Development and Application of Spectral Databases and Mathematical Models in the Study of Plant Natural Products Biosynthesis
Johnson, Sean Robert
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Plant natural products are useful for many different applications, including medicines, flavors and fragrances, and industrial uses. Two important aspects of plant natural products research are the identification of compounds in their source plants, and the characterization of the processes involved in their biosynthesis. To aid in the identification of plant natural products, we developed the Spektraris family of databases. These databases include high-performance liquid chromatography mass spectrometry data, and 13C and 1H nuclear magnetic resonance data, which are searchable through an online interface. The utility of Spektraris was validated by using it to identify compounds in plant extracts and as part of a workflow to elucidate the structure of a previously undescribed compound. Mints have a long history of use as model systems for studying the processes of terpene natural products biosynthesis in specialized plant tissues. The mint family (Lamiaceae), synthesizes and stores volatile terpenes in glandular trichomes. Using a comparative transcriptomic approach, we identified differences in gene expression of monoterpene biosynthetic genes among mint species with different oil profiles. We also assembled the genome of a mint species, Mentha longifolia. The genome assembly will be valuable for future mint research. To further investigate biosynthetic processes in mint, I developed a detailed mathematical model of the metabolism of peppermint glandular trichomes. The model incorporates multiple sources of data, including transcriptome data, metabolite data, enzymatic data from the peppermint literature, and previously developed models of plant metabolism. The creation of a new metabolic modeling software package, called YASMEnv, facilitated construction of the model. Model-based simulated reaction knockouts using flux balance analysis revealed that fermentation may be important for ATP regeneration in secretory phase glandular trichomes. Follow up experiments confirmed high levels of alcohol dehydrogenase activity in secretory phase isolated trichomes. Simulations also supported an essential role for ferredoxin and ferredoxin-NADP reductase. Transcriptome analysis revealed the presence of an isoform of ferredoxin in trichomes distinct from the one expressed in root. The presence of a distinct ferredoxin isoform in trichomes supports the hypothesis that selection pressure for efficient natural products biosynthesis may also act on the enzymes of primary metabolism.