The kinetics of ribozyme cleavage: a tool to analyze RNA folding as a function of catalysis.

As catalytically active RNAs, ribozymes can be characterized by kinetic measurements similar to classical enzyme kinetics. However, in contrast to standard protein enzymes, for which reactions can usually be started by mixing the enzyme with its substrate, ribozymes are typically self-cleaving. The reaction has to be initiated by folding the RNA into its active conformation.

The low incidence of diversity-generating retroelements in sequenced genomes.

The insertion of a retrotransposable element is usually associated with adverse or, at best, neutral effects on the host. Diversity-generating retroelements (DGRs) are the first elements that seem to offer a direct selective advantage to their phage or prokaryote host by exact replacement of a short, defined region of a host gene with a hypermutated variant. In a previous study, we presented the software DiGReF for identification of DGRs in genome sequences, and compiled the first comprehensive set of diversity-generating retroelements in public databases.

Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF.

Background: Diversity Generating Retroelements (DGRs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to "selfish" retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential.

Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron.

The autocatalytic group II intron ai5γ from Saccharomyces cerevisiae self-splices under high-salt conditions in vitro, but requires the assistance of the DEAD-box protein Mss116 in vivo and under near-physiological conditions in vitro. Here, we show that Mss116 influences the folding mechanism in several ways. By comparing intron precursor RNAs with long (∼300 nt) and short (∼20 nt) exons, we observe that long exon sequences are a major obstacle for self-splicing in vitro.

Protein-facilitated ribozyme folding and catalysis.

In vivo, large RNAs rely on proteins to fold to their native conformation. In the case of the S. cerevisiae group II intron ai5 gamma, the DEAD-box protein Mss116 has been shown to promote the formation of the catalytically active structure.