ESTs from the microsporidian Edhazardia aedis

Mathematical modelling of the interactive dynamics of wild and Microsporidia MB-infected mosquitoes

A recent discovery highlighted that mosquitoes infected with Microsporidia MB are unable to transmit the Plasmodium to humans. Microsporidia MB is a symbiont transmitted vertically and horizontally in the mosquito population, and these transmission routes are known to favor the persistence of the parasite in the mosquito population. Despite the dual transmission, data from field experiments reveal a low prevalence of MB-infected mosquitoes in nature. This study proposes a compartmental model to understand the prevalence of MB-infected mosquitoes. The dynamic of the model is obtained through the computation of the basic reproduction number and the analysis of the stability of the MB-free and coexistence equilibria. The model shows that, in spite of the high vertical transmission efficiency of Microsporidia MB, there can still be a low prevalence of MB-infected mosquitoes. Numerical analysis of the model shows that male-to-female horizontal transmission contributes more than female-to-male horizontal transmission to the spread of MB-infected mosquitoes. Moreover, the female-to-male horizontal transmission contributes to the spread of the symbiont only if there are multiple mating occurrences for male mosquitoes. Furthermore, when fixing the efficiencies of vertical transmission, the parameters having the greater influence on the ratio of MB-positive to wild mosquitoes are identified. In addition, by assuming a similar impact of the temperature on wild and MB-infected mosquitoes, our model shows the seasonal fluctuation of MB-infected mosquitoes. This study serves as a reference for further studies, on the release strategies of MB-infected mosquitoes, to avoid overestimating the MB-infection spread.

Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum

The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. These parasites invade and replicate within the circulating red blood cells of infected individuals leading to numerous disease manifestations, including severe anemia, altered circulation, and tissue inflammation. Malaria parasites are also known for their ability to maintain a chronic infection through antigenic variation, the ability to systematically alter the antigens displayed on the surface of infected cells and thereby avoid clearance by the host's antibody response. The genome of P. falciparum includes several large, multicopy gene families that encode highly variable forms of the surface proteins that are the targets of host immunity. Alterations in expression of genes within these families are responsible for antigenic variation. This process requires the continuous generation of new antigenic variants within these gene families, and studies have shown that new variants arise through extensive recombination and gene conversion events between family members. Malaria parasites possess an unusual complement of DNA repair pathways, thus the study of recombination between variant antigen encoding genes provides a unique view into the evolution of mobile DNA in an organism distantly related to the more closely studied model eukaryotes.

Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis

Background

Trachipleistophora hominis was isolated from an HIV/AIDS patient and is a member of a highly successful group of obligate intracellular parasites.

Methods

Here we have investigated the evolution of the parasite and the interplay between host and parasite gene expression using transcriptomics of T. hominis-infected rabbit kidney cells.

Results

T. hominis has about 30 % more genes than small-genome microsporidians. Highly expressed genes include those involved in growth, replication, defence against oxidative stress, and a large fraction of uncharacterised genes. Chaperones are also highly expressed and may buffer the deleterious effects of the large number of non-synonymous mutations observed in essential T. hominis genes. Host expression suggests a general cellular shutdown upon infection, but ATP, amino sugar and nucleotide sugar production appear enhanced, potentially providing the parasite with substrates it cannot make itself. Expression divergence of duplicated genes, including transporters used to acquire host metabolites, demonstrates ongoing functional diversification during microsporidian evolution. We identified overlapping transcription at more than 100 loci in the sparse T. hominis genome, demonstrating that this feature is not caused by genome compaction. The detection of additional transposons of insect origin strongly suggests that the natural host for T. hominis is an insect.

Conclusions

Our results reveal that the evolution of contemporary microsporidian genomes is highly dynamic and innovative. Moreover, highly expressed T. hominis genes of unknown function include a cohort that are shared among all microsporidians, indicating that some strongly conserved features of the biology of these enormously successful parasites remain uncharacterised.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1989-z) contains supplementary material, which is available to authorized users.

Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes

Obligate intracellular pathogens depend on their host for growth yet must also evade detection by host defenses. Here we investigate host adaptation in two Microsporidia, the specialist Edhazardia aedis and the generalist Vavraia culicis, pathogens of disease vector mosquitoes. Genomic analysis and deep RNA-Seq across infection time courses reveal fundamental differences between these pathogens. E. aedis retains enhanced cell surface modification and signalling capacity, upregulating protein trafficking and secretion dynamically during infection. V. culicis is less dependent on its host for basic metabolites and retains a subset of spliceosomal components, with a transcriptome broadly focused on growth and replication. Transcriptional profiling of mosquito immune responses reveals that response to infection by E. aedis differs dramatically depending on the mode of infection, and that antimicrobial defensins may play a general role in mosquito defense against Microsporidia. This analysis illuminates fundamentally different evolutionary paths and host interplay of specialist and generalist pathogens.

Microsporidia and 'the art of living together'

Parasitism, aptly defined as one of the 'living-together' strategies (Trager, 1986), presents a dynamic system in which the parasite and its host are under evolutionary pressure to evolve new and specific adaptations, thus enabling the coexistence of the two closely interacting partners. Microsporidia are very frequently encountered obligatory intracellular protistan parasites that can infect both animals and some protists and are a consummate example of various aspects of the 'living-together' strategy. Microsporidia, relatives of fungi in the superkingdom Opisthokonta, belong to the relatively small group of parasites for which the host cell cytoplasm is the site of both reproduction and maturation. The structural and physiological reduction of their vegetative stage, together with the manipulation of host cell physiology, enables microsporidia to live in the cytosolic environment for most of their life cycle in a way resembling endocytobionts. The ability to form structurally complex spores and the invention and assembly of a unique injection mechanism enable microsporidia to disperse within host tissues and between host organisms, resulting in long-lasting infections. Microsporidia have adapted their genomes to the intracellular way of life, evolved strategies how to obtain nutrients directly from the host and how to manipulate not only the infected cells, but also the hosts themselves. The enormous variability of host organisms and their tissues provide microsporidian parasites a virtually limitless terrain for diversification and ecological expansion. This review attempts to present a general overview of microsporidia, emphasising some less known and/or more recently discovered facets of their biology.

Characterization of active ribosomal RNA harboring MITEs insertion in microsporidian Nosema bombycis genome

Microsporidia are a group of obligate intracellular parasites of medical and agricultural importance, which can infect almost all animals, including human beings. Using the genome data of Nosema bombycis, four families of miniature inverted-repeat transposable elements (MITEs) in ribosomal DNA (rDNA) were characterized in the microsporidian N. bombycis and were named LSUME1, ITSME1, SSUME1, and SSUME2, respectively. The genome-wide investigation of these MITEs shows that these MITEs families distribute randomly in N. bombycis genome. All insertion sequences have conserved characteristics of MITEs, the direct repeat sequence and terminal inverted-repeat sequence at both ends of each MITEs sequence. Additionally, using the CLC RNA Workbench Software, secondary structures of rRNA containing MITEs sequence have been predicted and were located in variable region or expansion segment. Furthermore, using two different probes, one is prepared by MITE sequence only (short probe) and the other is prepared by MITE sequence flanking partial rDNA sequence (long probe); northern blotting and dot blotting have been performed to detect the transcriptional and functional activity of the rDNA containing MITEs insertion. Fortunately, we found that the rDNA, which harbors the MITE, not only can be transcripted but also can form a complete ribosome. This is an interesting thing that one gene can keep active even when it has been inserted with another sequence. But the biological and structural significance of this observation is not readily apparent.

Gut pathology and responses to the microsporidium Nosema ceranae in the honey bee Apis mellifera

The microsporidium Nosema ceranae is a newly prevalent parasite of the European honey bee (Apis mellifera). Although this parasite is presently spreading across the world into its novel host, the mechanisms by it which affects the bees and how bees respond are not well understood. We therefore performed an extensive characterization of the parasite effects at the molecular level by using genetic and biochemical tools. The transcriptome modifications at the midgut level were characterized seven days post-infection with tiling microarrays. Then we tested the bee midgut response to infection by measuring activity of antioxidant and detoxification enzymes (superoxide dismutases, glutathione peroxidases, glutathione reductase, and glutathione-S-transferase). At the gene-expression level, the bee midgut responded to N. ceranae infection by an increase in oxidative stress concurrent with the generation of antioxidant enzymes, defense and protective response specifically observed in the gut of mammals and insects. However, at the enzymatic level, the protective response was not confirmed, with only glutathione-S-transferase exhibiting a higher activity in infected bees. The oxidative stress was associated with a higher transcription of sugar transporter in the gut. Finally, a dramatic effect of the microsporidia infection was the inhibition of genes involved in the homeostasis and renewal of intestinal tissues (Wnt signaling pathway), a phenomenon that was confirmed at the histological level. This tissue degeneration and prevention of gut epithelium renewal may explain early bee death. In conclusion, our integrated approach not only gives new insights into the pathological effects of N. ceranae and the bee gut response, but also demonstrate that the honey bee gut is an interesting model system for studying host defense responses.

Causes and consequences of genome expansion in fungi

Fungi display a large diversity in genome size and complexity, variation that is often considered to be adaptive. But because nonadaptive processes can also have important consequences on the features of genomes, we investigated the relationship of genetic drift and genome size in the phylum Ascomycota using multiple indicators of genetic drift. We detected a complex relationship between genetic drift and genome size in fungi: genetic drift is associated with genome expansion on broad evolutionary timescales, as hypothesized for other eukaryotes; but within subphyla over smaller timescales, the opposite trend is observed. Moreover, fungi and bacteria display similar patterns of genome degradation that are associated with initial effects of genetic drift. We conclude that changes in genome size within Ascomycota have occurred using two different routes: large-scale genome expansions are catalyzed by increasing drift as predicted by the mutation-hazard model of genome evolution and small-scale modifications in genome size are independent of drift.

Extreme reduction and compaction of microsporidian genomes

Microsporidia are fungi-related obligate intracellular parasites with a highly reduced and compact genome, as for Encephalitozoon species which harbor a genome smaller than 3 Mbp. Genome compaction is reflected by high gene density and, for larger microsporidian genomes, size variation is due to repeat elements that do not drastically affect gene density. Furthermore, these pathogens present strong host dependency illustrated by extensive gene loss. Such adaptations associated with genome compaction induced gene size reduction but also simplification of cellular processes such as transcription. Thus, microsporidia are excellent models for eukaryotic genome evolution and gene expression in the context of host-pathogen relationships.

The intriguing nature of microsporidian genomes

Microsporidia are a group of highly adapted unicellular fungi that are known to infect a wide range of animals, including humans and species of great economic importance. These organisms are best known for their very simple cellular and genomic features, an adaptive consequence of their obligate intracellular parasitism. In the last decade, the acquisition of a large amount of genomic and transcriptomic data from several microsporidian species has greatly improved our understanding of the consequences of a purely intracellular lifestyle. In particular, genome sequence data from these pathogens has revealed how obligate intracellular parasitism can result in radical changes in the composition and structure of nuclear genomes and how these changes can affect cellular and evolutionary mechanisms that are otherwise well conserved among eukaryotes. This article reviews our current understanding of the genome content and structure of microsporidia, discussing their evolutionary origin and cataloguing the mechanisms that have often been involved in their extreme reduction.

The ecology and evolution of microsporidian parasites

The phylum Microspora is ancient and diverse and affects a wide range of hosts. There is unusually high use of vertical transmission and this has significant consequences for transmission and pathogenicity. Vertical transmission is associated with low pathogenesis but nevertheless can have significant impact through associated traits such as sex ratio distortion. The majority of microsporidia have mixed transmission cycles and it is not clear whether they are able to modify their phenotype according to environmental circumstances. There is a great need to understand the mechanisms controlling transmission and one of the first challenges for the genomics era is to find genes associated with life cycle stages. Similarly we cannot currently predict the ease with which these parasites might switch between host groups. Phylogenetic analysis suggests that there are strong relationships between Microsporidia and their hosts. However closer typing of parasite isolates, in relation to host range and disease phenotype, is required to assess future environmental risk from these pathogens.

Identification of NbME MITE families: potential molecular markers in the microsporidia Nosema bombycis

Six novel families of miniature inverted-repeat transposable elements (MITEs) were characterized in the microsporidia Nosema bombycis and were named NbMEs. The structural characteristics and the distribution of NbME copies in the N. bombycis genome were investigated, and it was found that portions of NbMEs are associated with gene sections. Potential molecular markers for various N. bombycis strains were identified in this study through utilization of the MITE-AFLP technique. Three distinct pathogenic isolates collected from different areas were distinguished, and polymorphisms were detected using the NbME5 marker, thereby establishing this NbME as a potential marker for studying isolate variation in N. bombycis.

Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

BACKGROUND

The highly compacted 2.9-Mb genome of Encephalitozoon cuniculi placed the microsporidia in the spotlight, encoding a mere 2,000 proteins and a highly reduced suite of biochemical pathways. This extreme level of reduction is not universal across the microsporidia, with genomes known to vary up to sixfold in size, suggesting that some genomes may harbor a gene content that is not as reduced as that of Enc. cuniculi. In this study, we present an in-depth survey of the large genome of Octosporea bayeri, a pathogen of Daphnia magna, with an estimated genome size of 24 Mb, in order to shed light on the organization and content of a large microsporidian genome.

RESULTS

Using Illumina sequencing, 898 Mb of O. bayeri genome sequence was generated, resulting in 13.3 Mb of unique sequence. We annotated a total of 2,174 genes, of which 893 encodes proteins with assigned function. The gene density of the O. bayeri genome is very low on average, but also highly uneven, so gene-dense regions also occur. The data presented here suggest that the O. bayeri proteome is well represented in this analysis and is more complex that that of Enc. cuniculi. Functional annotation of O. bayeri proteins suggests that this species might be less biochemically dependent on its host for its metabolism than its more reduced relatives.

CONCLUSIONS

The combination of the data presented here, together with the imminent annotated genome of Daphnia magna, will provide a wealth of genetic and genomic tools to study host-parasite interactions in an interesting model for pathogenesis.

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees

Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive N. ceranae proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in E. cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee–Nosema interactions.

Honey bee colonies are in decline in many parts of the world, in part due to pressures from a diverse assemblage of parasites and pathogens. The range and prevalence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we describe the N. ceranae genome, presenting genome traits, gene models and regulatory motifs. N. ceranae has an extremely reduced and AT-biased genome, yet one with substantial numbers of repetitive elements. We identify novel genes that appear to be conserved among microsporidia but undetected outside this phylum, which are of special interest as potential virulence factors for these obligate pathogens. A previously unrecognized motif is found upstream of many start codons and likely plays a role in gene regulation across the microsporidia. These and other comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and provide the first genetic tools for understanding how this pathogen interacts with honey bee hosts.