Circular RNAs with hammerhead ribozymes encoded in eukaryotic genomes: The enemy at home

Abstract

A new family of non-autonomous retrotransposons with self-cleaving hammerhead ribozymes, the so called retrozymes, has recently been found encoded in diverse plant genomes. These retroelements can be actively transcribed, and their RNAs accumulate in the cells as abundant non-coding circular RNAs (circRNAs) of small size (600-1000 nt). Related circRNAs with self-cleaving ribozymes had already been described in plants, and belong to a group of infectious RNA agents with an uncertain origin: the viroids and viroid-like satellites of plant RNA viruses. These pathogenic circRNAs show many structural similarities with retrozyme circRNAs, and both have been found to occur in flowering plants as heterogeneous RNA molecules of positive and negative polarities. Taking all these data together, we hypothesize that circRNAs encoded by genomic retrozymes could have given origin to infectious circRNAs with self-cleaving ribozymes. Moreover, we propose that retrozymes in time could have evolved from the ancient family of Penelope-like retroelements, which also harbour hammerhead ribozymes. Putative retrozyme sequences with hammerhead ribozymes have been detected as well in metazoan genomes, opening the door to a common occurrence of circRNAs with self-cleaving motifs among eukaryotes.

Keywords: Circular RNA; retrotransposons; ribozyme; viral satellite RNA; viroid.

Figure 1.

Representation of the possible hammerhead ribozyme (HHR) topologies. The conserved nucleotides of the HHR are boxed. Loop-loop interactions are also indicated. Dotted and continuous lines refer to non-canonical and Watson-Crick base pairs, respectively. The most typical lengths of the helix stems for each HHR type are drawn. N stands for any nucleotide, whereas R stands for purines (A or G), Y for pyrimidines (U or C) and H for either A, U or C.

Figure 2.

Sequence features of genomic retrozymes. (A) Schematic representation (top) of a full genomic retrozyme element. Target Site Duplications (TSDs) delimiting the retrozyme are shown in gray. Long terminal repeats (LTRs) are shown in blue. The positions of the primer binding site (PBS), the polypurine tract (PPT) and the hammerhead ribozymes (HHR) are indicated. The self-cleavage sites (SC) delimiting the retrozyme RNA are indicated with arrows. The resulting self-cleaved retrozyme RNA after transcription (middle) and circularization (bottom) are indicated. (B) Schematic representation of 2 examples of plant small non-autonomous LTR-retrotransposons such as TRIMs (top) and SMARTs (bottom) retroelements.

Figure 3.

Minimum free energy secondary structure predictions for (A) a retrozyme circRNA of Jatropha curcas (Entry KX273075.1), (B) the avsunviroid PLMVd (Entry M83545.1) and (C) the Nepovirus satellite RNA sTRSV (Entry M14879.1). HHR sequences are shown in purple (positive polarity) and green (negative polarity), and the PBS and PPT motifs of the retrozyme are shown in orange and blue, respectively. The corresponding structures of the HHRs motifs are shown under each circRNA structure and, with the exception of PLMVd HHRs, dotted lines indicate putative tertiary interactions between HHR loops. Self-cleavage sites are indicated with arrows. Kissing-loop interaction of PLMVd is also shown. Numbering for each circRNA starts at the self-cleavage site of the positive polarity HHR.