Biomedical subjects

J Tommassen

Publications and source records attributed to J Tommassen.

At least 91 records · Page 5Linked to original sources

PubMed1994

Sequence variability of the 40-kDa outer membrane proteins of Fusobacterium nucleatum strains and a model for the topology of the proteins.

The complete nucleotide sequences of the fomA genes encoding the 40-kDa outer membrane proteins (OMPs) of strains ATCC 10953 and ATCC 25586 of Fusobacterium nucleatum were determined using the genomic DNA, or DNA fragments ligated into a vector plasmid, as template in a polymerase chain reaction. The deduced amino acid sequences of these two proteins were aligned with the amino acid sequence of the corresponding protein of F. nucleatum strain Fev1 and examined for conserved/variable polypeptide segments. A model for the topology of the 40-kDa OMPs is proposed on the basis of this alignment and application of the structural principles derived for OMPs of Escherichia coli. According to this model, sixteen polypeptide segments, which are highly conserved, traverse the outer membrane, thereby creating eight external loops, most of which are highly variable.

Amino Acid Sequence↗

PubMed1994

Requirement for conformational flexibility in the signal sequence of precursor protein.

According to the "unlooping" model (de Vrije, T., Batenburg, A. M., Killian, J. A., and de Kruijff, B. (1990) Mol. Microbiol. 4, 143-150), proposed to explain how signal sequences serve to target proteins into the secretory pathway, the initial interaction of the signal sequence with the membrane in a helix-turn-helix conformation (spanning half of the bilayer) plays an important role in the initiation of the translocation reaction. To test this model we have introduced 2 cysteines (at positions -5 and -19) in the signal sequence of the Escherichia coli outer membrane protein PhoE. The mutations did not influence the translocation of precursor PhoE in vivo or in vitro. The 2 cysteines were oxidized to form a disulfide bridge. In vitro translocation of the looped precursor into inner membrane vesicles was disturbed. The looped precursor competed with translocation of wild type precursor PhoE, and looped precursor that was first bound to inner membrane vesicles could be translocated after the addition of dithiothreitol. Apparently, the mutant precursor with a disulfide bridge in the signal sequence is arrested as a very early intermediate in the translocation process. All of these results are consistent with the proposed unlooping model and show that, besides the primary structure characteristics of a signal sequence, conformational flexibility is needed to initiate the translocation reaction.

Amino Acid Sequence↗

PubMed1994

Molecular characterization of the structural gene for the lactoferrin receptor of the meningococcal strain H44/76.

The meningococcal lactoferrin receptor is a promising vaccine candidate since it seems to be antigenically rather stable. Monoclonal antibodies against this protein reacted with more than 50% of the strains tested. To gain further insight in its variability, the IbpA gene from strain H44/76, encoding this protein, was cloned and sequenced. This strain does not cross-react with monoclonal antibodies that recognize LbpA of strain BNCV. The deduced amino acid sequence was found to be 95% homologous to the previously established sequence of LbpA of strain BNCV. A topology model was proposed for LbpA, making use of the sequence comparisons and some general rules for the folding of outer membrane proteins. The protein is supposed to traverse the membrane 26 times in a beta-sheet conformation. The epitope recognized by the monoclonals was mapped and found to reside in the largest predicted surface-exposed loop. No iron-regulation of LbpA expression was found in E. coli, probably because IbpA is located in an operon, the promoter of which was not cloned. Upstream of IbpA, a part of an open reading frame was found. Whereas the LbpA protein shows homology to the transferrin-binding protein 1 (Tbp1), the putative protein encoded by the open reading frame upstream of IbpA shows extensive homology to Tbp2, suggesting that iron-acquisition from lactoferrin, like from transferrin, requires two specific proteins in the outer membrane. The upstream open reading frame is tentatively designated IbpB.

Amino Acid Sequence↗

PubMed1994

Immunogenicity of a mycobacterial T-cell epitope expressed in outer membrane protein PhoE of Escherichia coli.

The outer membrane protein PhoE of Escherichia coli can be used for the expression of foreign antigenic determinants. Previously, a T-cell epitope of the 65 kDa heat shock protein (hsp65) of Mycobacterium tuberculosis, comprising amino acids 180 to 188, was expressed in PhoE. The hybrid protein induced proliferation of epitope-specific T-cell clones in vitro. In this report, the potential of the hybrid protein to induce an in vivo T-cell response against the 180-188 T-cell epitope was assessed. Popliteal lymph node cells, isolated from rats immunized with PhoE containing the hsp65 epitope, showed high proliferative responses to a synthetic peptide consisting of amino acids 180 to 188 of hsp65, indicating that the epitope is immunogenic in the PhoE-associated conformation.

Animals↗

PubMed1994

Influence of amino acids of a carrier protein flanking an inserted T cell determinant on T cell stimulation.

CD4+ helper T cells recognize antigen in association with MHC class II molecules. To investigate the role of the context of a minimal T cell epitope on presentation and recognition in association with MHC class II molecules, an epitope of the 65 kDa heat shock protein of Mycobacterium tuberculosis was inserted at four different sites in the outer membrane protein PhoE of Escherichia coli. Only some of the constructs could stimulate the epitope-specific T cell clone A2b in vitro. One non-stimulatory construct could be made stimulatory by denaturation, suggesting that the protein conformation prevents correct presentation of the epitope. Other non-stimulatory constructs did not become stimulatory with denaturation. One of these constructs could be made stimulatory by substitution of either one of the two amino acids directly preceding the minimal epitope in the recombinant protein. In synthetic peptides the presence of these upstream residues did not interfere with T cell recognition, suggesting that these residues influence processing of the recombinant protein. Flanking amino acids also influenced induction of a T cell response against the inserted epitope in vivo. These results demonstrate that insertion of minimal T cell epitopes in carrier proteins for the design of vaccines might fail because of the inhibiting effects of flanking residues.

Amino Acid Sequence↗

PubMed1994

Construction of phoE-caa, a novel PCR- and immunologically detectable marker gene for Pseudomonas putida.

In this paper we describe the construction and use in Pseudomonas putida WCS358 of phoE-caa, a novel hybrid marker gene, which allows monitoring both at the protein level by immunological methods and at the DNA level by PCR. The marker is based on the Escherichia coli outer membrane protein gene phoE and 75 bp of E. coli caa, which encode a nonbacteriocinic fragment of colicin A. This fragment contains an epitope which is recognized by monoclonal antibody (MAb) 1C11. As the epitope is contained in one of the cell surface-exposed loops of PhoE, whole cells of bacteria expressing the protein can be detected by using the MAb. The marker gene contains only E. coli sequences not coding for toxins and therefore can be considered environmentally safe. The hybrid PhoE-ColA protein was expressed in E. coli under conditions of phosphate starvation, and single cells could be detected by immunofluorescence microscopy with MAb 1C11. Using a wide-host-range vector the phoE-caa gene was introduced into P. putida WCS358. The gene appeared to be expressed under phosphate limitation in this species, and the gene product was present in the membrane fraction and reacted with MAb 1C11. The hybrid PhoE-ColA protein could be detected on whole cells of WCS358 mutant strains lacking (part of) the O-antigen of the lipopolysaccharide but not on wild-type WCS358 cells, unless these cells had previously been washed with 10 mM EDTA. In addition to immunodetection, the phoE-caa marker gene could be specifically detected by PCR with one primer directed to a part of the phoE sequence and a second primer that annealed to the caa insert.

Base Sequence↗

PubMed1994

Overexpression of algE in Escherichia coli: subcellular localization, purification, and ion channel properties.

Alginate-producing (mucoid) strains of Pseudomonas aeruginosa possess a 54-kDa outer membrane (OM) protein (AlgE) which is missing in nonmucoid bacteria. The coding region of the algE gene from mucoid P. aeruginosa CF3/M1 was subcloned in the expression vector pT7-7 and expressed in Escherichia coli. The level of expression of recombinant AlgE was seven times higher than that of the native protein in P. aeruginosa. Recombinant AlgE was found mainly in the OM. A putative precursor protein (56 kDa) of AlgE could be immunologically detected in the cytoplasmic membrane (CM). Surface exposition of AlgE in the OM of E. coli was indicated by labeling lysine residues with N-hydroxysuccinimide-biotin. Secondary-structure analysis suggested that AlgE is anchored in the OM by 18 membrane-spanning beta-strands, probably forming a beta-barrel. Recombinant AlgE was purified, and isoelectric focusing revealed a pI of 4.4. Recombinant AlgE was spontaneously incorporated into planar lipid bilayers, forming ion channels with a single-channel conductance of 0.76 nS in 1 M KCl and a mean lifetime of 0.7 ms. Single-channel current measurements in the presence of other salts as well as reversal potential measurements in salt gradients revealed that the AlgE channel was strongly anion selective. For chloride ions, a weak binding constant (Km = 0.75 M) was calculated, suggesting that AlgE might constitute an ion channel specific for another particular anion, e.g., polymannuronic acid, which is a precursor of alginate. Consistent with this idea, the open-state probability of the channel decreased when GDP-mannuronic acid was added. The AlgE channel was inactivated when membrane voltages higher than +85 mV were applied. The electrophysiological characteristics of AlgE, including its rectifying properties, are quite different from those of typical porins.

Amino Acid Sequence↗

PubMed1994

Characterization of type IV pilus genes in plant growth-promoting Pseudomonas putida WCS358.

In a search for factors that could contribute to the ability of the plant growth-stimulating Pseudomonas putida WCS358 to colonize plant roots, the organism was analyzed for the presence of genes required for pilus biosynthesis. The pilD gene of Pseudomonas aeruginosa, which has also been designated xcpA, is involved in protein secretion and in the biogenesis of type IV pili. It encodes a peptidase that processes the precursors of the pilin subunits and of several components of the secretion apparatus. Prepilin processing activity could be demonstrated in P. putida WCS358, suggesting that this nonpathogenic strain may contain type IV pili as well. A DNA fragment containing the pilD (xcpA) gene of P. putida was cloned and found to complement a pilD (xcpA) mutation in P. aeruginosa. Nucleotide sequencing revealed, next to the pilD (xcpA) gene, the presence of two additional genes, pilA and pilC, that are highly homologous to genes involved in the biogenesis of type IV pili. The pilA gene encodes the pilin subunit, and pilC is an accessory gene, required for the assembly of the subunits into pili. In comparison with the pil gene cluster in P. aeruginosa, a gene homologous to pilB is lacking in the P. putida gene cluster. Pili were not detected on the cell surface of P. putida itself, not even when pilA was expressed from the tac promoter on a plasmid, indicating that not all the genes required for pilus biogenesis were expressed under the conditions tested. Expression of pilA of P. putida in P. aeruginosa resulted in the production of pili containing P. putida PilA subunits.

Amino Acid Sequence↗

PubMed1994

Molecular characterization of enterobacterial pldA genes encoding outer membrane phospholipase A.

The pldA gene of Escherichia coli encodes an outer membrane phospholipase A. A strain carrying the most commonly used mutant pldA allele appeared to express a correctly assembled PldA protein in the outer membrane. Nucleotide sequence analysis revealed that the only difference between the wild type and the mutant is the replacement of the serine residue in position 152 by phenylalanine. Since mutants that lack the pldA gene were normally viable under laboratory conditions and had no apparent phenotype except for the lack of outer membrane phospholipase activity, the exact role of the enzyme remains unknown. Nevertheless, the enzyme seems to be important for the bacteria, since Western blotting (immunoblotting) and enzyme assays showed that it is widely spread among species of the family Enterobacteriaceae. To characterize the PldA protein further, the pldA genes of Salmonella typhimurium, Klebsiella pneumoniae, and Proteus vulgaris were cloned and sequenced. The cloned genes were expressed in E. coli, and their gene products were enzymatically active. Comparison of the predicted PldA primary structures with that of E. coli PldA revealed a high degree of homology, with 79% of the amino acid residues being identical in all four proteins. Implications of the sequence comparison for the structure and the structure-function relationship of PldA protein are discussed.

Amino Acid Sequence↗

PubMed1994

Identification of the iroA gene product of Neisseria meningitidis as a lactoferrin receptor.

The iroA gene product is an iron limitation-inducible outer membrane protein of Neisseria meningitidis. A spontaneous mutant lacking the gene was unable to bind lactoferrin. Furthermore, Escherichia coli strains expressing the IroA protein were capable of binding lactoferrin. Apparently, the IroA protein functions as a lactoferrin receptor.

Bacterial Outer Membrane Proteins↗

PubMed1994

PhoE protein as a carrier for foreign epitopes.

Outer membrane protein PhoE of E. coli appears to be a suitable carrier for the expression of foreign antigenic determinants at the bacterial cell-surface. Insertion of stretches of amino acids in the cell-surface exposed regions of PhoE does not interfere with the biogenesis of the protein. Dependent on the cell-surface exposed loop used for insertion and the character of the inserted amino acids up to 50 amino acids could be inserted. Both B-cell epitopes and T-cell epitopes remain antigenic and immunogenic in the PhoE-associated conformation. However, flanking amino acids can interfere with the antigenicity and immunogenicity of T-cell epitopes inserted in PhoE. Because E. coli PhoE can be expressed in attenuated Salmonella and Shigella strains, it seems to be a suitable vaccine carrier candidate.

Amino Acid Sequence↗

PubMed1993

Effect of different positively charged amino acids, C-terminally of the signal peptidase cleavage site, on the translocation kinetics of a precursor protein in Escherichia coli K-12.

Introduction of positively charged amino acids immediately downstream of the signal sequence in prokaryotic precursor proteins is known to affect the export process. However, it is not clear whether different positively charged amino acids affect the export process similarly. To investigate this, the glutamate at position +2 of outer membrane protein PhoE was substituted by arginine, lysine or histidine. Pulse-chase experiments revealed that the Lys and Arg residues at position +2 caused a reduced processing rate, and that the effect was markedly more severe in the case of the Arg residue. Trypsin accessibility experiments revealed that the accumulated precursors were present in the cytoplasm. Since the degree of the inhibitory effect corresponded to the pKa of the different positively charged amino acids, this suggests that the positively charged residues must be deprotonated during the secretory process.

Amino Acids↗

PubMed1993

Polymerase chain reaction for the specific detection of Escherichia coli/Shigella.

The outer membrane protein PhoE of members of the family Enterobacteriaceae consists of conserved membrane-spanning segments and hypervariable surface-exposed regions. Two oligonucleotides based on DNA sequences encoding two different cell-surface-exposed regions of the Escherichia coli K12 PhoE protein were tested for their specificity in polymerase chain reactions. They reacted with all strains of the species E. coli/Shigella tested, except for strain S. boydii serovar 13, which is known to represent a different DNA-relatedness group. The probes did not react with any other Enterobacteriaceae tested, including strains of Escherichia blattae, Escherichia hermanii, Escherichia vulneris and Escherichia adecarboxylata, except for an Escherichia fergusonnii strain, which is most closely related to E. coli. Therefore, the primer couple showed a high degree of species-specificity. In addition, a second primer couple based on two conserved regions of the phoE genes was tested. This primer couple recognized a broad group of closely related enteric bacteria including Salmonella and Shigella.

Bacterial Outer Membrane Proteins↗

PubMed1993

Use of the enterobacterial outer membrane protein PhoE in the development of new vaccines and DNA probes.

PhoE protein is a major outer membrane protein of Escherichia coli. The polypeptide spans the membrane 16 times, thereby exposing 8 regions at the cell surface. Insertions in these regions did not affect the biogenesis of the protein. Therefore, we considered the possibility of using PhoE as a vector for the exposure of foreign antigenic determinants at the cell surface, with the ultimate goal of constructing new (live oral) vaccines. Via recombinant DNA techniques, B-cell epitopes of VP1 protein of foot-and-mouth-disease virus were inserted in the exposed regions of PhoE. The inserted epitopes were antigenic and immunogenic in the PhoE-associated conformation. Guinea pigs, immunized with such a hybrid protein were protected against viral challenge. Similarly, a T-cell epitope of the 65 kDa heat-shock protein of Mycobacterium tuberculosis remained antigenic and immunogenic in the PhoE-associated conformation, although recognition by the cells of the immune system was dependent on the amino acids, flanking the epitope. When the amino acid sequences of the PhoE proteins of different members of the family of Enterobacteriaceae are compared, the cell surface-exposed regions are hypervariable. Therefore, we considered the possibility that the DNA segments encoding these regions are species-specific. By using synthetic oligonucleotides corresponding to such DNA segments, primer couples for the specific detection and identification of different enterobacterial species, including Salmonella, by polymerase chain reactions have been developed.

Amino Acid Sequence↗

PubMed1993

Identification and characterization of the exbB, exbD and tonB genes of Pseudomonas putida WCS358: their involvement in ferric-pseudobactin transport.

Catechol-cephalosporins are siderophore-like antibiotics which are taken up by cells of Pseudomonas putida WCS358 via the ferric-siderophore transport pathway. Mutants of strain WCS358 were isolated that are resistant to high concentrations of these antibiotics. These mutants failed to grow under iron-limiting conditions, and could not utilize different ferric-siderophores. The mutants fall in three complementation groups. The nucleotide sequence determination identified three contiguous open reading frames, which were homologous to the exbB, exbD and tonB genes of Escherichia coli respectively. The deduced amino acid sequence of P. putida ExbB showed 58.6% homology with its E. coli homologue, but, unlike the E. coli protein, it has a N-terminal extension of 91 amino acids. The ExbD proteins are 64.8% homologous, whereas the TonB proteins only show 27.7% homology. The P. putida exbB gene could complement an E. coli exbB mutation, but the TonB proteins were not interchangeable between the species. It is concluded that P. putida WCS358 contains an energy-coupling system between the membranes, for active transport across the outer membrane, which is comprised of a TonB-like energy-transducing protein and two accessory proteins. This system is similar to, but not completely compatible with, the E. coli system.

Amino Acid Sequence↗

PubMed1993

Topology of PhoE porin: the 'eyelet' region.

A model for the topology of the PhoE porin has been proposed according to which the polypeptide traverses the outer membrane sixteen times mostly as amphipathic beta-sheets, thereby exposing eight loops at the cell surface. Until now, no evidence has been obtained for the surface exposure of the third loop. Recently, the structure of porin of Rhodobacter capsulatus has been determined. The proposed model of PhoE is very similar to the structure of the R. capsulatus porin, which has an 'eyelet' region, extending into the interior of the pore. The proposed third external loop of PhoE might form a similar 'eyelet' region. To determine the location of the predicted third external loop of PhoE, multiple copies of an oligonucleotide linker encoding an antigenic determinant of VP1 protein of foot-and-mouth disease virus (FMDV) were inserted. All hybrid proteins were properly inserted in the outer membrane. The monoclonal antibody MA11, directed against the linear FMDV epitope, was able to bind only to intact cells expressing a hybrid PhoE protein with at least three copies of the FMDV epitope present. Antibiotic sensitivity tests and single-channel conductance measurements revealed that the insertions influenced the channel size. These results are consistent with a location of the third loop of PhoE within the pore channel.

Amino Acid Sequence↗

PubMed1993

Expression of the pspA gene stimulates efficient protein export in Escherichia coli.

Expression of several mutant forms of outer membrane protein PhoE of Escherichia coli, which are disturbed in normal biogenesis, resulted in high expression of a 26 kDa protein. This 26 kDa protein fractionated as a peripherally bound inner membrane protein. It appeared to be identical to a previously identified protein (PspA = phage shock protein A) of unknown function that is induced upon infection of E. coli with filamentous phages. PspA was not expressed upon synthesis of mutant PhoE proteins in a secB mutant, nor upon expression of a PhoE mutant that lacks the signal sequence, suggesting that entrance into the export pathway of prePhoE is essential for induction. PspA synthesis was also induced under other conditions that are known to block the export apparatus, i.e. in secA, secD and secF mutants when grown at their non-permissive temperature or upon induction of the synthesis of MalE-LacZ or LamB-LacZ hybrid proteins. The inducing conditions for PspA synthesis suggested a role for this protein in export. In vivo pulse-chase experiments showed that the translocation of (mutant) prePhoE and of the precursors of other exported proteins was retarded in a pspA mutant strain. Also, in in vitro translocation assays, a role for PspA in protein transport could be demonstrated.

Bacterial Outer Membrane Proteins↗

PubMed1993

Topology of the PhoR protein of Escherichia coli and functional analysis of internal deletion mutants.

The PhoR protein of Escherichia coli K-12 belongs to a family of structurally related sensor-kinases that regulate responses to environmental stimuli. These proteins are often located in the inner membrane with two membrane-spanning segments that are separated by a periplasmic domain, which is supposed to sense the environmental stimuli. However, the hydrophobicity plot of PhoR suggests a somewhat different topology in which a large periplasmic domain is lacking and an extended cytoplasmic domain is present besides the kinase domain. In protease-accessibility experiments and by using phoR-phoA gene fusions, the topology of PhoR was investigated and the absence of a large periplasmic domain was confirmed. Furthermore, the function of the extended cytoplasmic domain was studied by creating internal deletions. The mutations in this domain resulted in a constitutive expression of the pho regulon, indicating that the mutant PhoR proteins are locked in their kinase function. We propose that this extended cytoplasmic domain functions by sensing an internal signal that represses the kinase function of the PhoR protein.

Bacterial Proteins↗