In vivo selection and in vivo evolution of a trans- splicing ribozyme

Group I introns are catalytic RNAs (ribozymes) that are capable of self-splicing out of primary transcripts. Through two consecutive transesterification reactions, the intron is removed and flanking exons are ligated. The group I intron sequence evolved for cis-splicing in nature. However, sequence modifications allow this ribozyme to catalyze a trans-splicing reaction as well. If the 5'-portion of the intron is truncated so that it no longer contains an exon, the ribozyme can then bind in trans at its 5'-end to an RNA substrate, cleave the substrate and replace the 3'-terminal portion of the substrate with its own 3'-exon. When the splice site is upstream of a mutation in a messenger RNA (mRNA) sequence, the transfer of the 3'-exon can replace and repair the downstream portion of the mRNA. Thus, this reaction can be utilized as a type of gene therapy on the mRNA level. Repairing mRNA offers the benefit of maintaining natural gene regulation and the ability to target gain-of-function mutations that gene therapy via gene transfer does not. Although the idea of utilizing a group I intron for gene therapy is not new, to date no gene therapy trials have used this trans-splicing reaction. This is in part due to the low efficiency of the ribozyme under clinically relevant conditions. This thesis represents an effort to increase trans-splicing efficiency of the Tetrahymena thermophila group I intron toward the development of a gene therapy. To find ribozyme variants with increased trans-splicing efficiency an in vivo selection procedure was developed in which the most efficient ribozymes are selected from millions of ribozyme variants. Ribozymes with an improved 5'-terminus were selected from a library with 9 x 106 ribozyme variants. Ribozymes with an improved internal sequence resulted from 21 rounds of evolution, which included mutagenesis and recombination. The in vivo evolution produced a highly efficient repair ribozyme that appears to be recruiting a cellular protein to increase activity. Future experiments that establish an analogous selection strategy in mammalian cells may make it possible to develop trans-splicing ribozymes for treating genetic diseases