A helix 1-extended hairpin ribozyme exhibits altered cleavage behavior in vitro

Induction of RNA interference in Caenorhabditis elegans by RNAs derived from plants exhibiting post-transcriptional gene silencing

The term 'gene silencing' refers to transcriptional and post-transcriptional control of gene expression. Related processes are found across kingdoms in plants and animals. We intended to test whether particular RNA constituents of a silenced plant can induce silencing in an animal. We generated Nicotiana benthamiana lines that expressed green fluorescent protein (GFP) from a transgene. Plants in which GFP expression was spontaneously silenced showed siRNAs characteristic of post-transcriptional gene silencing (PTGS). RNA extracts prepared from silenced plants were injected into a GFP-expressing strain of Caenorhabditis elegans, where they induced RNA interference (RNAi). Extracts from non-silenced plants were inactive. This directly demonstrates a relationship and a mechanistic link between PTGS and RNAi. Controls confirmed that the silencing agent was an RNA. Size fractionation on denaturing gels revealed that an RNA of approximately 85 nt was most active in inducing silencing in the worm. Northern blot analysis of the region in question did not detect a prominent GFP-specific RNA of sense or antisense polarity, indicating that the RNA species which induced silencing was present only in low concentration or did not hybridize due to formation of an intramolecular double strand. In view of its high activity, it is possible that this agent is responsible for the systemic spread of silencing in plants and it might represent the aberrant RNA, a previously postulated inducer of silencing.

Comparative kinetic analysis of structural variants of the hairpin ribozyme reveals further potential to optimize its catalytic performance

The hairpin ribozyme derived from the minus strand of the satellite RNA associated with the tobacco ringspot virus is one of the small catalytic RNAs that has been shown to catalyze trans-cleavage reactions. There is much interest in designing hairpin ribozymes with improved catalytic activity for the development of new therapeutic agents. Extensive mutagenesis studies as well as in vitro selection experiments have been performed to define the structure and optimize its catalytic activity. This communication describes a comparative kinetic analysis of four structural variants, introduced, either alone, or in combination, into the hairpin ribozyme. We have shown that extension of the helix 2 from 4 to 6 bp resulted in a significant decrease in K(M). Furthermore, the combination of this extension with the simultaneous stabilization of helix 4, led to a more than two-fold increase in the catalytic efficiency. This variant showed a 15-fold reduction in the K(M) value in respect to the wild-type ribozyme. This could be of great interest for the in vivo application of this catalytic motif. The 9-bp enlargement of helix 4 implied about a three-fold improvement in the catalytic activity. Similarly, the U39C substitution brought up the efficiency of the ribozyme slightly. However, introduction of nucleotides at the hinge region between A and B domains reduced the catalytic activity. This reduction was gradually increased with the number of nucleotides. Results obtained with variants carrying more than one modification always agreed with the ones obtained from each single variant.

Ribozymes: the characteristics and properties of catalytic RNAs

Ribozymes, or catalytic RNAs, were discovered a little more than 15 years ago. They are found in the organelles of plants and lower eukaryotes, in amphibians, in prokaryotes, in bacteriophages, and in viroids and satellite viruses that infect plants. An example is also known of a ribozyme in hepatitis delta virus, a serious human pathogen. Additional ribozymes are bound to be found in the future, and it is tempting to regard the RNA component(s) of various ribonucleoprotein complexes as the catalytic engine, while the proteins serve as mere scaffolding--an unheard-of notion 15 years ago! In nature, ribozymes are involved in the processing of RNA precursors. However, all the characterized ribozymes have been converted, with some clever engineering, into RNA enzymes that can cleave or modify targeted RNAs (or even DNAs) without becoming altered themselves. While their success in vitro is unquestioned, ribozymes are increasingly used in vivo as valuable tools for studying and regulating gene expression. This review is intended as a brief introduction to the characteristics of the different identified ribozymes and their properties.

The antisense sequence of the HIV-1 TAR stem-loop structure covalently linked to the hairpin ribozyme enhances its catalytic activity against two artificial substrates

This work is an in vitro study of the efficiency of catalytic antisense RNAs whose catalytic domain is the wild-type sequence of the hairpin ribozyme, derived from the minus strand of the tobacco ringspot virus satellite RNA. The sequence in the target RNA recognized by the antisense molecule was the stem-loop structure of the human immunodeficiency virus-1 (HIV-1) TAR region. This region was able to form a complex with its antisense RNA with a binding rate of 2 x 10(4) M(-1)s(-1). Any deletion of the antisense RNA comprising nucleotides of the stem-loop resulted in a decrease in binding rate. Sequences 3' of the stem in the sense RNA also contributed to binding. This stem-loop TAR-antisense segment, covalently linked to a hairpin ribozyme, enhanced its catalytic activity. The highest cleavage rate was obtained when the stem-loop structure was present in both ribozyme and substrate RNAs and they were complementary. Similarly, an extension at the 5'-end of the hairpin ribozyme increased the cleavage rate when its complementary sequence was present in the substrate. Inclusion of the stem-loop at the 3'-end and the extension at the 5'-end of the hairpin ribozyme abolished the positive effect of both antisense units independently. These results may help in the design of hairpin ribozymes for gene silencing.

The hairpin ribozyme: structure, assembly and catalysis

Recent studies of the hairpin ribozyme have revealed a distinct catalytic mechanism for this small RNA motif. Inner-sphere coordinated metal ions are not required, as the inert metal ion complex cobalt hexammine promotes catalysis. Detailed kinetic analyses have defined rates of individual steps in the catalytic cycle. Functional group modification, NMR studies of subdomains and cross-linking experiments, in combination with computer modeling, have led to a proposal for domain interactions in the substrate-ribozyme complex.