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

Anika Schmith; Thomas Spaller; Friedemann Gaube; Åsa Fransson; Benjamin Boesler; Sandeep Ojha; Wolfgang Nellen; Christian Hammann; Fredrik Söderbom; Thomas Winckler

doi:10.1186/s13100-015-0045-5

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

Mob DNA. 2015 Sep 3:6:14. doi: 10.1186/s13100-015-0045-5. eCollection 2015.

Authors

Affiliations

¹ Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany.
² Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden ; Present address: Aprea AB, Karolinska Institutet Science Park, Nobels väg 3, 17175 Solna, Sweden.
³ Institute of Biology - Genetics, University of Kassel, Kassel, Germany.
⁴ Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany.
⁵ Institute of Biology - Genetics, University of Kassel, Kassel, Germany ; Present address: Department of Biology, Brawijaya University, Jl. Veteran, Malang, East Java Indonesia.
⁶ Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.

Abstract

Background: In 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.

Results: The 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.

Conclusions: The 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.

Keywords: Argonaute; Dictyostelium; RNAi; Retrotransposition; siRNA.