Recent advances in Schistosoma genomics.

Schistosome research has entered the genomic era with the publications reporting the Schistosoma mansoni and Schistosoma japonicum genomes. Schistosome genomics is motivated by the need for new control tools. However, much can also be learned about the biology of Schistosoma, which is a tractable experimental model. In this article, we review the recent achievements in the field of schistosome research and discuss future perspectives on genomics and how it can be integrated in a usable format, on the genetic mapping and how it has improved the genome assembly and provided new research approaches, on how epigenetics provides interesting insights into the biology of the species and on new functional genomics tools that will contribute to the understanding of the function of genes, many of which are parasite- or taxon specific.

Small gene family encoding an eggshell (chorion) protein of the human parasite Schistosoma mansoni.

We have isolated six independent genomic clones encoding schistosome chorion or eggshell proteins from a Schistosoma mansoni genomic library. A linkage may of five of the clones spanning 35 kilobase pair (kbp) of the S. mansoni genome was constructed. The region contained two eggshell protein genes closely linked, separated by 7.5 kbp of intergenic DNA. The two genes of the cluster were arranged in the same orientation, that is, they were transcribed from the same strand. The sixth clone probably represents a third copy of the eggshell gene that is not contained within the 35-kbp region. The 5' end of the mRNA transcribed from these genes was defined by primer extension directly off the RNA. The ATCAT cap site sequence was homologous to a silkmoth chorion PuTCATT cap site sequence, where Pu indicates any purine. DNA sequence analysis showed that there were no introns in these genes. The DNA sequences of the three genes were very homologous to each other and to a cDNA clone, pSMf61-46, differing only in three or four nucleotides. A multiple TATA box was located at positions -23 to -31, and a CAAAT sequence was located at -52 upstream of the eggshell transcription unit. Comparison of sequences in regions further upstream with silkmoth and Drosophila sequences revealed several very short elements that were shared. One such element, TCACGT, recently shown to be an essential cis-regulatory element for silkmoth chorion gene promoter function, was found at a similar position in all three organisms.

DNA probes for identifying chromosomes 5, 6, and 7 of Schistosoma mansoni.

Schistosoma mansoni has a genome of 270 Mb contained on 8 pairs of chromosomes. C-banding has been a useful technique in identifying the 7 autosomal and sex chromosomes. However, even with C-banding, S. mansoni chromosomes 5, 6, and 7 are difficult to discriminate from each other, because of their small sizes, morphological similarity, and poor banding patterns. We have identified probes that specifically paint chromosomes 5, 6, and 7 of S. mansoni with the use of chromosome microdissection and the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). Exact chromosome identification is required for accurate chromosome mapping of genomic clones and genetic elements, which is an essential component of the schistosome genome project.

Monitoring the efficacy of drugs for neglected tropical diseases controlled by preventive chemotherapy.

In the last decade, pharmaceutical companies, governments and global health organisations under the leadership of the World Health Organization (WHO) have pledged large-scale donations of anthelmintic drugs, including ivermectin (IVM), praziquantel (PZQ), albendazole (ALB) and mebendazole (MEB). This worldwide scale-up in drug donations calls for strong monitoring systems to detect any changes in anthelmintic drug efficacy. This review reports on the outcome of the WHO Global Working Group on Monitoring of Neglected Tropical Diseases Drug Efficacy, which consists of three subgroups: (i) soil-transmitted helminthiases (ALB and MEB); (ii) onchocerciasis and lymphatic filariasis (IVM); and (iii) schistosomiasis (PZQ). Progress of ongoing work, challenges and research needs for each of the four main drugs used in helminthic preventive chemotherapy (PC) are reported, laying the ground for appropriate implementation of drug efficacy monitoring programmes under the co-ordination and guidelines of the WHO. Best practices for monitoring drug efficacy should be made available and capacity built as an integral part of neglected tropical disease (NTD) programme monitoring. Development of a disease-specific model to predict the impact of PC programmes, to detect outliers and to solicit responses is essential. Research studies on genetic polymorphisms in relation to low-efficacy phenotypes should be carried out to identify markers of putative resistance against all NTD drugs and ultimately to develop diagnostic assays. Development of combination and co-administration of NTD drugs as well as of new drug entities to boost the armamentarium of the few drugs available for NTD control and elimination should be pursued in parallel.

Cloning the gene encoding Schistosoma mansoni p50, an immunophilin.

A 2.2-kb fragment of genomic DNA encoding Schistosoma mansoni immunophilin p50 (Smp50) was identified on a 14-kb genomic clone. The sequence of Smp50 reveals seven exons interrupted by six small introns ranging from 28-35 bp in size. The transcription start point, defined by primer extension analysis of schistosome RNA, begins at 30 bp upstream from the start AUG codon. Smp50 lacks a TATA box and appears to be a single-copy gene.

RXR-2, a member of the retinoid x receptor family in Schistosoma mansoni.

A cDNA encoding a second full-length member of the Schistosoma mansoni RXR family (SmRXR-2) was identified. The nucleotide sequence of SmRXR-2 translates into a protein of 784 amino acids with a pI of 7.63 and an approximate mass of 78kDa making it the largest reported RXR to date. Phylogenetic tree analysis provides evidence that SmRXR-2 is the most ancient full-length RXR identified. SmRXR-2 exhibits unique sequence features compared with other RXRs. RT-PCR results demonstrate that the SmRXR-2 gene is constitutively expressed and thus must play multiple roles throughout schistosome development in the vertebrate host.

Characterization of the Ras homologue of Schistosoma mansoni.

Ras is a member of a super-family of guanine-binding or G-proteins. Ras functions as a molecular switch in the transduction of signals generated by the activation of a variety of cell surface receptors and relays the signals to downstream effectors. Little is known about signal transduction in schistosomes. In order for Schistosoma mansoni to survive different immune responses triggered by the host as well as to migrate from the site of penetration at the skin to the final destination in portal circulation, they must receive signals from the host environment and respond to them in a way that allows their survival. We have isolated the schistosome Ras cDNA by using sequence information of the schistosome Ras homologue submitted to the Genbank database. Analysis of the encoded peptide revealed 81% identity and 92% similarity with K-Ras from various species. Ras is a single copy gene as determined by quantitative hybridization experiments. The cDNA was cloned into pGEX-4T and the expressed peptide was used to generate specific antibody reagents. Affinity purified antibodies identified a 23 kDa native protein that localizes to the subtegument. Ras is not associated with the tegument. Ras is expressed in all the developmental stages of the parasite. However, Ras is over-expressed in female worms compared to males. Schistosome Ras was also shown to be post-translationally modified by addition of farnesyl isoprenoid moiety to the cysteine residue in the C-terminal box. Using a schistosome extract in vitro SmRas farnesylation was inhibited by the farnesyl transferase inhibitor, FTI-277, at concentrations comparable to those required to inhibit K-Ras processing. These initial studies on signal transduction in schistosomes should provide a solid basis for improving our understanding of schistosome-host interactions.

Schistosoma mansoni p48 eggshell protein gene: characterization, developmentally regulated expression and comparison to the p14 eggshell protein gene.

Egg production by worm pairs is a major cause of pathogenesis in schistosomiasis. To further the understanding of female reproductive development, we have isolated and characterized a complete copy of an eggshell protein precursor gene, p48. Sequence analysis reveals that the gene has 3 open reading frames and does not contain an intron. One of the open reading frames, ORF1, encodes a polypeptide of 50 kDa which shows strong homology to insect chorion proteins. Determination of the position of the mRNA cap-site facilitated identification of putative regulatory elements in the 5' upstream region of the gene. Some of these elements (e.g., TCACGT) have been shown to play a role in the regulation of chorion gene expression in insects. p48 mRNA is detectable only in mature female worms and the ability to detect the mRNA coincides temporally with worm pairing. Quantitative comparisons, during female reproductive development, of p48 transcripts to those from another eggshell protein precursor gene, p14, show that the p48 mRNA is significantly less abundant than p14 mRNA. In mature female worms, p48 mRNA can only be detected in vitelline cells. Antibodies made against the polypeptide sequence deduced from ORF1 of the p48 gene recognize a 50-kDa molecule in extracts from mature female worms, but not in extracts from immature females or males.

Identification and functional characterization of a member of the PUR-alpha family from Schistosoma mansoni.

Schistosoma mansoni p14 gene encodes an eggshell precursor that is expressed only in vitelline cells of mature female worms in response to a male stimulus. The upstream region of the p14 gene contains several potential cis-acting regulatory sequences. We used the upstream region of the p14 gene as bait in a yeast-one-hybrid screen of a S. mansoni cDNA library to identify interacting proteins. We report the identification and characterization of a cDNA (S. mansoni PUR-alpha (SmPUR-alpha)) encoding a protein homologous to single-stranded DNA transcription activator PUR-alpha, that binds to the p14 upstream region and activates transcription of the HIS3 reporter gene in yeast. SmPUR-alpha has a predicted molecular mass of 30 kDa and shares an overall homology of 63% with mammalian PUR-alpha. The DNA binding domain of SmPUR-alpha is highly conserved. We show by gel shift assays that GST-SmPUR-alpha binds to oligonucleotides comprising the p14 upstream region. SmPUR-alpha binds preferentially to single-stranded DNA and also binds RNA. Unlike the mammalian homologue, SmPUR-alpha exhibits little specificity for the PUR element GGn, but shows strong preference for a sequence containing alternating pyrimidines. Our data support that SmPUR-alpha is a single-copy gene and through reverse transcriptase-polymerase chain reaction and in situ hybridization, we show that SmPUR-alpha is constitutively transcribed in many cell types and thus likely plays a role as a general transcription activator in schistosomes.

Organization of the ribosomal RNA genes in Schistosoma mansoni.

The organization of the rRNA genes of Schistosoma mansoni has been determined by Southern blot analysis of genomic DNA digested with restriction enzymes, by isolation of the entire repeat on a single fragment of about 11 kilobase pairs from a genomic DNA library constructed in bacteriophage lambda and by characterization of three cloned EcoRI fragments which span the entire repeat. The segments encoding both the large and small rRNA subunits have been identified using specific cloned yeast rDNA fragments as probes and EcoRI, HindIII and BamHI restriction enzyme maps of the rRNA genes were constructed. The ends of the RNAs have been precisely mapped on the genomic DNA by S1 protection experiments. Our data indicate that the rRNA genes are present as a tight cluster. The total length of the rDNA repeat is about 10 kilobase pairs. There appears to be no variation in the size of transcribed and non-transcribed spacer DNA. At the RNA level we have characterized and mapped a small gap in the 28S RNA molecule. The interruption causes the RNA to dissociate into two equal sized fragments when analyzed under denaturing conditions.

Characterization of a 54-nucleotide gap region in the 28S rRNA gene of Schistosoma mansoni.

We have analyzed 572 bp in the 28S rDNA of the human blood fluke Schistosoma mansoni which correspond to expansion segment 5 of domain IV as defined by Clark et al. for the Xenopus laevis 28S rRNA. S1 nuclease mapping and primer extension analysis comparing this region with the mature 28S rRNA indicate that there are 54 nucleotides present in the 28S rDNA which are absent from the mature rRNA. This defines a gap that creates two 28S rRNA subunits (28S alpha and 28S beta). Comparison of the S. mansoni sequence with rDNAs of other organisms which contain gaps in their 28S rRNA shows that the overall features are conserved except that the S. mansoni gap is less A + T-rich. The conserved features include: (1) the location of the gap within the 28S rRNA; (2) the predicted secondary structure of the gap, containing a stem-loop with a UAAU sequence within the loop; and (3) a conserved CGAAAGGG on the 3' side of the gap.

Characterization of Sm20.8, a member of a family of schistosome tegumental antigens.

Two cDNA clones each encoding a 20.8-kDa protein (Sm20.8) were identified from the human blood fluke Schistosoma mansoni sporocyst and adult worm cDNA expression libraries by antibodies derived from rabbits vaccinated with irradiated cercariae and purified over an NP-40 extract of 3h schistosomula. Each identified cDNA has an open reading frame encoding a protein of 181 amino acids and shows homology (29-30%) with Sm21.7, Sm22.6, and Sj22.6, previously identified as belonging to a family of soluble schistosome tegumental antigens. An EF-hand calcium-binding motif is found in Sm20.8 protein in two different positions. However, neither motif binds 45calcium (45Ca) Recombinant Sm20.8 showed immunoreactivity with sera from infected humans and rabbits vaccinated with irradiated cercariae. Polyclonal rabbit sera against the Sm20.8 recognized the native protein in an extract of infected snail (sporocyst), cercariae, 3 hour schistosomules (3 h NP-40) and an adult worm preparation but not in uninfected snail tissue or eggs. Further demonstration that Sm20.8 was expressed in the different developmental stages of the parasite was by RT-PCR. Confocal microscopy demonstrates that Sm20.8 localizes to the tegument of adult worms and 3 h np-40. The IgG fraction specific to Sm20.8 mediated complement killing of schistosomules in vitro by 34%. Vaccination of mice with naked DNA containing the Sm20.8 gene and subsequently challenged with cercariae showed 30% reduction in worm burden compared to controls.

Evaluation of Schistosoma mansoni retinoid X receptor (SmRXR1 and SmRXR2) activity and tissue distribution.

Recently, we reported the identification of cDNA's encoding retinoid X receptor (RXR) homologues in Schistosoma mansoni. RXRs are known to be involved in the regulation of genes important for homeostasis and development. Previous studies indicated that SmRXR1 plays a role in the regulation of the female-specific gene, p14. Herein, we report that SmRXR2 also binds to cis-elements present in the p14 upstream region when evaluated in yeast reporter strains. SmRXR2 shows a pattern of recognition of cis-sequences present in the p14 gene upstream region different than SmRXR1. However, the SmRXR2 C (DNA binding) domain binds promiscuously in electrophoretic mobility shift assays to cis-elements of the p14 upstream region. The SmRXRs differ in their ability to activate transcription. The N-terminal A/B domain of SmRXR1 is necessary and sufficient for autonomous transcription activation function (AF) in yeast. SmRXR2 does not exhibit an equivalent autonomous AF. SmRXR1 and SmRXR2 fail to dimerize when investigated both in the yeast two-hybrid system and in immunoprecipitation experiments. In situ hybridization experiments using paraffin sections of adult worms demonstrate that SmRXR1 and SmRXR2 exhibit both common and unique cell type distribution which indicates that SmRXR1 and SmRXR2 both play a role in regulating gene expression in certain cells, yet each plays a distinct role in modulating the expression of genes in other cell types. Both SmRXR1 and SmRXR2 localize to vitelline cells. These studies provide a solid basis for improving our understanding of RXRs and their importance in female-specific gene regulation.

A cloned DNA probe identifies the sex of Schistosoma mansoni cercariae.

This report describes a method for the identification of the sex of Schistosoma mansoni cercariae using a cloned DNA probe which is female-specific. The probe is a 339 bp repeat; the sequence is presented. Cercariae from nine mono-miracidially infected snails were used in a double blind study. Mice were infected and the sex of adult worms observed. DNA was isolated from cercariae, digested with EcoRI, subjected to agarose gel electrophoresis, transferred to a matrix and hybridized with the cloned female-specific DNA probe. In all nine cases the sex of the cercariae as determined by DNA analysis agreed with the sex of the adult parasites.

Y-box binding protein from Schistosoma mansoni: interaction with DNA and RNA.

A Schistosoma mansoni homologue of the human Y-box binding protein (SMYB1), as well as truncated proteins containing its N-terminal Cold Shock Domain (CSD) or its C-terminal domain (TAIL) were cloned into the p-MAL-c2 expression vector and produced in Escherichia coli. In order to characterize the interactions of these proteins to an inverted CCAAT motif present in a number of gene promoters, their binding to DNA was measured by Electrophoretic Mobility Shift Assays. SMYB1 bound to single- and double-stranded DNA containing the CCAAT motif and could bind also to RNA. The truncated CSD and TAIL domain proteins bound to dsDNA and RNA, but exhibited distinct binding patterns. Protein-DNA interaction was also investigated in vivo, using the Yeast One-Hybrid System. The plasmid constructs were GSTTRI, a DNA fragment composed of three copies of the CCAAT motif of the S. mansoni glutathione S-transferase gene promoter and four oligonucleotides spanning different regions of the S. mansoni p14 gene promoter. None of the yeast clones transformed with the above plasmids was able to grow in selective medium or to activate the transcription of the HIS3 reporter gene, suggesting that SMYB1 could not interact with these promoters in vivo.

Identification and characterization of Schistosoma mansoni p17.7, a cyclophilin.

Antibodies affinity purified against tegumental components of schistosomula were used to screen a Schistosoma mansoni lambda gt11 adult worm cDNA expression library. One of the reactive clones was determined by sequence analysis to encode a protein homologous to cyclophilins of other species, in particular cyclophilin A. The 0.8-kb cDNA clone contained an open reading frame of 483 nucleotides which corresponds to a translation product of 161 amino acids with a deduced molecular size of 17.7 kDa. We have chosen to designate this clone as S. mansoni p17.7 (Smp17.7). The overexpressed and purified recombinant Smp17.7 (rSmp17.7) was demonstrated to possess peptidylprolyl cis-trans isomerase (PPIase) or rotamase activity typical of cyclophilins. Western blot analysis of Nonidet P-40 and a total soluble extract of adult schistosomes probed with affinity-purified antisera to rSmp17.7, demonstrated the presence of this protein in the parasite. Immunofluorescence studies using the purified antisera indicates a localization in various tissues including the tegument and the gut. As cyclophilin is able to interact with cyclosporin A (CsA), which has been shown to be antischistosomal in mice infected with S. mansoni, the characterization of this S. mansoni cyclophilin homologue may allow a better understanding of the schistosomicidal nature of cyclosporin A and lead to a novel strategy of therapy for schistosomiasis.

Cloning of the gene for phosphoglycerate kinase from Schistosoma mansoni and characterization of its gene product.

As molecules on the surface or associated with the outer covering (tegument) of Schistosoma mansoni are a major focus as potential vaccine candidates, affinity purified antibodies which are specific to the tegumental antigens were used to immunoscreen a lambda gt11 S. mansoni cercarial cDNA library. One of the identified clones was found to encode the glycolytic enzyme phosphoglycerate kinase (PGK, EC 2.7.2.3). The 1.5-kb cDNA clone has a single open reading frame encoding 416 amino acids and exhibits over 60% identity to PGKs from a number of eukaryotic species. Recombinant S. mansoni PGK (SmPGK) was overexpressed in Escherichia coli, purified, and shown to have PGK enzyme activity. Native protein affinity purified from S. mansoni adult worms was shown by microsequencing to have the same amino-acid sequence as deduced from the cDNA sequence, thus confirming the cDNA clone we identified encodes S. mansoni phosphoglycerate kinase. Antibodies localize the native SmPGK to various tissues including the tegument of 3-h schistosomula and 42-day adult worms.

Yeast artificial chromosome (YAC)-based genome mapping of Schistosoma mansoni.

Schistosoma mansoni has 7 pairs of autosomal chromosomes and one pair of sex chromosomes (ZZ for a male worm and ZW for a female), of a haploid genome size of 2.7 x 10(8) bp. We initiated the molecular genetic approach for the detailed characterization and understanding of the evolutionary biology of schistosomes. We have constructed a yeast artificial chromosome (YAC)-library with partially digested parasite genomic DNA, and the chromosome location of each insert was detected by fluorescent in situ hybridization (FISH). The library contains > 2283 clones with an average insert size of 358 kb, which represents a 2.6-fold coverage of the genome (> 7.2 x 10(8) bp). 100 randomly selected YAC clones were localized by FISH and found to be distributed widely among all chromosomes. The assembly of 14 YACs distributed almost the whole region of chromosome 3. Generated expressed sequenced tags (ESTs) derived from a unidirectional cDNA library were also used for further characterization of the YAC inserts. These results indicate that an extensive contig assembly of the entire chromosomes and a reasonably detailed gene map should be feasible in the near future.

Amebocytic accumulations in Biomphalaria glabrata: fine structure.

Internal pathologic conditions in four stocks of Biomphalaria glabrata involve amebocytes. Most snails exhibiting these conditions are also nonsusceptible to infection with Schistosoma mansoni. Fine structure studies reveal that periaortic and atrial amebocytic accumulations show two responses that involve heart tissue: a generalized response in which amebocytes have infiltrated the myocardium and focal areas of nodules in which heart tissue is encapsulated and destroyed. In pericardial accumulations amebocytes are subspherical at the periphery with their numerous filopodia intertwining; centrally they elongate and flatten to form a nodule. Hemocoelic accumulations are similar to pericardial ones but more compact. Hyalinocytes and granulocytes were both found in the four types of amebocytic accumulations; each contained phagocytized material. Acid phosphatase reaction product was detected in the Golgi bodies, primary phagosomes, multivesicular bodies and myelin bodies of granulocytes.

Fractionated sera from Schistosoma mansoni infected patients confers passive protection in mice.

Sera from humans with chronic Schistosoma mansoni infections (CHS) were chromatographed with CNBr-activated Sepharose 4 B conjugated with NP-40 extracts obtained from live 3 hr schistosomula. Both unbound (CHSUB) and bound (CHSB) fractions which contained IgG and IgM isotypes were characterized by ELISA, immunofluorescence, and complement-mediated in vitro killing assays. ELISA data showed that the CHSB fraction recognized schistosomula NP-40 extracts, whereas the CHSUB fraction did not. However, both CHSUB and CHSB fractions recognized 8 M urea adult worm extracts and 8 M urea egg extracts. By indirect immunofluorescence assay, the CHSB fraction recognized epitopes on the surface of live schistosomula 3 hr-29 days of age, whereas the CHSUB fraction showed surface fluorescence only on 24- and 29-day-old worms. The CHSB fraction mediated 95% killing of schistosomula in a complement dependent in vitro assay, the CHSUB fraction and the unfractionated CHS did not exhibit killing ability. The CHSUB fraction was able to titrate out the killing ability of the CHSB fraction in in vitro cytotoxic assays when mixed with the CHSB fraction at increasing concentrations. In passive immunization experiments, the CHSB fraction provided approximately 30% passive protection in mice when injected 1 day or 6 days after challenge and 20% protection when injected at 15 days, but failed to provide protection when administered greater than or equal to 24 days after challenge. Unfractionated CHS failed to mediate passive protection.