This dissertation contains a study about acetyl-CoA metabolism in Arabidopsis thaliana and describes the storage and production of specialized acetyl-CoA-derived polyketide phytochemicals in Hypericum gentianoides. Chapter 2 focuses on the transcriptomic and metabolomic impacts of reducing the activity of ATP-citrate lyase in Arabidopsis and the subsequent rescue of these plants by the application of malonate. Chapter 3 centers on structural studies of H. gentianoides translucent glands, which contain bioactive polyketides. Chapter 4 closes the dissertation. This dissertation also contains three appendices. Appendix A is a manuscript about a novel visualization and statistical analysis computer program exploRase that has been published in the Journal of Statistical Software, and that I have used to analyze transcriptomic and metabolomic data. A manuscript that is being submitted to Plant Physiology about the MetNetDB database and its labeled graph structure is featured in Appendix B. Appendix C discusses several challenges in overexpressing ACL in the plastids of Arabidopsis. Acetyl-CoA Metabolism Acetyl-CoA is critical for the formation of many important secondary biomolecules in plants, including isoprenoids, anthocyanins, and elongated fatty acids. The CoA moiety is quite large and it is thought to be unable to pass though biological membranes, thus acetyl-CoA must be synthesized within the compartment in which it is going to be utilized (Brooks and Stumpf, 1966). ATP-citrate lyase produces the cytoplasmic pool of acetyl-CoA via the cleavage of citrate to form oxaloacetate and acetyl-CoA in an ATP-dependent manner ATP-Citrate Lyase ACL is the enzyme responsible for generating the pool of cytosolic acetyl-CoA in Arabidopsis (Fatland et al., 2002). ACL activity has also been detected in a number of other plant species including: Pisum sativum (Kaethner and ap Rees, 1985), Glycine max (Nelson and Rinne, 1975) and Brassica napus (Ratledge et al., 1997). Two subunits compose the ACL heteromer in Arabidopsis: ACLA and ACLB (Fatland, 2002). It is likely the Arabidopsis ACL is an octoheteromer having an A 4 B 4 configuration (Fatland, 2002). The Arabidopsis genome contains three genes that encode ACLA (ACLA-1, At1g10670; ACLA-2, At1g60810; ACLA-3, At1g09430) and two genes encoding ACLB (ACLB-1, At3g06650; ACLB-2, At5g49460) (Fatland et al., 2002; Fatland et al., 2005). The expression of ACL subunit transcripts are coordinated in both space and time in flower development, early seed development and developing trichomes (Fatland, 2002). The expression of ACL subunits is also coordinated with the expression of homomeric acetyl-CoA carboxylase, the enzyme responsible for utilizing acetyl-CoA to elongate fatty acids in the cytosol. Experiments in yeast have shown that ACL activity is present only when both ACLA-1 and ACLB-2 polypeptides are present. Yeast expressing only one subunit of ACL (ACLA or ACLB) lack ACL activity (Fatland, 2002). Arabidopsis plant lines having an antisense copy of ACLA-1 inserted into their genome...