or inclusion bodies with cyanogen bromide and Staphylococcus aureus GluC, yielded peptides 162-174(LSLGVSYRFGQGE). Western blot and chemical assays indicated that the peptide was covalently modified by oligo-(R)-3-hydroxybutyrate (cOHB), a flexible, amphipathic oligoester. MALDI/MS was consistent with modification of peptides 162-174 by up to ten R-3-hydroxybutyrate (HB) residues. Western blot analysis of mutants of the peptide, using anti-OHB IgG, indicated that cOHB modification was not inhibited by the single mutations S163G, S167G, Y168F, R169N or R169D; however, cOHB was not detected on peptides containing the double mutations S163G:S167G S163G:V166G, L162G:S167G, and L164G:S167G. MALDI/MS/MS of double mutant S163G:S167G confirmed the absence of cOHB-modification. The results suggest that cOHB may be attached to one or both serines, and point to the importance of the flanking hydrophobic residues. Modification by cOHB may play a role in outer membrane targeting and assembly of OmpA.

OmpA: gating and dynamics via molecular dynamics simulations

Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of approximately 25 OMPs are currently known, there is relatively little known about their dynamics in different environments. The outer membrane protein, OmpA from Escherichia coli has been studied extensively in different environments both experimentally and computationally, and thus provides an ideal test case for the study of the dynamics and environmental interactions of outer membrane proteins. We review molecular dynamics simulations of OmpA and its homologues in a variety of different environments and discuss possible mechanisms of pore gating. The transmembrane domain of E. coli OmpA shows subtle differences in dynamics and interactions between a detergent micelle and a lipid bilayer environment. Simulations of the crystallographic unit cell reveal a micelle-like network of detergent molecules interacting with the protein monomers. Simulation and modelling studies emphasise the role of an electrostatic-switch mechanism in the pore-gating mechanism. Simulation studies have been extended to comparative models of OmpA homologues from Pseudomonas aeruginosa (OprF) and Pasteurella multocida (PmOmpA), the latter model including the periplasmic C-terminal domain.