Schistosoma gene discovery project update

The Brazilian contribution to the study of the Schistosoma mansoni transcriptome

Brazilian scientists have made definitive contributions towards the understanding of the transcriptome of Schistosoma mansoni. The transcriptome, as a collection of expressed genes, was studied with two basic approaches, the sequencing of cloned cDNA ends and the production and sequencing of random fragments of cDNA. The data that was generated covers nearly the entire set of transcribed genes. These data have been important for gene discovery and annotation of gene function, annotation of the genome, construction of microarrays, identification of peptides in the study of the proteome and can be mined for splice variants, polymorphisms such as single nucleotide polymorphisms and microsatellites, for example. This review will describe the advances achieved with the contribution of Brazilian researchers to the understanding of the transcribed regions of the S. mansoni genome.

The Schistosoma mansoni transcriptome: an update

Large scale EST sequencing projects have been carried out for Schistosoma mansoni and Schistosoma japonicum. This update will briefly review the most recent accomplishments in the area and discuss the use of EST data for the purposes of gene discovery, gene model development, genome annotation and SNP analysis. In addition, the use of ESTs for studying other features of the transcriptome such as splice site and transcription initiation variants will be discussed as well as approaches to assigning function to unknown transcripts. Although EST sequencing has contributed much for schistosome research, other data mining possibilities exist, including the identification of putative drug and vaccine targets.

Schistosoma mansoni genome project: an update

A schistosome genome project was initiated by the World Health Organization in 1994 with the notion that the best prospects for identifying new targets for drugs, vaccines, and diagnostic development lie in schistosome gene discovery, development of chromosome maps, whole genome sequencing and genome analysis. Schistosoma mansoni has a haploid genome of 270 Mb contained on 8 pairs of chromosomes. It is estimated that the S. mansoni genome contains between 15000 and 25000 genes. There are approximately 16689 ESTs obtained from diverse libraries representing different developmental stages of S. mansoni, deposited in the NCBI EST database. More than half of the deposited sequences correspond to genes of unknown function. Approximately 40-50% of the sequences form unique clusters, suggesting that approximately 20-25% of the total schistosome genes have been discovered. Efforts to develop low resolution chromosome maps are in progress. There is a genome sequencing program underway that will provide 3X sequence coverage of the S. mansoni genome that will result in approximately 95% gene discovery. The genomics era has provided the resources to usher in the era of functional genomics that will involve microarrays to focus on specific metabolic pathways, proteomics to identify relevant proteins and protein-protein interactions to understand critical parasite pathways. Functional genomics is expected to accelerate the development of control and treatment strategies for schistosomiasis.

Genome and genomics of schistosomes

Schistosomes infect over 200 million people and 600 million are at risk. Genomics and post-genomic studies of schistosomes will contribute greatly to developing new reagents for diagnostic purposes and new vaccines that are of interest to the biotechnology industry. In this review, the most recent advances in these fields as well as new projects and future perspectives will de described. A vast quantity of data is publicly available, including short cDNA and genomic sequences, complete large genomic fragments, and the mitochondrial genomes of three species of the genus Schistosoma. The physical structure of the genome is being studied by physically mapping large genomic fragments and characterizing the highly abundant repetitive DNA elements. Bioinformatic manipulations of the data have already been carried out, mostly dealing with the functional analysis of the genes described. Specific search tools have also been developed. Sequence variability has been used to better understand the phylogeny of the species and for population studies, and new polymorphic genomic markers are currently being developed. The information generated has been used for the development of post-genomic projects. A small microarray detected genes that were differentially expressed between male and female worms. The identification of two-dimensional spots by mass spectrometry has also been demonstrated.

Molecular characterization of an interleukin-4-inducing factor from Schistosoma mansoni eggs

The eggs of the parasitic trematode Schistosoma mansoni are powerful inducers of a T helper type 2 (Th2) immune response and immunoglobulin E (IgE) production. S. mansoni egg extract (SmEA) stimulates human basophils to rapidly release large amounts of interleukin (IL)-4, the key promoter of a Th2 response. Here we show purification and sequence of the IL-4-inducing principle of S. mansoni eggs (IPSE). Stimulation studies with human basophils using SmEA fractions and natural and recombinant IPSE as well as neutralization and immunodepletion studies using antibodies to recombinant IPSE demonstrate that IPSE is the bioactive principle in SmEA leading to activation of basophils and to expression of IL-4 and IL-13. Regarding the mechanism of action, blot analysis showed that IPSE is an IgE-binding factor, suggesting that it becomes effective via cross-linking receptor-bound IgE on basophils. Immunohistology revealed that IPSE is enriched in and secreted from the subshell area of the schistosome egg. We conclude from these data that IPSE may be an important parasite-derived component for skewing the immune response toward Th2.

The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences

Expressed sequence tag (EST) sequencing and analysis is a primary research tool to identify and characterize the Schistosoma mansoni transcriptome. As part of our gene discovery effort, a total of 5,793 ESTs have been generated from clones selected randomly from complementary DNA (cDNA) libraries constructed from male and female adult worms. Assembly analysis of all the 16,813 public S. mansoni ESTs has identified 1,920 distinct tentative consensus sequences (TCs) and 5,571 nonoverlapping ESTs (singletons). Of these, 376 TCs (20%) and 1,449 singletons (26%) are unique to the SUNY/TIGR sequencing effort. Tentative consensus sequences and singletons were distributed into various categories of biological roles associated with cell structure, metabolism, protein fate, signal transduction, transcription, protein synthesis, transporters, and cell growth. The TCs and singletons represent transcripts that can be used as a resource for functional annotation of genomic sequence data, comparative sequence analysis, and cDNA clone selection for microarray projects. The utility of EST analysis is demonstrated by identifying new protease genes, which may be involved in hemoglobin degradation.

Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.