A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein

Abstract

BackgroundIn the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies continuously in D. discoideum cells even though it produces considerable amounts of minus-strand (antisense) RNA in the presence of an active RNA interference machinery. Removal of the host-encoded C-module-binding factor (CbfA) from D. discoideum cells resulted in a more than 90 % reduction of both plus- and minus-strand RNA of TRE5-A and a strong decrease of the retrotransposition activity of the cellular TRE5-A population. Transcriptome analysis revealed an approximately 230-fold overexpression of the gene coding for the Argonaute-like protein AgnC in a CbfA-depleted mutant.ResultsThe D. discoideum genome contains orthologs of RNA-dependent RNA polymerases, Dicer-like proteins, and Argonaute proteins that are supposed to represent RNA interference pathways. We analyzed available mutants in these genes for altered expression of TRE5-A. We found that the retrotransposon was overexpressed in mutants lacking the Argonaute proteins AgnC and AgnE. Because the agnC gene is barely expressed in wild-type cells, probably due to repression by CbfA, we employed a new method of promoter-swapping to overexpress agnC in a CbfA-independent manner. In these strains we established an in vivo retrotransposition assay that determines the retrotransposition frequency of the cellular TRE5-A population. We observed that both the TRE5-A steady-state RNA level and retrotransposition rate dropped to less than 10 % of wild-type in the agnC overexpressor strains.ConclusionsThe data suggest that TRE5-A amplification is controlled by a distinct pathway of the Dictyostelium RNA interference machinery that does not require RNA-dependent RNA polymerases but involves AgnC. This control is at least partially overcome by the activity of CbfA, a factor derived from the retrotransposon’s host. This unusual regulation of mobile element activity most likely had a profound effect on genome evolution in D. discoideum.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-015-0045-5) contains supplementary material, which is available to authorized users.

Retrotransposon Domestication and Control in Dictyostelium discoideum

“…Next to Argonaute proteins, RNA-dependent RNA polymerases (RdRPs) and Dicer proteins are key components of RNAi, and several representatives of these families exist in D. discoideum (Martens et al, 2002 ; Kuhlmann et al, 2005 ; Boesler et al, 2014 ; Wiegand et al, 2014 ; Kruse et al, 2016 ; Meier et al, 2016 ). Indeed, TRE5-A was found overexpressed in an agnC deletion strain, and downregulated in an AgnC overexpressing strain, resulting in a reduced retrotransposition rate (Schmith et al, 2015 ). No indication was found for an involvement of the three RdRPs of the amoeba, nor of its two Dicer proteins.…”