Evolution of Susceptibility to Ingested Double-Stranded RNAs in Caenorhabditis Nematodes

Abstract

BackgroundThe nematode Caenorhabditis elegans is able to take up external double-stranded RNAs (dsRNAs) and mount an RNA interference response, leading to the inactivation of specific gene expression. The uptake of ingested dsRNAs into intestinal cells has been shown to require the SID-2 transmembrane protein in C. elegans. By contrast, C. briggsae was shown to be naturally insensitive to ingested dsRNAs, yet could be rendered sensitive by transgenesis with the C. elegans sid-2 gene. Here we aimed to elucidate the evolution of the susceptibility to external RNAi in the Caenorhabditis genus.Principal FindingsWe study the sensitivity of many new species of Caenorhabditis to ingested dsRNAs matching a conserved actin gene sequence from the nematode Oscheius tipulae. We find ample variation in the Caenorhabditis genus in the ability to mount an RNAi response. We map this sensitivity onto a phylogenetic tree, and show that sensitivity or insensitivity have evolved convergently several times. We uncover several evolutionary losses in sensitivity, which may have occurred through distinct mechanisms. We could render C. remanei and C. briggsae sensitive to ingested dsRNAs by transgenesis of the Cel-sid-2 gene. We thus provide tools for RNA interference studies in these species. We also show that transgenesis by injection is possible in many Caenorhabditis species.ConclusionsThe ability of animals to take up dsRNAs or to respond to them by gene inactivation is under rapid evolution in the Caenorhabditis genus. This study provides a framework and tools to use RNA interference and transgenesis in various Caenorhabditis species for further comparative and evolutionary studies.

Manipulation of Karyotype inCaenorhabditis elegansReveals Multiple Inputs Driving Pairwise Chromosome Synapsis During Meiosis

“…Although most Lon worm obtained by the selfing strategy proved to be sterile, we did successfully generate one tetraploid strain using this approach; for comparison, each of the 3 Lon putative triploids obtained through the original crossing scheme gave rise to tetraploid strains. We also successfully used the selfing strategy to generate a tetraploid derivative of C. briggsae JU1018 ( Figure 3G), a transgenic strain that is sensitive to RNAi by feeding (Nuez and Felix 2012).…”

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

“…Bristol (N2), C. briggsae (AF16), C. remanei (SB146), C. brenneri (CB5161), C. sinica (JU1201), C. nigoni (JU1325), C. latens (VX88), C. wallacei (JU1873), C. tropicalis (JU1373), C. doughertyi (JU1333), and C. japonica (DF5081) were used as the wild-type (WT) strain for each respective species. C. briggsae RNA interference (RNAi) sensitive by feeding strain JU1018:mfIs42[Cel-sid-2 + Cel-myo-2::DsRed] was generated by Nuez and Felix (2012). Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health (NIH) National Center for Research Resources.…”

“…Interestingly, mutation of MET-2 abrogated H3K9me2 deposition but did not affect H3K9me3 accumulation, while inactivation of the Polycomb Repressive Complex 2-related histone methyltransferase MES-2 (Holdeman et al 1998) resulted in depletion of H3K9me3 but not H3K9me2, suggesting that these marks are acquired independently in the C. elegans germ line (Bessler et al 2010). To examine the gene network responsible for deposition of H3K9me2 and H3K9me3 in the germ line in a species that accumulates H3K9me3 on sex chromosomes, we depleted histone methyltransferases in C. briggsae strains expressing C. elegans SID-2 from an integrated chromosomal array, which makes them susceptible to RNAi by feeding (Nuez and Felix 2012). Additionally, these strains allowed us to examine the chromatin state of a multicopy array, which in C. elegans is enriched for H3K9me3 in germ cells when the array carries a somatically expressed gene (Bessler et al 2010).…”

Environmental RNAi in herbivorous insects

“…Currently, most knowledge in this field has been generated in nematode model systems. Although insightful, even in nematodes of the same genus, the capacity for eRNAi is quite variable indicating a potential complex interplay between function and selective pressures in the environment (Nuez and Félix 2012). Other species that have demonstrated eRNAi (e.g., insects) do not show clear mechanistic orthologs to key components such as dsRNA transporter SID-2 (Winston et al 2007;Huvenne and Smagghe 2010), or do have some homologous genes known to be essential to the process in C. elegans (e.g., SID-1), yet with differential contribution in the examined insects' ability to uptake and distribute dsRNA (Miyata et al 2014).…”