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© Mart Krupovic, Junfeng Liu
Scanning electron micrograph of Saccharolobus islandicus cells (light blue) infected with the lemon-shaped virus STSV2 (yellow). Artistic rendering by Ala Krupovic.
Publication : Cell

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Cell - 02 Feb 2023

Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, , Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV

Link to Pubmed [PMID] – 36696902

Link to DOI – 10.1016/j.cell.2022.12.039S0092-8674(22)01582-3

Cell 2023 Feb; 186(3): 646-661.e4

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.

https://pubmed.ncbi.nlm.nih.gov/36696902