Argonaute Proteins Affect siRNA Levels and Accumulation of a Novel Extrachromosomal DNA from the Dictyostelium Retrotransposon DIRS-1

Boesler, Benjamin; Meier, Doreen; Förstner, Konrad U.; Friedrich, Michael W.; Hammann, Christian; Sharma, Cynthia M.; Nellen, Wolfgang

doi:10.1074/jbc.m114.612663

Cited by 9 publications

(24 citation statements)

References 51 publications

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“…The enzyme is thought to integrate into the genome circular intermediates (Poulter and Goodwin, 2005), the existance of which we recently verified experimentally (Boesler et al, 2014). Full length DIRS-1 contains three, partially overlapping ORFs that are surrounded by two inverted LTRs (Figure 2A).…”

Section: Dirs-1mentioning

confidence: 64%

Retrotransposon Domestication and Control in Dictyostelium discoideum

2017

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Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.

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Section: Dirs-1mentioning

confidence: 64%

Retrotransposon Domestication and Control in Dictyostelium discoideum

2017

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“…The silencing of the retrotransposon DIRS-1 is a model to study RNAi pathways in D. discoideum [ 14 , 15 , 17 , 22 ]. Previous deep sequencing of small RNAs revealed high levels of DIRS-1-derived ~21 nt siRNAs [ 15 ] that add up to 20 % of all small RNAs detected in D. discoideum cells [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

“…4 ). Thus, the RNAi pathways that regulate DIRS-1 and TRE5-A may overlap at the stage of primary siRNA formation, presumably involving the Dicer homolog DrnA, but use different RISCs that contain either AgnA for DIRS-1 silencing [ 22 ] or AgnC/AgnE for TRE5-A suppression.…”

Section: Discussionmentioning

confidence: 99%

“…At least the overexpression of DIRS-1 in JH.D cells could be explained by the weak, but reproducible overexpression of the genes rrpC and agnA (Fig. 2 ), which were both shown to be involved in the downregulation of DIRS-1 [ 22 ]. Thus, DIRS-1 and TRE5-A may be suppressed by different RNAi pathways and are affected indirectly by CbfA’s broad-ranging gene-regulatory activity.…”

Section: Discussionmentioning

confidence: 99%

“…Clearly, D. discoideum cells could take advantage of TRE5-A’s minus-strand RNA production to downregulate TRE5-A plus-strand RNA, the substrate for retrotransposition, using an RNAi pathway. This strategy is actually realized in the silencing of the tyrosine recombinase retrotransposon DIRS-1 in D. discoideum cells [ 22 ]. To suppress TRE5-A amplification, promoter activity of the C-module, the distinguished minus-strand RNA promoter at the 3′ end of the TRE5-A element, could be positively regulated by a host-encoded transcription factor.…”

Section: Introductionmentioning

confidence: 99%

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

Schmith¹,

Spaller²,

Gaube³

et al. 2015

Mobile DNA

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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.

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DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates

Malicki

Spaller

Winckler

et al. 2020

Nucleic Acids Research

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The Dictyostelium Intermediate Repeat Sequence 1 (DIRS-1) is the name-giving member of the DIRS order of tyrosine recombinase retrotransposons. In Dictyostelium discoideum, DIRS-1 is highly amplified and enriched in heterochromatic centromers of the D. discoideum genome. We show here that DIRS-1 it tightly controlled by the D. discoideum RNA interference machinery and is only mobilized in mutants lacking either the RNA dependent RNA polymerase RrpC or the Argonaute protein AgnA. DIRS retrotransposons contain an internal complementary region (ICR) that is thought to be required to reconstitute a full-length element from incomplete RNA transcripts. Using different versions of D. discoideum DIRS-1 equipped with retrotransposition marker genes, we show experimentally that the ICR is in fact essential to complete retrotransposition. We further show that DIRS-1 produces a mixture of single-stranded, mostly linear extrachromosomal cDNA intermediates. If this cDNA is isolated and transformed into D. discoideum cells, it can be used by DIRS-1 proteins to complete productive retrotransposition. This work provides the first experimental evidence to propose a general retrotransposition mechanism of the class of DIRS like tyrosine recombinase retrotransposons.

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Argonaute Proteins Affect siRNA Levels and Accumulation of a Novel Extrachromosomal DNA from the Dictyostelium Retrotransposon DIRS-1

Cited by 9 publications

References 51 publications

Retrotransposon Domestication and Control in Dictyostelium discoideum

Retrotransposon Domestication and Control in Dictyostelium discoideum

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

DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates

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