A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

  • Ashe A
  • Bélicard T
  • Le Pen J
  • et al.
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Abstract

RNA interference defends against viral infection in plant and animal cells. The nematode Caenorhabditis elegans and its natural pathogen, the positive-strand RNA virus Orsay, have recently emerged as a new animal model of host-virus interaction. Using a genome-wide association study in C. elegans wild populations and quantitative trait locus mapping, we identify a 159 base-pair deletion in the conserved drh-1 gene (encoding a RIG-I-like helicase) as a major determinant of viral sensitivity. We show that DRH-1 is required for the initiation of an antiviral RNAi pathway and the generation of virus-derived siRNAs (viRNAs). In mammals, RIG-I-domain containing proteins trigger an interferon-based innate immunity pathway in response to RNA virus infection. Our work in C. elegans demonstrates that the RIG-I domain has an ancient role in viral recognition. We propose that RIG-I acts as modular viral recognition factor that couples viral recognition to different effector pathways including RNAi and interferon responses.Most organisms—from bacteria to mammals—have at least a rudimentary immune system that can detect and defend against pathogens, particularly viruses. This defense mechanism, which is known as the innate immune system, uses sensor proteins to recognize viral RNA, and then mobilizes other immune components to attack the invaders.The specific mechanisms used to destroy viruses differ between species. In mammals, a protein called RIG-1 binds to viral RNA and activates a signaling pathway that leads to the production of interferons: immune proteins named after their ability to ‘interfere’ with viral replication. Plants and insects do not use interferons, but instead use a mechanism called RNA interference, in which long double-stranded RNAs are cleaved into shorter fragments.The nematode worm C. elegans also deploys RNA interference against viruses but, in contrast to insects and plants, worms do not possess a specific set of RNA interference enzymes that participate solely in the antiviral response. They do, however, express a protein called DRH-1 that is related to the RIG-I protein found in mammals.To investigate whether DRH-1 contributes to innate immunity in C. elegans, Ashe et al. infected 97 strains of C. elegans from around the world with a virus, and showed that some strains were more sensitive to the virus than others, with certain strains showing complete resistance. By comparing a sensitive strain with a resistant one, Ashe et al. revealed that viral sensitivity was caused by a mutation in the gene encoding DRH-1.Further experiments showed that DRH-1 is required for the first step in RNA interference. Ashe et al. have thus identified a conserved role for RIG-1 in initiating antiviral responses, and propose that the protein couples virus recognition to distinct defense mechanisms in different evolutionary groups.

Figures

  • Figure 1. A deletion polymorphism in drh-1 is a major determinant of Orsay virus sensitivity in wild isolates of C. elegans. (A) Genome-wide association analysis of Orsay virus sensitivity in 97 wild isolates of C. elegans. The mapped trait is the viral load of animals, measured by qRT-PCR on the Orsay virus RNA2 genome after 7 days of infection, using three independent infection experiments. The horizontal grey line is a Bonferroni-corrected threshold of Figure 1. Continued on next page
  • Figure 2. Geographic distribution and evolutionary genetic context of drh-1 alleles. (A) Geographic distribution of drh-1 alleles. The respective frequencies of the niDf250 and N2 alleles of drh-1 are represented for each world region in blue and red, respectively, based on genotyping of the 97 wild isolates. (B) Competition experiment between the N2 reference and the JU2196 introgression line. In the absence of the Orsay virus, the proportion of the N2 genotype remains close to 50% throughout the experiment (48.6 ± 5.3%). In the presence of the Orsay virus, the proportion of the N2 genotype increases and appears to stabilize around 90% after nine transfers (88.1 ± 4.6%). The presence of the virus has a significant effect (linear model, p=1.6 × 10−4). Error bars represents standard deviation. (C) Neighbor-network of the 97 isolates in the chromosome IV central region associated with Orsay virus sensitivity. Only one isolate per haplotype is represented; font size is relative to the number (n) of isolates sharing this haplotype. Haplotypes in blue or red carry the niDf250 allele of drh-1, respectively. (D) Distribution of SNPs along chromosome IV between N2 and JU1580, based on JU1580 whole-genome sequencing. (E) Molecular diversity (left y axis scale) is plotted along chromosome IV for isolates carrying the niDf250 or the N2 allele as blue or red lines, respectively. Linkage Disequilibrium D′ values (right y axis scale) between polymorphic RAD sites along chromosome IV and the niDf250 or N2 alleles of drh-1 are represented with blue or red circles, respectively. DOI: 10.7554/eLife.00994.006 Figure 2. Continued on next page
  • Figure 3. DRH-1 is required for the Orsay antiviral response and primary viRNA generation. (A) qRT-PCR analysis of viral load after 4 days of infection with the Orsay virus. *, dcr-1 mutants are sterile, data shown are homozygous mutant animals from heterozygous mothers. (B) Primary viRNA populations in strains as indicated. 5′ dependent small RNA sequencing captures only primary siRNAs with a 5′ monophosphate. Data are grouped as sense or antisense and according to length and the identity of the first nucleotide. From the same samples viral load was measured by qRT-PCR of the Orsay virus RNA1 genome after four days of infection (heatmap, see also Figure 3A and Figure 3—figure supplement 1B). (C) Analysis of phasing of 23 nt primary Figure 3. Continued on next page
  • Figure 4. DRH-1 acts upstream of a 22G secondary siRNA pathway. (A–M) Primary and secondary viRNA populations in strains as indicated. 5′ independent small RNA sequencing captures 5′ primary siRNAs (5′ monophosphate) and secondary siRNAs (5′ triphosphate). Data are grouped as sense or antisense and according to length and the identity of the first nucleotide. From the same samples viral load was measured by RT-qPCR of the Orsay virus RNA1 genome after 4 days of infection (heatmap, see also Figure 3A and Figure 3—figure supplement 1). DOI: 10.7554/eLife.00994.013 Figure 4. Continued on next page
  • Figure 5. Model: DRH-1 triggers a hierarchical antiviral RNAi pathway. Upon infection of the N2 C. elegans strain by the Orsay virus, DRH-1 recruits DCR-1 and its partner RDE-4 to the viral dsRNA replication intermediate. DCR-1 cleaves the viral genome into 23 nt viRNA duplexes with a 2 nt 3′ overhang. Duplex viRNAs are incorporated into the Argonaute protein RDE-1 and one strand is lost to give rise to primary viral siRNAs (primary viRNAs). Primary viRNAs and RDE-1 recruit an RdRP complex to the viral genome to synthesize secondary viral siRNAs, which act to silence viral transcripts or inhibit virus replication. The antiviral RNAi pathway is dependent on the SAGO-2 secondary Argonaute protein (Figure 3—figure supplement 1C). The antiviral RNAi pathway has parallels to the exogenous RNAi pathway and the endogenous RNAi pathway thought to recognize aberrant endogenous transcripts (Gu et al., 2009). A complex of DRH-1, DCR-1 and RDE-4 has previously been observed in whole animal lysates (Tabara et al., 2002; Duchaine et al., 2006; Thivierge et al., 2012). We refer to this complex as the Viral Recognition Complex (ViRC). ERI, other ERI factors. ERIC, ERI Complex. DOI: 10.7554/eLife.00994.018
  • Table 1. Evolution of Dicer and RIG-I family proteins

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Ashe, A., Bélicard, T., Le Pen, J., Sarkies, P., Frézal, L., Lehrbach, N. J., … Miska, E. A. (2013). A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity. ELife, 2. https://doi.org/10.7554/elife.00994

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