Hybrids of RNA viruses and viroid-like elements replicate in fungi

Abstract

Earth’s life may have originated as self-replicating RNA, and it has been argued that RNA viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses are defined by linear RNA genomes encoding an RNA-dependent RNA polymerase (RdRp), whereas viroid-like elements consist of small, single-stranded, circular RNA genomes that, in some cases, encode paired self-cleaving ribozymes. Here we show that the number of candidate viroid-like elements occurring in geographically and ecologically diverse niches is much higher than previously thought. We report that, amongst these circular genomes, fungal ambiviruses are viroid-like elements that undergo rolling circle replication and encode their own viral RdRp. Thus, ambiviruses are distinct infectious RNAs showing hybrid features of viroid-like RNAs and viruses. We also detected similar circular RNAs, containing active ribozymes and encoding RdRps, related to mitochondrial-like fungal viruses, highlighting fungi as an evolutionary hub for RNA viruses and viroid-like elements. Our findings point to a deep co-evolutionary history between RNA viruses and subviral elements and offer new perspectives in the origin and evolution of primordial infectious agents, and RNA life.

Design principles and applications of synthetic self‐replicating RNAs

“…Nonetheless, small gene-free srRNAs are still of considerable interest as they are readily generated by simple in vitro replication/serial transfer (Bansho et al, 2012;Mills et al, 1967;Wagner et al, 2022) and can be used as scaffolds for synthetic srRNAs, that is, by adding compatible RdRP genes. As mentioned before, small gene-free srRNAs might also be the evolutionary origin of the newly discovered ambiviruses (Forgia et al, 2023).…”

“…Remarkably, the recently discovered ambiviruses (ssRNA viruses with coding sequences on both strands) as well as some segmented ssRNA viruses with ambisense genomes (combination of segments with sense or antisense polarity) do not fall into either group IV or group V, but rather form their own group (Koonin et al, 2021;Sutela et al, 2020). Furthermore, in case of ribozyviruses, viroids, and potentially also some ambiviruses, the ssRNA genome can be circularized, thus protecting the RNA ends from exo-ribonucleases (Flores et al, 2011;Forgia et al, 2023).…”

“…Despite their low independence, viroids and satellite viruses may be re-engineered to encode their cognate RdRP. Indeed, Forgia et al propose that the acquisition of an RdRP by these short replicators might be the evolutionary origin of the newly discovered ambiviruses, due to their striking similarity to viroids and ribozyviruses like HDV (Forgia et al, 2023). In contrast to these simple RNA pathogens, all non-satellite RNA viruses encode at least the catalytic subunit of an RdRP even though additional host factors are often required for their genome replication.…”

Decoding the RNA virome of the tree parasite Armillaria provides new insights into the viral community of soil‐borne fungi

“…Ambiviruses were only recently described as circular ssRNA genomes with viroid‐like self‐cleaving elements (Forgia et al, 2023). Because the delineation criterion for ambiviruses has not yet been established, we have adhered to a threshold of 90% for the classification of new species, as recently proposed (Turina et al, 2023).…”

“…Characteristic conserved motifs of mitoviruses were also detected in the RdRP-based alignment of AbMV1 and AMV1 with other selected mitoviruses (Figure S1d). In the BLASTp search, AbMV1 exhibited 83.2% identity with the AbMV1 2011A isolate and AMV1 exhibited Reported ambiviruses have a circular ssRNA genome with self-cleaving elements (Forgia et al, 2023).…”