SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum

A novel Schistosoma japonicum endonuclease homologous to DNase II

Background

Recent advances in studies of the Schistosoma japonicum genome have opened new avenues for the elucidation of parasite biology and the identification of novel targets for vaccines, drug development and early diagnostic tools.

Results

In this study, we surveyed the S. japonicum genome database for genes encoding nucleases. A total of 130 nucleases of 3 classes were found. Transcriptional analysis of these genes using a genomic DNA microarray revealed that the majority of the nucleases were differentially expressed in parasites of different developmental stages or different genders, whereas no obvious transcriptional variation was detected in parasites from different hosts. Further analysis of the putative DNases of S. japonicum revealed a novel DNase II homologue (Sjda) that contained a highly conserved catalytic domain. A recombinant Sjda-GST protein efficiently hydrolysed genomic DNA in the absence of divalent iron. Western-blot and immunofluorescence assays showed that Sjda was mainly expressed on the teguments of female adult parasites and induced early humoral immune responses in infected mice.

Conclusions

A novel DNase II homologue, Sjda, was identified in S. japonicum. Sjda was mainly distributed on the teguments of adult female parasites and possessed a typical divalent iron-independent DNA catalytic activity. This protein may play an important role in the host–parasite interaction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1319-5) contains supplementary material, which is available to authorized users.

Inferences on the biochemical and environmental regulation of universal stress proteins from Schistosomiasis parasites

BACKGROUND

Human schistosomiasis is a freshwater snail-transmitted disease caused by parasitic flatworms of the Schistosoma genus. Schistosoma haematobium, Schistosoma mansoni, and Schistosoma japonicum are the three major species infecting humans. These parasites undergo a complex developmental life cycle, in which they encounter a plethora of environmental signals. The presence of genes encoding the universal stress protein (USP) domain in the genomes of Schistosoma spp. suggests these flatworms are equipped to respond to unfavorable conditions. Though data on gene expression is available for USP genes, their biochemical and environmental regulation are incompletely understood. The identification of additional regulatory molecules for Schistosoma. USPs, which may be present in the human, snail, or water environments, could also be useful for schistosomiasis interventions.

METHODS

We developed a protocol that includes a visual analytics stage to facilitate integration, visualization, and decision making, from the results of sequence analyses and data collection on a set of 13 USPs from S. mansoni and S. japonicum.

RESULTS

Multiple sequence alignment identified conserved sites that could be key residues regulating the function of USPs of the Schistosoma spp. Based on the consistency and completeness of sequence annotation, we prioritized for further research the gene for a 184-amino-acid-long USP that is present in the genomes of the three human-infecting Schistosoma spp. Calcium, zinc, and magnesium ions were predicted to interact with the protein product of the gene.

CONCLUSION

Given that the initial effects of praziquantel on schistosomes include the influx of calcium ions, additional investigations are required to (1) functionally characterize the interactions of calcium ions with the amino acid residues of Schistosoma USPs; and (2) determine the transcriptional response of Schistosoma. USP genes to praziquantel. The data sets produced, and the visual analytics views that were developed, can be easily reused to develop new hypotheses.

Proteomics analysis of differentially expressed proteins in schistosomula and adult worms of Schistosoma japonicum

Schistosoma japonicum has a complex lifecycle and exhibits dramatic changes in its biology and morphology at different developmental stages. The schistosomulum and adult worm are two stages of this complex lifecycle and differentially expressed proteins in these two stages should be important for survival, development, and reproduction of the parasites. In this study, soluble and hydrophobic proteins were extracted from eggs, cercariae, schistosomula (8d and 19d), and male and female adult worms (42d) of Schistosoma japonicum, and separated by two-dimensional (2D) gel electrophoresis. A total of 1376±52, 928±61, 1465±41, 1230±30, 904±34, and 1080±26 soluble proteins and 1437±44, 845±53, 986±22, 1145±35, 1066±39, and 1123±45 hydrophobic proteins were separated from eggs, cercariae, schistosomula (8d and 19d), and male and female adult worms (42d), respectively. There were 65±14, 27±7, 37±17 and 48±9 soluble protein spots only present in schistosomula (8d and/or 19d) and adult schistosomes (male and/or female). We successfully identified 22 spots from schistosomula and 11 spots from adult schistosomes by mass spectrometry. Quantitative real-time RT-PCR was used to examine six differentially expressed proteins at the transcription level. These proteins only found in schistosomula or adults stage by the proteomics analysis were highly expressed in the corresponding stage at mRNA level. Bioinformatics analysis showed that the differentially expressed proteins from schistosomula were mainly involved in cellular metabolic processes, stress response and developmental process. Differentially expressed proteins from adult schistosomes were involved with gene expression and protein metabolism processes. The results of this study might provide new insights to stimulate further exploration of the mechanism of growth and development in schistosomes and help identify candidate molecules for developing new vaccines or drugs.

Transcriptional responses of in vivo praziquantel exposure in schistosomes identifies a functional role for calcium signalling pathway member CamKII

Treatment for clinical schistosomiasis has relied centrally on the broad spectrum anthelmintic praziquantel; however, there is limited information on its mode of action or the molecular response of the parasite. This paper presents a transcriptional and functional approach to defining the molecular responses of schistosomes to praziquantel. Differential gene expression in Schistosoma japonicum was investigated by transcriptome-wide microarray analysis of adult worms perfused from infected mice after 0.5 to 24 hours after oral administration of sub-lethal doses of praziquantel. Genes up-regulated initially in male parasites were associated with "Tegument/Muscle Repair" and "Lipid/Ion Regulation" functions and were followed by "Drug Resistance" and "Ion Regulation" associated genes. Prominent responses induced in female worms included up-regulation of "Ca(2+) Regulation" and "Drug Resistance" genes and later by transcripts of "Detoxification" and "Pathogen Defense" mechanisms. A subset of highly over-expressed genes, with putative drug resistance/detoxification roles or Ca(2+)-dependant/modulatory functions, were validated by qPCR. The leading candidate among these was CamKII, a putative calcium/calmodulin-dependent protein kinase type II delta chain. RNA interference was employed to knockdown CamKII in S. japonicum to determine the role of CamKII in the response to praziquantel. After partial-knockdown, schistosomes were analysed using IC50 concentrations (50% worm motility) and quantitative monitoring of parasite movement. When CamKII transcription was reduced by 50-69% in S. japonicum, the subsequent effect of an IC50 dosage of praziquantel was exacerbated, reducing motility from 47% to 27% in female worms and from 61% to 23% in males. These observations indicated that CamKII mitigates the effects of praziquantel, probably through stabilising Ca(2+) fluxes within parasite muscles and tegument. Together, these studies comprehensively charted transcriptional changes upon exposure to praziquantel and, notably, identified CamKII as potentially central to the, as yet undefined, mode of action of praziquantel.

Differences in genomic architecture between two distinct geographical strains of the blood fluke Schistosoma japonicum reveal potential phenotype basis

The Chinese (SjC) and Philippine (SjP) strains of the blood fluke Schistosoma japonicum have been shown to present clearly different phenotypes in fecundity, pathology, drug sensitivity and immunology. We used microarray based comparative genomic hybridisation (aCGH) to investigate structural differences in the genomes of the two strains and identified seven distinct regions of the S. japonicum genome that present differential aCGH representing either deletion or duplication regions in SjP. Within these regions, genes predicted to be associated with the recognised phenotypic differences were identified and that may provide new insights into the biology and evolution of the two strains, with implications for the epidemiology and control of schistosomiasis japonica in China and the Philippines.

SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags

Background

Sparganum (plerocercoid of Spirometra erinacei) is a parasite that possesses the remarkable ability to survive by successfully modifying its physiology and morphology to suit various hosts and can be found in various tissues, even the nervous system. However, surprisingly little is known about the molecular function of genes that are expressed during the course of the parasite life cycle. To begin to decipher the molecular processes underlying gene function, we constructed a database of expressed sequence tags (ESTs) generated from sparganum.

Findings

SpiroESTdb is a web-based information resource that is built upon the annotation and curation of 5,655 ESTs data. SpiroESTdb provides an integrated platform for expressed sequence data, expression dynamics, functional genes, genetic markers including single nucleotide polymorphisms and tandem repeats, gene ontology and KEGG pathway information. Moreover, SpiroESTdb supports easy access to gene pages, such as (i) curation and query forms, (ii) in silico expression profiling and (iii) BLAST search tools. Comprehensive descriptions of the sparganum content of all sequenced data are available, including summary reports. The contents of SpiroESTdb can be viewed and downloaded from the web (http://pathod.cdc.go.kr/spiroestdb).

Conclusions

This integrative web-based database of sequence data, functional annotations and expression profiling data will serve as a useful tool to help understand and expand the characterization of parasitic infections. It can also be used to identify potential industrial drug targets and vaccine candidate genes.

Identification of novel antigens within the Schistosoma japonicum tetraspanin family based on molecular characterization

Tetraspanins (TSPs) are proteins found on the surface of the parasite Schistosoma mansoni that have been regarded as potential protective antigens. However, divergent evolution may occur among the species of S. mansoni and Schistosoma japonicum under different environmental pressure. Thus, it was essential to characterize the S. japonicum TSP family members before selecting potential candidate TSP antigens. In this study, we used bioinformatics and experimental validation to investigate 29 TSP members from S. japonicum, including all known genes, Sj23, TE736, Sj25, and Sj-TSP-2. Five TSP members were found to be variable, and two others (Sj-tsp genes) were alternatively spliced. The phylogenetic analysis showed that schistosome TSPs were highly divergent from those of other phyla. Quantitative RT-PCR revealed that the Sj-tsp genes were differentially transcribed in the developmental stages of cercariae, schistosomula, adult worms, and eggs. Six Sj-tsp genes were significantly up-regulated during the transformation from cercariae to schistosomula. Four Sj-tsp genes, including Sj-tsp-1, Sj-tsp-8, Sj-tsp-14, and Sj-tsp-26 were confirmed as potential protective antigens based on the molecular characterization. RNAi was preformed against the conserved Sj-tsp genes which were highly expressed in schistosomula to explore gene functions. These data will promote the identification of candidate antigens within the TSP family for developing novel vaccines against S. japonicum infections.

A portrait of the transcriptome of the neglected trematode, Fasciola gigantica--biological and biotechnological implications

Fasciola gigantica (Digenea) is an important foodborne trematode that causes liver fluke disease (fascioliasis) in mammals, including ungulates and humans, mainly in tropical climatic zones of the world. Despite its socioeconomic impact, almost nothing is known about the molecular biology of this parasite, its interplay with its hosts, and the pathogenesis of fascioliasis. Modern genomic technologies now provide unique opportunities to rapidly tackle these exciting areas. The present study reports the first transcriptome representing the adult stage of F. gigantica (of bovid origin), defined using a massively parallel sequencing-coupled bioinformatic approach. From >20 million raw sequence reads, >30,000 contiguous sequences were assembled, of which most were novel. Relative levels of transcription were determined for individual molecules, which were also characterized (at the inferred amino acid level) based on homology, gene ontology, and/or pathway mapping. Comparisons of the transcriptome of F. gigantica with those of other trematodes, including F. hepatica, revealed similarities in transcription for molecules inferred to have key roles in parasite-host interactions. Overall, the present dataset should provide a solid foundation for future fundamental genomic, proteomic, and metabolomic explorations of F. gigantica, as well as a basis for applied outcomes such as the development of novel methods of intervention against this neglected parasite.

Fasciola gigantica (Digenea) is a socioeconomically important liver fluke of humans and other mammals. It is the predominant cause of fascioliasis in the tropics and has a serious impact on the lives of tens of millions of people and other animals; yet, very little is known about this parasite and its relationship with its hosts at the molecular level. Here, advanced sequencing and bioinformatic technologies were employed to explore the genes transcribed in the adult stage of F. gigantica. From >20 million raw reads, >30,000 contiguous sequences were assembled. Relative levels of transcription were estimated; and molecules were characterized based on homology, gene ontology, and/or pathway mapping. Comparisons of the transcriptome of F. gigantica with those of other trematodes, including F. hepatica, showed similarities in transcription for molecules predicted to play roles in parasite-host interactions. The findings of the present study provide a foundation for a wide range of fundamental molecular studies of this neglected parasite, as well as research focused on developing new methods for the treatment, diagnosis, and control of fascioliasis.

RNA interference in Schistosoma mansoni schistosomula: selectivity, sensitivity and operation for larger-scale screening

BACKGROUND

The possible emergence of resistance to the only available drug for schistosomiasis spurs drug discovery that has been recently incentivized by the availability of improved transcriptome and genome sequence information. Transient RNAi has emerged as a straightforward and important technique to interrogate that information through decreased or loss of gene function and identify potential drug targets. To date, RNAi studies in schistosome stages infecting humans have focused on single (or up to 3) genes of interest. Therefore, in the context of standardizing larger RNAi screens, data are limited on the extent of possible off-targeting effects, gene-to-gene variability in RNAi efficiency and the operational capabilities and limits of RNAi.

METHODOLOGY/PRINCIPAL FINDINGS

We investigated in vitro the sensitivity and selectivity of RNAi using double-stranded (ds)RNA (approximately 500 bp) designed to target 11 Schistosoma mansoni genes that are expressed in different tissues; the gut, tegument and otherwise. Among the genes investigated were 5 that had been previously predicted to be essential for parasite survival. We employed mechanically transformed schistosomula that are relevant to parasitism in humans, amenable to screen automation and easier to obtain in greater numbers than adult parasites. The operational parameters investigated included defined culture media for optimal parasite maintenance, transfection strategy, time- and dose-dependency of RNAi, and dosing limits. Of 7 defined culture media tested, Basch Medium 169 was optimal for parasite maintenance. RNAi was best achieved by co-incubating parasites and dsRNA (standardized to 30 µg/ml for 6 days); electroporation provided no added benefit. RNAi, including interference of more than one transcript, was selective to the gene target(s) within the pools of transcripts representative of each tissue. Concentrations of dsRNA above 90 µg/ml were directly toxic. RNAi efficiency was transcript-dependent (from 40 to >75% knockdown relative to controls) and this may have contributed to the lack of obvious phenotypes observed, even after prolonged incubations of 3 weeks. Within minutes of their mechanical preparation from cercariae, schistosomula accumulated fluorescent macromolecules in the gut indicating that the gut is an important route through which RNAi is expedited in the developing parasite.

CONCLUSIONS

Transient RNAi operates gene-selectively in S. mansoni newly transformed schistosomula yet the sensitivity of individual gene targets varies. These findings and the operational parameters defined will facilitate larger RNAi screens.

Our wormy world genomics, proteomics and transcriptomics in East and southeast Asia

Helminths are the cause of some of the major infectious diseases of humanity in what is still a "wormy" world. There is, in East and Southeast Asia, a high prevalence of several helminthiases which occur primarily in rural, impoverished areas of low-income and developing countries throughout the tropics and subtropics. Subsequent to various parasite genome projects that commenced in the early 1990s, under the aegis of the World Health Organization (WHO), the draft genomes of three major helminth species (Schistosoma japonicum, S. mansoni and Brugia malayi) have been sequenced, and many other helminth parasites have now been targeted for intensive genomics investigation. The continuing release of genome sequences has catalyzed the emergence of transcriptomics, proteomics and related "-omics" analyses of helminth parasites, which provide unprecedented approaches to understanding their biology that will result in new clues for the development of novel control interventions. In this review, we present a summary of current approaches employed in helminth "-omics" studies and review recent advances in helminth genomics and post-genomics in the Southeast Asian setting.

Culture for genetic manipulation of developmental stages of Schistosoma mansoni

Genomes of the major human helminth parasites, and indeed many others of agricultural significance, are now the research focus of intensive genome sequencing and annotation. A draft genome sequence of the filarial parasite Brugia malayi was reported in 2007 and draft genomes of two of the human schistosomes, Schistosoma japonicum and S. mansoni reported in 2009. These genome data provide the basis for a comprehensive understanding of the molecular mechanisms involved in schistosome nutrition and metabolism, host-dependent development and maturation, immune evasion and invertebrate evolution. In addition, new potential vaccine candidates and drug targets will likely be predicted. However, testing these predictions is often not straightforward with schistosomes because of the difficulty and expense in maintenance of the developmental cycle. To facilitate this goal, several developmental stages can be maintained in vitro for shorter or longer intervals of time, and these are amenable to manipulation. Our research interests focus on experimental studies of schistosome gene functions, and more recently have focused on development of transgenesis and RNA interference with the longer term aim of heritable gene manipulation. Here we review methods to isolate and culture developmental stages of Schistosoma mansoni, including eggs, sporocysts, schistosomules and adults, in particular as these procedures relate to approaches for gene manipulation. We also discuss recent advances in genetic manipulation of schistosomes including the deployment of square wave electroporation to introduce reporter genes into cultured schistosomes.

Helminth genomics: The implications for human health

More than two billion people (one-third of humanity) are infected with parasitic roundworms or flatworms, collectively known as helminth parasites. These infections cause diseases that are responsible for enormous levels of morbidity and mortality, delays in the physical development of children, loss of productivity among the workforce, and maintenance of poverty. Genomes of the major helminth species that affect humans, and many others of agricultural and veterinary significance, are now the subject of intensive genome sequencing and annotation. Draft genome sequences of the filarial worm Brugia malayi and two of the human schistosomes, Schistosoma japonicum and S. mansoni, are now available, among others. These genome data will provide the basis for a comprehensive understanding of the molecular mechanisms involved in helminth nutrition and metabolism, host-dependent development and maturation, immune evasion, and evolution. They are likely also to predict new potential vaccine candidates and drug targets. In this review, we present an overview of these efforts and emphasize the potential impact and importance of these new findings.

Exposed proteins of the Schistosoma japonicum tegument

The ability of the mammalian blood fluke Schistosoma japonicum to survive in the inhospitable environment of the mammalian bloodstream can be attributed, at least in part, to its host-exposed outer surface, called the tegument. The tegument is a dynamic organ and is involved in nutrition, immune evasion and modulation, excretion, osmoregulation and signal transduction. Given its importance for parasite survival, proteins exposed to the host at the surface of the tegument are ideal targets for the development of vaccines and drugs. By biotinylating live adult worms and using a combination of OFFGEL electrophoresis and tandem mass spectrometry 54 proteins were identified as putatively host-exposed in S. japonicum. These included glucose transport proteins, an amino permease, a leucine aminopeptidase and a range of transporters, heat shock proteins and novel immune-active proteins. Members of the tetraspanin protein family and a homologue of Sm 29, a tegument membrane protein from Schistosoma mansoni, both effective vaccine antigens in S. mansoni, were also identified. The fate of labelled surface proteins was monitored over time using electron microscopy and revealed that biotinylated proteins were rapidly internalised from the surface of the tegument and trafficked into the cytoplasmic bridges that connect the distal cytoplasm of the tegument to the underlying cell bodies. The results reported herein dramatically increase the number of S. japonicum proteins known to be exposed to the host and, hence, those of interest as therapeutic targets. The ability of the parasite to rapidly internalise proteins at its surface has implications for the development of vaccines and may explain how these parasites are able to avoid the host immune system for long periods of time.

Schistosoma genomics: new perspectives on schistosome biology and host-parasite interaction

Schistosomiasis, caused mainly by Schistosoma japonicum, S. mansoni, and S. hematobium, remains one of the most prevalent and serious parasitic diseases worldwide. The blood flukes have a complex life cycle requiring adaptation for survival in fresh water as free-living forms and as parasites in snail intermediate and vertebrate definitive hosts. Functional genomics analyses, including transcriptomic and proteomic approaches, have been performed on schistosomes, in particular S. mansoni and S. japonicum, using powerful high-throughput methodologies. These investigations have not only chartered gene expression profiles across genders and developmental stages within mammalian and snail hosts, but have also characterized the features of the surface tegument, the eggshell and excretory-secretory proteomes of schistosomes. The integration of the genomic, transcriptomic, and proteomic information, together with genetic manipulation on individual genes, will provide a global insight into the molecular architecture of the biology, pathogenesis, and host-parasite interactions of the human blood flukes. Importantly, these functional genomics analyses lay a foundation on which to develop new antischistosome vaccines as well as drug targets and diagnostic markers for treatment and control of schistosomiasis.

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

BACKGROUND

Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available.

RESULTS

A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs.

CONCLUSION

The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.

A wake up call for urinary schistosomiasis: reconciling research effort with public health importance

This review considers the current status of urinary schistosomiasis, caused by infection with Schistosoma haematobium, and argues that greater research effort and focus are needed to improve understanding of this neglected tropical disease (NTD). The inappropriateness of relying solely on data concerning the much more extensively studied intestinal form of schistosomiasis caused by S. mansoni is highlighted. The current lack of genome and transcriptome information for S. haematobium is directly hindering further targeted research and must be quickly rectified. Recent molecular phylogenies caution the expectation of similarities between schistosome species and highlight the close relationships of species within the S. haematobium group. Treatment, current and prospective drugs and vaccines, together with diagnosis are considered, highlighting the differences associated with urinary schistosomiasis. This infection has a significant and specific impact on the urino-genital system and has a strong association with bladder cancer, leading to severe and chronic morbidity. There is a clear need for new clinical initiatives in this area to better quantify the disease burden. Furthermore, emerging associations with HIV and other pathogens need to be closely monitored. Research is urgently needed to improve current knowledge in order to develop the next generation of control tools.

Schistosomes--proteomics studies for potential novel vaccines and drug targets

Schistosomiasis is a major health problem and, despite decades of research, only one effective drug, Praziquantel is currently available. Recent expansion of sequence databases on Schistosoma mansoni and S. japonicum has permitted a wealth of novel proteomic studies on several aspects of the organization and development of the parasite in the human host. This unprecedented accumulation of molecular data is allowing a more rational approach to propose drug targets and vaccine candidates, such as proteins located at the parasite surface. Successful preliminary trials of two vaccine candidates that have been detected at the parasite surface by proteomics give grounds for believing that such an approach may provide a fresh start for the field.