Biology subjects

De la Pena, M.

Publications and source records attributed to De la Pena, M..

3 recordsLinked to original sources

bioRxiv2024

Self-cleaving ribozymes conserved in RNA viruses unveil a new role in protein translation

Small self-cleaving ribozymes are catalytic RNAs originally discovered in viroid-like agents, which are replicating circular RNAs (circRNAs) postulated as relics of a prebiotic RNA world. In the last decade, however, small ribozymes have also been detected across the tree of life, from bacterial to human genomes, and more recently, in unusual circRNA viruses. Here we report the conserved occurrence of diverse small ribozymes within the linear genomes of typical double- and single-stranded RNA virus families from fungi and plants. Type I hammerhead ribozyme motifs occur in the 5-UTR regions of chrysovirids and fusarivirids, displaying self-cleaving activity in vitro and in vivo. Similar hammerhead, as well as hepatitis delta and twister ribozymes, are also found in diverse megabirna-, hypo-, fusagra-, toti-or tombus-like viruses among others. The ribozymes occur not only as isolated motifs within UTRs but also as tandem pairs that encompass small RNA segments (186-399 nt) resembling Zetavirus-like sequences. In vivo characterization of the 5-UTR with a ribozyme from a chrysovirid revealed that the RNA-cleaving activity is essential for protein translation initiation in fungi. Analogous experiments in plants with diverse ribozyme motifs indicated that just the presence of a self-cleaving activity can induce cap-independent translation. We conclude that RNA self-cleaving activity, historically linked to the rolling circle replication of viroid-like circRNAs, appears to be co-opted by linear RNA viruses for translational roles.

microbiology↗

bioRxiv2024

Viroid-like colonists of human microbiomes

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA [~]1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the "Oblins". We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in [~]7% of analysed stool metatranscriptomes (29/440) and in [~]50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.

microbiology↗

bioRxiv2019

Small circRNAs with self-cleaving ribozymes are frequently expressed in metazoan transcriptomes

Ribozymes are catalytic RNAs present in modern genomes but considered as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of diverse animals are contained within a novel family of non-autonomous non-LTR retrotransposons. These retroelements are expressed as abundant linear and circular RNAs of [~]170-400 nt in different animal tissues. In vitro analyses confirm an efficient self-cleavage of the HHRs harboured in invertebrate retrozymes, whereas those in retrozymes of vertebrates, such as the axolotl, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, in eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which will allow the development of biotechnological tools in the emerging field of circRNAs.

genomics↗