| HDV ribozymes catalyze their own scission from the transcript during rolling circle replication of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human genomic library revealed an HDV-like ribozyme in the second intron of the human CPEB3 gene and recent results suggest this RNA affects episodic memory performance.;Bioinformatic searches based on the secondary structure were used to identify sequences capable of forming HDV/CPEB3 fold, and their self-cleavage activity was confirmed in vitro. Active sequences were uncovered in several marine organisms, two nematodes, an arthropod, a bacterium, and an insect virus, often in multiple sequence families and copies. Sequence searches based on identified ribozymes showed that plants, fungi, and a unicellular eukaryote also harbor the ribozymes.;Genomic mapping of these RNAs suggested several biological roles, one of which is the 5' processing of non-LTR retrotransposons. Using structure-based bioinformatics, several classes of retrotransposons were found in phyla spanning arthropods, nematodes, and chordates, which utilize HDV-like self-cleaving ribozymes for processing their 5' termini. Ribozyme-terminated retrotransposons include rDNA-specific R2, R4 and R6; telomere-specific SART; and Baggins and RTE elements.;Peripheral elements of HDV-like ribozymes affect the ribozyme cleavage by changing the stability of the overall structure. The R2 ribozyme's self-scission is strongly modulated by the insertion site sequence in the rDNA. Structured leader sequence promotes faster kinetics in drz-Fpra-1. J1/2 element regulates the ribozyme cleavage through proper assembly of the core structure. Longer tail sequence in Agam-2-1 altered the cleavage rate by extending P2 helix.;Intermolecular HDV-like ribozyme and substrate were constructed from drz-Agam-2-1 by splitting the J1/2 and P1 regions. The cleavage involves the reaction of ribozyme-substrate complex assembled from ribozyme and substrate, phosphodiester backbone scission, and product release from the ribozyme-product complex. Kinetic rate constants for each step were determined in this study.;A structure-based search based on the HDV-like fold revealed putative trans-acting ribozyme and substrates from Anopheles gambiae. Both of the substrates map to the first exon, and one of them maps to the first nucleotide of the first exon in the EST indicating that there might be a cleaving process operated by trans ribozyme. The family of HDV-like ribozymes thus continues to grow in numbers and biological importance. |
