A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes

Abstract

Circular DNAs, such as most prokaryotic and phage genomes, are a frequent form of nucleic acids, whereas circular RNAs had been regarded as unusual macromolecules until very recently. The first reported RNA circles were the family of small infectious genomes of viroids and circular RNA (circRNA) satellites of plant viruses, some of which contain small self-cleaving RNA motifs, such as the hammerhead (HHR) and hairpin ribozymes. A similar infectious circRNA, the unique human hepatitis delta virus (HDV), is another viral satellite that also encodes self-cleaving motifs called HDV ribozymes. Very recently, different animals have been reported to contain HDV-like circRNAs with typical HDV ribozymes, but also conserved HHR motifs, as we describe here. On the other hand, eukaryotic and prokaryotic genomes encode sequences able to self-excise as circRNAs, like the autocatalytic Group I and II introns, which are widespread genomic mobile elements. In the 1990s, the first circRNAs encoded in a mammalian genome were anecdotally reported, but their abundance and importance have not been unveiled until recently. These gene-encoded circRNAs are produced by events of alternative splicing in a process generally known as backsplicing. However, we have found a second natural pathway of circRNA expression conserved in numerous plant and animal genomes, which efficiently promotes the accumulation of small non-coding RNA circles through the participation of HHRs. Most of these genome-encoded circRNAs with HHRs are the transposition intermediates of a novel family of non-autonomous retrotransposons called retrozymes, with intriguing potential as new forms of gene regulation.

Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes

“…2016 ; Cervera and de la Peña 2020 ), or the heterogenous family of infectious circRNA genomes ( Flores et al. 2016 ; de la Peña et al. 2020 ).…”

“…Interestingly, the retrotransposition intermediates of both LTR and non-LTR retrozymes are small circular RNAs that accumulate at high levels in different organisms, and share many characteristics with infectious HHR-containing circRNAs of plants ( de la Peña and Cervera 2017 ). The conserved presence of diverse self-cleaving ribozymes in infectious agents as well as in retrotransposons hints at a complex evolutionary relationship among all these mobile elements ( de la Peña et al. 2020 ).…”

Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?

“…The retrozymes consist of a 300-700 nt non-coding sequence flanked by long terminal repeats (LTRs) and, apart from the presence of the HHR, resemble other small, non-autonomous retrotransposons that are abundant in plants, such as terminal-repeat retrotransposons in miniature (TRIMs) [72] or small LTR retrotransposons (SMARTs) [73]. The retrozymes are actively transcribed, the transcripts are self-cleaved by HHR and form abundant cccRNAs of both polarities [74,75]. Notably, the circularization is catalyzed by chloroplast tRNA ligase as is the case also in avsunviroids.…”

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

“…For the second prerequisite there is evidence from naturally existing RNAs as well as from experiments that ribozymes can remain catalytically active when they are part of longer RNA molecules. For example, active hammerhead ribozyme domains are embedded in the larger circular ssRNA genomes of Avsunviroidae viroids [64], virus satellite circRNAs [65] and hepatitis delta virus [66] as well as in various retroelements such as short interspersed nuclear elements (SINEs) [67], Penelope-like elements [68] and retrozymes [69]. Moreover, various artificial RNAs with multiple active ribozyme domains have been successfully generated, including two-ribozyme constructs [70][71][72], RNAs with four [73,74], up to nine [75] and up to ten ribozyme domains [76].…”