TY - CHAP ID - 11829 TI - Hammerhead Ribozymes Against Virus and Viroid RNAs T2 - From Nucleic Acids Sequences to Molecular Medicine PB - RNA Technologies PY - 2012 SP - 411-427 AU - Carbonell, A. AU - Flores, R. AU - Gago, S. AU - VL - UR - SN - 978-3-642-27426-8 DO - 10.1007/978-3-642-27426-8_16 AB - The hammerhead ribozyme, a small catalytic motif that promotes self-cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically in trans other RNAs in the presence of Mg2+. To be really effective, hammerheads need to operate at the low concentration of Mg2+ existing in vivo. Evidence has been gathered along the last years showing that tertiary stabilizing motifs (TSMs), particularly interactions between peripheral loops, are critical for the catalytic activity of hammerheads at physiological levels of Mg2+. These TSMs, in two alternative formats, have been incorporated into a new generation of more efficient trans-cleaving hammerheads, some of which are active in vitro and in planta when targeted against the highly structured RNA of a viroid (a small plant pathogen). This strategy has potential to confer protection against other RNA replicons, like RNA viruses infecting plants and animals. A2 - Erdmann, V. A. & Barciszewski, J., eds. C1 - Molecular Signal Processing ER - TY - JOUR ID - 13205 TI - Viroid Replication: Rolling-Circles, Enzymes and Ribozymes JO - Viruses PY - 2009 SP - 317-334 AU - Flores, R. AU - Gas, M.-E. AU - Molina-Serrano, D. AU - Nohales, M.-?. AU - Carbonell, A. AU - Gago, S. AU - De la Peña, M. AU - Daròs, J.-A. AU - VL - 1 UR - DO - 10.3390/v1020317 AB - Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae) and the chloroplast (family Avsunviroidae). Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i) synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii) circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5’ and 3’ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue. A2 - C1 - Molecular Signal Processing ER -