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.
Highlights
In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability
C-module-binding factor (CbfA) regulates the expression of the Argonaute-like protein AgnC Even though the accumulation of tRNA gene-targeted retroelement 5-A (TRE5-A) RNA in D. discoideum cells strictly depends on CbfA and this factor binds to the C-module of TRE5-A in vitro, it does not regulate the C-module’s promoter activity in vivo [21]
A probable explanation for this paradox could be that CbfA exerts an indirect effect by regulating an RNA interference (RNAi) pathway that is involved in the control of TRE5-A expression
Summary
In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. Transposable elements are found in virtually all organisms and play central roles in shaping their host’s genomes The amplification of these genomic parasites is a constant threat to host fitness due to the intrinsic process of integration into the genomic DNA that can cause mutagenesis of genes and force illegitimate recombinations between distant transposon copies [1,2,3,4]. Eukaryotic cells have evolved several pathways of RNA interference (RNAi) to restrain the amplification of transposons at the posttranscriptional level [5,6,7,8] In this process, long RNA duplexes (dsRNA), which may occur in cells as intermediates of transposon or RNA virus replication, are typically processed into 20–30 nucleotide double-stranded small interfering RNAs (siRNAs) by ribonuclease III-type enzymes such as Dicer. If slicing is precluded by mismatches between the annealing guide RNA and cellular mRNA, translation is repressed and mRNA can be degraded by deadenylation and decapping
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