Functional Analysis of PPR-SMR-related Proteins in Zea mays (Maize) and Arabidopsis thaliana

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Plastid gene expression is essential for all metabolic processes in plastids and for plant viability. The regulation of plastid gene expression occurs at various levels of transcription, transcript maturation and protein assembly processes. Numerous nucleus encoded factors are needed for the regulation of plastid gene expression. Pentatricopeptide repeat (PPR) proteins appear to play a particularly important role, and participate in many types of RNA metabolism. In my Ph.D. work, I identified a novel type of PPR protein that is characterized by a second functional motif called SMR (small MutS-releated). Proteins harboring both PPR and SMR domains comprise a small ¿subfamily¿ within the large PPR family. The SMR domain has been shown to have nicking endonuclease activity. This, together with current understanding of PPR motifs, suggests that the PPR-SMR subfamily may participate in DNA or RNA metabolism, DNA repair, transcriptional and/or translational processes by acting as endonucleases. In this project I will explore these possibilities by studying four predicted plastid PPR-SMR proteins in Zea mays (maize) and the orthologous proteins in Arabidopsis; use of the two organisms will be synergistic as they each offer different experimental advantages. Work will include determinations of specific nucleic acid target sequences, endonuclease assays and comparative phenotypic, molecular and biochemical analyses of mutants in maize and Arabidopsis. I will determine whether each protein interacts with specific RNA and/or DNA sequences in vivo, and whether the metabolism of the corresponding nucleic acids is disrupted in the mutant background.