Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions

Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber's pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 "mixed" proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host-parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.

Excretion/secretion products from Schistosoma mansoni adults, eggs and schistosomula have unique peptidase specificity profiles

Schistosomiasis is one of a number of chronic helminth diseases of poverty that severely impact personal and societal well-being and productivity. Peptidases (proteases) are vital to successful parasitism, and can modulate host physiology and immunology. Interference of peptidase action by specific drugs or vaccines can be therapeutically beneficial. To date, research on peptidases in the schistosome parasite has focused on either the functional characterization of individual peptidases or their annotation as part of global genome or transcriptome studies. We were interested in functionally characterizing the complexity of peptidase activity operating at the host-parasite interface, therefore the excretory-secretory products of key developmental stages of Schistosoma mansoni that parasitize the human were examined. Using class specific peptidase inhibitors in combination with a multiplex substrate profiling assay, a number of unique activities derived from endo- and exo-peptidases were revealed in the excretory-secretory products of schistosomula (larval migratory worms), adults and eggs. The data highlight the complexity of the functional degradome for each developmental stage of this parasite and facilitate further enquiry to establish peptidase identity, physiological and immunological function, and utility as drug or vaccine candidates.

Schistosomiasis in Egypt: A never-ending story?

Schistosomiasis has plagued the Egyptian population since the antiquity. The disease is still a public health problem in Egypt, despite the tendency of being overlooked. In the first part of this review, the past and current trends of schistosomiasis in Egypt are reviewed, including history, epidemiology, morbidity, therapy, and control of the disease. Most of these aspects are more or less relevant to other schistosome-endemic regions all over the world. As only one drug is currently available for individual treatment and preventive mass chemotherapy, the quest for complementary measures is urgently warranted. Indeed, one promising approach is the discovery of a vaccine. Herein, we point out the efforts of the Egyptian scientists to develop an efficacious and affordable vaccine against schistosomiasis - a step forward in the battle of elimination of Schistosoma infection. Based on the candidate vaccine antigens, four types of vaccine formulations are discussed: purified antigen vaccines, DNA constructs, attenuated cercariae, and excretory-secretory antigen vaccines. Finally, this review provides insights into this ancient seemingly long-lasting parasitic disease.

Kicking in the Guts: Schistosoma mansoni Digestive Tract Proteins are Potential Candidates for Vaccine Development

Schistosomiasis is a debilitating disease that represents a major health problem in at least 74 tropical and subtropical countries. Current disease control strategies consist mainly of chemotherapy, which cannot prevent recurrent re-infection of people living in endemic area. In the last decades, many researchers made a remarkable effort in the search for an effective vaccine to provide long-term protection. Parasitic platyhelminthes of Schistosoma genus, which cause the disease, live in the blood vessels of definitive hosts where they are bathed in host blood for many years. Among the most promising molecules as vaccine candidates are the proteins present in the host–parasite interface, so numerous tegument antigens have been assessed and the achieved protection never got even close to 100%. Besides the tegument, the digestive tract is the other major site of host–parasite interface. Since parasites feed on blood, they need to swallow a considerable amount of blood for nutrient acquisition. Host blood ingested by schistosomes passes through the esophagus and reaches the gut where many peptidases catalyze the proteolysis of blood cells. Recent studies show the emergence of antigens related to the parasite blood feeding, such as esophageal gland proteins, proteases, and other proteins related to nutrient uptake. Herein, we review what is known about Schistosoma mansoni digestive tract proteins, emphasizing the ones described as potential vaccine candidates.

Expression profile of the Schistosoma japonicum degradome reveals differential protease expression patterns and potential anti-schistosomal intervention targets

Blood fluke proteases play pivotal roles in the processes of invasion, nutrition acquisition, immune evasion, and other host-parasite interactions. Hundreds of genes encoding putative proteases have been identified in the recently published schistosome genomes. However, the expression profiles of these proteases in Schistosoma species have not yet been systematically analyzed. We retrieved and culled the redundant protease sequences of Schistosoma japonicum, Schistosoma mansoni, Echinococcus multilocularis, and Clonorchis sinensis from public databases utilizing bioinformatic approaches. The degradomes of the four parasitic organisms and Homo sapiens were then comparatively analyzed. A total of 262 S. japonicum protease sequences were obtained and the expression profiles generated using whole-genome microarray. Four main clusters of protease genes with different expression patterns were identified: proteases up-regulated in hepatic schistosomula and adult worms, egg-specific or predominantly expressed proteases, cercaria-specific or predominantly expressed proteases, and constantly expressed proteases. A subset of protease genes with different expression patterns were further validated using real-time quantitative PCR. The present study represents the most comprehensive analysis of a degradome in Schistosoma species to date. These results provide a firm foundation for future research on the specific function(s) of individual proteases and may help to refine anti-proteolytic strategies in blood flukes.

Parasite proteases play critical roles in host-parasite interactions and thus are considered to be potential anti-schistosomal targets. Although numerous schistosome proteases have been predicted based on recently published genomes, no systematic analysis of their expression in Schistosoma species has been performed. Thus, we comparatively analyzed the degradomes of four parasitic organisms and human host, and performed whole-genome microarray analysis to analyze the expression profile of the Schistosoma japonicum degradome at four developmental stages. The expression profile generated for the S. japonicum degradome was divided into four main clusters with different expression patterns, and a subset of selected proteases were further validated using real-time quantitative PCR. Our work is the most comprehensive analysis of a degradome in Schistosoma species to date. Many protease genes were first characterized in blood flukes, and some could be treated as potential anti-schistosomal targets for intensive research in the future. The results provide a firm foundation for deep study on the specific function(s) of individual proteases or protease families in schistosomes.

Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium

Background

Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets.

Results

Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases.

Conclusion

Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-428) contains supplementary material, which is available to authorized users.

Cysteine peptidases as schistosomiasis vaccines with inbuilt adjuvanticity

Schistosomiasis is caused by several worm species of the genus Schistosoma and afflicts up to 600 million people in 74 tropical and sub-tropical countries in the developing world. Present disease control depends on treatment with the only available drug praziquantel. No vaccine exists despite the intense search for molecular candidates and adjuvant formulations over the last three decades. Cysteine peptidases such as papain and Der p 1 are well known environmental allergens that sensitize the immune system driving potent Th2-responses. Recently, we showed that the administration of active papain to mice induced significant protection (P<0.02, 50%) against an experimental challenge infection with Schistosoma mansoni. Since schistosomes express and secrete papain-like cysteine peptidases we reasoned that these could be employed as vaccines with inbuilt adjuvanticity to protect against these parasites. Here we demonstrate that sub-cutaneous injection of functionally active S. mansoni cathepsin B1 (SmCB1), or a cathepsin L from a related parasite Fasciola hepatica (FhCL1), elicits highly significant (P<0.0001) protection (up to 73%) against an experimental challenge worm infection. Protection and reduction in worm egg burden were further increased (up to 83%) when the cysteine peptidases were combined with other S. mansoni vaccine candidates, glyceraldehyde 3-phosphate dehydrogenase (SG3PDH) and peroxiredoxin (PRX-MAP), without the need to add chemical adjuvants. These studies demonstrate the capacity of helminth cysteine peptidases to behave simultaneously as immunogens and adjuvants, and offer an innovative approach towards developing schistosomiasis vaccines

Evolutionary histories of expanded peptidase families in Schistosoma mansoni

Schistosoma mansoni is one of the three main causative agents of human schistosomiasis, a major health problem with a vast socio-economic impact. Recent advances in the proteomic analysis of schistosomes have revealed that peptidases are the main virulence factors involved in the pathogenesis of this disease. In this context, evolutionary studies can be applied to identify peptidase families that have been expanded in genomes over time in response to different selection pressures. Using a phylogenomic approach, we searched for expanded endopeptidase families in the S. mansoni predicted proteome with the aim of contributing to the knowledge of such enzymes as potential therapeutic targets. We found three endopeptidase families that comprise leishmanolysins (metallopeptidase M8 family), cercarial elastases (serine peptidase S1 family) and cathepsin D proteins (aspartic peptidase A1 family). Our results suggest that the Schistosoma members of these families originated from successive gene duplication events in the parasite lineage after its diversification from other metazoans. Overall, critical residues are conserved among the duplicated genes/proteins. Furthermore, each protein family displays a distinct evolutionary history. Altogether, this work provides an evolutionary view of three S. mansoni peptidase families, which allows for a deeper understanding of the genomic complexity and lineage-specific adaptations potentially related to the parasitic lifestyle.

Schistosomiasis: from drug deployment to drug development

PURPOSE OF REVIEW

Schistosomiasis is a chronic and morbid disease that affects hundreds of millions of the poorest individuals in (sub)tropical regions, particularly sub-Saharan Africa. Just one drug, praziquantel (PZQ), is available. As discussed, efforts to expand mass drug administration programs may accelerate the emergence of resistance. In addition, PZQ's peculiar pharmacological profile and undefined mechanism of action(s) complicate discriminating incomplete efficacy from true resistance. Accordingly, and in spite of the challenges associated with developing new antischistosomals as discussed herein, alternatives to PZQ should be identified. Various strategies to do this are highlighted here.

RECENT FINDINGS

The last 2 years have witnessed more engagement of the necessary infrastructure combined with the application of the latest strategies and technologies to facilitate antischistosomal drug discovery. Preclinical and clinical evaluation of new chemistries has benefited from various consortia and institutions that underwrite drug development for antiparasitics in general. Drug repositioning, target-based drug design, improved automation for compound screening, genomics and functional genomics are just some of the tools now being applied to identify possible new drugs and drug targets.

SUMMARY

The new momentum toward the discovery of alternatives to PZQ is encouraging but needs to be sustained by a stronger advocacy for drug development, in addition to drug deployment.

A snapshot of the Ixodes scapularis degradome

Parasitic encoded proteases are essential to regulating interactions between parasites and their hosts and thus they represent attractive anti-parasitic druggable and/or vaccine target. We have utilized annotations of Ixodes scapularis proteases in gene bank and version 9.3 MEROPS database to compile an index of at least 233 putatively active and 150 putatively inactive protease enzymes that are encoded by the I. scapularis genome. The 233 putatively active protease homologs hereafter referred to as the degradome (the full repertoire of proteases encoded by the I. scapularis genome) represent ~1.14% of the 20485 putative I. scapularis protein content. Consistent with observations in other animals, the content of the I. scapularis degradome is ~6.0% (14/233) aspartic, ~19% (44/233) cysteine, ~40% (93/233) metallo, ~28.3% (66/233) serine and ~6.4% (15/233) threonine proteases. When scanned against other tick sequences, ~11% (25/233) of I. scapularis putatively active proteases are conserved in other tick species with ≥ 60% amino acid identity levels. The I. scapularis genome does not apparently encode for putatively inactive aspartic proteases. Of the 150 putative inactive protease homologs none are from the aspartic protease class, ~8% (12/150) are cysteine, ~58.7% (88/150) metallo, 30% (45/150) serine and ~3.3% (5/150) are threonine proteases. The I. scapularis tick genome appears to have evolutionarily lost proteolytic activity of at least 6 protease families, C56 and C64 (cysteine), M20 and M23 (metallo), S24 and S28 (serine) as revealed by a lack of the putatively active proteases in these families. The overall protease content is comparable to other organisms. However, the paucity of the S1 chymotrypsin/trypsin-like serine protease family in the I. scapularis genome where it is ~12.7% (28/233) of the degradome as opposed to ~22-48% content in other blood feeding arthropods, Pediculus humanus humanus, Anopheles gambiae, Aedes Aegypti and Culex pipiens quinquefasciatus is notable. The data is presented as a one-stop index of proteases encoded by the I. scapularis genome.

Gene Atlasing of digestive and reproductive tissues in Schistosoma mansoni

Background

While considerable genomic and transcriptomic data are available for Schistosoma mansoni, many of its genes lack significant annotation. A transcriptomic study of individual tissues and organs of schistosomes could play an important role in functional annotation of the unknown genes, particularly by providing rapid localisation data and thus giving insight into the potential roles of these molecules in parasite development, reproduction and homeostasis, and in the complex host-parasite interaction.

Methodology/Principal Findings

Quantification of gene expression in tissues of S. mansoni was achieved by a combination of laser microdissection microscopy (LMM) and oligonucleotide microarray analysis. We compared the gene expression profile of the adult female gastrodermis and male and female reproductive tissues with whole worm controls. The results revealed a total of 393 genes (contigs) that were up-regulated two-fold or more in the gastrodermis, 4,450 in the ovary, 384 in the vitelline tissues of female parasites, and 2,171 in the testes. We have also supplemented these data with the identification of highly expressed genes in different regions of manually dissected male and female S. mansoni. Though relatively crude, this dissection strategy provides low resolution localisation data for critical regions of the adult parasites that are not amenable to LMM isolation.

Conclusions

This is the first detailed transcriptomic study of the reproductive tissues and gastrodermis of S. mansoni. The results obtained will help direct future research on the functional aspects of these tissues, expediting the characterisation of currently unannotated gene products of S. mansoni and the discovery of new drug and vaccine targets.

There is currently only one drug available for treatment of schistosomiasis mansoni and no vaccine. The searches for possible new drug and vaccine candidates remain two major areas of current research in schistosomiasis. There are considerable amounts of data available on the genomics, transcriptomics and proteomics of Schistosoma mansoni from which useful candidates for future drug and vaccine development can be identified. Arranging these data into a biologically relevant context through the characterisation of gene expression profiles of the different tissues of this complex metazoan parasite, is an essential step in identifying molecules with potential therapeutic value. We have used laser microdissection microscopy and microarray analysis to show that many tissue-specific genes are up-regulated in the digestive and reproductive tissues of S. mansoni. This new knowledge provides an avenue to investigate the molecular components associated with fundamental aspects of schistosome biology.

Cytogenetic study of the effect of Schistosoma mansoni infection on human peripheral blood lymphocytes and the role of β-carotene and vitamin E in modulating this effect

This study has been made to determine the potential genotoxicity of Schistosoma mansoni on lymphocytes of infected patients using different mutagenic end points. The protective role of antioxidants pro vitamin β-carotene and vitamin E in minimizing these genotoxic effect was also studied. The study focused on the effect of schistosomiasis on the induction of sister chromatid exchange (SCEs) and other chromosomal aberrations. This work was conducted on 24 Schistosoma mansoni infected patients and 10 healthy adults as a control group. Lymphocytes from peripheral blood of patients and control group were used for culture and subsequent cytogenetic studies. The results indicated that schistosomiasis was genotoxic in all examined tests. It induced a significant increase in the percentage of structural chromosomal aberrations and the frequency of SCEs. It also inhibited cell division and caused cell cycle delay. Lymphocyte cultures of S. mansoni patients treated with 10 μg/ml β-carotene or 20 mg/ml vitamin E showed a significant decrease in the percentage of structural chromosomal aberrations and the frequency of SCEs. Schistosomiasis has a genotoxic effect on peripheral blood lymphocytes. The use of the antioxidants β-carotene and vitamin E can be considered a promising approach not only toward inhibiting the genetic damage of schistosomiasis but also as prophylactic agents against infection with S mansoni. Furthermore, higher doses of antioxidant drugs, β-carotene and vitamin E, should be tried as an adjuvants to conventional therapy in a trial to improve treatment of schistosomiasis.

Cathepsin B proteases of flukes: the key to facilitating parasite control?

Cysteine proteases are important virulence factors for parasites. This review will focus on the cathepsin B proteases of trematodes (also known as flukes) which are abundant in juvenile and immature flukes. Recent research, primarily in Fasciola, using inhibitors, RNA interference (RNAi) and vaccination studies indicates that cathepsin Bs play a key role in the biology of trematodes. As these proteases are largely expressed by infective parasite stages, their inactivation by chemotherapy or vaccination will greatly reduce the damage wrought by flukes as they invade host tissues. This validates cathepsin Bs as key strategic targets for fluke control.

Massively parallel sequencing and analysis of the Necator americanus transcriptome

Background

The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.

Methodology/Principal Findings

A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%), proteinase inhibitors (7.8%) or calcium-binding EF-hand proteins (6.7%). Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%), oxidative phosphorylation (63%) and/or proteases (60%); most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins) were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins) or amino acid metabolism (e.g., asparagine t-RNA synthetase).

Conclusions

This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human hookworm, A. duodenale, for both fundamental and applied purposes, including the prevalidation of anti-hookworm drug targets.

The blood-feeding hookworm Necator americanus infects hundreds of millions of people. To elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of adult Necator americanus was studied using next-generation sequencing and in silico analyses. Contigs (n = 19,997) were assembled from the sequence data; 6,771 of them had known orthologues in the free-living nematode Caenorhabditis elegans, and most encoded proteins with WD40 repeats (10.6%), proteinase inhibitors (7.8%) or calcium-binding EF-hand proteins (6.7%). Bioinformatic analyses inferred that C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%), oxidative phosphorylation (63%) and/or proteases (60%). Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. Essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have human homologues. These candidate targets were inferred to be linked to mitochondrial metabolism or amino acid synthesis. This investigation provides detailed insights into the transcriptome of the adult stage of N. americanus.

Schistosome genomes: a wealth of information

The blood flukes Schistosoma japonicum and Schistosoma mansoni are the first major human platyhelminth pathogens to have their genome sequences published. The work of two large international consortia offers draft sequence information and detailed analyses presenting a wealth of information addressing, in particular, metabolic and signalling pathways, host-parasite interactions and potential new drug targets. We comment on these breakthroughs and their potential applications in the study and control of schistosomes.