Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

A comprehensive analysis of covalently closed circular RNA across ecosystems reveals that viroids infect a diverse collection of host species, including those that aren't plants. The study also discovers other types of ribozyme activity and functional properties in these molecules.

Benjamin D. Lee, Uri Neri, Simon Roux, Uri Gophna, Valerian V. Dolja and Eugeni V. Koonin worked together on a research project to investigate the diversity and extent of viroid-like covalently closed circular (ccc) RNAs and viroids. The project was titled "Investigating the Diversity and Extent of Viroid-Like CCC RNAs and Viroids."

Examples of minimum replicators include viroids and viroid-like RNAs. Neither of these types of RNAs encodes any proteins, but they do rely on enzymes produced by cells in order to replicate. In order for the researchers to achieve their objective, they developed a computer pipeline, which they then applied to the process of analyzing 5,131 plant metatranscriptomes and 1,344 plant transcriptomes.

Because of this, scientists were able to identify 11,378 viroid-like cccRNAs that span 4,409 species-level clusters. This represents a five-fold increase from the number of viroid-like elements that had been found earlier. Within this diverse group, the researchers discovered a significant number of possible viroids, retrozymes, ribozyme-like viruses and satellite RNAs.

According to the findings of the study, certain mito-like viruses, ambiviruses and capsid-encoding satellite virus-like cccRNAs have self-cleaving ribozymes in their genomes. In addition, the research discovered rare ribozymes as well as a variety of other ribozyme combinations within the cccRNAs. The existence of matches to CRISPR spacers suggests that certain cccRNAs may be capable of replicating in prokaryotes. The discovery of viroid-like cccRNAs in a wide variety of transcriptomes and ecosystems lends credence to the hypothesis that their host range encompasses a wider variety of organisms than is presently understood. In addition to this, the detection of these cccRNAs hints that the host range of these organisms is likely to be much wider than is now understood.