Plant mutator-like transposable elements (MULEs): Their evolutionary dynamics, interaction with genes, and recapitulation of transposition activity in yeast

Transposable elements (TEs) are genomic sequences that can move from one position to another within a genome, where the movement is catalyzed by transposases. Mutator-like transposable elements (MULEs) are a highly mutagenic TE superfamily, which is widespread in a range of organisms. This dissertation focuses on studying the evolution and biology of MULEs in plants, specifically 1) Mechanisms underlying differential abundance of MULEs in maize and rice; 2) Transposition of a rice MULE in yeast; 3) Insertions of MULEs and their impact on gene expression in the Illinois Long-Term Selection Maize population.;While the maize genome (2,500 Mb) is six times larger than the rice genome (380 Mb), it contains fewer MULEs than the latter (12,900 vs. 32,000). The differential amplification of MULEs in the two genomes prompted us to investigate the status of MULEs containing transposase (coding-MULEs). Examination of the two genomes indicates that they harbor similar amount of candidate coding-MULEs; however, the majority of candidate coding-MULEs in maize are defective. This is partly due to the higher amount of LTR retrotransposons that disrupt the coding region of MULEs in maize. Additionally, the candidate coding-MULEs seem to be subjected to higher indel rate in maize than that in rice, which accelerate the deterioration of maize elements. Collectively, nested insertions and accumulation of indels may explain the low abundance of MULEs in maize than that in rice.;To date, MULEs have been only shown to be active in their native hosts. In this study, transposition of a rice MULE was recapitulated in yeast, representing the first report of MULE transposition in a heterologous species. The wild-type transposase induced low transposition frequency, however, it could be improved by a variety of transposase modifications, including deletion, substitution, and fusion of an enhanced yellow fluorescent protein (EYFP). Deletion of the N-terminal 129 amino acids led to enhanced transposition frequency as well as altered cellular localization of the transposase. Mutational analysis revealed a critical region of the transposase, where changes of the amino acid compositions resulted in either enhanced or repressed activity. Additionally, fusion of an EYFP to the N-terminal deleted transposase also enhanced transposition frequency, which is the first report of transposition activity enhancement by protein fusion. Taken together, the establishment of the MULE transposition system in yeast laid the foundation for further studying MULE biology.;MULEs have the propensity to insert into genic regions, which influence the expression of adjacent genes as well as the relevant developmental processes. To determine whether MULEs played any role in the Illinois Long-Term Selection Experiment (ILTSE) maize strains, MULE insertions that are co-segregating with either high or low protein maize strains were studied. Consistent with previous studies, most insertions (~79%) were located in low-copy regions. Interestingly, compared with MULEs in the B73 maize genome, co-segregating insertions are over-represented in exons and equally represented in the 5' and 3' regions of genes, which is in contrast to the 5' insertion preference of MULEs reported in previous studies. Expression analysis revealed that out of 55 genes with adjacent co-segregating insertions, over 1/4 exhibited altered expression levels and may be associated with the selected trait. Further studies are needed to test whether there are causal relationships between these co-segregating MULE insertions and the selected trait.