Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?

Abstract

BackgroundRetrotransposons are key players in the evolution of eukaryotic genomes. Moreover, it is now known that some retrotransposon classes, like the abundant and plant-specific Sireviruses, have intriguingly distinctive host preferences. Yet, it is largely unknown if this bias is supported by different genome structures.ResultsWe performed sensitive comparative analysis of the genomes of a large set of Ty1/copia retrotransposons. We discovered that Sireviruses are unique among Pseudoviridae in that they constitute an ancient genus characterized by vastly divergent members, which however contain highly conserved motifs in key non-coding regions: multiple polypurine tract (PPT) copies cluster upstream of the 3' long terminal repeat (3'LTR), of which the terminal PPT tethers to a distinctive attachment site and is flanked by a precisely positioned inverted repeat. Their LTRs possess a novel type of repeated motif (RM) defined by its exceptionally high copy number, symmetry and core CGG-CCG signature. These RM boxes form CpG islands and lie a short distance upstream of a conserved promoter region thus hinting towards regulatory functions. Intriguingly, in the envelope-containing Sireviruses additional boxes cluster at the 5' vicinity of the envelope. The 5'LTR/internal domain junction and a polyC-rich integrase signal are also highly conserved domains of the Sirevirus genome.ConclusionsOur comparative analysis of retrotransposon genomes using advanced in silico methods highlighted the unique genome organization of Sireviruses. Their structure may dictate a life cycle with different regulation and transmission strategy compared to other Pseudoviridae, which may contribute towards their pattern of distribution within and across plants.

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

“…Retrofit and Sire are shown in Figure 1D and E. The most striking feature is a highly conserved TATATA motif. This motif has previously been found in Bare-1 [30], Tnt1 [31], both related to Sire; and another clade of Sireviruses [32], phylogenetically distinct from the ones used in the present study. The TATATA motif is known to function as a TATA box [30].…”

Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons

“…The best known mechanism by which genomes maintain LTR-RTs silencing is by methylation of the LTRs [9]. Low complexity CpG rich regions just upstream of the TATA box have been previously described in LTR-RTs in the monocots [37]. These CpG islands are generally found unmethylated in the promoter regions of active genes, hypermethylation of these islands results in an epigenetically silent state.…”

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

“…They are unique in structure among LTR retrotransposons, because they contain highly conserved motifs in their noncoding regions ( Fig. 1A; Bousios et al 2010). These motifs include junctions between the LTRs and the internal (INT) domain of the elements, as well as characteristic features such as palindromic repeats within the upstream half of the LTRs that represents the cis-regulatory center of LTR retrotransposons (Grandbastien 2015).…”