Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Maintenance of the levels of nucleoside triphosphates (NTPs) as well as their corresponding deoxy derivatives (dNTPs) is crucial to all growth and developmental processes. The enzyme nucleoside diphosphate kinase (NDK) utilises an autophosporylated enzyme intermediate to catalyse the transfer of 5’ terminal phosphate from NTPs (mostly ATP) to nucleoside diphosphates (NDPs) via a reversible mechanism as given below. N1TP + NDK ↔N1DP+ −NDK-His* (1) N2DP + NDK-His* P ↔N2TP + NDK−His. (2) In the γ-phosphoryl group transfer, the highly conserved His 117 active site residue becomes autocatalytically phosphorylated, in the enzyme intermediate (NDK-H*). This phosphoryl group is transferred to ribo-or deoxyribonucleotides (N2DP) in a substrate non-specific manner. In addition to its fundamental role in nucleotide metabolism, NDP kinase is also involved in a number of cellular regulatory functions such as growth and developmental control, tumor metastasis suppression, signal transduction and so on. From mycobacterial genera, NDK of Mycobacterium tuberculosis (MtNDK) has been crystallised, structure was solved and biochemical functions were elucidated. However, there has not been any such study on the NDK of Mycobacterium smegmatis, except on the possible interaction with other proteins which modulates the NTP synthesising activity of MsNDK, towards specific NTPs. M. smegmatis, being a saprophytic, fast growing and non-pathogenic mycobacterium that is widely used as an experimental model mycobacterial system to study various biological processes in mycobacteria, it was thought appropriate to study NDK from this organism. The outcome of current study is presented in five chapters. The First Chapter gives a detailed introduction on the structural and functional aspects of NDK from diverse organisms, from bacteria to humans. Chapter 2. Molecular Cloning, Expression and Characterisation of Biochemical Activities of Nucleoside Diphosphate Kinase from Mycobacterium smegmatis mc 155 The research work starts with the molecular cloning, overexpression, purification, and characterisation of biochemical activities of recombinant MsNDK protein. In brief, ndk gene from M. smegmatis (Msndk) has been cloned, efficiently overexpressed as a soluble 6xHis-tagged recombinant protein, purified through affinity chromatography, and its biochemical characterisation for ATPase, GTPase and NTP synthesising activities have been demonstrated. Catalytic mutant of MsNDK, MsNDK-H117Q, was generated using site-directed mutagenesis approach and H117 was shown to be essential for the catalytic activity. Further experiments revealed that it is the same H117 that is required for mediating autophosphorylation as well, which is an intermediate in the transphosphorylation reaction of NDK. Chapter 3. Characterisation of Oligomerisation Property of M. smegmatis Nucleoside Diphosphate Kinase: the Possible Role of Hydrogen Bond and Hydrophobic Interactions The present study revealed that presence of homodimer of MsNDK could be observed in the presence of heat and SDS. Chemical cross-linking experiments revealed that MsNDK forms dimer, tetramer and hexamer. Homology modeling of MsNDK on the MtNDK crystal structure supported the existence of hexamer as three homodimers. Gln 17, Ser 24 and Glu 27 were found to be positioned at the dimer interface. Mutations on these residues did not abolish the stability of the respective mutant dimers in the presence of SDS and heat. Modeled structure of MsNDK revealed the existence of hydrophobic interactions at the dimer interface. In silico approach helped in mapping the existence of hydrophobic interactions at the dimer interface as two consecutive β-strands. Exposure of hydrophobic residues, using organic solvent methanol, abolished the dimer completely, indicating the vital role of hydrophobic interactions in the dimer stability. In solution, the native MsNDK was found to be a hexamer. Chapter 4. Mycobacterial Nucleoside Diphosphate Kinase Functions as GTPase Activating Protein for Mycobacterial Cytokinetic Protein FtsZ In Vitro Mammalian, plant, and bacterial NDKs can function as GTPase activating protein (GAP) for small G proteins namely, p21 Ras, Rad, and Rho-GTPases in animals and Pra1, Pra2, and GPA1 in Arabidopsis thaliana in vitro. We examined whether NDK of M. tuberculosis (MtNDK) can function as GAP in vitro for the cytokinetic protein FtsZ of Mycobacterium tuberculosis (MtFtsZ), which is a protein with a classical G-protein fold, possessing GTP-binding and GTPase activities (like G proteins). Both MtNDK and MsNDK could function as GAP for MtFtsZ and FtsZ of M. smegmatis (MsFtsZ) respectively in vitro. Similarly, MtNDK could function as GAP for MsFtsZ and reciprocally MsNDK could function as GAP from MtFtsZ. Interaction of NDK with respective FtsZ could be observed. Physiological implications of GAP activity of NDK on FtsZ are discussed. Chapter 5. Transcriptional Analyses of Nucleoside Diphosphate Kinase Gene of Mycobacterium smegmatis mc 155 Although there are studies on the structural and functional aspects of NDK, there are not many studies available on the transcriptional analysis of nucleoside diphosphate kinase (NDK) gene expression in general and nothing in particular in mycobacterial systems. Therefore we studied the transcriptional analysis of expression of Msndk gene, in order to map the Transcriptional Start Site (TSS), identification of promoter elements, and elucidated of transcriptional activity of the promoters. Expression of Msndk gene was analysed in exponential growth phase and under two different stress conditions wherein DNA replication gets arrested. Hydroxy Urea (HU), which reduce dNTP pools by inhibiting ribonucleotide reductase and Phenethyl Alcohol (PEA), which affects membrane structure resulting in DNA replication arrest, were used. Two transcripts and their promoter elements were mapped and their promoter activities were demonstrated. The profile of transcripts was found to be identical under the three different conditions examined.

Background: Peroxisome proliferator-activated receptor δ (PPARδ) is a versatile regulator of distinct biological processes and overexpression of PPARδ in cancer may be partially related to its suppression of its own co-regulators. Aims: To determine whether recruited suppressor proteins bind to and regulate PPARδ expression, activity and PPARδ-dependent cholangiocarcinoma proliferation. Methods: Yeast two-hybrid assays were done using murine PPARδ as bait. PPARδ mRNA expression was determined by qPCR. Protein expression was measured by western blot. Immunohistochemistry and fluorescence microscopy were used to determine PPARδ expression and co-localization with NDP Kinase alpha (NM23-H2). Cell proliferation assays were performed to determine cell numbers. Results: Yeast two-hybrid screening identified NM23-H2 as a PPARδ binding protein and their interaction was confirmed. Overexpressed PPARδ or treatment with the agonist GW501516 resulted in increased cell proliferation. NM23-H2 siRNA activated PPARδ luciferase promoter activity, upregulated PPARδ RNA and protein expression and increased GW501516-stimulated CCA growth. Overexpression of NM23-H2 inhibited PPARδ luciferase promoter activity, downregulated PPARδ expression and AKT phosphorylation and reduced GW501516-stimulated CCA growth. Conclusions: We report the novel association of NM23-H2 with PPARδ and the negative regulation of PPARδ expression by NM23-H2 binding to the C-terminal region of PPARδ. These findings provide evidence that the metastasis suppressor NM23-H2 is involved in the regulation of PPARδ-mediated proliferation.

Les peroxyrédoxines (PRXs) forment une famille de peroxydases communes à tous les organismes vivants et ubiquitaires dans la cellule. Leur particularité provient d’un ou deux résidus cystéines accomplissant un cycle d’oxydo-réduction à l’aide d’un donneur d’électron. Ces protéines thiols sensibles au potentiel redox sont impliquées dans le mécanisme de détoxification du H2O2, une molécule oxydante induite lors de situations de stress. Les PRXs pourraient être induites par le stress et régulées par phosphorylation. En effet, des expérimentations in vitro ont démontré que la nucléoside diphosphate kinase 1 (NDPK1) a la capacité de phosphoryler une PRX cytosolique de pomme de terre. Ce mémoire décrit les travaux expérimentaux effectués pour caractériser la fonction de la PRX. Pour cela, le clonage d’une isoforme a été effectué, suivi d’une caractérisation biochimique et d’une étude d’expression de la protéine. Les données de séquençage révèlent qu’il s’agit d’une PRX de type II phylogénétiquement liée aux PRXs cytosoliques. L’ADNc codant pour cette peroxyrédoxine (PRX1) a été cloné chez Solanum chacoense. Une protéine recombinante portant une étiquette (6xHis) en N-terminale a été produite. Des essais enzymatiques ont confirmé la fonction antioxydante de la protéine recombinante et un anticorps polyclonal a été généré chez le lapin puis utilisé en conjonction avec un anticorps anti-NDPK1 pour déterminer les patrons d’expression généraux de ces protéines chez Solanum lycopersicum et Solanum tuberosum lors de situations de stress. Les données démontrent que les deux protéines sont généralement co-exprimées mais pas co-régulées et que la PRX1 est induite en certaines situations de stress. / The peroxiredoxins (PRXs) are a recently discovered family of peroxidases found in all organisms and ubiquitous in the cell. An important particularity of these proteins is the presence of one or two active cysteines that accomplish an oxydo-reduction cycle with an electron donor. The PRXs are sensitive to the redox potential and are implicated in the detoxification of the H2O2, an oxidante molecule induced in stress situations. The PRXs should be induced in stress situations and regulated by phosphorylation. Indeed, in vitro experimentations have shown that the NDPK1 can phosphorylate a cytosolic PRX isoform of the potato. This dissertation describes the experimentation made to acquire a preliminary understanding of the function of the PRX. For this purpose, we cloned a PRX isoform, followed by a biochemical characterization and expression studies of the protein. The sequencing data shown a type II PRX phylogenetically related to the cytosolic isoforms. The cDNA of this peroxiredoxin (PRX1) has been cloned in Solanum chacoense. The recombinant protein produced had a N-terminal (6xHis) tag. Enzymatic assays confirmed the antioxidant activity of the recombinant protein and a polyclonal antibody has been generated from the rabbit. This antibody was used in conjunction with an antibody anti-NDPK1 to determine the general expression patterns of those proteins during stresses in Solanum lycopersicum and Solanum tuberosum. The results obtained showed that the two proteins are generally co-expressed but not co-regulated. Obvious experimental facts displayed an induction of the PRX1 in biotic and abiotic stresses situations.

Les peroxyrédoxines (PRXs) forment une famille de peroxydases communes à tous les organismes vivants et ubiquitaires dans la cellule. Leur particularité provient d’un ou deux résidus cystéines accomplissant un cycle d’oxydo-réduction à l’aide d’un donneur d’électron. Ces protéines thiols sensibles au potentiel redox sont impliquées dans le mécanisme de détoxification du H2O2, une molécule oxydante induite lors de situations de stress. Les PRXs pourraient être induites par le stress et régulées par phosphorylation. En effet, des expérimentations in vitro ont démontré que la nucléoside diphosphate kinase 1 (NDPK1) a la capacité de phosphoryler une PRX cytosolique de pomme de terre. Ce mémoire décrit les travaux expérimentaux effectués pour caractériser la fonction de la PRX. Pour cela, le clonage d’une isoforme a été effectué, suivi d’une caractérisation biochimique et d’une étude d’expression de la protéine. Les données de séquençage révèlent qu’il s’agit d’une PRX de type II phylogénétiquement liée aux PRXs cytosoliques. L’ADNc codant pour cette peroxyrédoxine (PRX1) a été cloné chez Solanum chacoense. Une protéine recombinante portant une étiquette (6xHis) en N-terminale a été produite. Des essais enzymatiques ont confirmé la fonction antioxydante de la protéine recombinante et un anticorps polyclonal a été généré chez le lapin puis utilisé en conjonction avec un anticorps anti-NDPK1 pour déterminer les patrons d’expression généraux de ces protéines chez Solanum lycopersicum et Solanum tuberosum lors de situations de stress. Les données démontrent que les deux protéines sont généralement co-exprimées mais pas co-régulées et que la PRX1 est induite en certaines situations de stress. / The peroxiredoxins (PRXs) are a recently discovered family of peroxidases found in all organisms and ubiquitous in the cell. An important particularity of these proteins is the presence of one or two active cysteines that accomplish an oxydo-reduction cycle with an electron donor. The PRXs are sensitive to the redox potential and are implicated in the detoxification of the H2O2, an oxidante molecule induced in stress situations. The PRXs should be induced in stress situations and regulated by phosphorylation. Indeed, in vitro experimentations have shown that the NDPK1 can phosphorylate a cytosolic PRX isoform of the potato. This dissertation describes the experimentation made to acquire a preliminary understanding of the function of the PRX. For this purpose, we cloned a PRX isoform, followed by a biochemical characterization and expression studies of the protein. The sequencing data shown a type II PRX phylogenetically related to the cytosolic isoforms. The cDNA of this peroxiredoxin (PRX1) has been cloned in Solanum chacoense. The recombinant protein produced had a N-terminal (6xHis) tag. Enzymatic assays confirmed the antioxidant activity of the recombinant protein and a polyclonal antibody has been generated from the rabbit. This antibody was used in conjunction with an antibody anti-NDPK1 to determine the general expression patterns of those proteins during stresses in Solanum lycopersicum and Solanum tuberosum. The results obtained showed that the two proteins are generally co-expressed but not co-regulated. Obvious experimental facts displayed an induction of the PRX1 in biotic and abiotic stresses situations.

Les isoenzymes de nucléoside diphosphate kinase (NDPK) sont connues depuis maintenant presque 60 ans et n'ont été considérées que pour leur activité catalytique de transfert de groupement phosphoryle. La découverte du gène nme, un gène antimétastatique codant une NDPK, a renouvelé l'intérêt scientifique pour cette famille d'enzymes. Il est désormais connu que la multiplication des gènes durant l'évolution a été accompagnée de diversifications structurales et fonctionnelles. J'ai étudié la fixation des NDPK-A, -B et –D (retrouvées associées aux membranes biologiques, bien que le rôle de cette association soit encore méconnu) à des membranes modèles, et j'ai trouvé des différences dans les mécanismes de fixation. J'ai montré la capacité de la NDPK-D, isoforme mitochondriale, à interagir avec des membranes anioniques ou zwitterioniques, à augmenter leur fluidité et à former des domaines protéolipidiques en présence de CL, lipide anionique spécifique de la membrane mitochondriale interne. J'ai observé cette capacité à former des domaines protéolipidiques avec d'autres protéines interagissant avec la CL, comme la créatine kinase mais pas le cytochrome C. La NDPK-A ne se fixe pas aux phospholipides du feuillet interne de la membrane plastique, ce qui suggère un autre partenaire in vivo. La NDPK-B n'interagit qu'avec des membranes anioniques via un processus en deux étapes, provoque une diminution de fluidité et est capable de former des domaines protéolipidiques. La ségrégation des lipides anioniques induite par la fixation de protéines pourrait contribuer à la formation de plateformes au sein de la membrane susceptibles de servir de point d'ancrage à de nombreuses molécules, modulant ainsi les fonctions cellulaires / Nucleoside diphosphate kinase isoenzymes (NDPK) have been known for nearly 60 years and, until recently, have been considered as housekeeping enzymes. The discovery of a nme gene, an antimetastatic gene that codes for a NDPK, revived the interest for this family. It is now known that the multiplication of nme genes throughout evolution has been accompanied with structural and functional diversification. I studied the binding of NDPK-A, -B and –D (which ae retrieved associated to cellular membranes where they are thought to play several roles) to model membranes and found differences in their behavior towards different compositions of phospholipids. I showed the ability of the NDPKD mitochondrial isoform to interact with both anionic and zwitterionic membranes, to modify their fluidity and to form proteolipidic domains in presence of CL, a mitochondrial inner membrane specific anionic lipid. I observed this ability to form proteo-cardiolipin domains with other CL interacting protein like creatine kinase but not with cytochrome c. NDPK-A was not able to bind to inner leaflet plasma membrane mimicking systems suggesting another partner in vivo. Concerning NDPK-B, it interacted only with anionic membranes via a two step-process, induced a decrease of the membrane fluidity and was able to form proteolipidic domains. Such anionic lipid segregation triggered by protein binding may contribute to platforms formation within membranes. Those platforms are then susceptible to provide a functional docking platform for numerous molecules and thus to modulate cellular functions

Living organisms employ different kinds of mechanisms, to regulate the functions of genes or their products, which may help in maintaining homeostasis inside the cell or may help in fighting hostile environment in the case of pathogenic organisms. These mechanisms act at the transcriptional, post-transcriptional, translational, and post-translational levels. In order to understand the physiology of an organism, it is essential to obtain an in-depth knowledge of such mechanisms, in which several proteins participate in interlinked pathways. In this regard, the present study focuses on two such proteins: (i). the newly identified Fic (Filamentation induced by cAMP) protein; and (ii). NDK (Nucleoside Diphosphate Kinase), which had been studied for decades. Fic protein and NDK share several common features: (i). both use nucleoside triphosphate (NTPs) or nucleoside diphosphate (NDPs) or their derivatives as one of their substrates; (ii). they have been found to be involved in diverse cellular pathways, involving different types of substrates that form the second substrate of these proteins; (iii). both are ubiquitously present in all the living organisms - from bacteria to humans to plants. However, there is very little information on these proteins from mycobacterial systems, which include some major human pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, which are the causative agents of Tuberculosis and Leprosy, respectively. In view of these reasons, in the present study, the structural and/or functional features of the Fic and NDK proteins from Mycobacterium tuberculosis, were analysed, as it might be of medical significance for effectively combating the pathogen. The Chapter 1 of the thesis contains the Introduction to the research work and Chapter 2 is on the overall Materials and Methods. The remaining chapters pertain to the data obtained on the structural and/or functional features of the Fic and NDK proteins from Mycobacterium tuberculosis. Chapter 3. Cloning, Expression and Purification of Mycobacterium tuberculosis Fic The role of FIC (Filamentation induced by cAMP) domain containing proteins in the regulation of many vital pathways, mostly through the transfer of NMPs from NTPs to specific target proteins (NMPylylation), in microorganisms, higher eukaryotes, and plants is emerging. In order to understand the biological role of FIC domain containing proteins in mycobacteria, the gene for the FIC domain containing protein of the human pathogen, Mycobacterium tuberculosis, MtuFic, was cloned, overexpressed, purified to homogeneity, and biochemically characterised. Neither the His-tagged nor the GST-tagged MtuFic protein, overexpressed in Escherichia coli, nor expression of Mtufic in Mycobacterium smegmatis, yielded the protein in the soluble fraction. However, the maltose binding protein (MBP) tagged MtuFic (MBP-MtuFic) could be obtained partly in the soluble fraction. Denatured-refolded protein was used for the antibody generation in mice and rabbit. The cellular localisation and secretion of MtuFic were characterised using the antibody. Chapter 4. Biochemical Characterisation of Mycobacterium tuberculosis Fic Sequence alignment with several FIC motif containing proteins, complemented with homology modeling on the FIC motif containing protein, VbhT of Bartonella schoenbuchensis as the template, showed conservation and interaction of residues constituting the FIC domain. MtuFic, possesses the critical His144 residue, in the characteristic FIC Motif, HPFREGNGRSTR (HPFxxGNGRxxR), spanning 144th to 155th residue. Site-specific mutagenesis of the His144, or Glu148, or Asn150 of the FIC motif, or of Arg87 residue that constitutes the FIC domain, or complete deletion of the FIC motif, abolished the NTP to NMP conversion activity. The activity of MtuFic was consistent with the biochemical activities hitherto reported for a variety of bacterial FIC domain containing proteins. Studies were also carried out on NMPylylation in the presence of eukaryotic proteins and eukaryotic and mycobacterial cell lysates. Although formation of NMPs from NTPs mediated by MBP-MtuFic could be detected, we could not identify any protein as the target substrate either in the human macrophage (THP1) cells or in the M. tuberculosis cells. VopSΔ30 (kind gift from Dr. Kim Orth), along with human G proteins as targets, were used as the positive controls. Various possibilities for the inability to detect a protein target substrate are discussed. Chapter 5. Transcriptional Analysis of Mycobacterium tuberculosis fic Gene (Mtufic) In parallel, in order to understand the transcriptional regulation of Mtufic, primer extension analysis was carried out. The Transcription Start Site (TSS; +1 site) of Mtufic were mapped under different growth/stress conditions, which tubercle bacilli encounter in human host. Mtufic got expressed mainly through two transcripts, T1 and T2, arising from two different transcription start sites (TSS). Putative promoter regions were cloned in a promoter probe vector, which expresses a GFP protein of very high intensity, in order to qualitatively detect the activity of the promoters. The half-life of the gfp mRNA was determined to be 4 min and therefore justifiably quantitated the Mtufic promoter activity by determining the gfp mRNA levels. The levels of Mtufic mRNA were two-fold higher under nutrient-depleted stationary phase of growth, as compared to the levels at mid-log phase. The activity of P1 and P2, as quantitated real-time using the short half-life gfpm2+ mRNA levels in Mycobacterium smegmatis transformants, showed that the activity of P2 was upregulated two-fold under nutrient-depleted stationary phase of growth, while that of P1 remained unaltered while of P1 and P2 were low under hypoxia. Co-transcription of Mtufic, with the immediate upstream gene, Rv3642c, of unknown function, was observed. Taken together, the data strongly indicated that the expression of Mtufic gets altered under nutrient-depleted and hypoxic conditions, which are the stress conditions experienced by tubercle bacilli in granuloma in tuberculosis patients. Chapter 6. Functional Characterisation of Mycobacterial FtsZ-NDK Interaction During the past few decades, our laboratory has been carrying out extensive molecular and functional studies on the cytokinetic protein, FtsZ, of different mycobacterial species, and of a variety of other mycobacterial proteins that are believed to be interacting with the cell division machinery. In this regard, in parallel to the work on MtuFic, we carried out work on the identification and characterisation of the proteins that interact with mycobacterial FtsZ. In this context, we found for the first time that the nucleoside diphosphate kinase (NDK), which can generate NTPs from ATP/GTP and NDPs, interacts with FtsZ and that the interaction was conserved across several mycobacterial species. Therefore, the FtsZ-NDK interaction was extensively characterised in vitro, using the recombinant, purified FtsZ and NDK proteins from different mycobacterial species. This novel finding on the interaction of NDK with FtsZ adds another role to NDK, namely in bacterial cell division.