The presence of thiols in living systems is critical for the maintenance of cellular redox homeostasis, the maintenance of protein thiol-disulfide ratios and the protection of cells from reactive oxygen species. In addition to the well studied tripeptide glutathione (??-Glu-Cys-Gly), a number of compounds have been identified that contribute to these essential cellular roles. Many of these molecules are of great clinical interest due to their essential role in the biochemistry of a number of deadly pathogens, as well as their possible role as therapeutic agents in the treatment of a number of diseases. A series of studies were undertaken using theoretical, chemical and biochemical approaches on a selection of thiols, ergothioneine, the ovothiols and mycothiol, to further our understanding of these necessary biological components. Ergothioneine is present at significant physiological levels in humans and other mammals; however, a definitive role for this thiol has yet to be determined. It has been implicated in radical scavenging in vivo and shows promise as a therapeutic agent against disease states caused by oxidative damage. Given the clinical importance of this intracellular thiol, further investigation into the behaviour of ergothioneine appeared warranted. A high level theoretical study was performed to determine the thermodynamic driving force behind the instability of the ergothioneine disulfide, as well as the thermodynamics of the reactions of ergothioneine with a selection of biologically relevant reactive oxygen species. These results were compared to those determined for a glutathione model compound, as well as the related ovothiols. The latter are believed to act as hydrogen peroxide scavengers in vivo and are currently under review as possible therapeutics against oxidative damage. The structural differences between the ovothiols and ergothioneine dramatically affect their reactivity and this study investigates the thermodynamic driving forces behind these differences. Mycothiol is the major thiol found in the Actinomycetales bacteria, which include the causative agent of tuberculosis, and the enzymes which use mycothiol have been identified as important targets for the development of novel antimicrobials. To better understand the in vivo behaviour of mycothiol, a thorough conformational search was performed to determine what, if any, trends exist among the low energy conformers expected to be present in solution. Knowledge of the conformations preferred by mycothiol may aid in the design of substrate-based inhibitors targeted at mycothiol-dependent enzymes. In addition, the efforts towards the identification of a mycothiol-dependent glyoxalase system are described. The glyoxalase system is essential for the detoxification of methylglyoxal, a toxic by-product of glycolysis, and this system would serve as a target for the design of new therapeutics against tuberculosis and other pathogenic Actinomycetales bacteria. In addition to the study of intracellular thiols, this work details a preliminary theoretical study of the thermodynamics of the phosphorylation of proteinaceous serine residues by inositol pyrophosphates in eukaryotic cell-free extracts. It has been postulated that this observed activity may represent a novel signalling pathway in eukaryotes. This study focused on the effect of inositol pyrophosphate structure and overall charge on the thermodynamics of these reactions. This information should contribute to our understanding of this novel cellular phosphorylation process.

Inositol pyrophosphates (PP-InsPs) are a family of molecules recently discovered to be implicated in a number of plant pathways such as auxin regulation, phosphate (Pi) sensing, and jasmonate-(JA)-regulated plant defense. Transgenic plants that overexpress inositol tetrakisphosphate 1-kinase (ITPK1) and the kinase domain of the dual domain diphosphoinositol pentakisphosphate kinase 2 (VIP2KD) have been previously studied to display uniquely elevated PP-InsPs. Here it is reported that the JA defense pathway is constitutively upregulated in VIP2KD OX plants, resulting in a lower rate of herbivory on the transgenic plants. ITPK1 OX, although also having elevated PP-InsPs, was fed upon by insect larvae comparably to Wild-Type Arabidopsis (WT). The data implicate VIP2, InsP8, and possibly the PP-InsP biosynthesis as a whole. / Master of Science in Life Sciences / Plants and insects have been evolving defenses against each other since they first emerged together post-Cambrian explosion. They each have evolved targeted metabolic pathways to produce chemicals with which to repel, harm, or even trick one another. In Arabidopsis thaliana, one of the most widely studied defense mechanisms is the jasmonic acid defense pathway, which responds to the herbivory of insects like caterpillars by setting off an array of genetic switches. The plant enters a stressed state wherein it represses the genes focused on growth and development and encourages the expression of genes focused on protecting vital resources and thwarting the attacker. This work examines a connection between the phosphate-sensing pathways and the jasmonic acid defense pathways in plants, and the following data show that plants with elevated inositol pyrophosphates (a phosphate storage molecule) are resistant to the herbivory of common pest caterpillars.

The presence of thiols in living systems is critical for the maintenance of cellular redox homeostasis, the maintenance of protein thiol-disulfide ratios and the protection of cells from reactive oxygen species. In addition to the well studied tripeptide glutathione (γ-Glu-Cys-Gly), a number of compounds have been identified that contribute to these essential cellular roles. Many of these molecules are of great clinical interest due to their essential role in the biochemistry of a number of deadly pathogens, as well as their possible role as therapeutic agents in the treatment of a number of diseases. A series of studies were undertaken using theoretical, chemical and biochemical approaches on a selection of thiols, ergothioneine, the ovothiols and mycothiol, to further our understanding of these necessary biological components. Ergothioneine is present at significant physiological levels in humans and other mammals; however, a definitive role for this thiol has yet to be determined. It has been implicated in radical scavenging in vivo and shows promise as a therapeutic agent against disease states caused by oxidative damage. Given the clinical importance of this intracellular thiol, further investigation into the behaviour of ergothioneine appeared warranted. A high level theoretical study was performed to determine the thermodynamic driving force behind the instability of the ergothioneine disulfide, as well as the thermodynamics of the reactions of ergothioneine with a selection of biologically relevant reactive oxygen species. These results were compared to those determined for a glutathione model compound, as well as the related ovothiols. The latter are believed to act as hydrogen peroxide scavengers in vivo and are currently under review as possible therapeutics against oxidative damage. The structural differences between the ovothiols and ergothioneine dramatically affect their reactivity and this study investigates the thermodynamic driving forces behind these differences. Mycothiol is the major thiol found in the Actinomycetales bacteria, which include the causative agent of tuberculosis, and the enzymes which use mycothiol have been identified as important targets for the development of novel antimicrobials. To better understand the in vivo behaviour of mycothiol, a thorough conformational search was performed to determine what, if any, trends exist among the low energy conformers expected to be present in solution. Knowledge of the conformations preferred by mycothiol may aid in the design of substrate-based inhibitors targeted at mycothiol-dependent enzymes. In addition, the efforts towards the identification of a mycothiol-dependent glyoxalase system are described. The glyoxalase system is essential for the detoxification of methylglyoxal, a toxic by-product of glycolysis, and this system would serve as a target for the design of new therapeutics against tuberculosis and other pathogenic Actinomycetales bacteria. In addition to the study of intracellular thiols, this work details a preliminary theoretical study of the thermodynamics of the phosphorylation of proteinaceous serine residues by inositol pyrophosphates in eukaryotic cell-free extracts. It has been postulated that this observed activity may represent a novel signalling pathway in eukaryotes. This study focused on the effect of inositol pyrophosphate structure and overall charge on the thermodynamics of these reactions. This information should contribute to our understanding of this novel cellular phosphorylation process.

The myo-inositol signaling pathway in plants allows them to sense external environmental stimuli and respond to them. This signaling pathway depends on the dynamic levels of the second messenger, inositol(1,4,5)trisphosphate, which in turn is regulated by inositol polyphosphate 5-phosphatases (5PTases). Previous studies have shown that 5PTase 13 binds an important energy sensor, Sucrose non-fermenting (Snf) 1-related kinase (SnRK1.1) and also a novel protein P80. Studies from the lab have also shown that P80 is a part of a deubiquitinating enzyme complex along with WDR20 and Ubiquitin-specific protease called UBP3. Our p80 mutants have a root deficient phenotype under low energy conditions which is normalized by addition of sucrose. p80 mutants show reduced growth and early senescence under specific environmental conditions. This is opposite in nature to SnRK1.1 overexpressors. In this study, I have examined the possible interaction of P80 with SnRK1. I have studied the effects of expression of the exogenous SnRK1.1:GFP transgene under the control of the 35S CaMV promoter in the p80 mutant. This will facilitate the delineation of mechanisms that plants use for the control of energy sensing. I also examined the effects of the overexpression of SnRK1.2:GFP in the p80 mutant. Further, I have explored the presence of a new class of molecules, inositol phosphate molecules (InsPs) containing pyrophosphate bonds (PPx) in p80 mutants. Recent evidence has shown that this class of molecules has roles in sensing and signaling. I have demonstrated that InsP7 is present in developing seeds and vegetative tissue of higher plants. I have also demonstrated that p80 mutants have an alteration in the levels of PPx-InsPs. In addition, I have established spatial expression patterns of two enzymes involved in the synthesis of PPx-InsPx, known as VIP kinases. These studies will help resolve how PPx-InsPs are regulated in plants and thus help in their functional characterization. / Master of Science

To compensate for the sessile nature of plants, thousands of years of evolution have led to the development of many sophisticated signaling pathways that help plants sense and respond appropriately to different environmental cues. One such signaling pathway is called inositol phosphate signaling. This research dissertation focuses on the inositol phosphate signaling pathway in plants, with emphasis on elucidating how a new class of signaling molecules collectively referred to inositol pyrophosphates are synthesized. Inositol pyrophosphates are an emerging class of "high-energy" intracellular signaling molecules containing one or two diphosphate groups attached to an inositol ring, with suggested roles in bioenergetic homeostasis and inorganic phosphate sensing. Information regarding the biosynthesis of this unique class of signaling molecules in plants is scarce, however the enzymes responsible for their biosynthesis in other eukaryotes have been well described. This work aims to characterize the biochemical activity of the kinase domain (KD) of the Arabidopsis plant diphosphoinositol pentakisphosphate kinase enzymes (AtVIP1 and AtVIP2), and elucidate the biosynthesis pathway of inositol pyrophosphates in plants. Our data indicate that AtVIP1-KD and AtVIP2-KD function primarily as diphosphoinositol pentakisphosphate 5 kinases that phosphorylate this substrate at the 1-position. We also discovered a previously unreported inositol hexakisphosphate kinase activity for the Arabidopsis inositol(1,3,4) triphosphate 5/6kinase enzymes, that can convert InsP6 to InsP7. Together, these enzymes can function in plants to produce inositol pyrophosphates, which have been implicated in signal transduction and phosphate sensing pathways. The significance and potential application of these findings in terms of reduced phytate content and phosphate pollution, improved plant fitness, and improved nutrient use efficiency are discussed. The future outlook of inositol phosphate signaling research is also discussed. / Doctor of Philosophy / Inositol Pyrophosphate Biosynthesis and Subcellular Distribution of Enzymes. Notably, InsP6 which represents the major precursor of PP-InsPs in plants is synthesized in the cytosol, however, it can also be transported into the vacuole by the ABC transporter MRP5. Subcellular localization of enzymes involved in PP-InsP biosynthesis including AtITPK and the kinase domains of AtVIP suggests that these molecules are present in the cytosol and nucleus, and to a smaller extent in the ER. Not shown are the full length and phosphatase domain of AtVIP, which are absent from the nucleus. See document for accompanied illustration.