Infections of virulent and avirulent viruses differentially influenced the expression of dicer-1, ago-1, and microRNAs in Bombus terrestris

Transcriptomic Characterization of miRNAs in Apis cerana Larvae Responding to Ascosphaera apis Infection

Ascosphaera apis is a fungal pathogen that specifically infects bee larvae, causing an outbreak of chalkbrood disease in the bee colony and a decline in the number of bee colonies. The role of miRNA regulation in honeybees in response to A. apis infection is unclear. In this study, based on small RNA-seq, we identified the differentially expressed miRNAs (DEmiRNAs) and their regulatory networks and functions in the gut of Apis cerana cerana on the first day (AcT1), the second day (AcT2) and the third day (AcT3) after A. apis infection, and analyzed the immune response mechanism of A. apis through the miRNAs-mRNA regulation network of A. apis infection. A total of 537 miRNAs were obtained, and 10, 27, and 54 DEmiRNAs were screened in the AcT1, AcT2, and AcT3 groups, respectively. The number of DEmiRNAs gradually increased with the infection time. Stem-loop RT-PCR results showed that most of the DEmiRNAs were truly expressed, and the expression trend of DEmiRNAs was consistent with the results of sRNA-seq. The top five GO terms of DEmiRNA-targeted mRNA were binding, cellular process, catalytic activity, metabolic process, and single-organism process. The main pathways enriched by KEGG were endocytosis, ubiquitin-mediated proteolysis, phagosome, and the JAK-STAT immune-related signaling pathways. The number of DEmiRNAs and target mRNAs of these related pathway genes increased with infection time. The miRNA-mRNA regulatory network analysis showed that ace-miR-539-y was the core miRNA of the early immune response in the gut of larvae infected with A. apis in the JAK-STAT pathway and phagosome, and ace-miR-1277-x was the core miRNA of the late immune response in the gut of larvae infected with A. apis in the JAK-STAT signaling pathway and phagosome. The results showed that miRNA participated in the immune response of honeybees to A. apis infection by regulating the host's energy metabolism, cellular immunity, and humoral immunity. The results of this study provide a basis for the regulation of miRNAs in A. c. cerana larvae in response to A. apis infection and provide new insights into host-pathogen interactions.

Wolbachia mediates crosstalk between miRNA and Toll pathways to enhance resistance to dengue virus in Aedes aegypti

The obligate endosymbiont Wolbachia induces pathogen interference in the primary disease vector Aedes aegypti, facilitating the utilization of Wolbachia-based mosquito control for arbovirus prevention, particularly against dengue virus (DENV). However, the mechanisms underlying Wolbachia-mediated virus blockade have not been fully elucidated. Here, we report that Wolbachia activates the host cytoplasmic miRNA biogenesis pathway to suppress DENV infection. Through the suppression of the long noncoding RNA aae-lnc-2268 by Wolbachia wAlbB, aae-miR-34-3p, a miRNA upregulated by the Wolbachia strains wAlbB and wMelPop, promoted the expression of the antiviral effector defensin and cecropin genes through the Toll pathway regulator MyD88. Notably, anti-DENV resistance induced by Wolbachia can be further enhanced, with the potential to achieve complete virus blockade by increasing the expression of aae-miR-34-3p in Ae. aegypti. Furthermore, the downregulation of aae-miR-34-3p compromised Wolbachia-mediated virus blockade. These findings reveal a novel mechanism by which Wolbachia establishes crosstalk between the cytoplasmic miRNA pathway and the Toll pathway via aae-miR-34-3p to strengthen antiviral immune responses against DENV. Our results will aid in the advancement of Wolbachia for arbovirus control by enhancing its virus-blocking efficiency.

Evolutionary immunology to explore original antiviral strategies

Over the past 25 years, the field of evolutionary developmental biology (evo-devo) has used genomics and genetics to gain insight on the developmental mechanisms underlying the evolution of morphological diversity of animals. Evo-devo exploits the key insight that conserved toolkits of development (e.g. Hox genes) are used in animals to produce genetic novelties that provide adaptation to a new environment. Like development, immunity is forged by interactions with the environment, namely the microbial world. Yet, when it comes to the study of immune defence mechanisms in invertebrates, interest primarily focuses on evolutionarily conserved molecules also present in humans. Here, focusing on antiviral immunity, we argue that immune genes not conserved in humans represent an unexplored resource for the discovery of new antiviral strategies. We review recent findings on the cGAS-STING pathway and explain how cyclic dinucleotides produced by cGAS-like receptors may be used to investigate the portfolio of antiviral genes in a broad range of species. This will set the stage for evo-immuno approaches, exploiting the investment in antiviral defences made by metazoans over hundreds of millions of years of evolution. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response

Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.

The Honey Bee Gene Bee Antiviral Protein-1 Is a Taxonomically Restricted Antiviral Immune Gene

Insects have evolved a wide range of strategies to combat invading pathogens, including viruses. Genes that encode proteins involved in immune responses often evolve under positive selection due to their co-evolution with pathogens. Insect antiviral defense includes the RNA interference (RNAi) mechanism, which is triggered by recognition of non-self, virally produced, double-stranded RNAs. Indeed, insect RNAi genes (e.g., dicer and argonaute-2) are under high selective pressure. Honey bees (Apis mellifera) are eusocial insects that respond to viral infections via both sequence specific RNAi and a non-sequence specific dsRNA triggered pathway, which is less well-characterized. A transcriptome-level study of virus-infected and/or dsRNA-treated honey bees revealed increased expression of a novel antiviral gene, GenBank: MF116383, and in vivo experiments confirmed its antiviral function. Due to in silico annotation and sequence similarity, MF116383 was originally annotated as a probable cyclin-dependent serine/threonine-protein kinase. In this study, we confirmed that MF116383 limits virus infection, and carried out further bioinformatic and phylogenetic analyses to better characterize this important gene-which we renamed bee antiviral protein-1 (bap1). Phylogenetic analysis revealed that bap1 is taxonomically restricted to Hymenoptera and Blatella germanica (the German cockroach) and that the majority of bap1 amino acids are evolving under neutral selection. This is in-line with the results from structural prediction tools that indicate Bap1 is a highly disordered protein, which likely has relaxed structural constraints. Assessment of honey bee gene expression using a weighted gene correlation network analysis revealed that bap1 expression was highly correlated with several immune genes-most notably argonaute-2. The coexpression of bap1 and argonaute-2 was confirmed in an independent dataset that accounted for the effect of virus abundance. Together, these data demonstrate that bap1 is a taxonomically restricted, rapidly evolving antiviral immune gene. Future work will determine the role of bap1 in limiting replication of other viruses and examine the signal cascade responsible for regulating the expression of bap1 and other honey bee antiviral defense genes, including coexpressed ago-2, and determine whether the virus limiting function of bap1 acts in parallel or in tandem with RNAi.

Possible Spillover of Pathogens between Bee Communities Foraging on the Same Floral Resource

Simple Summary

Floral resource availability is one of the keys to preserving the health of bee communities. However, flowers also present a risk of pathogen transmission, as infected pollinators could deposit pathogens while foraging, exposing other pollinators to infection via the consumption of contaminated nectar or pollen. Here, we studied, over time, the prevalence of seven viruses in bee communities that share the same small surface of floral resource in order to assess the risk of virus spillover. In total, 2057 bee specimens from 30 species were caught, identified and checked for the presence of viruses. Specimens from the Halictidae family were the dominant wild bees. The prevalence of viruses was quite high: at least one virus was detected in 78% of the samples, and co-infections were frequent. The genetic diversity of the viruses was also investigated to look for the possible association of geographic origin or host with shared ancestry.

Abstract

Viruses are known to contribute to bee population decline. Possible spillover is suspected from the co-occurrence of viruses in wild bees and honey bees. In order to study the risk of virus transmission between wild and managed bee species sharing the same floral resource, we tried to maximize the possible cross-infections using Phacelia tanacetifolia, which is highly attractive to honey bees and a broad range of wild bee species. Virus prevalence was compared over two years in Southern France. A total of 1137 wild bees from 29 wild bee species (based on COI barcoding) and 920 honey bees (Apis mellifera) were checked for the seven most common honey bee RNA viruses. Halictid bees were the most abundant. Co-infections were frequent, and Sacbrood virus (SBV), Black queen cell virus (BQCV), Acute bee paralysis virus (ABPV) and Israeli acute paralysis virus (IAPV) were widespread in the hymenopteran pollinator community. Conversely, Deformed wing virus (DWV) was detected at low levels in wild bees, whereas it was highly prevalent in honey bees (78.3% of the samples). Both wild bee and honey bee virus isolates were sequenced to look for possible host-specificity or geographical structuring. ABPV phylogeny suggested a specific cluster for Eucera bees, while isolates of DWV from bumble bees (Bombus spp.) clustered together with honey bee isolates, suggesting a possible spillover.

Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies

A necessary pre-processing data analysis step is the removal of adapter sequences from the raw reads. While most adapter trimming tools require adapter sequence as an essential input, adapter information is often incomplete or missing. This can impact quantification of features, reproducibility of the study and might even lead to erroneous conclusions. Here, we provide examples to highlight the importance of specifying the adapter sequence by demonstrating the effect of using similar but different adapter sequences and identify additional potential sources of errors in the adapter trimming step. Finally, we propose solutions by which users can ensure their small RNA-seq data is fully annotated with adapter information.

Dicer regulates Nosema ceranae proliferation in honeybees

Nosema ceranae is a microsporidian parasite that infects the honeybee midgut epithelium. The protein-coding gene Dicer is lost in most microsporidian genomes but is present in N. ceranae. By feeding infected honeybees with small interfering RNA targeting the N. ceranae gene coding Dicer (siRNA-Dicer), we found that N. ceranae spore loads were significantly reduced. In addition, over 10% of total parasite protein-coding genes showed significantly divergent expression profiles after siRNA-Dicer treatment. Parasite genes for cell proliferation, ABC transporters and hexokinase were downregulated at 3 days postinfection, a key point in the middle of parasite replication cycles. In addition, genes involved in metabolic pathways of honeybees and N. ceranae showed significant co-expression. Furthermore, the siRNA-Dicer treatment partly reversed the expression patterns of honeybee genes. The honeybee gene mucin-2-like showed significantly upregulation in the siRNA-Dicer group compared with the infection group continually at 4, 5 and 6 days postinfection, suggesting that the siRNA-Dicer feeding promoted the strength of the mucus barrier resulted from interrupted parasite proliferation. As the gene Dicer broadly regulates N. ceranae proliferation and honeybee metabolism, our data suggest the RNA interference pathway is an important infection strategy for N. ceranae.

Dynamic miRNA-mRNA regulations are essential for maintaining Drosophila immune homeostasis during Micrococcus luteus infection

Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M. luteus infection. The pathway enrichment analysis indicates that differentially expressed genes are involved in diverse signaling pathways, including Toll and Imd as well as orther signaling pathways at three time points during Drosophila with M. luteus infection. Remarkably, the dynamic change of miRNA expression is delayed by compared to mRNA expression change over three time points, implying that the "time" parameter should be considered when the function of miRNA/mRNA is further studied. In particular, the dynamic miRNA-mRNA regulatory networks have shown that miRNAs may synergistically regulate gene expressions of different signaling pathways to promote or inhibit innate immune responses and maintain homeostasis in Drosophila, and some new regulators involved in Drosophila innate immune response have been identified. Our findings strongly suggest that miRNA regulation is a key mechanism involved in fine-tuning cooperatively gene expressions of diverse signaling pathways to maintain innate immune response and homeostasis in Drosophila. Taken together, the present study reveals a novel role of dynamic miRNA-mRNA regulation in immune response to bacteria infection, and provides a new insight into the underlying molecular regulatory mechanism of Drosophila innate immune responses.