Fungal, plant and animal retrotransposon elements

This chapter discusses the structural chemistry and the biological aspects of fungal, plant and animal retrotransposon. Retrotransposons infest the genomes of all eukaryotes, in which they have replicated for eons using retrotransposon-encoded reverse transcriptases to make new copies of themselves. These elements easily make up the majority by weight of most plant genomes and even the human genome is ∼35% retrotransposon sequence by weight. However, the major types of retrotransposons found in plants and animals differ in a very significant way. Whereas, the major human retrotransposon, LI (or LINE-1), does not encode any recognizable protease and the typical plant (and fungal) transposon encodes an aspartyl protease, PR. These two classes of retrotransposons differ in several other important aspects; most notably, the protease-containing class contains LTRs and generally resembles, in both structure and replication mechanism, the retroviruses, which encode aspartyl proteases of family A2. The life cycle of the yeast LTR retrotransposon Tyl, which can be extrapolated in outline to most LTR retrotransposons, is summarized in the chapter.