In an effort to test the feasibility of intracellular expression of enzyme-targeted antibodies to alter metabolism, recombinant antibody fragments in the single-chain format (scFv) were isolated from a phage display library using Arabidopsis chalcone isomerase (CHI) of the flavonoid biosynthetic pathway as the antigen. Each of the genes encoding the scFv's was cloned into a plant transformation vector, which was subsequently used to generate transgenic plants. One transgenic line with low expression of one of the scFv's appeared to have an altered flavonoid metabolism, as evidenced by a reduced capacity for anthocyanin accumulation and a reduction in flavonol glycosides in seedlings. Strong corroborating evidence that implicated the binding of scFv to CHI in the phenotypic alterations was obtained from protein mobility shift assays. Taken together, the results indicate that scFv-mediated metabolic alteration is possible in plants. Thus, we show that intracellular expression of scFv's can be exploited as an additional tool for metabolic engineering. / Ph. D.

Terpenes comprise a large diverse class of natural products and many of them attract interest because of their physiological function, therapeutic and industrial values. Triterpene oils including squalene (C30), botrycococcene (C30) and their methylated derivatives (C31-C37) generated by the green algae Botryococcus braunii race B, which have recently received significant attention because of their utility for advanced biofuels. However, the slow growth habit of B. braunii makes it impractical as a robust biofuel production system. In this thesis, we firstly evaluated the potential of generating high levels of triterpene (C30) production in tobacco plants by diverting carbon flux from cytosolic MVA pathway or plastidic MEP pathway by overexpressing avian farnesyl diphosphate synthase along with triterpene synthase targeted to the cytoplasm or the chloroplast of cells. Up to 1,000 µg/g fresh weight of squalene and 544 µg/g fresh weight of botryococcene was achieved in our transgenic plants with this metabolism direct to the chloroplasts, which is about approximately 100-times greater than that accumulating in the plants engineered for cytosolic production. To test if methylated triterpenes can be produced in tobacco, we also engineered triterpene methyltransferases (TMTs) into wild type plants and transgenic tobacco plants selected for high level triterpene accumulation. We observed that up to 91% of the total triterpene content was converted to methylated forms (C31, C32) by targeting the TMTs to the chloroplasts of transgenic plants, whereas only 4-14% of total triterpenes were methylated when TMTs were directed to the cytoplasm. Select transgenic lines were growing in field studies from 2011 to 2014 to evaluate their physiological performance under field conditions. Surprisingly, the field studies suggested that the growth and agronomic performance of the transgenic lines accumulating squalene were not compromised, while those accumulating high levels of botryococcene were only 72%-76% as tall, had about 59%-75% of the leaf area, and about 55%-75% of the biomass as wild type plants. Yet, these transgenic plants had photosynthetic capacity equal to the wild type plants.

In the first part of this research, we constructed a Genome scale Metabolic Model (GEM) of Taxus cuspidata, a medicinal plant used to produce paclitaxel (Taxol®). The construction of the T. cuspidata GEM was predicated on recent acquisition of a transcriptome of T. cuspidata metabolism under methyl jasmonate (MJ) elicited conditions (when paclitaxel is produced) and unelicited conditions (when paclitaxel is not produced). Construction of the draft model, in which transcriptomic data from elicited and unelicited conditions were included, utilized tools including the ModelSEED developed by Argonne National Laboratory. Although a model was successfully created and gapfilled by ModelSEED using their software, we were not able to reproduce their results using COBRA, a widely accepted FBA software package. Further work needs to be done to figure out how to run ModelSEED models on commonly available software. In the second part of this research, we modeled the MJ elicited/defense response phenotype in Arabidopsis thaliana. Previously published models of A. thaliana were tested for suitability in modeling the MJ elicited phenotype using publicly available computation tools. MJ elicited and unelicited datasets were compared to ascertain differences in metabolism between these two phenotypes. The MJ elicited and unelicited datasets were significantly different in many respects, including the expression levels of many genes associated with secondary metabolism. However, it was found that the expression of genes related to growth and central metabolism were not generally significantly different for the MJ+ and MJ- datasets, the pathways associated with secondary metabolism were incomplete and could not be modeled, and FBA methods did not show the difference in growth that was expected. These results suggest that behavior associated with the MJ+ phenotype such as slow growth and secondary metabolite production may be controlled by factors not easily modeled with transcriptome data alone. Additional research was performed in the area of cryosectioning and immunostaining of fixed Taxus aggregates. Protocols developed for this work can be found in Appendix B.