An evolutionary approach to the structure and activities of group II introns

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Group II introns are novel genetic elements that possess properties of both catalytic RNAs and retroelements. The introns consist of two components: 1) a catalytic RNA (ribozyme) component that carries out a self-splicing reaction; and 2) an intron-encoded reverse transcriptase (RT) that facilitates the splicing reaction and allows the introns to insert into new genomic locations through a retrotransposition (i.e., reverse transcription) mechanism. This remarkable and coordinated series of reactions by the ribozyme and RT is itself worthy of study; however, group II introns have attracted additional attention because of their relationships to other important eukaryotic elements. The ribozyme of group II introns is widely believed to be the ancestor of spliceosomal introns (~25% of the human genome), while the RT is related to RTs of retroelements, retroviruses and telomerase. Group II introns are considered ancestral to non-LTR retroelements (~20% of the human genome), as well as spliceosomal introns. Because group II introns are relatively simple systems (two molecules), studying their mechanisms is expected to shed light on spliceosomal introns and non-LTR retroelements, as has been the case in the past. This application proposes to continue the research program of my lab, in which we use a comparative approach to address the breadth of group II intron structures and properties, as well as the evolutionary development and differentiation of the introns. Specific aims are: 1) to extend phylogenetic studies of group II intron sequences to reconstruct a more complete history of the introns; 2) to use sequence covariation data to infer RNA structural information about differentiated subclasses of introns, and to test validity of the predictions experimentally; 3) to biochemically investigate self-splicing properties of the IIC intron B.h.I1; and 4) to address the three-dimensional RNA structures of subclasses of group II introns through modeling and biochemical experimentation. Together these studies will advance our understanding of the mechanisms of a unique genetic element, and help elucidate how the introns evolved and eventually proliferated to occupy a large fraction of eukaryotic genomes.