Post-Transcriptional Gene Regulation in Plants

Many elements contribute to the regulation of protein expression in eukaryotes. One such element, the upstream open reading frame (uORF), is the focus of this dissertation because it has not previously been well-characterized on a genome-wide scale. To undertake this project, an evaluation and improvement of full-length cDNA collections was implemented (Chapter 2). Most uORF amino acid sequences are not conserved in evolution, but those that are conserved seem likely to play sequence-specific roles in translational control of downstream, or major, open reading frames (mORF). By comparing full-length cDNA sequence libraries from Arabidopsis and rice we identified 26 homology groups of conserved peptide uORFs, only two of which had been reported previously. The conserved uORF amino acid sequences of each homology group were distinct from those of any other homology group, and within each uORF homology group mORFs always code for similar proteins in Arabidopsis and rice. Essentially all uORFs and their associated mORFs have been subject to purifying selection as determined by Ka/Ks analysis. The mORFs of conserved uORF transcripts encode transcription factors at a much higher frequency than expected (31% vs. 6% for the genome as a whole, p=10-7); a variety of different types of transcription factors are represented among these mORFs. Duplicate copies of conserved uORF-possessing genes that were created by whole genome duplication in an Arabidopsis ancestor are much more likely to have been retained in extant Arabidopsis than duplicates of the average gene (39% vs. 14%, p=5x10-3). Two of the 26 uORF homology groups were also found to be present in animals, indicating a high degree of sequence conservation and an ancient origin for these groups. The evolutionary history of one of these groups suggests that some uORFs arise by a 'transcriptional fusion' model