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

Abstract

Background: Retrotransposons 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.

Results: We 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.

Conclusions: Our 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.

Figure 1

Genome diversity of Ty1/copia retrotransposons. Pairwise score identity of the various genomic regions of Sireviruses and classic elements and of the Sirevirus conserved motifs. Classic Ty1/copia elements with linker domain smaller than 25 bp are not included in the respective analysis. Most domains that are shared between the two retrotransposon datasets appear to be equally divergent (see also Table 1). SV, Sirevirus; Cl, Classic elements; Full, full length element; LD, linker domain; GP, gag-pol; PBS, conserved 5'LTR/internal domain junction; PPT, linker domain/3'LTR junction; IntS, integrase signal; TATA, TATA box-like motif.

Figure 2

The organization of the linker domain/3'LTR junction of Ty1/copia retrotransposons. (A) Genome structure of Ty1/copia retrotransposons, of which Sireviruses may contain an envelope-like gene. (B, C) Organization of the Sirevirus and classic elements linker domain/3'LTR junction. The IR arms (yellow) surround the loop sequence, of which the terminal PPT octamer (red) occupies the outmost 5' side. Classic elements with nucleotides in bold indicate the region, where the left arm is located at the 3' end of the pol gene region, due to the very short linker domain.

Figure 3

The diversity of the PPT/3'LTR junction of classic Ty1/copia retrotransposons. Alignment of the conserved Sirevirus PPT/3'LTR junction to the respective region of classic Ty1/copia retrotransposons. Underlined bases represent the 3' terminus of the IR left arm, and nucleotides shaded in black indicate the beginning of the 3'LTR. The location of the IR left arm is universally conserved in all Pseudoviridae.

Figure 4

Sequence composition and distribution of the novel Sirevirus RMs. (A) Alignment of the Sirevirus palindromic RM boxes (refer to Table 3 for the intervening bases of each RM), (B) and their organization (pink boxes) in four elements at the 5' side of the ENV gene (only HOPIE and Inga), and upstream of the TATA box (blue circle) in the 3'LTR. All or a section of the RM clusters define the borders of CpG islands (orange bar) (all elements are shown in Figure S4 in Additional file 2)

Figure 5

Alignment of the Sirevirus conserved TATA box region (A), 5'LTR/internal domain junction (B), and polyC-rich integrase signal (C).

Figure 6

The organization of the highly conserved microdomains in the Sirevirus genome. The coloring follows the pattern of previous figures. The conserved 16 mer of the 5'LTR/PBS junction is shown in orange, whilst the integrase signal at the 3' terminus of the LTRs in light blue. The size difference of Sireviruses and classic retrotransposons is approximately drawn to scale (see also Table 2).