<p> Plants produce a variety of small molecules, including those essential for survival in all conditions (primary metabolites) or for more ecologically specific conditions (secondary metabolites). While primary metabolic pathways are broadly shared among plants, secondary metabolism is under constant selective pressure towards chemical innovation, given the continual fluctuation of the environment. Thus, plant secondary metabolism - whose constituents number in the hundreds of thousands - is lineage-specific, highly structurally diverse, and ultimately of high value to medicine, agriculture, and industry. Efforts to optimize the production of specific metabolites or to discover new compounds remain difficult primarily due to inadequate understandings of the metabolic genes involved and how these genes are regulated. This work first examines co-regulation, a major form of organization by which plant secondary metabolic genes are organized. In response to the bacterial crop pathogen <i>Pseudomonas syringae, Arabidopsis thaliana</i> and its relatives in the mustard family produce numerous secondary metabolites from the amino acid tryptophan, including the antimicrobial compound camalexin. However, hundreds of biosynthetic genes of unknown function are also simultaneously upregulated. Using metabolic profiling and co-expression analysis, I helped to identify the complete biosynthetic pathway to the indole-3-carbonylnitriles (ICNs), a previously unknown class of compounds. When the cytochrome P450 gene <i>CYP82C2</i> is mutated, biosynthesis of the compound 4-hydroxy-ICN (4OH-ICN) is abolished, and plant defense against <i>P. syringae</i> is impaired. Conversely, addition of 4OH-ICN to plants is sufficient to suppress bacterial growth. Next, this work examines the evolution of camalexin and 4OH-ICN metabolism. Cytochrome P450-directed secondary metabolism has been shown almost without exception to be evolutionarily derived from changes to enzymes with broad substrate specificity. By contrast, I observe through genetics, enzyme phylogenetic analysis, and transient expression assays that the ICN and camalexin biosynthetic pathways evolved from a common chemical substrate. In particular, changes to camalexin catalysis by the newly duplicated gene <i>CYP71A12</i> led to the formation of ICN metabolism in several mustard species, although both compounds are directly derived from indole cyanohydrin. Furthermore, 40H-ICN is an extremely recently evolved metabolite, derived from a flurry of genic, epigenetic and transposon-mediated rearrangements of a yet-more recent gene duplicate (<i>CYP82C2</i>). These regulatory changes to <i>CYP82C2</i> lead to its pathogen-inducibility solely in the species <i>A. thaliana</i>. I additionally identify WRKY33 and MYB51 as two sets of defense regulators that carefully fine-tune 40H-ICN metabolism by direct biosynthetic gene regulation. WRKY33 transcription factor, which is involved in the species-specific regulation of <i>CYP82C2</i>, is conserved throughout flowering plants, indicating that transcriptional recruitment is an important feature in the expansion of secondary metabolism. Finally, this work probes possible molecular functions of 40H-ICN and camalexin by exploring the molecular mechanisms underlying their secretion from roots and regulation of cell death processes. This study ultimately reveals that the proliferation of diverse chemical arsenals in plants is greatly aided by the regulatory capture of new and rapidly evolving genes by evolutionarily more stable transcription factors. Future emphases on transcriptional regulators of secondary metabolism may thus aid in the discovery of new secondary metabolic pathways on a more rapid scale.</p><p>

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2006. / "Title from dissertation home page (viewed July 11, 2007)." Source: Dissertation Abstracts International, Volume: 67-08, Section: B, page: 4258. Adviser: Jeffrey D. Palmer.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008. / Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 2706. Adviser: Geoffrey A. Levin. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

<p> The redistribution of nitrogen from old leaves to young leaves during senescence is crucial for plant survival. The <i>Arabidopsis thaliana </i> chloroplast residential protease S33Ab (At5g11650) was predicted to contribute to the degradation of chloroplast stromal proteins during senescence by bioinformatics tools. Rubisco degradation did not co-segregate with the T-DNA insertion mutant <i>s33Ab.</i> The location of T-DNA insertions into <i>S33Ac</i> (At1g18360) and <i>S33Ad</i> (At1g73480) were confirmed by sequencing. Total leaf proteins from <i>Ab, Ac, Ad </i> single, <i>Ab/Ac, Ab/Ad, Ac/Ad</i> double and <i> Ab/Ac/Ad</i> triple mutants were isolated from senescing leaves, subjected to immunoblot analysis to quantify Rubisco large subunit (LSU), glutamine synthase 2 (GS2), Rubisco activase (RCA), and light harvesting complex protein for photosystem II, b (Lhcb1) and compared to wild type. There is no significant difference among all the genotypes. This genetic analysis shows that S33Ab and its two closely related homologs, S33Ac and S33Ad do not individually contribute or work additively in chloroplast stromal protein degradation.</p>

<p> Auxin is a phytohormone that has long been known to control many aspects of plant growth and development. The YUCCA (YUC) gene family is a large group of genes that catalyze auxin biosynthesis and have been shown to be critical for vegetative growth and inflorescence development in grasses. There is genetic redundancy present with <i>Arabidopsis YUCs,</i> but in <i> Zea mays</i> (maize), a single gene knockout of <i>ZmSPI1</i> causes a severe inflorescence phenotype. Since <i>Oryza sativa</i> (rice), another grass species, does not show an inflorescence phenotype when <i> OsYUC1/SPI1</i> is knocked down, <i>SPI1</i> appears to have undergone an evolutionary shift in function within the grass family. This study shows that <i>SPI1</i> expression in PACMAD (Panicoideae, Arundinoideae, Chlorodoideae, Micrairoideae, Aristidoideae, and Danthoniodeae subfamilies) clade grasses <i>Sorghum bicolor</i> and <i>Setaria italica</i> occurs at sites of inflorescence branching and is consistent with maize, but in BEP (Bambusoideae, Ehrhartoideae, and Pooideae subfamilies) clade grasses rice and <i>Brachypodium distachyon SPI1</i> shifts from localized expression to more generalized expression and potentially becomes weaker. Artificial microRNA (amiRNA) knockdowns of <i>SPI1 </i> expression in <i>Brachypodium</i> did not show a phenotype when expression was reduced to 28.01% (+/- 6.39%) of wild type. In rice and <i> Brachypodium,</i> other <i>YUC</i> genes were shown to be expressed in the inflorescence by quantitative RT-PCR (qPCR), suggesting YUC proteins are more redundant in BEP grasses such as <i>B. distachyon</i> and <i> O. sativa,</i> than in maize and potentially its relatives.</p>

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2008. / Title from PDF t.p. (viewed on Oct. 7, 2009). Source: Dissertation Abstracts International, Volume: 70-02, Section: B, page: 0781. Adviser: Scott D. Michaels.

<p> Nitrogen deficiency is the most common and widespread nutritional deficiency affecting plants worldwide. Ectomycorrhizal symbiosis involves the beneficial interaction of plants with soil fungi and plays a critical role in nutrient cycling, including the uptake of nitrogen from the environment. The main goal of this study is to understand how limiting nitrogen in the presence or absence of an ectomycorrhizal fungi, <i>Laccaria bicolor,</i> affects the health of aspen trees, <i>Populus tremuloides.</i> Under limited nitrogen conditions, aspen tree growth and development is reduced, and mycorrhizal symbiosis may significantly improve plant biomass, providing sufficient nitrogen is available. The results of biochemical analysis also indicate that the supply of carbon to fungus associated with aspen roots is reduced as a result of aspen utilizing more sugar resources for the production of sucrose and starch within shoot tissues. Identification of metabolic pathways in aspen tree roots revealed that carbohydrate and nitrate metabolism was impacted by changing environmental conditions, including interactions with the fungi.</p>