Abstract
Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the “RNA world” hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.
Highlights
The higher order of organization through dimerization, i.e., the formation of bonded dimers, is a particular feature of Avocado Sun Blotch Viroid (ASBVd) to do more under tight evolutionary constraints for such small genomes that should preserve functional hammerhead ribozyme (HHR) [74,75]
The simultaneous presence of viroids or viroid-like RNAs with different catalytic profiles: from inactive or bad catalysts as single-hammerhead structures to intermediate and good 11 catalysts can be the result of the adaptation process to specific hosts and of the survival of properties which originate from the RNA World
The host range of viroids that is restricted to plants has often been presented as an argument against the hypothesis to consider viroids as relics from the RNA World
Summary
We know today that RNA is present in all living organisms, in which it performs a variety of structural and metabolic functions. Due to its very small size and structural features, the HDV RNA is deemed to be related to viroids [15,16,17,18,19,20,21] From these perspectives, they are similar to the hammerhead ribozymes which are found in retrotransposons [22,23]. Hammerhead ribozyme (HHR) motifs were found in the haloarchaeal tailed viruses [28,29] These new biological functions have to be identified, it was shown that they may affect gene expression to different extents depending on the genomic and genetic contexts [30]. Our recent results on these two topics with the Avocado Sun Blotch Viroid (ASBVd) will be presented as illustrations
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