Helicobacter pylori physiology predicted from genomic comparison of two strains.

Helicobacter pylori is a gram-negative bacteria which colonizes the gastric mucosa of humans and is implicated in a wide range of gastroduodenal diseases. This paper reviews the physiology of this bacterium as predicted from the sequenced genomes of two unrelated strains and reconciles these predictions with the literature. In general, the predicted capabilities are in good agreement with reported experimental observations. H. pylori is limited in carbohydrate utilization and will use amino acids, for which it has transporter systems, as sources of carbon. Energy can be generated by fermentation, and the bacterium possesses components necessary for both aerobic and anaerobic respiration. Sulfur metabolism is limited, whereas nitrogen metabolism is extensive. There is active uptake of DNA via transformation and ample restriction-modification activities. The cell contains numerous outer membrane proteins, some of which are porins or involved in iron uptake. Some of these outer membrane proteins and the lipopolysaccharide may be regulated by a slipped-strand repair mechanism which probably results in phase variation and plays a role in colonization. In contrast to a commonly held belief that H. pylori is a very diverse species, few differences were predicted in the physiology of these two unrelated strains, indicating that host and environmental factors probably play a significant role in the outcome of H. pylori-related disease.

Molecular analysis of an A-protein secretion mutant of Aeromonas salmonicida reveals a surface layer-specific protein secretion pathway.

The Aeromonas salmonicida Tn5 mutant, A449-TM1, is unable to secrete the surface layer protein (A-protein) through the outer membrane. Immunogold labeling of thin sections of A449-TM1, with polyclonal antisera against the A-protein, showed the accumulation of large quantities of A-protein in an enlarged periplasm. The majority of the labeled A-protein could be seen at the poles of the cells. The ability of A449-TM1 to secrete other extracellular proteins such as hemolysin and protease was not impaired by the Tn5 insertion, which indicates that the mutation in A449-TM1 interferes with a secretion pathway specifically for the translocation of the A-protein through the outer membrane. The mutant, A449-TM1, was shown to be avirulent for fish. A cosmid clone from a gene library of A449-TM1, which contains the Tn5 insertion from the chromosome, was used to identify a 1.4 kb SaII/ClaI fragment from immediately adjacent to the Tn5 insertion. This fragment was used to identify and clone a 4 kb HindIII fragment from a chromosomal DNA digest from the wild-type strain, A449. DNA sequence analysis of this clone identified an open reading frame (ORF) of 1656 bp. The deduced product of this ORF showed sequence similarity to a family of ATP-binding secretion proteins, but appeared to be phylogenetically distinct from these proteins, consistent with its participation in a secretory pathway specific for surface layer protein.

Tyrosine phosphorylation of the tetragonal paracrystalline array of Aeromonas hydrophila: molecular cloning and high-level expression of the S-layer protein gene.

High virulence strains of the fish pathogenic bacterium Aeromonas hydrophila produce a tetragonally arranged paracrystalline surface protein array (S-layer). The gene (ahsA) encoding the S-protein subunit of A. hydrophila TF7 was cloned into lambda EMBL 3, and sub-cloned into pUC 18. Transformation into Escherichia coli led to stable high-level expression of full-size S-protein under the control of its native promoter. The DNA sequence revealed a 1406 base-pair open reading frame encoding a protein consisting of a 19 amino acid residue signal peptide, and a 448 residue 45,400 Da molecular mass mature protein with a predicted isoelectric point (pI) of 6.72 compared with the measured M(r) of 52,000 and pI of 4.6. This suggested that the S-protein was post-translationally modified and in vivo cell labelling with [32P]orthophosphate, acid phosphatase digestion of S-protein, ascending thin-layer chromatography of partially acid hydrolysed S-protein and Western blot analysis with monoclonal anti-phosphotyrosine antibody showed that the S-protein of strain TF7 contained phosphotyrosine. S-proteins produced by the other strains of motile aeromonads tested also reacted with this anti-phosphotyrosine antibody. Cell fractionation studies employing plasmid-encoded ahsA showed that in A. hydrophila the S-protein subunits were secreted across the outer membrane by the native S-protein secretion pathway, while in E. coli and A. salmonicida the cloned A. hydrophila S-protein inserted into the outer membrane of the foreign host. These findings indicate that the process employed to translocate Aeromonas S-proteins across the outer membrane is highly specific.

Mutagenesis of the paracrystalline surface protein array of Aeromonas salmonicida by endogenous insertion elements.

The tetragonal paracrystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor and bacteria which are unable to produce A-layer are attenuated in their ability to kill fish. Ten independent mutants of Aeromonas salmonicida which were unable to produce A-layer were isolated by growth at 30 degrees C. These mutants displayed either reduced synthesis of the A-layer subunit, synthesis of a truncated subunit, or complete loss of the ability to produce the subunit protein. Restriction mapping and analysis by polymerase chain reaction showed that the mutations had resulted from insertion of two different insertion sequence (IS) elements into different sites in the A-layer subunit gene (vapA) and its promoter. Sequence comparisons indicated that ISAS1 is unique among reported IS elements. It is 1223 bp long with imperfect terminal inverted repeats of 22 bp and insertion resulted in a duplicated 8 bp target sequence in vapA. ISAS1 expressed a 42,000 molecular weight (M(r)) protein in mini-cells. ISAS2 was 1084 bp long, expressed proteins of M(r) 38,000 and 39,000 in vitro, had imperfect 29 bp terminal inverted repeats and had duplicated a 3 bp target sequence. Sequence comparisons indicated that ISAS2 was also unique to A. salmonicida; however, the proteins encoded by ISAS2 showed strong homology to the putative transposases encoded by the IS30 family of IS elements. Southern analyses showed that both ISAS1 and ISAS2 were restricted to A. salmonicida strains A449 and A450 where they were present in low copy number. The ability of these two IS elements to mutate the ability of A. salmonicida to produce its paracrystalline surface array provides a novel method for the attenuation of virulence.

Significance of duplicated flagellin genes in Campylobacter.

The complex flagellum of Campylobacter coli VC167 contains two highly related (98%) flagellin subunit proteins which are produced from two 92% homologous, tandemly orientated genes, flaA and flaB. Mutants expressing only flaA form a full-length flagellar filament that confers slightly less than wild-type motility to the bacterium. However, flagellin mutants expressing only flaB produce extremely short, truncated filaments, and are only slightly motile. We have shown that the presence of two essentially identical genes is advantageous, in that flaAflaB+ mutants become highly motile upon passage by an event which allows the production of a full length simple flagellar filament containing a single FlaA-FlaB chimeric flagellin protein. Furthermore, we have demonstrated that the reassortment of DNA that results in this chimeric protein can occur by two mechanisms: intragenomic recombination and transformation-mediated intergenomic recombination.

Distribution of surface-exposed and non-accessible amino acid sequences among the two major structural domains of the S-layer protein of Aeromonas salmonicida.

The tetragonally arranged crystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor. Circular dichroism studies in the presence or absence of 0.1% sodium dodecyl sulfate showed that the secondary structure of A-protein, and its 39,439 molecular weight amino-terminal trypsin-resistant peptide, were altered. In both cases alpha-helix was increased significantly at the expense of beta-structure when SDS was added. Western and dot immunoblotting, immuno-microscopy and enzyme-linked immunosorbent assay with monospecific polyclonal antiserum and eight monoclonal antibodies specific for epitopes exposed on the surface of native A-layer showed that the 481 residue A-protein subunit and the surface of A-layer were conserved antigenically. Mimeotope analysis of nonapeptides representing the sequence of A-protein allowed identification of 146 residues in presumed linear epitopes accessible on the surface of A-layer. Inaccessible or non-epitopic residues accounted for 70% of the protein. The majority of inaccessible residues were in the N-terminal 301 residues of A-protein. Dispersed among these were 65 surface-accessible residues in five linear epitope clusters illustrating the complex folding of this major structural domain of A-protein. The C-terminal 180 residues carried fewer linear epitopes but contained the major region of A-layers surface-accessible sequence, including four linear epitopes in predominantly hydrophobic sequence. Four A-layer surface-binding monoclonal antibodies also bound to this minor structural domain, although the epitopes of only two were identified by mimeotope analysis. The epitopes of six A-layer surface-binding monoclonals could not be identified, suggesting that A-layer may also contain conformation dependent surface epitopes.

Roles of structural domains in the morphology and surface anchoring of the tetragonal paracrystalline array of Aeromonas hydrophila. Biochemical characterization of the major structural domain.

The tetragonally arranged S-layer of Aeromonas hydrophila contains two morphological domains. The mature S-layer protein of A. hydrophila has a subunit molecular weight of 52,000, and has been reported to contain two structural domains. Here a mutant has been isolated which produces an S-layer of subunit molecular weight 38,650 as determined by sedimentation analysis. This truncated S-protein was exported via the periplasm to the cell surface, but could not self-assemble into a tetragonal array or be anchored to the cell surface. Instead the truncated protein formed cup-like structures which were purified and characterized biochemically. Automated Edman degradation showed that the truncated protein comprised the amino-terminal structural domain of the S-protein. This domain had an increased hydrophobic amino acid content relative to the wild-type protein, and contained approximately 42% beta-sheet, 10% alpha-helix, and 19% beta-turn. Differences in alpha-helix and beta-turn contents between the wild-type and truncated proteins were observed when the effects of pH and SDS were examined, indicating that the carboxy terminus influences the effects of environmental change on the conformation of the S-protein. This lesser carboxy-terminal array also appears to be required for both correct array morphology, and array anchoring, while the greater amino-terminal domain appears to comprise the major morphological core of the surface array.

Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.

Infection with Helicobacter pylori has been linked to numerous severe gastroduodenal diseases including peptic ulcer and gastric cancer. Several techniques have been used to measure the genetic heterogeneity of H. pylori at several different levels and to determine whether there is any correlation with severity of disease. The availability of two completed genome sequences from unrelated strains (J99 and 26,695) has allowed an analysis of the level of diversity from a large-scale yet detailed perspective. Although the two chromosomes are organized differently in a limited number of discrete regions, the genome size and gene order of these two "high-virulence" (cagA+ and vacA+) H. pylori isolates was found to be highly similar. The regions of organizational difference are associated with insertion sequences, DNA restriction/modification genes, repeat sequences, or a combination of the above. A significant level of variation at the nucleotide level is seen across the genome, providing an explanation for why the nucleotide-based typing techniques have such high discriminatory power among independent H. pylori isolates. This nucleotide variation together with the organizational rearrangements appears to have provided an over-estimation of the gene order diversity of H. pylori as assessed by pulse-field gel electrophoresis. Functional assignments are assigned to approximately only 60% of the gene products in each strain, with one-half of the remaining gene products of unknown function having homologues in other bacteria, while the remainder appear to be H. pylori-specific. Between 6% and 7% of the coding capacity of each strain are genes that are absent from the other strain, with almost one-half of these strain-specific genes located in a single hypervariable region called the plasticity zone. The majority of the strain-specific genes in each strain are also H. pylori-specific, with no homologues being identified in the public databases. Significantly, over one-half of the functionally assigned strain-specific genes in both H. pylori J99 and 26695 encode DNA restriction/modification enzymes. Analysis of the level of conservation between orthologues from the two strains indicates that the H. pylori specific genes have a lower level of conservation than those orthologues to which a putative function can be assigned. The plasticity zone represents one of several regions across each genome that is comprised of lower (G+C)% content DNA, some of which has been detected in self-replicating plasmids, suggesting that both horizontal transfer from other species and plasmid integration are responsible for the strain-specific diversity at this locus. These analyses have yielded results with important implications for understanding the genetic diversity of H. pylori and its associated diseases, and imply a need to reassess the respective roles of bacterial and host factors in H. pylori associated diseases.

An Aeromonas salmonicida gene required for the establishment of infection in rainbow trout (Oncorhynchus mykiss).

The asoB gene of Aeromonas salmonicida is located approximately 9 kb downstream of the structural gene (vapA) for the surface layer (A-layer). The nucleotide sequence of asoB was determined and found to encode a putative polytopic cytoplasmic membrane protein which exhibited homology to a number of bacterial transport proteins. Allele exchange mutagenesis of asoB resulted in a mutant (A449-D) which was avirulent when administered by bath immersion. However, when administered by intraperitoneal injection, A449-D is as lethal as wild type. Characterization of the phenotype of A449-D showed that there were pleiotropic effects on VapA secretion, haemolysis and outer membrane protein composition. Mobilization of cloned asoB on a broad-host-range plasmid into A449-D resulted in the complementation of VapA translocation, haemolytic activity and virulence.

Cloning, characterization and expression of the recA gene of Aeromonas salmonicida.

The Aeromonas salmonicida A449 recA gene has been cloned, sequenced and expressed in vitro. The predicted amino acid sequence of A. salmonicida RecA was determined and, when compared to other RecA, was found to possess a number of domains identical to those characterized in Escherichia coli RecA. The A. salmonicida recA was mobilized into an E. coli recA mutant strain and was shown to allow increased survival in the presence of the chemical mutagen MMS and after ultraviolet (UV) irradiation. The A. salmonicida recA also possesses a potential regulatory SOS box in the DNA 5' of the gene. The rate of A. salmonicida-mediated recombination in E. coli was increased by exposure to UV light, which suggests that SOS induction in A. salmonicida parallels that of E. coli.

Construction of new Campylobacter cloning vectors and a new mutational cat cassette.

We have developed new Campylobacter shuttle vectors which are 6.5-6.8-kb plasmids carrying Campylobacter and Escherichia coli replicons, a multiple cloning site (MCS), the lacZ alpha gene, oriT and either a kanamycin or chloramphenicol resistance-encoding gene (KmR or CmR) from Campylobacter which functions in both hosts. These vectors can be mobilized efficiently from E. coli into C. jejuni or C. coli, and stably maintained in these hosts. Plasmids pRY107 and pRY108 carry a KmR marker and 17 unique cloning sites in two different orientations in lacZ alpha, allowing easy blue/white color selection. Plasmids pRY111 and pRY112 contain a CmR gene and 17 unique sites in both orientations. In addition, MCS are flanked by T7 and T3 late promoters and M13 forward and reverse primer sites, facilitating expression in T7 or T3 expression systems and sequence analysis. A Campylobacter CmR gene cartridge, bracketed by six restriction sites, has been developed for use in site-specific mutagenesis of Campylobacter genes.

Effect of heat denaturation of target DNA on the PCR amplification.

The polymerase chain reaction (PCR) and amplification of specific regions of DNA in vitro is a widely used and powerful technique, and the optimization of conditions used to maximize PCR product yield has received much attention. We have shown that lengthy denaturation times of template DNA ranging from 1 to 7 min at pH 7.0-8.0, that are often employed prior to the start of a PCR reaction, result in marked degradation of the template. This can result in a significant reduction in the yield of PCR products larger than 500 bp, by up to 99%. This effect was demonstrated for both complex genomic template DNA, and also for a 2691-bp linear piece of template DNA using both a rapid hot-air thermocycler and a conventional block thermocycler. This decrease in product yield is likely due to the increased degradation of the template or target DNA as a result of pre-amplification denaturation (PAD). We therefore recommend that when amplifying larger pieces of DNA, the template DNA should not be exposed to PAD prior to a PCR reaction, irrespective of the starting pH of the template solution.

The synthesis, secretion and role in virulence of the paracrystalline surface protein layers of Aeromonas salmonicida and A. hydrophila.

The S-layers of the Aeromonas spp. studied to date are composed of identical protein subunits which are translocated across the cytoplasmic membrane, periplasm and outer membrane to the cell surface, where they are assembled and tethered to the cell via an interaction with the O-polysaccharide side chains of the lipopolysaccharide. Aeromonas S-layers have the ability to bind a number of host factors such as fibronectin, laminin and vitronectin as well as providing resistance to serum killing and protease digestion. Aeromonas mutants unable to produce an S-layer are altered in their ability to cause disease. In the case of Aeromonas salmonicida, the loss of ability to produce an S-layer effectively abolishes virulence. However, in the case of A. hydrophila, the reduction in virulence caused by the loss of the S-layer is less significant.

Helicobacter pylori induces an increase in inositol phosphates in cultured epithelial cells.

Helicobacter pylori is a bacterial pathogen of humans that infects the gastric mucosa. This infection has been associated with gastritis, peptic ulcers, and gastric carcinomas. Diverse in vitro studies have described efficient adherence of H. pylori to different types of epithelial cells. Because of its varied effects on host cells, we have analysed signal transduction events in H. pylori-infected epithelial cells. Our results show that H. pylori induces an increase in inositol phosphates in all cultured epithelial cells used, including HeLa, Henle 407, Hep-2, and the human gastric adenocarcinoma cell line AGS. Bacterial growth medium supernatants induce a similar response in the host cell. The increase in inositol phosphates is not related to redistribution of cytoskeletal proteins such as actin or alpha-actinin nor tyrosine-phosphorylation of host cell proteins. The inositol phosphate increase is also observed in cells infected with low or non-adherent H. pylori mutants or mutants defective in the vacuolating toxin or urease holoenzyme. These results indicate that inositol phosphate release in H. pylori-infected cells is not dependent on bacterial adherence, and that a soluble bacterial factor, but not the vacuolating toxin or urease holoenzyme, mediates such an effect.

Surface antigens of virulent strains of Aeromonas hydrophila.

Antiserum was raised in rabbits to whole cells of a representative strain from a group of A. hydrophila strains exhibiting enhanced virulence for fish. The major surface antigens of the strain were identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. The lipopolysaccharide (LPS) was examined using SDS-PAGE and silver staining. It was found to possess O polysaccharide chains of homogeneous length that were highly immunogenic. The LPS was conserved both morphologically and antigenically throughout the high virulence group. Heat-labile protein antigens were detected after absorption of the antiserum with boiled cells of the homologous strain. Only one major protein antigen, with a molecular weight of approximately 52,000, was present in outer membrane preparations or in whole cell lysates. A representative strain from the high virulence group, strain TF7, was shown by electron microscopy to be covered by a regular surface protein array (S-layer) which was found to be composed primarily of the 52 KD protein antigen. All the other members of the A. hydrophila high virulence group were shown to possess similar S-layers.

Molecular Characterization of H. pylori Surface Antigens.

Despite its clinical significance, relatively little is known about the components of Helicobacter pylori that allow it to colonize, persist, and elicit an inflammatory response within the host. Bacterial surface components frequently influence colonization and persistence of a pathogen, as well as the disease process (1). In the case of H. pylori, one macromolecular assembled protein component that is unequivocally located on the surface of the bacterium is the sheathed flagellum. Two other proteins that can be isolated in abundance from suspensions of H. pylori cells, but that are normally regarded as intracellular in other bacterial species, are urease and a GroEL analog, Hp60K (2-6). Whether these large macromolecular assemblies are surface proteins on H. pylori or are released as a result of cellular lysis is uncertain. However, numerous other intracellular proteins can be readily isolated from culture supernatants after mild shearing and extraction procedures, and these released proteins have initially been incorrectly interpreted as representing surface proteins (7-9).

Sterility of salmonid roe and practicality of hatching gnotobiotic salmonid fish.

The ventral surface of spawning salmonid fish was opened aseptically and the roe were removed aseptically. Roe obtained by using this technique were demonstrated to be sterile. Aseptic fertilization and incubation of eggs obtained in this manner resulted in the hatching of gnotobiotic salmonid fish.