Mechanistic Study of Arabidopsis Genes in Nuclear and Mitochondrial RNA Metabolism

RNA is the major functional molecule that connecting the genetics information (DNA) and the final product (protein). There are many post-transcriptional modifications on mRNAs before translation and are important to generate the complexities of proteins. The RNA metabolisms in eukaryotes include transcription, RNA splicing, 5’ capping, 3’ processing, and polyadenylation in the nuclear genome. On the other hand, there are other unique RNA metabolic processes such as 5’ and 3’ end processing, and RNA editing in plant organelles genomes. How these metabolic processes are controlled is the critical question in RNA studies. In the first portion of this dissertation, the biological and molecular functions of Arabidopsis P-type PPR protein, PPME, were addressed. The null T-DNA mutant of ppme exhibited severe developmental defects, including retarded seedling growth, draft, seed abortion, shriveled seeds, and reduced seed viabilities. Besides, the RNA editing of mitochondrial nad1-898 and nad-937 was lost, leading to amino-acid shifts within NAD1 protein that resulted in the reduced complex I activity in the ppme mutant. Different from other P-type PPR members, the P-type PPR protein, PPME, was the first identified that functioned as an editing factor to modulate RNA editing in the mitochondrial nad1 transcripts and was important for plant development. In the second part of this dissertation, the important processing factor, Arabidopsis CstF64 in the nucleus, was studied. The cstf64 T-DNA insertional mutants are defective in post-embryonic development. Interestingly, there are many genes exhibited variable mRNA 3’ end length in the cstf64-1 knockdown mutant in our RNA-sequencing profile and the specific cis-elements AAG/NAAA was isolated from those genes showing variable mRNA 3’ end lengths in the cstf64-1 mutant. This AAG/NAAA motifs were randomly distributed within the regions nearby poly(A) sites in those genes with variable mRNA 3’ end length. Therefore, we speculate that Arabidopsis CstF64 may serve as barriers to block non-specific poly(A) signal usages by directly binding to the AAG/NAAA variants during transcription, and this mechanism was different from those in mammals and important for other trans-factors to recognize the major poly(A) signal.