BARE Retrotransposons Are Translated and Replicated Via Distinct RNA Pools

Retrotransposons, also called Class I transposable elements, and their fragments can constitute considerably more than 50% of higher plant genomes. The most abundant subclass, the Long Terminal Repeat (LTR) retrotransposons, are transcribed from promoters in the LTRs and encode proteins for packaging of the transcripts, their reverse transcription into cDNA, and integration of the cDNA back into the genome. In addition, the genome contains non-autonomous LTR retrotransposons, which utilize the proteins of autonomous elements for their replication and propagation. A major question for both retrotransposons and retroviruses is how the two conflicting roles for their transcripts, translation and reverse transcription, are managed. Here, we show that the copia-like BARE retrotransposon of barley, despite its simple organization into only one open reading frame, produces three distinct classes of transcripts, one that is capped, polyadenylated, and translated but which cannot be reverse transcribed and another that is not capped or polyadenylated, but destined instead for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor produce a subgenomic RNA encoding only Gag, the capsid protein that forms the virus-like particles (VLPs).  Moreover, the BARE2 subfamily, which cannot synthesize Gag and is dependent on BARE1 for this protein, does not produce the spliced sub-genomic RNA but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.