Characterization of unknown plastid targeted genes involved in production of metabolic compounds in medicinally active plants

Plants have been used as medicine throughout human history. However, many of the medicinally relevant compounds are synthesized via pathways that are only partially characterized. In order to maximize the efficient production of these valuable compounds in their native species or in a heterologous plant species, elucidation of the genes involved in these pathways is key. For many of these pathways, key steps are known or suspected to occur within the highly reductive environment of the plastid. Precursors such as terpenes and aromatic amino acids are also produced in plastids, giving this organelle an unparalleled degree of control over biochemical flux. Production of the antimalarial drug quinine (Cinchona pubescens), the neurotransmitter antagonist atropine (Datura innoxia), and the anticancer drug paclitaxel (Taxus x media) are known to be largely plastid-synthesized. We are characterizing the predicted plastid-targeted proteomes of these species using clustering algorithms to elucidate common and unique genes from each species. We analyzed RNAseq data from these species using a custom assembly and analysis workflow. The resulting assemblies were used to derive peptide sequences that were further analyzed using TargetP to identify plastid targeted genes. Comparative analysis of predicted plastid targeted proteomes was performed using a recently published approach (Schaeffer et al., 2014). This analysis is expected to yield gene candidates involved in respective medicinal compound biosynthesis, and will facilitate the unraveling of the biochemical pathways involved in the synthesis of these drugs.