A life of research on circular RNAs and ribozymes: towards the origin of viroids, deltaviruses and life

Viroids and Retrozymes: Plant Circular RNAs Capable of Autonomous Replication

Among the long non-coding RNAs that are currently recognized as important regulatory molecules influencing a plethora of processes in eukaryotic cells, circular RNAs (circRNAs) represent a distinct class of RNAs that are predominantly produced by back-splicing of pre-mRNA. The most studied regulatory mechanisms involving circRNAs are acting as miRNA sponges, forming R-loops with genomic DNA, and encoding functional proteins. In addition to circRNAs generated by back-splicing, two types of circRNAs capable of autonomous RNA-RNA replication and systemic transport have been described in plants: viroids, which are infectious RNAs that cause a number of plant diseases, and retrozymes, which are transcripts of retrotransposon genomic loci that are capable of circularization due to ribozymes. Based on a number of common features, viroids and retrozymes are considered to be evolutionarily related. Here, we provide an overview of the biogenesis mechanisms and regulatory functions of non-replicating circRNAs produced by back-splicing and further discuss in detail the currently available data on viroids and retrozymes, focusing on their structural features, replication mechanisms, interaction with cellular components, and transport in plants. In addition, biotechnological approaches involving replication-capable plant circRNAs are discussed, as well as their potential applications in research and agriculture.

Uncovered diversity of infectious circular RNAs: A new paradigm for the minimal parasites?

Infectious circular RNAs (circRNAs) have been considered as biological oddities only occurring in plants, with limited exceptions. However, a great diversity of viroid-like circRNAs has been recently uncovered by the high-throughput exploration of transcriptomic data of geographically and ecologically diverse niches. In my opinion, this suggests a change in basic assumptions regarding our knowledge about these minimal parasites. The potentially infectious circRNAs found are diverse in size, type of ribozymes, encoded proteins and potential host organisms. The distinction between viroids and RNA viruses has been blurred by the detection of circular mitoviruses and ambiviruses which encode for their own RNA-dependent RNA polymerase. Thus, their taxonomic classification might pose a challenge because of the apparent extensive horizontal transfer and recombination of sequences. Many aspects of the predicted circRNAs remain to be uncovered, such as their pathogenicity or host range, and experimental validations are essential. For example, viroid-like circRNAs similar in size to plant viroids have been found to replicate and cause symptoms in fungi, with an isolate being the smallest replicon characterized so far. Despite an ancestral prebiotic origin for viroid-like sequences has been proposed, their dependence of viral or cellular proteins seems, to my view, more compatible with a cellular escape and/or viral genome reduction. This wide variety of potentially infectious agents might pose a biohazard concern of which we were previously unaware, and thus it would be convenient that more efforts are assigned for their characterization.

In-Plant Persistence and Systemic Transport of Nicotiana benthamiana Retrozyme RNA

Retrozymes are nonautonomous retrotransposons with hammerhead ribozymes in their long terminal repeats (LTRs). Retrozyme transcripts can be self-cleaved by the LTR ribozyme, circularized, and can undergo RNA-to-RNA replication. Here, we demonstrate that the Nicotiana benthamiana genome contains hundreds of retrozyme loci, of which nine represent full-length retrozymes. The LTR contains a promoter directing retrozyme transcription. Although retrozyme RNA is easily detected in plants, the LTR region is heavily methylated, pointing to its transcriptional silencing, which can be mediated by 24 nucleotide-long retrozyme-specific RNAs identified in N. benthamiana. A transcriptome analysis revealed that half of the retrozyme-specific RNAs in plant leaves have no exact matches to genomic retrozyme loci, containing up to 13% mismatches with the closest genomic sequences, and could arise as a result of many rounds of RNA-to-RNA replication leading to error accumulation. Using a cloned retrozyme copy, we show that retrozyme RNA is capable of replication and systemic transport in plants. The presented data suggest that retrozyme loci in the N. benthamiana genome are transcriptionally inactive, and that circular retrozyme RNA can persist in cells due to its RNA-to-RNA replication and be transported systemically, emphasizing functional and, possibly, evolutionary links of retrozymes to viroids-noncoding circular RNAs that infect plants.