The Evolutionary Loss of RNAi Key Determinants in Kinetoplastids as a Multiple Sporadic Phenomenon

Abstract

We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico. The alignments indicated that the genes are homologous with a high degree of confidence, and three-dimensional structural models strongly supported a functional relationship to previously characterized AGO1, DCL1, and DCL2 proteins. Phylogenetic analysis of these putative proteins showed that these genes, when present, evolved in parallel with other nuclear genes, arguing that the RNAi system genes share a common progenitor, likely across all Kinetoplastea. In addition, the genome segments bearing these genes are highly conserved and syntenic, even among those taxa in which they are absent. However, taxa in which these genes are apparently absent represent several widely divergent branches of kinetoplastids, arguing that these genes were independently lost at least six times in the evolutionary history of these organisms. The mechanisms responsible for the apparent coordinate loss of these RNAi system genes independently in several lineages of kinetoplastids, while being maintained in other related lineages, are currently unknown.

Gene family innovation, conservation and loss on the animal stem lineage

“…Argonaute and Dicer were each lost five times independently in choanoflagellates ( Figure 3—figure supplement 2 ), although these could both be overestimates if the genes were not expressed in our culture conditions. A similar pattern of repeated parallel loss has also been previously observed in kinetoplastids, a group of single-celled eukaryotes ( Matveyev et al, 2017 ). Curiously, in contrast to the case for kinetoplastids, where Argonaute and Dicer were generally lost together, we detect five choanoflagellate species in which Argonaute is present and Dicer is absent or vice versa.…”

Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania

“…Variation in the RNAi pathway may contribute to the observed patchiness in viral distribution, as this pathway acts as an antiviral defense mechanism in many species (95). In agreement with this, the RNAi pathway (believed to be ancestral to all eukaryotes) is absent in Phytomonas spp., Leptomonas seymouri, and LRV2-bearing Leishmania aethiopica and Leishmania major (23,96,97). The RNAi pathway may be especially important for narnaviruses, which are presumably defenseless because of the lack of capsids.…”

“…In addition, numerous Crithidia and Leptomonas spp. retain the RNAi pathway (96). It is thus possible that RNAi plays only a weak role in the evolutionary distribution of trypanosomatid viruses.…”

Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence

“…Some pseudogenes transcribed in T. brucei have been proposed to participate in RNAi-based natural antisense suppression [ 99 ]. The genes responsible for RNAi machinery are absent in all strains of T. cruzi examined to date and may only be present as pseudogenes in T. rangeli SC-58, but are present and intact in both T. rangeli AM80 and T. conorhini 025E [ 100 ]. Analysis of the transcriptional activities and structural organization of these pseudogenes is beyond the scope of this study, but may clarify their roles in generation of protein diversity or post-transcriptional regulation.…”