published_or_final_version / Zoology / Master / Master of Philosophy

Obesity is a medical condition in which excess body fat has been accumulated. It is most commonly caused by imbalance between energy intake and energy expenditure (lack of physical activity and lower metabolic rate, etc.). The control of energy metabolism involves multiple tissues and signalling pathways and there is a great need for further understanding of these different interactions. In this study, I use Caenorhabditis elegans to study these complex pathways at the level of a whole organism. The downstream target of mTOR, p70 S6 kinase (S6K), has been implicated in the phosphorylation of multiple substrates and the regulation of growth and metabolism. In this study the worm homolog of S6K, rsks-1, found to be important for fat metabolism. Previous work in our lab found that RSKS-1::GFP is expressed at high levels in a set of sensory neurons and upregulated in ASJ, ASE and BAG sensory neurons in starved worms or mutants with low insulin activity. In this study, I found that the upregulation of rsks-1 expression was affected by serotonin, but not by the other neurotransmitters. Combined with the result that rsks-1 is required for the expression of TGFβ and insulin in ASI, rsks-1 may control dietary sensing by affecting insulin and TGFβ signalling within nervous system. Quantification of fat accumulation by TLC/GC revealed that in comparison to wild type worms, rsks-1 mutants have more than two-fold higher levels of triglycerides. This was confirmed by FT-IR microspectroscopy analysis. rsks-1 mutants also contain disproportionately high levels of C16:1n9 and C18:1n9 lipids compared with wild type worms. Genetic analysis has shown that rsks-1 acts either downstream of, or in parallel to the insulin and TGFβ pathways to affect fat levels. My studies showed that rsks-1 affects fat metabolism by influencing mRNA levels of genes encoding proteins in the β-oxidation pathway. Combined with defects in dietary sensing, fatty acid absorption, fertility and mitochondria function, the loss of rsks-1 activity induced much more energy storage than wild type by making a profound metabolic shift. These results are consistent with the metabolomics data analysis. Tissue specific RNAi showed that rsks-1 was required in many different tissues to regulate fat metabolism. Taken together, it can be concluded that RSKS-1 activity is needed for co-ordination of metabolic states in C. elegans. In order to understand more about the physiology behind fat accumulation, I analysed a mutant, aex-5, that has significantly lowered lipid levels. I found that this defect is associated with a significant reduction in the rate at which dietary fatty acids are taken up from the intestinal lumen. The aex-5 gene, which encodes a Kex2/subtilisin-family, Ca2+-sensitive proprotein convertase, is required for a discrete step in an ultraradian rhythmic phenomenon called the defecation motor program (DMP). Combined with other results, we conclude that aex-5 and other defecation genes may affect fat uptake by promoting the correct distribution of acidity within the intestinal lumen. This dissertation also described how to use Fourier transform infrared (FT-IR) microspectroscopy to detect lipids, proteins and carbohydrates directly in single worm. In conclusion, in this thesis I have uncovered several components that play roles in dietary sensing, fatty acid synthesis, adiposity regulation and fatty acid absorption in C. elegans.

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Plants possess integrated signalling networks that mediate the responses to various environmental conditions. Mitogen-activated protein kinases (MAPKs) constitute a highly conserved family of enzymes in eukaryotes, and in plants MAPK-based signal transduction modules regulate a large number of physiological processes, including responses to environmental stresses and phytohormones. Regulated dephosphorylation of active MAPKs is a key component of the control of MAPK signalling cascades, and in mammals, members of the MAPK phosphatase (MKP) sub-class of dual-specificity tyrosine phosphatases have been recognized as key players for inactivating MAPKs. Five MKP homologues are found in Arabidopsis thaliana, but only limited information is available concerning their properties and biological roles. Based on initial data derived from my reverse genetics and protein interaction studies of these five potential MKPs, as well as gene function information in the literature, I chose to focus on two putative Arabidopsis MKPs, AtMKP2 and Indole-3-Butyric Acid-response 5 (IBR5). By using a combination of genetic and biochemical studies, I established that the previously uncharacterized MKP designated AtMKP2, participates in the regulation of cellular homeostasis in ozone-challenged tissue, and can influence the activation state of two MAPKs, MPK3 and MPK6. AtMKP2-suppressed plants displayed significantly prolonged MPK3 and MPK6 activation during ozone treatment, and recombinant AtMKP2 was able to dephosphorylate both phospho-MPK3 and phospho-MPK6 in vitro, providing direct evidence that AtMKP2 may target these oxidant-activated MAPKs. A mutation in IBR5, one of the five potential AtMKPs, was previously reported to confer reduced sensitivity to auxin and ABA in Arabidopsis. My protein interaction studies demonstrated that IBR5 and MPK12 are physically coupled and that the C-terminus of MPK12 is essential for its interaction with IBR5. In vitro dephosphorylation assays indicated that recombinant phosphoMPK12 is efficiently dephosphorylated by IBR5. In transgenic plants with reduced expression of the MPK12 gene, root growth is hypersensitive to exogenous auxins, consistent with the lower auxin sensitivity reported for ibr5 mutants. Taken together, my data demonstrate for the first time that both AtMKP2 and IBR5 are bona fide Arabidopsis MAPK phosphatases and that they serve as important regulators of oxidative stress and auxin signalling, respectively, in Arabidopsis.

Cell survival in conditions of severe oxygen deprivation depends on a wide variety of biochemical modifications, which result in a large-scale suppression of metabolism, preventing [ATP] from falling to fatally low levels. We investigated whether AMP-activated protein kinase (AMPK) has a role in the coordination of cellular modification during hypoxia, which leads to a regulated state of metabolic suppression in the goldfish (Carassius auratus). Energy charge, AMPK activity, protein and gene expression, as well as the translational capacity and phosphorylation state of a downstream target were measured in goldfish tissues during exposure to hypoxia (-0.3 mg 02/L) for up to 12 h. AMPK activity in the goldfish liver increased by 4-fold at 0.5 h hypoxia and was temporally associated with a —11-fold increase in calculated AMPfree/ATP. No change was observed in total AMPK protein or relative gene expression of identified AMPK isoforms. Changes in AMPK activity were also associated with a decreased rate of protein synthesis and an increase in the phosphorylated form of eukaryotic elongation factor-2 (eEF2; relative to total eEF2). Increases in AMPK activity were not seen in hypoxic goldfish muscle, brain, heart or gill, nor was a significant alteration in cellular energy charge seen in muscle. Still, the present study is the first to show that AMPK activity increases in liver in response to short-term severe hypoxia exposure in a hypoxia-tolerant fish. The decreased rates of protein synthesis, a well known component of metabolic suppression, combined with increased phosphorylation of eEF2, a downstream target of AMPK, potentially implicate the kinase in the cellular effort to suppress metabolism in hypoxia-tolerant species during oxygen deprivation.

The structure and mechanism of the Protein Tyrosine Phosphatase-like Phytases (PTPLPs) from Selenomonas ruminantium (PhyAsr) and Mitsuokella multacida (PhyAmm) were investigated using a combination of enzyme kinetics, site-directed mutagenesis, and X-ray crystallography. I show that PTPLPs use a classical protein tyrosine phosphatase catalytic mechanism and adopt a core PTP fold. Several unique structural features of PTPLPs confer specificity for inositol phosphates. The effect of ionic strength and oxidation on the kinetics and structure of PTPLPs was investigated. The structural consequences of reversible and irreversible oxidation on PTPLPs and PTPs are compared and discussed. We determine the structural basis of substrate specificity in PTPLPs and propose a novel reaction mechanism for the hydrolysis of inositol polyphosphates by PTPLPs. Finally, the structure and function of a unique tandemly repeated phytase has been determined. We show that the active sites of the tandem repeat possess significantly different specificities for inositol polyphosphate. / xix, 148 leaves : ill. (some col.) ; 29 cm

A novel bacterial protein tyrosine phosphatase (PTP)-like enzyme has recently been isolated that has a PTP-like active site and fold and the ability to dephosphorylate myo-inositol hexakisphosphate. In order to expand our knowledge of this novel class of enzyme, four new representative genes were cloned from 3 different anaerobic bacteria related to clostridia and the recombinant gene products were examined. A combination of site-directed mutagenesis, kinetic, and high-performance ion-pair chromatography studies were used to elucidate the mechanism of hydrolysis, substrate specificity, and pathways of Ins P6 dephosphorylation. The data indicate that these enzymes follow a classical PTP mechanism of hydrolysis and have a general specificity for polyphosphorylated myo-inositol substrates. These enzymes dephosphorylate Ins P6 in a distributive manner, and have the most highly ordered pathways of sequential dephosphorylation of InsP6 characterized to date. Bioinformatic analyses have indicated homologues that are involved in the regulation of cellular function. / x, 138 leaves ; 29 cm.

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No description available.

Programmed cell death (PCD) is a fundamentally important process delicately coordinated throughout an organism’s life cycle. In plants, PCD is an integral part of development, reproduction, and pathogenesis. Numerous types of proteins are involved in regulation of PCD in plants, like phosphatases, metacaspases, and protein kinases. In tomato resistance to the pathogen Pseudomonas syringae pv. tomato (Pst), a Ser/Thr protein kinase, Adi3 (AvrPto-dependent Pto-interacting protein 3), interacts with the pathogen’s avirulence protein AvrPto and the tomato resistance protein Pto. Adi3 is a member of the AGC protein kinase family, a group known to transmit signals via the secondary messengers cAMP, cGMP, and phospholipids. In an unchallenged system, the master regulator of AGC kinases, Pdk1, activates Adi3. Activation of Adi3 enables nuclear localization and cell death suppression – all of which is prevented when challenged by Pst. A BLAST_p search of the Arabidopsis thaliania genome with the amino acid sequence of Adi3 identified a 67% identical match, AGC1-3. Like Adi3, AGC1-3 at its activation-loop serine and another site, by Pdk1. With N-terminal deletions of AGC1-3, Pdk1 was found to phosphorylate AGC1-3 at two serines – one serine conserved among all Arabidopsis AGC kinases, the other a serine on the N-terminus of the kinase domain. The non-activation loop serine in AGC1-3, Ser269, is conserved at Ser212, in Adi3. Phosphorylation at Ser212 does not impact auto-catalytic activity of Adi3. However it does enhance trans-catalytic activity. Analysis of AGC1-4 and AGC1-7, two proteins closely related to AGC1-3, reveals that phosphorylation of non-activation loop residues by Pdk1 is not restricted to AGC1-3 and Adi3. Functional analysis of AGC1-3 in Arabidopsis protoplasts revealed that like Adi3, nuclear localization and activation-loop phosphorylation are essential for cell viability. In an effort to elucidate a signaling network controlled by AGC1-3, the KiC (Kinase-client) assay was employed. In the KiC assay, a 2,100-member peptide library was assayed against AGC1-3 and the constitutively active mutant AGC1-3^(S596D). By MS analysis, AGC1-3 and AGC1-3(S596D) phosphorylated 26 and 19 substrate peptides, respectively. Substrate peptides were mapped to proteins involved in central metabolism, transcription, and protein metabolism. The work presented in this dissertation provides conclusive evidence that Pdk1 phosphorylates AGC1-3 and Adi3 at a non-activation loop residue. The work also supports AGC1-3 as the Arabidopsis homologue of Adi3 and presents novel phosphorylation data of potential AGC1-3 substrates.