Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective

Abstract

In the model organism Drosophila melanogaster, the PIWI-interacing RNA pathway contributes in silencing transposable elements (TEs) through smallRNAs (piRNAs), which arise from genomic loci (piRNA clusters) that contain sequences of previously-acquired TEs. As such, they are a functionally-immune archive of previous TE invasions that is passed to the offspring. In the arboviral vector Aedes aegypti, piRNA clusters contain TEs and endogenous viral elements from nonretroviral RNA viruses (nrEVEs) which produce piRNAs, supporting the hypothesis that nrEVEs are heritable immunity effectors. However, direct evidence that nrEVEs mediate adaptive immunity is lacking. Here, by using an analytic approach intersecting population genomics with molecular biology we demonstrate that the composition of piRNA clusters is modular through acquisition and absence of nrEVEs. We show that the genomes of wild-caught mosquitoes have a different set of nrEVEs than those annotated in the reference genome, including population-specific integrations. nrEVEs are not distributed in mosquito genomes only by genetic drift, but some show signs of positive selection. Moreover, by comparing natural mosquito populations expressing or lacking two newly characterised nrEVEs with high sequence complementarity to cell fusing agent virus, we show that nrEVEs confer antiviral immunity in ovaries against the cognate virus. Our results confirm that some nrEVEs have been co-opted for adaptive immunity to viral infections. form an "archive" in the genome (Marraffini and Sontheimer, 2010; Koonin and Makarova 2017; Kofler 2019). CRISPR RNAs (Clustered Regularly Interspaced Palindromic Repeats, crRNAs) are produced from short fragments of foreign nucleic acids previously integrated into the repetitive CRISPR locus of the host genome. crRNAs assemble with specific CRISPR-associated proteins (Cas) proteins to form complexes that bind and cleave any phage or plasmid bearing sequence complementarity to the crRNA (Amitai and Sorek et al., 2016).piRNAs are a class of small RNAs of around 25-30 nt that guide PIWI proteins onto complementary target RNAs, resulting in gene silencing at the post-transcriptional or transcriptional level (Ozata et al., 2019). In D. melanogaster, piRNA precursors are generated from genomic loci, called piRNA clusters (Czech and Hannon, 2016). These regions are enriched for (remnants of) TE sequences and, as a consequence, cluster-derived piRNAs show sequence complementarity to TEs. It is thought that piRNA clusters act as traps for new TE invasions by horizontal transfer (Brennecke et al., 2007; Khurana et al., 2011;Parhad and Theurkauf, 2019). Thus, akin to CRISPR loci in prokaryotes for

In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes

“…Such association does not appear to be only a physical co-localization, but a result of putative antiviral mechanism mediated by the activity of some retrotransposon elements (Whitfield et al, 2017;Tasseto et al, 2019). Lastly, Crava et al (2020) have shown that TEs from BEL-Pao superfamily are enriched into piRNA clusters found in the AaegL5 Ae. aegypti genome assembly and this enrichment can influence their association with EVEs.…”

Endogenous piRNA-guided slicing triggers responder and trailer piRNA production from viral RNA inAedes aegyptimosquitoes

“…These non-retroviral sequence elements are enriched in piRNA clusters and, accordingly, give rise to abundant piRNAs (26), which may guide the slicing of cognate RNA from acutely infecting viruses. It has been recently shown that piRNAs derived from EVEs are indeed able to target and inhibit newly infecting viruses (31)(32)(33)), yet, it remains unknown whether piRNA phasing may serve as a mechanism to expand the vpiRNA pool after an initial cleavage by an endogenous, possibly EVE-derived, piRNA.…”

“…aegypti piRNA pathway differs from that in Drosophila in three important ways: i) the pathway is active in somatic tissues as well as germline tissues (21,22), ii) it processes noncanonical substrates such as de novo produced viral RNA (23)(24)(25), and iii) mosquito piRNA clusters contain large numbers of endogenous viral elements (EVEs): sequences of nonretroviral RNA viruses inserted in mosquito genomes (26)(27)(28). These EVEs give rise to abundant piRNAs (26,29,30) and mediate antiviral defense (31)(32)(33).…”

ViR: a tool to account for intrasample variability in the detection of viral integrations

“…Additionally, integrated viral sequences in both plants and animals derive not only from DNA viruses and retroviruses but also from non-retroviral RNA viruses and are enriched in repetitive regions of the genome (20,(23)(24)(25)28). To understand the widespread distribution of EVEs and their biological role, we need to characterize EVEs using WGS data from wild-collected samples or samples collected under hypothesis-driven experimental conditions.…”

“…Additionally EVEs of non-model organisms tend to occur in repetitive DNA, mostly in association with transposable element (TE) sequences and in Piwi-interacting RNA (piRNA) clusters (20,23,24). These newly-identified EVEs have been increasingly recognized as important players in different biological processes such as antiviral immunity and regulation of expression (25,26).…”