Helicobacter pylori and Schistosoma japonicum co-infection in a Chinese population: helminth infection alters humoral responses to H. pylori and serum pepsinogen I/II ratio.

The effects of helminth infection on humoral IgG responses and clinical outcome of gastric Helicobacter pylori infection are unknown. IgG and IgG subclass responses to H. pylori and serum pepsinogen I/II ratio, a marker of gastric atrophy, were investigated in a Schistosoma japonicum prevalent Chinese population. H. pylori, CagA and IgG subclass responses were assayed by ELISA. Serum pepsinogen I and pepsinogen II were assayed by ELISA and the pepsinogen I/II ratio determined. In 150 subjects, infection with S. japonicum and H. pylori was 55.3% and 51.3%, respectively. H. pylori IgG titres and CagA seropositivity were significantly lower (P<0.05) in co-infected subjects, and differences in H. pylori IgG isotype responses were evident. In H. pylori positives, a significantly higher (P<0.05) pepsinogen I/II ratio was observed in co-infected subjects. The difference between S. japonicum positive and negative subjects was only evident in H. pylori CagA seronegative subjects. In conclusion, S. japonicum co-infection with H. pylori is associated with alterations in IgG responses to H. pylori and less gastric atrophy.

TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins.

TMB-Hunt is a program that uses a modified k-nearest neighbour (k-NN) algorithm to classify protein sequences as transmembrane beta-barrel (TMB) or non-TMB on the basis of whole sequence amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, a discrimination accuracy of 92.5% was achieved, as tested using a rigorous cross-validation procedure. The TMB-Hunt web server, available at www.bioinformatics.leeds.ac.uk/betaBarrel, allows screening of up to 10,000 sequences in a single query and provides results and key statistics in a simple colour coded format.

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.

BACKGROUND: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes. RESULTS: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure. A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings. CONCLUSION: TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection.

ShAR1alpha and ShAR1beta: novel putative nicotinic acetylcholine receptor subunits from the platyhelminth blood fluke Schistosoma.

The cDNAs for two novel neuronal-type nicotinic acetylcholine receptor (nAChR) subunits have been cloned and characterised from the parasitic trematode blood fluke Schistosoma haematobium. One of these encodes a putative nAChR alpha-subunit named ShAR1alpha, whilst the second encodes a potential non-alpha subunit, ShAR1beta. These ShARs possess the key structural features common to all nAChRs, but they are unusual in that they have very large cytoplasmic domains spanning M3 and M4. Overall, the ShAR1alpha and ShAR1beta proteins share 37% identity and 53% similarity, but excluding the residues of the M3-M4 domain this rises to 52% identity and 71% similarity. Sequence comparisons with other nAChR polypeptides indicate that both ShARs are most similar to the invertebrate alpha7-like subunits identified in insects and nematodes, and to the vertebrate subunits alpha7 and alpha8. Outside of the M3-M4 domain, 45% and 40%, respectively, of the ShAR1alpha and ShAR1beta residues are conserved in the ACR-16 subunit from Caenorhabditis elegans. Phylogenetic analysis suggests that the ShARs share a common lineage with members of the ACR-16 group as well as alpha7 and alpha8. Immunolocalisation studies revealed distinct and non-overlapping patterns of distribution for ShAR1alpha and ShAR1beta within the parasite. ShAR1beta was localised within the musculature and on discrete cell bodies within the connective parenchyma. In contrast, ShAR1alpha was localised exclusively to the surface membranes, suggesting it may contribute to the regulatory nAChR we have characterised previously. In Xenopus oocyte expression studies, ShAR1alpha did not form functional channels on its own or in combination with ShAR1beta or the chick beta2 subunit. Furthermore, a chimera in which the M3-M4 domain of ShAR1alpha was replaced with that of chick alpha7 was also non-functional. We discuss our findings in the context of the proposed role for surface nAChRs in the regulation of glucose uptake in the parasite, and the potential exploitation of these receptors as targets for cholinergic schistosomicides.

Mapping and sequencing of acetylcholinesterase genes from the platyhelminth blood fluke Schistosoma.

Acetylcholinesterase (AChE) on the surface of the parasitic blood fluke Schistosoma is the likely target for schistosomicidal anticholinesterases. Determination of the molecular structure of this drug target is key for the development of improved anticholinesterase drugs and potentially a novel vaccine. We have recently cloned the cDNA encoding the AChE from the human parasite Schistosoma haematobium and succeeded in expressing functional recombinant protein. We now describe the cloning and molecular characterisation of homologues from two other schistosome species-Schistosoma mansoni and Schistosoma bovis, which are important parasites of man and cattle, respectively, but which differ in their sensitivity to the therapeutic anticholinesterase metrifonate. Comparison of the deduced amino acid sequences revealed that the AChE from all three species posses a high degree of identity, with conservation of all of the residues known to be important for substrate binding and catalytic activity. Also conserved is a unique C-terminal domain which is unusual in that it lacks the consensus for GPI modification, even though the native protein is considered to be GPI-anchored. We have also established the AChE gene structures for all three species and cloned the complete gene for S. haematobium AChE. The gene structure is relatively complex, comprising nine coding exons; the location of the splice sites is identical in all three species, but the size of the introns varies considerably. The two C-terminal splicing sites that are conserved in all species are also present in Schistosoma, but a third C-terminal conserved splicing site which is located 11-13 amino acids upstream of the histidine of the catalytic triad in all invertebrate AChE genes characterised to date is absent. We discuss our findings in the context of the molecular phylogeny of the AChE genes and the potential application to the control of schistosomiasis.

Molecular characterization of an acetylcholinesterase implicated in the regulation of glucose scavenging by the parasite Schistosoma.

Acetylcholinesterase (AChE) present on the surface of the trematode blood fluke Schistosoma has been implicated in the regulation of glucose scavenging from the host blood. Determination of the molecular structure and functional characteristics of this molecule is a crucial first step in understanding the novel function for AChE and in evaluating the potential of schistosome AChE as a target of new parasite control methods. We have determined the primary structure of acetylcholinesterase from Schistosoma haematobium. Immunolocalization studies confirmed that the enzyme was present on the parasite surface as well as in the muscle. The derived amino acid sequence possesses features common to acetylcholinesterases: the catalytic triad, six cysteines that form three intramolecular disulphide bonds, and aromatic residues lining the catalytic gorge. An unusual feature is that the fully processed native enzyme exists as a glycoinositol phospholipid (GPI)-anchored dimer, but the sequence of the C?terminus does not conform to the current consensus for GPI modification. The enzyme expressed in Xenopus oocytes showed conventional substrate specificity and sensitivity to established inhibitors of AChE, although it is relatively insensitive to the peripheral site inhibitor propidium iodide. Distinctions between host and parasite AChEs will allow the rational design of schistosome-specific drugs and vaccines.