Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

Abstract

Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

Chemistry and Biology of Self-Cleaving Ribozymes

“…For example, some eukaryotic HHRs that are found associated with Penelope-like elements (PLEs) , a family of retrotransposons, display an organization suggestive of dimerization [92]. The dimeric form, containing two sites of self-cleavage, is possible when HHRs occur in tandem and has been shown to lead to a more stable active structure compared to monomeric species of the ribozyme [93].…”

“…In rare instances, such as the Clec2 -associated HHRs and the CPEB3 HDV-like ribozymes, a single ribozyme sequence is conserved across multiple organisms [4, 37], demonstrating that the self-scission activity was preserved through evolutionary lineages. On the other hand, many instances of HHR, HDV-like, and twister ribozymes are found associated with mobile genetic elements and are thus not well conserved in terms of genetic loci or even sequence [5, 92, 94]. The extensive distribution of these ribozymes suggests they are common genomic features, perhaps distributed via (sub-)viral elements, retrotransposons and other repeats, but now associated with multiple biological functions.…”

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction

“…Now, thousands of hammerhead ribozyme sequences have been identified in a variety of species, spanning all domains of life. 2–5 While many viroids use hammerhead ribozyme sequences to process their RNA genomes, the physiological functions of the majority of these hammerhead-like sequences are still unclear.…”

Small circRNAs with self-cleaving ribozymes are frequently expressed in metazoan transcriptomes

“…Altogether, our data strongly suggest that metazoan retrozymes are intensively transcribed in most invertebrate tissues as small (~170-400 nt) and highly self-paired circRNAs (supplementary Figure S6). Moreover, retrozyme containing species such as mussels and other invertebrates also show the presence of autonomous PLEs retroelements carrying atypical type I HHR variants (23,37), supporting the genomic co-existence of both families of non-autonomous and autonomous retroelements with HHRs.…”

“…On the other hand, metazoan retrozymes, which lack any of the typical LTR features ( Figure 1B and C), should be mobilized by some other active member of the families of non-LTR retrotransposons, such as LINEs or PLEs among others. Interestingly, metazoan retrozymes and PLEs share some peculiarities, such as the presence of type I HHRs (23), their occurrence as tandem copies (48), and their co-existence in all the metazoans analysed, which suggest that autonomous PLEs are a strong candidate to complete retrozyme mobilization.…”