Leishmania guyanensis controls endogenous viral replication by a canonical RNA interference pathway

Protistan parasites of the genus Leishmania, infamous human and animal pathogens, can themselves be infected by endosymbiotic viruses, exemplified by Leishmania RNA viruses (LRVs). These viruses affect immune responses in vertebrate hosts and have been associated with adverse treatment outcomes. How parasites control replication of these viruses is not known. Intriguingly, functional RNA interference (RNAi) pathways that have been associated with antiviral responses across eukaryotes, are retained only in some Leishmania spp., including those of the subgenus Viannia. Here, we investigated effectors in the canonical RNAi response and the Piwi protein of the human pathogen L. (Viannia) guyanensis by gene ablation and identified Dicer-like 1 and Argonaute 1 proteins of the canonical RNAi pathway as critical for controlling viral RNA levels. Notably, we characterized virus-derived small interfering RNA (vsiRNA) levels and their unique properties including terminal modifications as well as, unusual for canonical Dicer cleavage, predominant perfectly matching sequence overlaps in blunt ended vsiRNA duplexes. Taken together, the data suggests that control of viral replication is directly mediated by the canonical RNAi response. This study opens the door to further investigations of antiviral RNAi in other protistan parasites and suggests that, where present, canonical RNAi is critical for such activities. Author summaryLeishmania parasites of humans and animals harbor endosymbiotic viruses, which, in some cases, have been shown to affect vertebrate immune responses and impact treatment. Thus, understanding how viral levels are controlled is critical to identify antiviral effectors, which, in turn, will allow studies on how viral levels impact parasite biology. Here, we investigated RNA interference pathways against its virus of the family Pseudototiviridae in a New World human pathogen L. guyanensis. To do that, we have produced and analyzed genetic knockouts of Dicer-like and Argonaute proteins involved in antiviral small RNA response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/743808v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@cffe40org.highwire.dtl.DTLVardef@13d4012org.highwire.dtl.DTLVardef@395e60org.highwire.dtl.DTLVardef@631fed_HPS_FORMAT_FIGEXP M_FIG C_FIG