Toward understanding the functional role of Ss-RIOK-1, a RIO protein kinase-encoding gene of Strongyloides stercoralis

A standard workflow for community-driven manual curation of Strongyloides genome annotations

Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of Strongyloides species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple Strongyloides species are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in two Strongyloides species highlights the potential for errors in a large percentage of current Strongyloides gene models. Here, we present three examples of gene annotation updates within the Strongyloides rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for Strongyloides genomes. We also extend our analysis to 405 previously curated Strongyloides genes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Expression of Heat Shock Protein 70 (HSP70) and Astacin Genes of Strongyloides stercoralis as well as HSP70 and HSP17.1 Genes of S. ratti in Adult and Larval Stages of S. stercoralis

Background

Uncovering the roles and characteristics of pathogenesis-related molecules can help us develop novel management methods in parasitology. In this study, we studied the expression levels of Strongyloides stercoralis heat shock protein70 (HSP70) (Sst-hsp-70) and astacin (Sst-ast) as pathogenesis-related genes as well as the expression of S. ratti HSP70 and HSP17.1 (Sra-hsp-70, Sra-hsp-17.1) in the larvae and adult stages of S. stercoralis.

Methods

A hyperinfection isolate of S. stercoralis from Gilan Province, northern Iran was cultivated on nutrient agar. After a couple of days, parasites in different stages of life were collected, and total RNA was extracted. The expression levels of astacin and HSP genes were compared by real-time PCR.

Results

Statistically higher expression levels of Sst-ast, Sst-hsp-70, and Sra-hsp-70 genes in L3 larvae than in adults were observed. However, the expression level of Sra-hsp-17.1 was non-significantly lower in the larval stage than in adult worms.

Conclusion

Higher expression levels of Sst-ast, Sst-hsp-70, and Sra-hsp-70 genes in the larval stages of S. stercoralis suggest the potential role of these enzymes in parasite cutaneous invasion and pathogenesis. However, higher expression of Srahsp-17.1 in adult forms is probably involved in resistance and survival mechanisms. The similarity in gene expression between S. stercoralis and S. ratti can provide helpful hints to better understand strongyloidiasis from various perspectives, including pathogenesis, proper diagnosis, and targeted treatment.

Domain definition and preliminary functional exploration of the endonuclease NOBP-1 in Strongyloides stercoralis

BACKGROUND

Ribosome biogenesis is the process of assembling ribosome complexes that regulate cell proliferation and differentiation with potential regulatory effects on development. Many factors regulate ribosome biological processes. Nin one binding protein (Nob1) has received widespread attention as key genes regulating ribosome biogenesis-the 3' end of the 20S rRNA is cleaved by Nob1 at cleavage site D to form 18S rRNA, generating translationally capable 40S subunit. As a ribosome biogenesis factor, Nob1 may regulate the development of organisms, but almost nothing is known about the function of Nob1 for any parasitic nematode. We explored the functional role of NOBP-1 (the homologous gene of Nob1) encoding gene from a parasitic nematode-Strongyloides stercoralis.

METHODS

The full-length cDNA, gDNA and promoter region of Ss-nobp-1 was identified using protein BLAST in WormBase ParaSite according to the Caenorhabditis elegans NOBP-1 sequence to analyze the gene structure. RNA sequencing (RNA-seq) data in wormbase were retrieved and analyzed to assess the transcript abundance of Ss-nobp-1 in seven developmental stages of S. stercoralis. The standard method for gonadal microinjection of constructs was carried out to determine the anatomic expression patterns of Ss-nobp-1. The interaction between Ss-NOBP-1 and partner of NOBP-1 (Ss-PNO-1) was assessed by yeast two-hybridization and bimolecular fluorescence complementarity (BiFC) experiments.

RESULTS

The NOBP-1 encoding gene Ss-nopb-1 from the zoonotic parasite S. stercoralis has been isolated and characterized. The genomic DNA representing Ss-nobp-1 includes a 1599-bp coding region and encodes a protein comprising 403 amino acids (aa), which contains conserved PIN domain and zinc ribbon domain. RNA-seq analysis revealed that Ss-nobp-1 transcripts are present throughout the seven developmental stages in S. stercoralis and have higher transcription levels in iL3, L3 and P Female. Ss-nobp-1 is expressed mainly in the intestine of transgenic S. stercoralis larvae, and there is a direct interaction between Ss-NOBP-1 and Ss-PNO-1.

CONCLUSIONS

Collectively, Ss-NOBP-1 has a potential role in embryo formation and the infective process, and findings from this study provide a sound foundation for investigating its function during the development of parasitic nematode.

First Evidence of Function for Schistosoma japonicumriok-1 and RIOK-1

Protein kinases are known as key molecules that regulate many biological processes in animals. The right open reading frame protein kinase (riok) genes are known to be essential regulators in model organisms such as the free-living nematode Caenorhabditis elegans. However, very little is known about their function in parasitic trematodes (flukes). In the present study, we characterized the riok-1 gene (Sj-riok-1) and the inferred protein (Sj-RIOK-1) in the parasitic blood fluke, Schistosoma japonicum. We gained a first insight into function of this gene/protein through double-stranded RNA interference (RNAi) and chemical inhibition. RNAi significantly reduced Sj-riok-1 transcription in both female and male worms compared with untreated control worms, and subtle morphological alterations were detected in the ovaries of female worms. Chemical knockdown of Sj-RIOK-1 with toyocamycin (a specific RIOK-1 inhibitor/probe) caused a substantial reduction in worm viability and a major accumulation of mature oocytes in the seminal receptacle (female worms), and of spermatozoa in the sperm vesicle (male worms). These phenotypic alterations indicate that the function of Sj-riok-1 is linked to developmental and/or reproductive processes in S. japonicum.

RIOK-2 protein is essential for egg hatching in a common parasitic nematode

The atypical protein kinase RIOK-2 is a non-ribosomal factor essential for ribosome maturation in yeast and human cells; however, little is known about its physiological role in pathogens. Our earlier work examined the expression profile of a RIOK-2 gene (Ss-riok-2) in Strongyloides stercoralis - a prevalent nematode parasite of dogs and humans. Herein, we demonstrate that Ss-RIOK-2 encodes a catalytically active kinase, distributed primarily in the cytoplasm of intestinal and hypodermal cells in transgenic larvae. Its expression oscillates as the free-living L1s develop into infective L3s. Overexpression of a catalytically impaired Ss-RIOK-2-D228A mutant delayed the development of transgenic larvae, while ectopic expression of another dominant negative isoform with a mutation in the ATP-binding site (K123A) abrogated the process of egg hatching, which could be rescued by co-expressing a wild-type Ss-RIOK-2 but not by its Ss-RIOK-1 ortholog. Collectively, our findings show a critical and specific role of Ss-RIOK-2 during the development of a pathogenic roundworm, which can be exploited to develop anti-infectives.

Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for the detection of the E198A SNP in the isotype-1 β-tubulin gene of Haemonchus contortus populations in China

Haemonchus contortus is one of the most important gastrointestinal nematodes of small ruminants around the world, seriously hampering the healthy development of the sheep industry. The control of this parasite mainly depends on anthelmintics, however, drug resistance of H. contortus has become a serious problems worldwide. Previous studies demonstrated that the E198A (GAA to GCA), a single nucleotide polymorphism (SNP) in the isotype-1 β-tubulin gene is associated with benzimidazole resistance in H. contortus. However, only PCR-RFLP and ARMS-PCR methods have been previously used for the detection of the E198A mutation. In the present study, a loop-mediated isothermal amplification (LAMP) assay was established for rapid detection of the E198A SNP in H. contortus. The results showed that optimization of LAMP reaction reagents and conditions could achieve this. The resulting amplicons were visualized by adding hydroxynaphthol blue dye (HNB) prior to amplification. The color of LAMP products amplified without DNA or from DNA from worms with the E198A homozygous susceptible genotype was still violet, but the products with DNA from worms with the E198A heterozygous genotype or the E198A resistant homozygous genotype changed to sky blue. The specificity of this method was further verified by sequencing, which confirmed the successful LAMP detection of the E198A mutation with high specificity. In conclusion, the developed LAMP method has high specificity and good reproducibility for screening the E198A SNP of isotype-1 β-tubulin gene of H. contortus of field samples without using sophisticated equipment, providing useful technique for the rapid detection and thus prevention and control of benzimidazole resistant H. contortus infections.

CRISPR/Cas9 Mutagenesis and Expression of Dominant Mutant Transgenes as Functional Genomic Approaches in Parasitic Nematodes

DNA transformation of parasitic nematodes enables novel approaches to validating predictions from genomic and transcriptomic studies of these important pathogens. Notably, proof of principle for CRISPR/Cas9 mutagenesis has been achieved in Strongyloides spp., allowing identification of molecules essential to the functions of sensory neurons that mediate behaviors comprising host finding, invasion, and location of predilection sites by parasitic nematodes. Likewise, CRISPR/Cas9 knockout of the developmental regulatory transcription factor Ss-daf-16 has validated its function in regulating morphogenesis of infective third-stage larvae in Strongyloides stercoralis. While encouraging, these studies underscore challenges that remain in achieving straightforward validation of essential intervention targets in parasitic nematodes. Chief among these is the likelihood that knockout of multifunctional regulators like Ss-DAF-16 or its downstream mediator, the nuclear receptor Ss-DAF-12, will produce phenotypes so complex as to defy interpretation and will render affected worms incapable of infecting their hosts, thus preventing establishment of stable mutant lines. Approaches to overcoming these impediments could involve refinements to current CRISPR/Cas9 methods in Strongyloides including regulatable Cas9 expression from integrated transgenes and CRISPR/Cas9 editing to ablate specific functional motifs in regulatory molecules without complete knockout. Another approach would express transgenes encoding regulatory molecules of interest with mutations designed to similarly ablate or degrade specific functional motifs such as the ligand binding domain of Ss-DAF-12 while preserving core functions such as DNA binding. Such mutant transgenes would be expected to exert a dominant interfering effect on their endogenous counterparts. Published reports validate the utility of such dominant-negative approaches in Strongyloides.

Functional genomic exploration reveals that Ss-RIOK-1 is essential for the development and survival of Strongyloides stercoralis larvae

Protein kinase RIOK-1 is a non-ribosomal factor essential for rRNA cleavage and ribosome small subunit maturation. It is encoded in all eukaryotic organisms. The RIOK-1 encoding gene of Caenorhabditis elegans (Ce-riok-1) is expressed in the neuronal and reproductive systems in larvae and adults of this free-living nematode, and it supports larval growth and development of the adult gonad. In spite of its recognised roles in model organisms such as C. elegans, little is known about the function of this molecule in parasitic nematodes. In a previous study, we characterised the structure, transcriptional profiles and in vivo transcriptional expression patterns of the Ss-riok-1 of human and canine parasitic nematode Strongyloides stercoralis. Here, we extend previous work to undertake functional studies, using transgenesis to assess the roles of Ss-RIOK-1 in the development of S. stercoralis. The results revealed that recombinant Ss-RIOK-1 with D282A mutation at its catalytic site lost its kinase phosphorylation activity in vitro. Both wild-type and mutant Ss-RIOK-1s were expressed in the cytoplasm of neurons and some hypodermal cells in the wild-type strain (UPD) of S. stercoralis. Larvae expressing the dominant negative mutant Ss-RIOK-1 that lost the catalytic activity had a decreased mobility and a severe defect in development to the infective L3 stage. Our findings demonstrated that Ss-RIOK-1 is essential for the development and survival of free-living larvae of S. stercoralis, and that catalytic activity is essential for its function in the parasitic nematode.

Transgenesis in Strongyloides and related parasitic nematodes: historical perspectives, current functional genomic applications and progress towards gene disruption and editing

Transgenesis for Strongyloides and Parastrongyloides was accomplished in 2006 and is based on techniques derived for Caenorhabditis elegans over two decades earlier. Adaptation of these techniques has been possible because Strongyloides and related parasite genera carry out at least one generation of free-living development, with adult males and females residing in soil contaminated by feces from an infected host. Transgenesis in this group of parasites is accomplished by microinjecting DNA constructs into the syncytia of the distal gonads of free-living females. In Strongyloides stercoralis, plasmid-encoded transgenes are expressed in promoter-regulated fashion in the F1 generation following gene transfer but are silenced subsequently. Stable inheritance and expression of transgenes in S. stercoralis requires their integration into the genome, and stable lines have been derived from integrants created using the piggyBac transposon system. More direct investigations of gene function involving expression of mutant transgene constructs designed to alter intracellular trafficking and developmental regulation have shed light on the function of the insulin-regulated transcription factor Ss-DAF-16. Transgenesis in Strongyloides and Parastrongyloides opens the possibility of powerful new methods for genome editing and transcriptional manipulation in this group of parasites. Proof of principle for one of these, CRISPR/Cas9, is presented in this review.

Proteomic Analysis of the Excretory and Secretory Proteins of Haemonchus contortus (HcESP) Binding to Goat PBMCs In Vivo Revealed Stage-Specific Binding Profiles

Haemonchus contortus is a parasitic gastrointestinal nematode, and its excretory and secretory products (HcESPs) interact extensively with the host cells. In this study, we report the interaction of proteins from HcESPs at different developmental stages to goat peripheral blood mononuclear cells (PBMCs) in vivo using liquid chromatography-tandem mass spectrometry. A total of 407 HcESPs that interacted with goat PBMCs at different time points were identified from a H. contortus protein database using SEQUEST searches. The L4 and L5 stages of H. contortus represented a higher proportion of the identified proteins compared with the early and late adult stages. Both stage-specific interacting proteins and proteins that were common to multiple stages were identified. Forty-seven interacting proteins were shared among all stages. The gene ontology (GO) distributions of the identified goat PBMC-interacting proteins were nearly identical among all developmental stages, with high representation of binding and catalytic activity. Cellular, metabolic and single-organism processes were also annotated as major biological processes, but interestingly, more proteins were annotated as localization processes at the L5 stage than at the L4 and adult stages. Based on the clustering of homologous proteins, we improved the functional annotations of un-annotated proteins identified at different developmental stages. Some unnamed H. contortus ATP-binding cassette proteins, including ADP-ribosylation factor and P-glycoprotein-9, were identified by STRING protein clustering analysis.

Genetics: modes of reproduction and genetic analysis

Classical and reverse genetics remain invaluable tools for the scientific investigation of model organisms. Genetic analysis of endoparasites is generally difficult because the sexual adults required for crossing and other manipulations are usually hidden within their host. Strongyloides spp. and Parastrongyloides spp. are notable exceptions to this and their free-living adults offer unique opportunities to manipulate these parasites experimentally. Here I review the modes of inheritance in the two generations of Strongyloides/Parastrongyloides and I discuss the opportunities and the limitations of the currently available methodology for the genetic analysis of these two genera.

Exploring features and function of Ss-riok-3, an enigmatic kinase gene from Strongyloides stercoralis

Background

Right open reading frame protein kinase 3 (RIOK-3) belongs to the atypical kinase family. Unlike the other two members, RIOK-1 and RIOK-2, which are conserved from Archaea to humans, RIOK-3 occurs only in multicellular organisms. Studies on HeLa cells indicate that human RIOK-3 is a component of the 40S small ribosome subunit and supports cancer cell growth and survival. However, almost nothing is known about the function of RIOK-3. We explored the functional role of RIOK-3 encoding gene from Strongyloides stercoralis, a parasitic nematode of humans and dogs.

Methods

To analyze the gene and promoter structure of Ss-riok-3, RACE-PCR and Genome-walker PCR were performed to isolate the full length cDNA, gDNA and promoter region of Ss-riok-3. RNA-seq was conducted to assess the transcript abundance of Ss-riok-3 in different stages of S. stercoralis. Transgenesis was employed to determine the anatomic expression patterns of Ss-riok-3.

Results

The RIOK-3 protein-encoding gene (designated Ss-riok-3) of S. stercoralis was characterized. The full-length complementary and genomic DNAs of the RIOK-3 encoding gene (riok-3) were isolated from this nematode. The cDNA of Ss-riok-3 is 1,757 bp in length, including a 23 bp 5’-UTR, a 36 bp 3’-UTR and a 1,698 bp coding region encoding a protein of 565 amino acids (aa) containing a RIO kinase domain. RNA sequencing (RNA-seq) analysis revealed that Ss-riok-3 is transcribed in all developmental stages of S. stercoralis assessed, with transcripts being particularly abundant in parasitic females. Gene structure analysis revealed that Ss-riok-3 contains no intron. The putative promoter contains conserved promoter elements, including four TATA, two GATA, one inverse GATA and one inverse CAAT boxes. The promoter of Ss-riok-3 drives GFP expression in the head neuron, intestine and body wall muscle of transgenic S. stercoralis larvae, and the TATA boxes present in the 3’-UTR of the gene immediately upstream of Ss-riok-3 initiate transcription.

Conclusions

The characterization of the RIOK-3 encoding gene from S. stercoralis provides a sound foundation for investigating in detail its function in the development and reproduction of this important pathogen.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-014-0561-z) contains supplementary material, which is available to authorized users.