Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes

Publisher Website
Google Scholar
Abstract
Since the advent of methodologies to analyze the content of whole genomes (e.g., renaturation kinetics and Cot analysis), it has been known that a large fraction of eukaryotic genomes is highly repetitive (1, 2). Recent computer-assisted analysis of several sequenced eukaryotic genomes, including Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and humans, has demonstrated that most repetitive DNA is composed of or derived from transposable elements (TEs). In the human genome, for example, TEs are the single most abundant component, accounting for over 40% of the total DNA (3). Although this amount of TEs is viewed as a hindrance to those engaged in the determination and assembly of DNA sequence, the availability of both complete and partial eukaryotic genome sequences is providing TE biologists with a bonanza of raw material that is being used to understand how genomes evolve. Before the report in PNAS by Kapitonov and Jurka (4), all eukaryotic TEs were thought to use one of two mechanisms for transposition. Class 1, or retrotransposons, transpose via an RNA intermediate in reactions catalyzed by element-encoded proteins, including reverse transcriptase. In contrast, the transposon itself is the intermediate for class 2 elements where an element-encoded transposase catalyzes reactions, resulting in TE excision from one site and reinsertion elsewhere in the genome (the so-called cut-and-paste mechanism). In addition to these two mechanisms, some prokaryotic TEs (called IS or insertion sequences), move by another mechanism called rolling circle (RC) transposition (5, 6). This process is similar to the RC replication of some plasmids, single-stranded (ss) bacteriophage, and plant geminiviruses. In a recent issue of PNAS, Kapitonov and Jurka (4) report that RC transposons also occur in eukaryotes where, surprisingly, they comprise about 2% of the genomes of A. thaliana and C. elegans. How could a …