Indiana University-Purdue University Indianapolis (IUPUI) / Glycogen is a major energy reserve in most eukaryotes and its rate of synthesis is controlled by glycogen synthase. The activity of eukaryotic glycogen synthase is regulated by the allosteric activator glucose-6-phosphate, which can overcome the inhibitory effects of phosphorylation. The effects of phosphorylation and glucose-6-phosphate on glycogen synthase are mediated by a cluster of six arginines located within a stretch of 12 amino acids near the C-terminus of the enzyme’s polypeptide chain. We studied isoform-2 of yeast glycogen synthase as a model to study the structural and molecular mechanisms that underlie the regulation of the eukaryotic enzymes and our primary tools of investigation were macromolecular X-ray crystallography, site-directed mutagenesis, intein-mediated peptide ligation and enzyme assays. We have solved the tetrameric structure of the yeast enzyme in two different activity states; the resting enzyme and the activated state when complexed with glucose-6-phosphate. Binding of glucose-6-phosphate to glycogen synthase induces large conformational changes that free the active site of the subunits to undergo conformational changes necessary to catalyze the reaction. Further, using site directed mutagenesis and intein-mediated peptide ligation to create specific phosphorylation states of the enzyme we were able to define specific roles for the arginine residues that mediate the regulatory effects of phosphorylation and glucose-6-phosphate activation. Based on these studies, we propose a three state structural model for the regulation of the enzyme, which relate the observed conformational states to specific activity levels. In addition to these regulatory studies, we have also solved the structure of the enzyme complexed with UDP and with substrate analogs, which provide detailed insight into the catalytic mechanism of the enzyme and the ability of glycogen synthase to remain tightly bound to its substrate glycogen.

Plant-pathogenic fungi harbor various specialized metabolites including diterpenoids that function as hormones and virulence factors. The fungus Magnaporthe oryzae is the causal agent of rice blast disease and can infect over 50 grass species. We demonstrate that the rice blast fungus encodes two diterpene synthases that produce normal pimara-8,15-diene and manoyl oxide scaffolds. Phylogenetic analysis of diterpene synthases among rice blast pathotypes showed functional conservation of the two core diterpene synthases amongst all pathotypes and suggests further expansion in select grass species. These insights into the blast fungal terpenome may inform efforts to counteract deleterious phytopathogens in crucial food crops.

Tableau d'honneur de la Faculté des études supérieures et postdoctorales, 2005-2006 / L'hypertension artérielle (HTA) associée à l'insuffisance rénale chronique (IRC) est une cause importante de morbidité-mortalité chez les patients dialysés. La physiopathologie de cette HTA est encore imprécise et implique un ensemble de désordres hémodynamiques incluant une expansion volémique et un changement de l'activité du système nerveux autonome et du système rénine-angiotensine. La dysfonction endothéliale constitue un facteur majeur de maintien et de progression de cette HTA. La diminution de la relâche endothéliale du monoxyde d'azote (NO) apparaît comme l'un des déterminants les plus importants de cette dysfonction endothéliale. En plus d'avoir un puissant effet vasodilatateur, le NO inhibe la production d'endothéline-1 (ET-1), module le taux de filtration glomérulaire (GFR) et est impliqué dans le processus de stress oxydatif. Cette étude vise à déterminer l'effet de la surexpression de l'enzyme NO synthase endothéliale (eNOS) sur la progression de l'HTA et de l'IRC chez le rat urémique. Un adénovirus codant pour la eNOS est administré par voie intraveineuse à des rats en urémie induite par néphrectomie sub-totale 5/6. Le transfert du gène est observé uniquement dans l'endothélium des vaisseaux. Après quatre semaines de suivi, le traitement avec l'AdeNOS/GFP a freiné l'élévation de la pression artérielle systolique (PAS), préservé la fonction rénale et prévenu l'apparition des dommages tissulaires rénaux. Ces effets protecteurs sont associés à une augmentation de la concentration circulante et urinaire de nitrites et de nitrates (NO2-/NO3-) indiquant une augmentation de la relâche de NO. Ainsi, la surexpression de la eNOS entraîne une augmentation de la biodisponibilité du NO et atténue le développement de l'HTA chez le rat urémique en plus de ralentir la progression de l'IRC, probablement en prévenant la dysfonction endothéliale.

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Adaptation to any undesirable change in the environment helps to ensure the survival of many microorganisms. During nutrient starvation, bacteria undergo a stringent response characterized by the accumulation of the alarmone (p)ppGpp. This results in the repression of stable RNA species and a change in colony morphology. In Gram-negative bacteria such as Escherichia coli, RelA and SpoT synthesize and hydrolyze these nucleotides, respectively, under conditions of nutrient starvation. In Gram-positive bacteria, the bifunctional enzyme Rei is responsible for the accumulation of (p)ppGpp. These enzymes catalyze the transfer of a pyrophosphate moiety from ATP to the 3' end of either GTP or GDP. The overproduction of (p)ppGpp has many diverse consequences on bacterial physiology such as sporulation, virulence, long term persistence of pathogenic bacteria, cell morphology, antibiotic synthesis and fatty acid metabolism. In Bacillus subtilis a novel (p)ppGpp synthase, YwaC, is also involved in the accumulation of (p)ppGpp but does not associate with the ribosome. Transcriptional analysis of ywaC has implicated it with cell wall stress especially associated with lesions in the teichoic acid biosynthetic pathway. The work described here includes a steady state kinetic analysis of the reaction catalyzed by YwaC. Recombinant YwaC was over-expressed in E. coli and purified to homogeneity. Steady-state kinetic experiments were performed utilizing a high-performance liquid chromatography assay. This examination yielded Km values for GDP and GTP of 5 J.1M and 6 J.1M respectively, while the kcat was measured to be 0.13 min"1 and 0.11 min"1 respectively. As is common with other (p)ppGpp synthases, the low activity ofYwaC may be increased in the presence of the appropriate effector molecule. To explore the functional phenotype associated with ywaC a deletion strain was made by replacing the gene on the chromosome of B. subtilis with a spectinomycin resistance cassette. A variety of antibiotics were used to probe the ywaC deletion strain in an attempt to detect antibiotic sensitivity in comparison to wildtype cells. In addition, the morphology of the ywaC deletion strain was investigated using phase contrast confocal microscopy. Length and shape remained the same in a ywaC knockout. Growth profiles performed over a 24-hour period showed that the knockout strain grew similarly to wildtype B. subtilis. Thus, the phenotype analysis described herein failed to further elucidate the function of YwaC. Nevertheless, rigorous biochemical analysis described here have established the enzymatic role of (p)ppGpp synthesis for YwaC, but there remains much room for further investigation. / Thesis / Master of Science (MSc)

Steroidal glycoalkaloids (SGAs) are secondary metabolites produced by approximately 350 species in the Solanaceae family. SGAs are reported to be important for pest resistance and flavor enhancement at low concentrations but are toxic to humans and other mammals at high concentrations. Studies on sterol / SGA biosynthesis have implicated squalene synthase as a key regulatory enzyme because it catalyzes an irreversible step from the mevalonic acid pathway. However, the regulatory mechanisms of squalene synthase are not yet known. A study was conducted to elucidate the distribution pattern of SGAs and to clone the squalene synthase gene in order to determine a relationship between SGAs and gene expression levels. Solanum chacoense, a wild potato species was used as a model plant from which tissues were harvested at specified developmental stages and analyzed for SGA content. The results from the SGA analysis suggest a qualitative and quantitative tissue- and age-dependent accumulation of SGAs. Regenerative tissues such as, axiliary shoots, flowers and floral buds had the highest levels of 88, 49 and 63 µmole/g DW, respectively. The roots, stems and tubers showed the lowest amounts of SGAs of 1 to 8, 5 to 15 and 7 to 15 µmole/g DW, respectively. Stolons and tubers accumulated higher amounts of α-chaconine (59 to 67%) than α-solanine (61 to 64%) at all developmental stages analyzed. On the other hand, in young expanding, fully expanded, and old senescing leaves where leptine and leptinines tend to dominate, α-solanine and α-chaconine together accounted for only 8 to 15%, 7 to 15%, and 8 to 45%, respectively. Plant organs that showed the highest biosynthetic activity for SGA production also had high levels of transcripts coding for genes of isoprenoid biosynthesis. The results from the cloning and characterization of squalene synthase suggest that the cloned cDNA fragment is a putative S. chacoense squalene synthase gene with an open reading frame / predicted protein precursor of 411 amino acids. The cloned cDNA has high similarity (68-100%) to known plant squalene synthase genes and contains six deduced peptide domains observed in other species. The 3â untranslated regions of floral buds, young leaves (early vegetative stage), and fully expanded leaves (anthesis) were different in length with, 249, 335, and 202 nucleotides, respectively. The Southern blot analysis suggests a single copy gene although the existence of a gene family cannot be ruled out. / Ph. D.

Roots and leaves are integrated structural elements that together sustain plant growth and development. Insect herbivores pose a constant threat to both above- and belowground plant tissues. To ward off herbivorous insects, plants have developed different strategies such as direct and indirect chemical defense mechanisms. Research has primarily focused on visible aboveground interactions between plants and herbivores. Root-feeding insects, although often overlooked, play a major role in inducing physical and physiological changes in plants. However, little is known about how plants deploy chemical defense against root herbivores. We have developed an Arabidopsis aeroponic culture system based on clay granulate, which provides access to root tissue and accommodates subterranean insect herbivores. Using this system, feeding performance and plant tissue damage by the root herbivore Bradysia (fungus gnat) were evaluated. Larval feeding was found to reduce Arabidopsis root biomass and water uptake. Furthermore, we have characterized a root-specific terpene synthase AtTPS08, which is responsible for the constitutive formation of the novel volatile diterpene compound, rhizathalene, in Arabidopsis roots. Rhizathalene synthase is a class I diterpene synthase that has high affinity for the substrate geranylgeranyl diphosphate (GGPP) and is targeted to the root leucoplast. Expression of the β-glucuronidase (GUS) reporter gene fused to the upstream genomic region of AtTPS08 demonstrated constitutive promoter activity in the root vascular tissue and root tips. Using the established bioassay with Arabidopsis and Bradysia larvae, in aeroponic culture we could show that roots deficient in rhizathalene synthesis were more susceptible to herbivory. Our work provides in vivo-evidence that diterpene compounds are involved in belowground direct defense against root-feeding insects. Future work is still required to improve our understanding of plant root defense. This study has provided a basis for future investigations on the biochemistry, molecular regulation and defensive function of Arabidopsis root chemicals in interaction with both above- and belowground herbivores (and pathogens). / Ph. D.