Innate, translation‐dependent silencing of an invasive transposon in Arabidopsis

Abstract

Co-evolution between hosts' and parasites' genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this response's activation, we studied the single-copy element EVAD E (EVD), one of few representatives of the large Ty1/ Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG-POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5'OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto-unrecognized "translationdependent silencing" (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.

Heterochromatin re-organization associated with the transcriptional reprogramming under viral infection inArabidopsis

“…DEGs regulated by epigenetic marks were confirmed to be targets of their respective pathways since they were identified as differentially expressed (adjusted p-value <0.05) in different combinations of mutants for genes involved in the homeostasis of DNA methylation ( mddcc 64 , ago4 65 , and polV 66 , 71% of DNA methylation-associated DEGs), H3K27me3 ( clf and elf6 ref6 jmj13 67 , 93% of H3K27me3-associated DEGs) and H3K9me2 ( kyp and ddm1 68 , 54% of H3K9me2-associated DEGs) (Fig 6a and Sup Table 4). The majority of overrepresented CMV-induced DEGs associated with epigenetic marks were classified as stress/stimulus responsive genes according to their annotated gene ontology (GO) biological function (Fig 6b and Sup Fig 8a).…”

“…DEGs regulated by epigenetic marks were confirmed to be targets of their respective pathways since they were identified as differentially expressed (adjusted p-value <0.05) in different combinations of mutants for genes involved in the homeostasis of DNA methylation (mddcc 64 , ago4 65 , and polV 66 , 71% of DNA methylation-associated DEGs), H3K27me3 (clf and elf6 ref6 jmj13 67 , 84% of H3K27me3-associated DEGs) and H3K9me2 (kyp and ddm1 68 , HSP70-2 74 and the main antiviral AGO protein, AGO2 75 (all associated with H3K9me2, Fig 6e). In addition, CMV-responsive DEGs associated with epigenetic marks included other stress-responsive genes that have not been previously associated with viral infections such as AT1G43910, AT1G13470 and AT1G67870, the lipid transfer protein EARLI1, the acyl-transferase protein CER26 or the FADbinding Berberine family protein ATBBE10 (Sup Fig 8c-e).…”

Atypical epigenetic and small RNA control of transposons in clonally reproducingSpirodela polyrhiza

“…S31 ). Although PTGS is a well-documented control mechanism against transcriptionally active TEs in Arabidopsis [27,56,58,148–150], we were intrigued by the presence of 22-nt siRNAs, given that any identifiable ortholog of DCL2, their cognate Dicer in plants [151–154], is missing in Spirodela and Lemnaceae genomes in general ( Fig. 2b, Supplemental Fig.…”

The plant siRNA landscape

“…PBSs are mandatory for LTR element reverse-transcription (RT) and hence are unlikely to withstand miRNA-counteracting mutations. Incidentally, RT is not part of DNA element biology, which is easiRNA free ( Oberlin et al 2022 ). Inverted-repeat copies of the “to-be targeted” TEs likely underlie the henceforth suggested MIRNA - TE coevolution ( Sarazin and Voinnet 2014 ), and indeed Arabidopsis MIR845 is a [5′LTR + PBS]-encompassing truncation inversion ( Borges et al 2018 ).…”

“…Nonetheless and as discussed ( Sarazin and Voinnet 2014 ), the predicted set of ≥50 TE-targeting (ea)miRNAs unlikely underpins, alone, the observed bulk of easiRNA production in ddm1 . For instance, the evolutionarily young (2 copies) COPIA element ÉVADÉ ( EVD ; Mirouze et al 2009 ) displays no overt miRNA target sites and indeed spawns comparable levels of RDR6-dependent easiRNA in both ddm1 and dcl1 dmm1 sporophytes ( Oberlin et al 2022 ; see section below). Moreover, TEs rearranged into IRs ( Slotkin et al 2003 ) likely spawn easiRNAs de facto RDR independently ( Fig.…”