Dissertations / Theses on the topic 'DNA topoisomerases; Cell growth'

Thesis (Ph.D)--University of Tennessee Health Science Center, 2008.
Title from title page screen (viewed on July 16, 2007). Research advisor: Mary-Ann Bjornsti, Ph.D. Document formatted into pages (xii, 123 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 118-123).

Parmi les medicaments anticancereux les plus actifs, les agents intercalants de l'adn (anthracyclines, acridines) produisent des lesions sur l'adn de type soit cassure du dna, soit pontage adn-proteine. Ces alterations sont analysees par elution alcaline, sedimentation de nucleotide et sedimentation alcaline. Ces lesions sont reversibles apres suppression des intercalants (culture cellulaire, cellules leuconiques(l1210)). Les dna topoisomerase 2 (enzyme de replication, de transcription, d'organisation de chromatine) sont responsables des lesions provoquees par les agents intercalants du dna, car dans ces conditions, elles forment les ponts proteine-dna. L'utilisation des cellules soit sensibles soit resistantes aux inhibiteurs de dna topoisomerase 2 a permis de mettre en evidence leur role dans la formation de ces alterations au dna

Mitochondrial DNA encodes thirteen protein subunits in the oxidative phosphorylation system (OXPHOS) that is responsible for cellular energy production. Mitochondrial disorders have been identified to be associated with mtDNA mutations. However, the molecular mechanisms of specific mtDNA mutations are still being explored in order to establish causative links. This study tries to elucidate the mutational effects of mtDNA on OXPHOS complex activities and cell growths. Using mouse 3T3 fibroblasts as a cell model, single-cell clones with different growth rates were isolated. The entire mtDNA genome was sequenced for mutations. The enzymatic activities of OXPHOS complex I to V were analysed. Three growth patterns represented by five clones were identified. Three clones (clone #2, #3, and #6) had the shortest doubling times (11.5 - 14.9 hours). Clone #1 had a medium growth rate (19.2 hous); and clone #5 had a significantly slow growth rate (22 hours). MtDNA sequencing results revealed that clone #5 had several heteroplasmic mutations (one in 16S rRNA, two in tRNAser (UCN), three in tRNAasp, one in tRNAlys, one in COI, five in COII, and one in ATPase8) while the other four clones showed sequence homology. Enzymatic analyses showed that on average clone #5 had significantly low complex III, IV, and V activities (p < 0.05). Changes in biochemical properties and protein structure were analyzed to deduct possible mechanisms for reduced respiration. In conclusion, the slow growth rate is associated with reduced OXPHOS enzyme functions. It is most likely that the combination of COI and COII mutations resulted in the reduction of complex IV function. It is still unclear whether the ATPase8 mutation (T7869A) in the non-conserved region alone can have such a pronounced phenotypic effect. A reduction in complex III also cannot be explained since there were no mutations in the only mtDNA-encoded complex III gene, but it is possible that there are mutations in the nDNA-encoded complex III genes. Mutations in tRNA and rRNA genes may also be responsible for reduced protein syntheses and consequently reduced OXPHOS activities. It is unclear why complex I activity was not affected. Although the mutational effect of individual mtDNA mutation observed cannot be clearly identified, this study establishes a correlation between mtDNA mutation and cell energy production and growth.

Pharmacology
Ph.D.
Cardiovascular disease (CVD) is the leading cause of death worldwide, and is projected to remain so for at least the next decade. Ever since its discovery in the urine and blood of children with inborn errors of metabolism, homocysteine (Hcy) at elevated plasma concentrations has been associated with CVD clinically and epidemiologically. Observational studies and meta-analyses have noted that changes in plasma Hcy by 5μM increase the odds ratio of developing coronary artery disease by 1.6-1.8 among other CVD. Clinical trials aimed at reducing plasma Hcy for benefit against development of subsequent cardiovascular events have had unconvincing results, but have moreover failed to address the mechanisms by which Hcy contributes to CVD. Recommendations from national agencies like the American Heart Association and the United States Preventive Services Task Force emphasize primordial prevention as a way to combat CVD. Reducing plasma Hcy as secondary and primary interventions does not fulfill this recommendation. In order to best understand the role of Hcy in CVD, an investigation into its mechanisms of action must be undertaken before measures of primordial prevention can be devised. Numerous experimental studies in the literature identify vascular endothelium as a target for the pathological effects of Hcy. Endothelial injury and impairment are contributory processes to atherosclerosis, and Hcy has been demonstrated to inhibit endothelial cell (EC) growth and proliferation through mechanisms involving cell cycle arrest, oxidative stress, and programmed cell death in vitro. Animal models have also confirmed that high levels of Hcy accelerate atherosclerotic plaque development and lead to impairment of vascular reendothelialization following injury. Hcy has been shown to have the opposite effect in vascular smooth muscle cells (SMC), causing their proliferation and again contributing to atherosclerosis. The cell-type specificity of Hcy remains to be understood, and among the aims of this research was to further characterize the effects of Hcy in EC. The overarching goal was discovery in order to direct future investigations of Hcy-mediated pathology. To begin, the first investigation considered the transcriptional and regulatory milieu in EC following exposure to Hcy. High-throughput screening using microarrays determined the effect of Hcy on 26,890 mRNA and 1,801 miRNA. Two different in vitro models of hyperhomocysteinemia (HHcy) were considered in this analysis. The first used a high dose of 500µ Hcy to mimic plasma concentrations of patients wherein the transsulfuration pathway of Hcy metabolism is impaired as in inborn cystathionine-ß-synthase deficiency. The other set of conditions used 50µ Hcy in the presence of adenosine to approximate impairment of the remethylation pathway of Hcy metabolism wherein s-adenosylhomocysteine accumulates, thus inhibiting s-adenosylmethionine formation and methylation reactions. These distinctions are important because most clinical trials do not distinguish between causes of HHcy, thereby ignoring the specific derangements underlying HHcy. mRNA and miRNA expression changes for both sets of treatment conditions identified CVD as a common network of Hcy-mediated pathology in EC. Moreover, methylation-specific conditions identified cell cycle modulation as a major contributory mechanism for this pathology, which agrees with recent findings in the literature. Analysis of significant mRNA changes and significant miRNA changes independently identified roles for Hcy in CVD and cell cycle regulation, thereby suggesting that miRNA may mediate the effects of Hcy in addition to gene expression changes alone. To investigate the role of Hcy in the cell cycle further, the next set of investigations considered the effect of Hcy under conditions approximating impaired remethylation in early cell cycle events. Previous studies have demonstrated that Hcy inhibits cyclin A transcription in EC via demethylation of its promoter. Conversely, Hcy induces cyclin A expression in SMC, again making the case for a cell type-specific mechanism in EC. Preceding cyclin A transcription and activation, canonical events in the early cell cycle include D-type cyclin activation, retinoblastoma protein (pRB) phosphorylation, and transcription factor E2F1 activation. In a series of in vitro experiments on EC, it was seen that Hcy inhibits expression of cyclin D2 and cyclin D3, but not cyclin D1. Next, pRB phosphorylation was seen to be decreased following treatment with Hcy. This also led to decreased E2F1 expression. However, this series of events could be reversed with E2F1 supplementation, allowing the cell cycle to proceed. As Hcy exerts a number of its effects via regulation of gene transcription, a final series of investigations aimed to predict potential targets of Hcy by examining patterns of transcription factor binding among known targets of Hcy regulation. Gene promoters of Hcy-modulated genes were analyzed in order to determine common transcription factors that potentially control their regulation. The locations of CpG-rich regions in promoters were identified to determine which regions would be most susceptible to regulation by DNA methylation. Next, high-throughput next-generation sequencing (NGS) and bisulfite NGS was performed for DNA from EC treated with Hcy in order to determine methylation changes after Hcy treatment. A number of potential transcription factors and their binding sites were identified as potential mediators of Hcy-mediated gene regulation. Taken together, these investigations represent an exploration of Hcy-mediated pathology in CVD, by focusing upon novel regulatory mechanisms in EC. Objective high-throughput arrays identified roles for Hcy in CVD and cell cycle pathways regulated by miRNA and gene expression, which were confirmed experimentally in vitro. These observations led to an investigation and identification of common transcription factors that potentially regulate Hcy-altered gene expression. This framework may be used to guide future investigations into the complex pathological network mediating the effects of Hcy in CVD. First, identification of a role for miRNA in mediating the effects of Hcy represents a novel regulatory mechanism, heretofore largely unexplored. Next, expanding the role of Hcy in EC cell cycle regulation to identify upstream mediators greatly adds to the published literature. Finally, noting that these changes center upon transcriptional and post-transcriptional regulation gives import to developing methods to characterize promoter and transcription factor regulation. The investigations presented herein and their results provide evidence that the future of Hcy research is vibrant, relevant, and not nearly surfeit.
Temple University--Theses

Mitochondria are the main sites for adenosine triphosphate (ATP) generation within most cells. Structural and functional alterations of mitochondria due to genetic abnormalities of mitochondria can cause respiratory chain dysfunction. In this study, the important role of mitochondria in energy metabolism was determined by comparing the effect of mitochondrial DNA (mtDNA) mutations on growth patterns and oxidative phosphorylation (OXPHOS) enzyme activities of six isolated clones (B5, B12, D4, D9, E1 and E8); as well as the effect of ATP supplement to culture using the slowest growing clone. The isolated clones had shown distinct growth pattern and morphology. The difference in proliferation rates among the clones was ascertained by the doubling times (B5=26.4h. B12=43.2h. D4=25.7h. D9=33.6h. E1=26.9h and E8=28.8h). The clone's slow growth rate was likely the result of mitochondrial mutations in the 16S rRNA gene, ND1, ND4, ND6 and COX III. Five heteroplasmic mutations were found in clone B12 (G2480T, C2513G, A2520T, C9527T and C14263G), one heteroplasmic mutation in clone D9 (A4137G) and one homoplasmic mutation in clone D4 (C11496). The mutations in clone B12 appeared to be deleterious to the cell by disrupting mitochondrial OXPHOS activities and reducing energy output. Additionally, extracellular ATP supplement to OXPHOS deficient clone B12 facilitated cell growth and enhances the gene expression. Increased expression of mtDNA-encoded respiratory chain complexes observed in clone B12 compared to clone D4 may reflect mitochondrial genomic adaptation to perturbations in cellular energy requirements. The stimulation of mitochondrial biogenesis may be a cellular response in compensation for defects in OXPHOS associated with mtDNA mutations. My data support the hypothesis that the variability in functional manifestations of mtDNA is attributed to the nature of the mutation, number of mutation and the gene specifically affected. These results will help to further our understanding of the relationship between mitochondrial mutation and cellular function.

Mycobacterium tuberculosis (Mtb) is one of the most virulent and prevalent bacterial pathogens across the world. As Mtb infects millions of people a year, it remains essential to study its physiology with the goal of developing new therapeutic interventions. A critical part of the bacteria’s ability to propagate is through successful cell division. Although the process of bacterial cell division and the key proteins therein are well understood in Escherichia coli, much remains to be understood about division in mycobacteria. Genetic and cell biological approaches have recently begun to identify key divisome components in Mycobacterium smegmatis. However, questions remain regarding the role and function of one divisome protein in particular, the DNA translocase FtsK. In this dissertation, I investigated the necessity of FtsK for the growth of mycobacteria. Using an inducible knockdown of FtsK, I present evidence that complete loss of FtsK is required to inhibit growth in both Mtb and M. smegmatis, and that these orthologs share a homologous function. Additional work suggests extended loss of FtsK may be lethal to bacteria. These observations support that FtsK is an essential member of the divisome in mycobacteria, facilitating the processes of growth and division.

In primary rat hepatocytes, we found that activation of the Pl3-kinase pathway is both necessary and sufficient to account for EGF-induced DNA synthesis. To identify the mechanism of EGF-induced Pl3-kinase activation, we demonstrated that three distinct p85-associated complexes were formed following EGF: ErbB3-p85, Shc-p85 and a large complex Gab2-Grb2-SHP2-p85. The latter accounted for >80% of total Pl3-kinase activity. Further experiments showed that these complexes are differentially localized in rat liver following EGF treatment. ErbB3-p85 and Shc-p85 complexes were localized to PM and Endosomes; whereas the multimeric Gab2-Grb2-SHP2-p85 complex was formed rapidly and exclusively in cytosol. A central role for Gab2 in EGF-induced Pl3-kinase activation and DNA synthesis was established when we observed that over-expression of wild-type Gab2 augmented these EGF actions, whereas a Gab2 mutant lacking p85 binding sites did not effect such augmentation. Over-expression of the PH-domain of Gab2 did not affect EGF-induced Gab2 phosphorylation, Pl3-kinase activation and DNA synthesis, whereas over-expressed Gab2 lacking the PH-domain was comparable to wild-type Gab2 in respect to these EGF-induced signals. These data demonstrated that Gab2 is phosphorylated and mediates EGF signaling in a PH-domain independent manner. We then explored the mechanism of Gab2 phosphorylation by EGF; our results demonstrated that PP1, a selective inhibitor of Src family kinases, blocked EGF-induced Gab2 tyrosine phosphorylation and downstream events. Moreover, Gab2 phosphorylation was increased in Csk knock-out cells in which Src family kinases are constitutively activated. A constitutive association between Gab2 and Src via proline rich sequences on Gab2 was demonstrated since deletion of proline rich sequences in Gab2 prevented EGF-induced association of Src with Gab2, Gab2 phosphorylation, Pl3-kinase/Akt activation, and DNA synthesis. The role of SHP2 was defin

Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains xviii, 157 p.; also includes graphics (some col.). Includes bibliographical references (p. 125-157). Available online via OhioLINK's ETD Center

Myeloid Derived Suppressor Cells (MDSC) represent a significant hurdle to cancer immunotherapy because they dampen anti-tumor cytotoxic T cell responses. Previous studies have reported on the myelo-depletive effects of certain chemotherapies. Using guadecitabine, a next-generation DNA methyltransferase inhibitor (DNMTi), we observed significantly reduced tumor burden in the 4T1 murine mammary carcinoma model. Guadecitabine treatment prevents excessive tumor-induced myeloid proliferation and systemic accumulation, and skews remaining MDSCs toward a beneficial antigen-presenting phenotype. Together, this alters the splenic environment to improve T cell activation and interferon-gamma (IFNg) production. Additionally, guadecitabine enhances the therapeutic effect of adoptively transferred antigen-experienced lymphocytes to diminish tumor growth and improve overall survival. Based on these findings, the immune-modulatory effects of guadecitabine can help rescue the anti-tumor immune response and could contribute to the overall effectiveness of current cancer immunotherapies. Allergies and asthma are common ailments that are on the rise around the world. Mast cells play a direct role in the signs and symptoms characteristic in allergic patients. The family of A Disintegrin And Metalloproteinases (ADAMs) are involved in regulating many cellular processes by cleaving surface receptors, ligands, and signaling molecules. We sought to determine the role of ADAM17 in mast cell activity. In studies using ADAM17-deficient mast cells, percent degranulation and cytokines released by IgE-mediated activation were significantly reduced. Interestingly, ionomycin-activation was unchanged, suggesting ADAM17 may be involved in IgE-mediated mast cell activation upstream of calcium release. Additionally, ADAM17MC-/- mice showed protection from IgE-, but not histamine-, mediated passive systemic anaphylaxis (PSA). The underlying mechanism behind the reduced degranulation occurs through signaling deficiencies downstream of Lyn phosphorylation. Together, the data suggest that ADAM17 is required for proper mast cell signaling through its interaction with the Src family kinase, Lyn.

The overexpression of several receptors and dysfunction of signal transduction pathways characterize the heterogeneity of many solid tumours. Targeted therapies against epidermal growth factor receptor (EGFR)-overexpressing tumours involve well tolerated EGFR inhibitors. However, the potency of these inhibitors is mitigated by several factors including mutations in signaling pathways and receptor heterogeneity. To circumvent this problem, we recently designed a novel strategy that seeks to synthesize molecules "programmed" to release an EGFR inhibitor and a cytotoxic DNA-damaging agent. This led to mixed EGFR-DNA targeting agents, termed "type I combi-molecules". Previous work demonstrated that these compounds: (1) inhibited EGFR and (2) damaged DNA. However, the correlation of their degradation, localization and distribution in the cell with their mechanism of action remained elusive. In this thesis, we designed a fluorescence-labeled combi-molecule AL237 "programmed" to release a blue fluorescent EGFR inhibitor and a green DNA targeting species. The results showed that AL237 blocked EGFR phosphorylation and downstream MAPK pathway, subsequently leading to downregulation of XRCC1 and ERCC1, two DNA repair enzymes. Following demonstration of the ability of AL237 to fully block the MAPK pathway, we studied its localization in the tumour cells by fluorescence microscopy. The results showed that the released quinazoline colocalized with EGFR in the perinuclear region and the green fluorescence was detected in isolated nuclei. This led to a model whereby combi-molecule entered the cell, bind to the EGFR at the plasma membrane to prevent signal transduction and abundantly localized in the perinuclear region from where the released alkylating species could diffuse to the nucleus. This mechanism explained the significantly high levels of DNA damaging species in the nuclei of cells expressing EGFR. Further studies exploiting AL237 fluorescence properties demonstrated that its potency did not depend on the P-gp status of the cells. The P-gp independence of AL237 effect was explained by its intracellular degradation that prevented the efflux of the intact structure. Further studies on combi-molecules that do not require hydrolysis to generate the two targeting species (type II combi-molecules) showed that they exhibited potency in the submicromolar range. Studies designed to elucidate the mechanism underlying the exquisite potency of ZR2008 showed that it induced significant levels of apoptosis, independently of the AKT status of the cells. A constant in its potency was its ability to block cells in G1/S and to downregulate the antiapoptotic protein survivin. Our findings suggest that pathways leading to the inhibition of survivin could be a major molecular determinant for the cytotoxicity of ZR2008. The results from this work in toto contributed to the elucidation of the mechanism of action of two classes of combi-molecules: type I and type II.
L'hétérogénéité de la plupart des tumeurs solides est caractérisée par la surexpression de plusieurs récepteurs et le disfonctionnement des voies de transduction des signaux. Les thérapies actuelles contre les tumeurs surexprimant le récepteur du facteur de croissance épidermique (EGFR) utilisent des inhibiteurs de l'EGFR, agents relativement bien tolérés en clinique. Cependant, l'efficacité de ces inhibiteurs est atténuée par plusieurs facteurs tels que les mutations dans les voies de signalisation et par l'hétérogénéité des récepteurs. Pour palier ce problème, nous avons récemment conçu une stratégie basée sur la synthèse des molécules «programmées» pour libérer un inhibiteur de l'EGFR et un agent cytotoxique capable d'endommager l'ADN. Ces molécules, combinant des agents ciblant l'EGFR et l'ADN, sont dénommées «combi-molécules de type I». Les travaux réalisés précédemment au laboratoire ont démontré que ces composés (1) inhibent la phosphorylation de l'EGFR et (2) endommagent l'ADN. Cependant, la corrélation entre leur dégradation, leur localisation et leur distribution au sein de la cellule et leur mécanisme d'action n'a pas encore été élucidée. Au cours de cette thèse de doctorat, nous avons élaboré une combi-molécule, AL237, marquée d'un groupe fluorescent et « programmée» pour libérer un inhibiteur de l'EGFR fluorescant dans le bleu et une entité fluorescant dans le vert ciblant l'ADN. Les résultats ont démontré que AL237 bloque la phosphorylation de l'EGFR et de la voie de signalisation des MAP kinases, accompagnée par la réduction sousjacente de l'expression de XRCC1 et ERCC1: deux enzymes impliquées dans la réparation de l'ADN. Après avoir démontré la capacité de AL237 à bloquer entièrement la voie de signalisation des MAP kinases, nous avons étudié la localisation de cette molécule dans des cellules cancéreuses par microscopie en fluorescence. Les résultats ont montré que la quinazoline libérée est colocalisée avec l'EGFR dans la région périnucléaire et que le signal de fluorescence vert est détecté dans les noyaux isolés. Ces résultats mettent en valeur un modèle ou la combi-molécule entre dans la cellule, s'associe au REGF au niveau de la membrane plasmique, empêchant ainsi la transduction des signaux, puis se localise abondamment dans la région périnucléaire où les espèces alkylantes sont libérées et peuvent ainsi diffuser dans le noyau. Ce mécanisme permet d'expliquer la forte concentration d'espèces ciblant l'ADN observée dans les noyaux des cellules exprimant l'EGFR. D'autre part, des études utilisant les propriétés de fluorescence de AL237 ont démontré que la toxicité de cette molécule n'est pas affectée par la présence de la P-glycoprotéine (P-gp) dans les cellules. Cette observation peut être expliquée par le fait que, AL237 se dégrade intracellulairement en deux petites molécules empêchant ainsi l'efflux de la macrostructure intacte. Au cours de cette thèse, d'autres travaux ont été réalisés sur des combi-molécules, dites de type II, qui ne nécessitent pas d'hydrolyse pour générer les deux espèces actives et montrent une toxicité élevée à des concentrations submicromolaires. Les études élaborées pour élucider le mécanisme de l'exceptionnelle activité de ZR2008, une combi-molécule exemple de type II, ont montré qu'elle induit des niveaux significatifs d'apoptose indépendamment du statut d'AKT dans les cellules. Une constante dans son activité est sa capacité à bloquer les cellules dans les phases G1/S du cycle cellulaire et à inhiber le niveau de la survivine, une protéine antiapoptotique. Nos résultats suggèrent que les voies de signalisation, menant à l'inhibition de la survivine, pourraient jouer un rôle déterminant pour la cytotoxicité de ZR2008. En conclusion, les travaux de cette thèse ont contribué à l'élucidation des mécanismes d'action des deux classes de combi-molécules : type I et type II.

Solid tumours are characterized by the overexpression of several receptors that promote growth and antiapoptotic signalling. Their overexpression is associated with tumour progression and reduced sensitivity to anticancer drugs. Thus, in order to block the progression of such tumours, strategies to block receptor and induce additional damage in the cells are required. Here, we studied molecules termed, "combi-molecules", designed to block one such receptor, the epidermal growth factor receptor, (EGFR) and damage DNA. Combi-molecules are classified into two types: type I and type II. Type I combi-molecules require hydrolytic cleavage for releasing the EGFR and DNA targeting species, whereas the type II can generate the two species without requirement for degradation. Despite significant evidence of the high potency of the two types of combi-molecules, the parameters governing their potency in vivo remained elusive. This thesis describes bioanalytical approaches to elucidate the inverse potency of type II combi-molecules ZR2003 in vitro vs. in vivo and to analyse the degradation pathways of type I combi-molecule ZRS1 in vitro and in vivo. ZR2003 was 6-fold more potent than the clinical drug Iressa in vitro but slightly less potent than the latter in vivo. Tumour analysis showed that the difference of potency in vivo may be due to lower levels of absorption of ZR2003 in vivo when compared to Iressa. These results were in agreement with the levels of absorption observed in human ovarian cancer cell OV90 aggregates, indicating that the latter 3D organ-like model could be used to predict ZR2003 absorption in vivo. Studies on type I combi-molecule ZRS1 showed that while the drug was stable ex vivo, its decomposition was rapid in vivo and this was in agreement with data obtained from the 3D organ-like model. However, a new metabolite of ZRS1, FD105Ac, was detected in vivo but not in vitro, suggesting that the 3D organ-like model could not predict ZRS1 in vivo metabolism. Overall, the study showed that the reverse magnitude of potency of Iressa and type II combi-molecule ZR2003 from in vitro to in vivo may not be due to differences in their mode of action but rather to their differential plasma and tumour absorption. The results from the analysis of type I combi-molecule ZRS1 suggests that while it is unstable in vivo, its degradation and metabolism lead to high concentrations of EGFR inhibitory metabolites.
Les tumeurs solides sont caractérisées par la surexpression de plusieurs récepteurs qui encouragent la croissance tumorale et la signalisation antiapoptotique. Leur surexpression est associée avec la progression de la tumeur ainsi qu'à une diminution de sa sensibilité aux drogues anticancéreuses. De façon à empêcher la progression de telles tumeurs, il est nécessaire de développer des stratégies visant à bloquer les récepteurs et à indure des dommages additionnels dans la cellule. Dans cette étude, nous avons étudié une classe de molécules appelées « combi-molécules », conÇues pour bloquer un de ces récepteurs, le récepteur du facteur de croissance de l'épiderme (EGFR), et pour induire un dommage à l'ADN. Bien qu'il existe des évidences significatives de la haute puissance de ces combi-molécules, les paramètres gouvernant leur puissance in vivo n'ont pas été élucidés. Cette thèse décrit l'approche bioanalytique qui a été utilisée pour déterminer la puissance d'une combi-molécule, ZR2003, in vitro comparativement à in vivo et pour analyser la voie de dégradation d'une seconde combi-molécule, ZRS1, in vitro ainsi qu'in vivo. Les combi-molécules sont classifiées en deux types : type I et type II. Les combi-molécules de type I sont destinées à être dégradées pour générer les agents ciblant EGFR et l'ADN, tandis que les combi-molécules de type II peuvent générer deux agents sans avoir recours à une décomposition au préalable. Nous avons démontré qu'un modèle d'organe en 3D fait de cellules de cancer ovarien, OV90, peut être une bonne plateforme pour prédire la décomposition et l'absorption des combi-molécules in vivo.Nous avons trouvé que ZR2003 est 6 fois plus puissant que l'Iressa in vitro mais légèrement moins puissant que ce dernier in vivo. L'analyse des tumeurs a démontré que la différence de puissance in vivo pourrait être due à une absorption moins efficace de ZR2003 in vivo comparativement à l'Iressa. Ce résultat concorde avec l'absorption qui est observée dans les modèles d'organe 3D indiquant que ce modèle pourrait servir à prédire la biodistribution de ZR2003. Pour l'analyse des combi-molécules de type I, il a été démontré avec ZRS1 qu'alors que la drogue est stable ex vivo, sa décomposition est rapide à l'intérieur des tumeurs, en accordance avec ce qui a été observé dans le modèle d'organe 3D. Par contre, un nouveau métabolite de ZRS1, le FD105 acétylé ou FD105Ac, a été observé in vivo mais non in vitro, suggérant que le modèle d'organe 3D ne peut prédire la métabolisation in vivo. De façon générale, cette étude démontre que les composants bioactifs du prototype de combi-molécule de type II ZR2003 est moins bioactif que les combi-molécules de type I qui peuvent être dégradées dans les fluides biologiques. De plus, le modèle d'organe 3D peut servir à prédire la biodisponibilité et la stabilité des combi-molécules mais pas leur métabolisation in vivo.

The cellular stress response (CSR) is one of the most highly conserved mechanisms among all organisms. Cellular stress can be defined as damage or the threat of damage to proteins, macromolecules and/or DNA. The response to damage can involve cell cycle regulation, protein chaperoning, DNA repair or, if macromolecular damage is too severe, apoptotic mechanisms can be initiated. This thesis details experiments that were designed to examine the cellular response to non-lethal environmental stressors at the protein level, using two fish species as study models. Two proteins that can cause cell cycle arrest and apoptosis mechanisms were examined. Expression of the CCAAT enhancer binding protein-delta (C/EBP-[delta]) was examined in the zebrafish, Danio rerio, exposed to acute, non-lethal hypoxic conditions. While C/EBP-[delta] was expressed constitutively in control individuals during all time points, exposure to hypoxic conditions did not have a consistent significant effect on C/EBP-[delta] expression (two-way ANOVA, P>0.05) in zebrafish white muscle tissue. In a second study, the expression of the growth arrest and DNA damage 45-alpha protein (gadd45-[alpha], a mediator of cell cycle arrest and perhaps apoptosis was examined in heat-stressed liver tissue of an extremely cold-adapted Antarctic fish, Trematomus bernacchii. Gadd45-[alpha] levels were higher in fish exposure to 2°C across all time points (one-way ANOVA; P

The proper maintenance of the pathways governing cell growth is critical to ensure cell survival and DNA fidelity. Much of our understanding of how the cell cycle is regulated comes from studies examining the relationship between DNA viruses and the mechanisms of cell proliferation control. There are numerous examples demonstrating that viruses can alter the host cell environment to their advantage. In particular, the small DNA tumor viruses, which include adenovirus, simian-virus 40 (SV-40), and human papillomavirus (HPV), can modulate the host cell cycle to facilitate viral DNA replication. Due to the fact that these viruses infect quiescent, non-cycling cells and lack the necessary enzymes and resources to replicate their DNA (e.g. DNA polymerase), the small DNA tumor viruses must activate the host cell replication machinery in order to expedite viral DNA replication. The capacity of these viruses to perturb normal cell proliferation control is dependent upon their oncogene products, which target p53 and members of the Retinoblastoma (RB) family of proteins and inactivate their respective functions. By targeting these key cell cycle regulatory proteins, the small DNA tumor viruses induce the infected host cells to enter S-phase and activate the components involved with host cell DNA synthesis thereby generating an environment that is conducive to viral DNA replication. In contrast, the larger, nuclear-replicating DNA viruses such as those from the family Herpesviridae, do not share the same stringent requirement as the small DNA viruses to induce the infected host cell to enter S-phase. The herpesviruses encode many of the components to stimulate nucleotide biosynthesis and the necessary factors to facilitate virus DNA replication including a viral DNA polymerase and other accessory factors. Additionally, many herpesviruses encode gene products that arrest the host cell cycle, in most instances, prior to the G1/S transition point. Inducing cells to growth arrest appears to be a prerequisite for the replication of most herpesviruses. However, in addition to encoding factors that inhibit the cell cycle, many herpesviruses encode proteins that can promote cell cycle progression in a manner similar to the small DNA tumor virus oncoproteins. By targeting members of the RB family and p53 protein, the herpesvirus proteins induce S-phase and activate S-phase associated factors that playa role in DNA replication. In this manner, the herpesviruses may promote an environment that is favorable for DNA replication. Consistent with the other herpesviruses, human cytomegalovirus (HCMV)induces human fibroblasts to growth arrest. However, in other cell types, virus infection causes cells to enter S-phase. In addition, HCMV replication requires several cellular factors that are present only during S-phase. Furthermore, HCMV induces the activation of S-phase-associated events as well as the increased expression of numerous S-phase genes following infection. HCMV encodes two immediate early (IE) gene products, IE1-72 and IE2-86, which can interact with members of the RB family of proteins. Additionally, the IE2-86 protein can bind to and inhibit p53 protein function. Given the functional resemblance between the HCMV IE proteins and the oncoproteins of the small DNA tumor viruses, we hypothesized that expression of the HCMV IE proteins could modulate cell cycle control. Specifically, we determined that expression of either IE1-72 or IE2-86 can induce quiescent cells to enter S-phase and delay cell cycle exit following serum withdrawal. Moreover, IE2-86 mediates this effect in the presence or absence of p53, whereas IE1-72 fails to do so in p53-expressing cells. Furthermore, both IE1-72 and IE2-86 induce p53 protein accumulation that is nuclear localized. Because IE1-72 fails to promote S-phase entry in cells expressing p53 and induces p53 protein levels, the mechanism by which IE1-72 alters p53 levels was examined. IE1-72 elevates p53 protein levels by inducing both p19ARF protein and an ATM-dependent phosphorylation of p53 at Ser15. IE1-72 also promotes p53 nuclear accumulation by abrogating p53 nuclear shuttling. As consequence of this IE1-72-mediated increase in p53 levels, p21 protein is induced leading to a p21-dependent growth arrest in cells expressing IE1-72. These findings demonstrate that the HCMV IE proteins can alter cell proliferation control and provide further support to the notion that HCMV, through the expression of its IE proteins, induces S-phase and factors associated with S-phase while blocking cell DNA synthesis, to possibly generate an environment that is suitable for viral DNA replication.

We have previously shown that the insulin-like growth factor 1 receptor (IGF-1R) translocates to the cell nucleus, where it binds to enhancer-like regions and increases gene transcription. Further studies have demonstrated that nuclear IGF-1R (nIGF-1R) physically and functionally interacts with some nuclear proteins, i.e. the lymphoid enhancer-binding factor 1 (Lef1), histone H3, and Brahma-related gene-1 proteins. In this study, we identified the proliferating cell nuclear antigen (PCNA) as a nIGF-1R-binding partner. PCNA is a pivotal component of the replication fork machinery and a main regulator of the DNA damage tolerance (DDT) pathway. We found that IGF-1R interacts with and phosphorylates PCNA in human embryonic stem cells and other cell lines. In vitro MS analysis of PCNA co-incubated with the IGF-1R kinase indicated tyrosine residues 60, 133, and 250 in PCNA as IGF-1R targets, and PCNA phosphorylation was followed by mono- and polyubiquitination. Co-immunoprecipitation experiments suggested that these ubiquitination events may be mediated by DDT-dependent E2/E3 ligases (e.g. RAD18 and SHPRH/HLTF). Absence of IGF-1R or mutation of Tyr-60, Tyr-133, or Tyr-250 in PCNA abrogated its ubiquitination. Unlike in cells expressing IGF-1R, externally induced DNA damage in IGF-1R-negative cells caused G(1) cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF-1R in DDT.

Neuroblastoma is the most common extra-cranial childhood solid tumour which arises from embryonic neural crest cells that fail to undergo a differentiation programme to form mature sympathetic neurones. Most children with advanced stage neuroblastoma have a 5-year event free survival rate of only 20%. However, the spontaneous differentiation of some early stage neuroblastoma into non-malignant gangliomas has prompted the search for agents that can induce neuroblastoma differentiation. Peroxisome proliferator-activated receptor gamma (PPARƴ) is a member of the nuclear receptor superfamily of ligand-dependent transcription factors which play a major role in adipocyte differentiation and exhibits anticancer activity against a range of tumour cells in vitro. High levels of PPARƴ have been shown to be associated with differentiated neuroblastoma and low levels of PPARƴ with poorly differentiated tumours. Therefore, the aim of this project is to investigate whether PPARƴ acts as a tumour suppressor gene in neuroblastoma. Our research shows that overexpression of PPARƴ in the human neuroblastoma cell line SK-N-AS cells inhibited cell growth but had no effect on cell viability or the degree of differentiation, suggesting that PPARƴ may modulate cell cycle progression in SK-N-AS neuroblastoma cells. Additionally, we show that PPARƴ strongly represses the DNMT1 promoter activity. This suggests that PPARƴ may in addition to regulating the cell cycle also modulate epigenetic processes within the cell.

The Runx family of transcription factors performs an essential role in animal development by controlling gene expression programs that mediate cell proliferation, growth and differentiation. The work described in this thesis is concerned with understanding mechanisms by which Runx proteins support this program of gene expression within the architectural context of the mammalian cell nucleus. Multiple aspects of nuclear architecture are influenced by Runx2 proteins including sequence-specific DNA binding at gene regulatory regions, organization of promoter chromatin structure, and higher-order compartmentalization of proteins in nuclear foci. This work provides evidence for several functional activities of Runx2 in relation to architectural parameters of gene. expression for the control of cell growth and differentiation. First, the coordination of SWI/SNF mediated chromatin alterations by Runx2 proteins is found to be a critical component of osteoblast differentiation for skeletal development. Several chromatin modifying enzymes and signaling factors interact with the developmentally essential Runx2 C-terminus. A patent-pending microscopic image analysis strategy invented as part of this thesis work - called intranuclear informatics - has contributed to defining the C-terminal portion of Runx2 as a molecular determinant for the nuclear organization of Runx2 foci and directly links Runx2 function with its organization in the nucleus. Intranuclear informatics also led to the discovery that nuclear organization of Runx2 foci is equivalently restored in progeny cells following mitotic division - a natural perturbation in nuclear structure and function. Additional microscopic studies revealed the sequential and selective reorganization of transcriptional regulators and RNA processing factors during progression of cell division to render progeny cells equivalently competent to support Runx2 mediated gene expression. Molecular studies provide evidence that the Runx proteins have an active role in retaining phenotype by interacting with target gene promoters through sequence-specific DNA binding during cell division to support lineage-specific control of transcriptional programs in progeny cells. Immunolocalization of Runx2 foci on mitotic chromosome spreads revealed several large foci with pairwise symmetry on sister chromatids; these foci co-localize with the RNA polymerase I transcription factor, Upstream Binding Factor (UBFl) at nucleolar organizing regions. A series of experiments were carried out to reveal that Runx2 interacts directly with ribosomal DNA loci in a cell cycle dependent manner; that Runx2 is localized to UBF foci within nucleoli during interphase; that Runx2 attenuates rRNA synthesis; and that this repression of ribosomal gene expression by Runx2 is associated with cell growth inhibition and induction of osteoblast-specific gene expression. This thesis has identified multiple novel mechanisms by which Runx2 proteins function within the hierarchy of nuclear architecture to control cell proliferation, growth and differentiation.

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Tese (Doutorado em Tecnologia Nuclear)
IPEN/T
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP
FAPESP:11/21708-6

Little is known about the signaling pathways that contribute to treatment response in advanced stage head and neck tumors. Increased expression of epidermal growth factor receptor (EGFR) and downstream pathways such as nuclear factor kappa B (NFκB) are implicated in aggressive tumor phenotypes and limited response to therapy. This study explored the rationale for combining the proteasome inhibitor bortezomib with the EGFR inhibitor gefitinib in a subset of head and neck squamous cell carcinomas with high EGFR gene amplification. Drug responses of gefitinib and bortezomib as single agents and in combination within head and neck squamous cell carcinoma cell lines were analyzed using MTS assays. The effects of gefitinib on the activation of EGFR and itsthree major downstream pathways, Akt, STAT3 and MAPK were determined by western blotting. The activation status of NFκB and the effects of bortezomib on the canonical pathway were assessed by DNA binding assays. Resistance to lower doses of gefitinib was associated with elevated EGFR and activated Akt expression. Gefitinib was able to effectively inhibit activation of STAT3, Akt and MAPK in HNSCC to varying degrees depending on EGFR expression status. Bortezomib treatment inhibited TNFα –induced nuclear NFκB/RelA expression but demonstrated variability in levels of baseline nuclear NFκB/RelA expression between sensitive and resistant cell lines. Bortezomib effectively suppresses NFκB/RelA nuclear activation but demonstrates additional modes of cellular toxicity beyond the NFκB pathway in sensitive cell lines. Further understanding of tumor response to the targeted inhibitors gefitinib and bortezomib may provide novel approaches in managing HNSCCs.

Many polypeptide growth factors act by binding to cell surface receptors that have intrinsic tyrosine kinase activity. Binding of these growth factors to their cognate receptors results in the initiation of mitogenic signals which then get transduced to the interior of the cell. A critical target for extracellular signals is the nucleus. A plethora of recent evidence indicates that extracellular signals can affect nuclear gene expression by modulating transcription factor activity. In this study, I have determined that the transactivation domain of c-Myc (protein product of the c-myc proto-oncogene) is a direct target of mitogen-activated signaling pathways involving protein kinases. Further, my study demonstrates that transactivation of gene expression by c-Myc is regulated as a function of the cell cycle. c-Myc is a sequence-specific DNA binding protein that forms leucine zipper complexes and can act as a transcription factor. Although, significant progress has been made in understanding the cellular properties of c-Myc, the precise molecular mechanism of c-Myc function in oncogenesis and in normal cell growth is not known. I have focused my attention on the property of c-Myc to function as a sequence-specific transcription factor. In my studies, I have employed a fusion protein strategy, where the transactivation domain of the transcription factor c-Myc is fused to the DNA binding domain and nuclear localization signal of the yeast transcription factor GAL4. This fusion protein was expressed together with a plasmid consisting of specific GAL4 binding sites cloned upstream of a minimal E1b promoter and a reporter gene. The activity of the c-Myc transactivation domain was measured as reporter gene activity in cell extracts. This experimental approach enabled me to directly monitor the activity of the c-Myc transactivation domain. Results listed in Chapter II demonstrate that the transactivation domain of c-Myc at Ser-62 is a target of regulation by mitogen-stimulated signaling pathways. Furthermore, I have determined that a mitogen activated protein kinase, p41mapk, can phosphorylate the c-Myc transactivation domain at Ser-62. Phosphorylation at this site results in a marked increase in transactivation of gene expression. A point mutation at the MAP kinase phosphorylation site (Ser-62) causes a decrease in transactivation. c-Myc expression is altered in many types of cancer cells, strongly implicating c-myc as a critical gene in cell growth control. The molecular mechanisms by which c-Myc regulates cellular proliferation are not understood. For instance, it is not clear where in the cell cycle c-Myc functions and what regulates its activity. In exponentially growing cells, the expression levels of c-Myc remain unchanged as the cells progress through the cell cycle. The function of c-Myc may therefore be regulated by a mechanism involving a post-translational modification, such as phosphorylation. Results described in chapter IV demonstrate that the level of c-Myc mediated transactivation oscillates as cells progress through the cell cycle and was greatly increased during the S to G2/M transition. Furthermore, mutation of the phosphorylation site Ser-62 in the c-Myc transactivation domain diminishes this effect, suggesting a functional role for this phosphorylation site in the cell cycle-specific regulation of c-Myc activity. Taken together, my dissertation study reveals a molecular mechanism for the regulation of nuclear gene expression in response to mitogenic stimuli.

Hintergrund Die Strahlentherapie ist neben der radikalen Prostatektomie eine Standardtherapie zur Behandlung von Prostatatumoren und führt zu sehr guten Ergebnissen für die lokale Tumorkontrolle und für das Überleben. Allerdings ist, wie bei der Operation auch, dabei das Risiko eines Rezidivs für fortgeschrittene Tumoren im Gegensatz zu Tumoren in früheren Stadien relativ hoch. Daher besteht eine hohe Dringlichkeit zur Verbesserung der Strahlentherapie vor allem bei fortgeschrittenen Tumoren. Ein Ansatz hierfür ist die Kombination der Bestrahlung mit molekularen Therapien. Ziel dabei ist es, bestimmte Zielproteine zu blockieren, um die Strahlensensibilität der Prostatakarzinomzellen zu erhöhen. Ein potentielles Target könnte hierbei die Blockade des VEGF-C/NRP-2/Akt-Signalwegs (VEGF-C – vascular endothelial growth factor C; NRP-2 – Neuropilin 2; Akt – Proteinkinase B) sein. Im Prostatakarzinom sind die Konzentrationen von VEGF-C und NRP-2 im Vergleich zu normalen Prostatazellen erhöht. Aus Untersuchungen ist bekannt, dass beide Proteine eine progressive Wirkung auf die Tumorgenese haben. In Vorarbeiten zeigen Muders et al. (2009) zudem eine Aktivierung von Akt über die VEGF-C/NRP-2-Achse und eine darüber vermittelte Resistenz gegenüber oxidativem Stress durch H2O2. Akt wirkt in verschiedenen Tumorentitäten außerdem protektiv gegenüber Bestrahlung. Es besteht die Annahme, dass dies auch für Prostatakarzinomzellen gilt. Zielstellung Im Rahmen dieser Arbeit wurde untersucht, ob und über welchen Mechanismus VEGF-C, NRP-2 und Akt die Strahlenresistenz in Prostatakarzinomzelllinien beeinflussen. Methoden Es wurden in vitro- und in vivo-Experimente in den humanen Prostatakarzinomzelllinen PC-3, DU145, LNCaP sowie in PC-3-Xenografts durchgeführt. Der Einfluss von VEGF-C und NRP-2 auf die Strahlenresistenz wurde in vitro nach Herunterregulierung der entsprechenden Gene mittels siRNA beziehungsweise nach Supplementierung mit humanem rekombinanten VEGF-C in Koloniebildungsassays untersucht. Zur Ermittlung des Einflusses von VEGF-C und von NRP-2 auf mögliche Zellüberlebensmechanismen wurden der autophagische Flux nach Blockade der Autophagie mit Bafilomycin A1 mittels Western Blot, die DNA-Doppelstrangbruch-Reparatur mittels Quantifizierung der γH2AX Foci sowie die Zellzyklusverteilung mittels Durchflusszytometrie untersucht. Die Signalweiterleitung von VEGF-C über Akt sowie, als weitere Möglichkeit, die Signalweiterleitung über ERK1/2 wurden nach siRNA-Transfektion mit und ohne Bestrahlung mittels Western Blot geprüft. Weitere Versuche zu Akt erfolgten in vitro und in vivo mit dem PI3K/Akt-Inhibitor Nelfinavir in PC-3-Zellen. Der in vitro Effekt von Nelfinavir auf die Strahlenresistenz wurde dabei mithilfe eines Koloniebildungsassays nach Behandlung der Zellen mit 10 µM Nelfinavir getestet. In vivo wurde die Wirkung von Nelfinavir ohne sowie in Kombination mit Bestrahlung in PC-3-Xenografts in Nacktmäusen untersucht. Für die Bestimmung der Tumorwachstumszeit wurden die Mäuse mit 80 mg Nelfinavir/kg Körpergewicht 30 mal innerhalb von 6 Wochen behandelt. In einem weiteren Versuch wurde die lokale Tumorkontrolle bei gleichzeitiger fraktionierter Bestrahlung mit Gesamtdosen von 30 bis 120 Gy und einer Nachbeobachtungszeit von 180 Tagen bestimmt. Ergebnisse Die Untersuchungen zur Strahlenresistenz über den VEGF-C/NRP-2/Akt-Signalweg haben ergeben, dass in den drei Prostatakarzinomzelllinien PC-3, DU145 und LNCaP VEGF-C signifikant Strahlenresistenz vermittelt. Für NRP-2 hingegen wurde festgestellt, dass es in Abhängigkeit von der Zelllinie entweder zur Strahlenresistenz (DU145) oder zur Strahlensensibilisierung (PC-3) führt. Weiterhin wurde nachgewiesen, dass durch VEGF-C in PC-3 und DU145 weder über Akt noch über ERK1/2 Strahlenresistenz vermittelt wird. Die Versuche zu Strahlenresistenz vermittelnden Mechanismen ergaben, dass VEGF-C in unbestrahlten PC-3-Zellen die Autophagie fördert, NRP-2 jedoch nicht. Unter Bestrahlung war ein Effekt von VEGF-C und NRP-2 auf die Autophagie nicht reproduzierbar nachweisbar. Ein weiterer Versuch hat gezeigt, dass in PC-3 Autophagie keinen Einfluss auf das klonogene Überleben nach Bestrahlung hat. Außerdem wurde festgestellt, dass VEGF-C in PC-3 die DNA-Doppelstrangbruch-Reparatur nicht beeinflusst. Darüber hinaus wurde nachgewiesen, dass eine Verminderung des VEGF-C-Gehalts in PC-3 zum G2/M-Arrest führt. In DU145 konnte jedoch kein Effekt beobachtet werden. In den Untersuchungen zum Einfluss von Akt auf die Strahlenresistenz unabhängig von VEGF-C und NRP-2 wirkte Nelfinavir inhibierend auf die Akt-Phosphorylierung am Ser473 und beeinflusste das klonogene Überleben von PC-3-Zellen minimal. In PC-3-Xenografts führte Nelfinavir zu keiner Tumorwachstumsverzögerung und wirkte in vitro und in vivo nicht strahlensensibilisierend. Schlussfolgerung In den Versuchen konnte gezeigt werden, dass VEGF-C in Prostatakarzinomzellen Strahlenresistenz vermittelt. Diese Erkenntnis könnte als ein Forschungsansatz zur Entwicklung einer kombinierten Therapie aus VEGF-C-Blockade und Bestrahlung dienen. Ein potentieller Mechanismus, über den VEGF-C die Strahlenresistenz vermittelt, ist, in Abhängigkeit von der Zelllinie, die Aufhebung des G2/M-Arrests. NRP-2 wirkt in der Vermittlung von Strahlenresistenz beziehungsweise sensibilität je nach Zelllinie unterschiedlich. Hierzu sollten weitere Untersuchungen bezüglich möglicher Interaktionen innerhalb anderer Signalwege mit strahlensensibilisierendem Einfluss erfolgen. Innerhalb des untersuchten Signalwegs konnte weiterhin festgestellt werden, dass VEGF-C Strahlenresistenz nicht über Akt vermittelt. Die vorliegende Arbeit enthält die erste Studie sowohl zur Untersuchung des Einflusses von Nelfinavir in Kombination mit Bestrahlung auf das Überleben von Prostatakarzinomzellen in vitro als auch auf die Tumorwachstumszeit und die lokale Tumorkontrolle in vivo. Hierin konnte keine strahlensensibilisierende Wirkung von Nelfinavir nachgewiesen werden. Da Nelfinavir in Zellen anderer Tumorentitäten strahlensensibilisierend wirkt und außerdem bekannt ist, dass es in eine Reihe von Signalwegen eingreift, die das Zellüberleben fördern oder hemmen, sollte weiter geklärt werden, ob Tumorzellen mit einem bestimmten genetischen Profil besser auf die Behandlung mit Nelfinavir ansprechen
Background In addition to radical prostatectomy, radiotherapy is a standard therapy for the treatment of prostate tumours and leads to good results for local tumour control and survival. However, as with the resection, the risk of recurrence for advanced tumours is relatively high compared to tumours in earlier stages. Therefore, there is a high urgency to improve radiotherapy especially for advanced stages. One approach is the combination of irradiation with molecular therapies. The aim is to block certain target proteins to increase the radiosensitivity of the prostate carcinoma cells. A potential target could be the blockade of the VEGF-C/NRP-2/Akt signalling pathway (VEGF-C – vascular endothelial growth factor C; NRP-2 – neuropilin 2; Akt – protein kinase B). In prostate cancer the concentrations of VEGF-C and NRP-2 are increased compared to normal prostate cells. Studies have shown that both proteins have a progressive effect on tumourigenesis. In preliminary work Muders et al. (2009) also showed the activation of Akt via the VEGF-C/NRP-2 axis and a resistance to H2O2 induced oxidative stress. Akt also has a protective effect against irradiation in various tumour entities. It is assumed that this also applies to prostate carcinoma cells. Aim of the study Within the framework of this thesis, it was investigated whether and via which mechanism VEGF-C, NRP-2, and Akt affect the radioresistance in prostate carcinoma cell lines. Methods In vitro and in vivo experiments were performed in the human prostate carcinoma cell lines PC-3, DU145, LNCaP, as well as in PC-3 xenografts. The influence of VEGF-C and NRP-2 on the radioresistance was examined in vitro after knock down of the corresponding genes using siRNA or after supplementation with human recombinant VEGF-C in colony formation assays. In order to determine the influence of VEGF-C and NRP-2 on possible cell survival mechanisms, the autophagic flux was examined after the blockade of autophagy with bafilomycin A1 using western blot, the DNA double strand break repair by quantification of the γH2AX foci, and the cell cycle distribution by flow cytometry. The signal transduction of VEGF-C via Akt as well as, as a further possibility, the signal transduction via ERK1/2 were tested after siRNA transfection with and without irradiation using western blot. Further experiments on Akt were performed in vitro and in vivo with the PI3K/Akt inhibitor nelfinavir in PC-3 cells. The in vitro effect of nelfinavir on radioresistance was tested using a colony formation assay after treatment of the cells with 10 μM nelfinavir. In vivo, the effect of nelfinavir without and in combination with irradiation in PC-3 xenografts was investigated in nude mice. For the determination of the tumour growth time, the mice were treated with 80 mg nelfinavir/kg body weight 30 times within 6 weeks. In a further experiment, the local tumour control was determined with simultaneous fractionated irradiation with total doses of 30 to 120 Gy and a follow-up time of 180 days. Results The investigations on radioresistance via the VEGF-C/NRP-2/Akt signalling pathway showed that in the three prostate carcinoma cell lines PC-3, DU145, and LNCaP VEGF-C significantly mediates radioresistance. For NRP-2 however, it was found that, depending on the cell line, it either leads to radioresistance (DU145) or radiosensitization (PC-3). Further, it was shown that in PC-3 and DU145 VEGF-C does not mediate radioresistance via Akt or ERK1/2. The experiments on radioresistance mediating mechanisms revealed that VEGF-C promotes autophagy in untreated PC-3 cells, but NRP-2 does not. Under irradiation, an effect of VEGF-C and NRP-2 on autophagy could not be detected reproducibly. A further experiment has shown that in PC-3 autophagy has no influence on the clonogenic survival after irradiation. In addition, it was found that VEGF-C does not affect the DNA double strand break repair in PC-3. Furthermore, it was shown that a reduction in the VEGF-C content leads to a G2/M arrest in PC-3. However, no effect could be observed in DU145. In studies regarding the influence of Akt on radioresistance independent of VEGF-C and NRP-2, nelfinavir inhibited Akt phosphorylation at Ser473 and minimally affected the clonogenic survival of PC-3 cells. In PC-3 xenografts, nelfinavir did not lead to any tumour growth delay and did not have a radiosensitizing effect in vitro or in vivo. Conclusion In the experiments, it was shown that VEGF-C mediates radioresistance in prostate cancer cells. This finding could serve as a research approach for the development of a combined therapy of a VEGF-C blockade and irradiation. A potential mechanism by which VEGF-C mediates radioresistance is the reverse of the G2/M arrest, depending on the cell line. NRP-2 acts differently in the mediation of radioresistance or radiosensitivity, depending on the cell line. On this, further investigations should be carried out with regard to possible interactions within other signalling pathways with a radiosensitizing influence. Within the investigated signalling pathway, it was further shown that VEGF-C does not mediate radioresistance via Akt. The present work contains the first study examining the effect of nelfinavir in combination with irradiation on prostate cancer cell survival in vitro as well as on growth time and local tumour control in vivo. Herein no radiosensitizing effects of nelfinavir could be detected. Since nelfinavir radiosensitizes cells of other tumour entities and is also known to interfere with a series of signalling pathways that promote or inhibit cell survival, it should be clarified whether tumour cells with a particular genetic profile are more responsive to treatment with nelfinavir

The nuclear pore complex (NPC) is perhaps the largest protein complex in the eukaryotic cell, and controls the movement of molecules across the nuclear envelope. The NPC is composed of up to 30 proteins termed nucleoporins (Nups), each grouped in different sub-complexes. The transmembrane ring sub-complex is composed of Nups responsible for anchoring the NPC to the nuclear envelope. Bioinformatic analysis has traced all major sub-complexes of the NPC back to the last eukaryotic common ancestor, meaning that the nuclear pore structure and function is conserved amongst all eukaryotes. In this study Arabidopsis T-DNA knockout lines for these genes were investigated to characterise gene function. Differences in plant growth and development were observed for the ndc1 knockout line compared to wild-type but gp210 plants showed no phenotypic differences. The double knockout line gp210 ndc1 was generated through crosses to observe plant response to the knockout of two anchoring-Nup genes. No synergistic affect from this double knockout was observed, suggesting that more, as yet unidentified Nups function the transmembrane ring in plants. The sensitivity to nuclear export inhibitor leptomycin B (LMB) was tested also for knockout lines, although growth sensitivity to the drug was not observed. Nucleocytoplasmic transport of knockout lines was measured in cells transformed by particle bombardment. To express fluorescent protein constructs actively transported through the NPC, localisation of protein determined the nucleocytoplasmic transport of the cell. The ndc1single knockout and the double knockout gp210 ndc1 exhibited decreased nuclear export. Further experiments in determining NDC1 localisation and identification of other Nups in the transmembrane ring sub-complex would bring a more comprehensive understanding to the plant NPC.

The eubacterial genome is maintained in a negatively supercoiled state which facilitates its compaction and storage in a small cellular space. Genome supercoiling can potentially influence various DNA transaction processes such as DNA replication, transcription, recombination, chromosome segregation and gene expression. Alterations in the genome supercoiling have global impact on the gene expression and cell growth. Inside the cell, the genome supercoiling is maintained judiciously by DNA topoisomerases to optimize DNA transaction processes. These enzymes solve the problems associated with the DNA topology by cutting and rejoining the DNA. Due to their essential cellular functions and global regulatory roles, DNA topoisomerases are fascinating candidates for the study of the effect of topology perturbation on a global scale. Genus Mycobacterium includes a large number of species including the well-studied Mycobacterium smegmatis (Msm) as well as various pathogens–Mycobacterium leprae, Mycobacterium abscessus and Mycobacterium tuberculosis (Mtb), the last one being the causative agent of the deadly disease Tuberculosis (TB), which claims millions of lives worldwide annually. The organism combats various stresses and alterations in its environment during the pathogenesis and virulence. During such adaptation, various metabolic pathways and transcriptional networks are reconfigured. Considering their global regulatory role, DNA topoisomerases and genome supercoiling may have an influence on the mycobacterial survival and adaptation. Biochemical studies from our laboratory have revealed several distinctive characteristics of mycobacterial DNA gyrase and topoisomerase I. DNA gyrase has been shown to be a strong decatenase apart from its characteristic supercoiling activity. Similarly, the mycobacterial topoisomerase I exhibits several distinct features such as the ability to bind both single- as well as double-stranded DNA, site specific DNA binding and absence of Zn2+ fingers required for DNA relaxation activity in other Type I enzymes. Although, efforts have been made to understand the biochemistry and mechanism of mycobacterial topoisomerases, in vivo significance and regulatory roles remain to be explored. The present study is aimed at understanding the mechanism, in vivo functions, regulation and genome wide distribution of mycobacterial topoisomerases. Chapter 1 of the thesis provides introduction on DNA topology, genome supercoiling and DNA topoisomerases. The importance of genome supercoiling and its regulatory roles has been discussed. Further, the regulation of topoisomerase activity and the role in the virulence gene regulation is described. Finally, a brief overview of Mtb genome, disease epidemiology, and pathogenesis is presented along with the description of the work on mycobacterial topoisomerases. In Chapter 2, the studies are directed to understand the DNA relaxation mechanism of mycobacterial Type IA topoisomerase which lack Zn2+ fingers. The N-terminal domain (NTD) of the Type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli TopoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial TopoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. It is elucidated that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the strand passage step of the catalysis. It is hypothesized that the loss of Zn2+ fingers from the mycobacterial TopoI could be associated with Zn2+ export and homeostasis. In Chapter 3, the studies have been carried out to understand the regulation of mycobacterial TopoI. Identification of Transcription Start Site (TSS) suggested the presence of multiple promoters which were found to be sensitive to genome supercoiling. The promoter activity was found to be specific to mycobacteria as the promoter(s) did not show activity in E. coli. Analysis of the putative promoter elements suggested the non-optimal spacing of the putative -35 and -10 promoter elements indicating the involvement of supercoiling for the optimal alignment during the transcription. Moreover, upon genome relaxation, the occupancy of RNA polymerase was decreased on the promoter region of topoI gene implicating the role of DNA topology in the Supercoiling Sensitive Transcription (SST) of TopoI gene from mycobacteria. The involvement of intrinsic promoter elements in such regulation has been proposed. In Chapter 4, the importance of TopoI for the Mtb growth and survival has been validated. Mtb contains only one Type IA topoisomerase (Rv3646c), a sole DNA relaxase in the cell, and hence a candidate drug target. To validate the essentiality of Mtb topoisomerase I for bacterial growth and survival, conditionally regulated strain of topoI in Mtb was generated. The conditional knockdown mutant exhibited delayed growth on agar plate and in liquid culture the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the Mtb growth and open up new avenues for targeting the enzyme. In Chapter 5, the influence of perturbation of TopoI activity on the Msm growth and physiology has been studied. Notably, Msm contains an additional DNA relaxation enzyme– an atypical Type II topoisomerase TopoNM. The TopoI depleted strain exhibited slow growth and drastic change in phenotypic characters. Moreover, the genome architecture was disturbed upon depletion of TopoI. Further, the proteomic and transcript analysis indicated the altered expression of the genes involved in central metabolic pathways and core DNA transaction processes in the mutant. The study suggests the importance of TopoI in the maintenance of cellular phenotype and growth characteristics of fast growing mycobacteria having additional topoisomerases. In Chapter 6, the ChIP-Seq method is used to decipher the genome wide distribution of the DNA gyrase, topoisomerase I (TopoI) and RNA polymerase (RNAP). Analysis of the ChIP-Seq data revealed the genome wide distribution of topoisomerases along with RNAP. Importantly, the signals of topoisomerases and RNAP was found to be co-localized on the genome suggesting their functional association in the twin supercoiled domain model, originally proposed by J. C. Wang. Closer inspection of the occupancy profile of topoisomerases and RNAP on transcription units (TUs) revealed their co-existence validating the topoisomerases occupancy within the twin supercoiled domains. On the genomic scale, the distribution of topoisomerases was found to be more at the ori domains compared to the ter domain which appeared to be an attribute of higher torsional stress at ori. The reappearance of gyrase binding at the ter domain (and the lack of it in the ter domain of E. coli) suggests a role for Mtb gyrase in the decatenation of the daughter chromosomes at the end of replication. The eubacterial genome is maintained in a negatively supercoiled state which facilitates its compaction and storage in a small cellular space. Genome supercoiling can potentially influence various DNA transaction processes such as DNA replication, transcription, recombination, chromosome segregation and gene expression. Alterations in the genome supercoiling have global impact on the gene expression and cell growth. Inside the cell, the genome supercoiling is maintained judiciously by DNA topoisomerases to optimize DNA transaction processes. These enzymes solve the problems associated with the DNA topology by cutting and rejoining the DNA. Due to their essential cellular functions and global regulatory roles, DNA topoisomerases are fascinating candidates for the study of the effect of topology perturbation on a global scale. Genus Mycobacterium includes a large number of species including the well-studied Mycobacterium smegmatis (Msm) as well as various pathogens–Mycobacterium leprae, Mycobacterium abscessus and Mycobacterium tuberculosis (Mtb), the last one being the causative agent of the deadly disease Tuberculosis (TB), which claims millions of lives worldwide annually. The organism combats various stresses and alterations in its environment during the pathogenesis and virulence. During such adaptation, various metabolic pathways and transcriptional networks are reconfigured. Considering their global regulatory role, DNA topoisomerases and genome supercoiling may have an influence on the mycobacterial survival and adaptation. Biochemical studies from our laboratory have revealed several distinctive characteristics of mycobacterial DNA gyrase and topoisomerase I. DNA gyrase has been shown to be a strong decatenase apart from its characteristic supercoiling activity. Similarly, the mycobacterial topoisomerase I exhibits several distinct features such as the ability to bind both single- as well as double-stranded DNA, site specific DNA binding and absence of Zn2+ fingers required for DNA relaxation activity in other Type I enzymes. Although, efforts have been made to understand the biochemistry and mechanism of mycobacterial topoisomerases, in vivo significance and regulatory roles remain to be explored. The present study is aimed at understanding the mechanism, in vivo functions, regulation and genome wide distribution of mycobacterial topoisomerases. Chapter 1 of the thesis provides introduction on DNA topology, genome supercoiling and DNA topoisomerases. The importance of genome supercoiling and its regulatory roles has been discussed. Further, the regulation of topoisomerase activity and the role in the virulence gene regulation is described. Finally, a brief overview of Mtb genome, disease epidemiology, and pathogenesis is presented along with the description of the work on mycobacterial topoisomerases. In Chapter 2, the studies are directed to understand the DNA relaxation mechanism of mycobacterial Type IA topoisomerase which lack Zn2+ fingers. The N-terminal domain (NTD) of the Type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli TopoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial TopoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. It is elucidated that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the strand passage step of the catalysis. It is hypothesized that the loss of Zn2+ fingers from the mycobacterial TopoI could be associated with Zn2+ export and homeostasis. In Chapter 3, the studies have been carried out to understand the regulation of mycobacterial TopoI. Identification of Transcription Start Site (TSS) suggested the presence of multiple promoters which were found to be sensitive to genome supercoiling. The promoter activity was found to be specific to mycobacteria as the promoter(s) did not show activity in E. coli. Analysis of the putative promoter elements suggested the non-optimal spacing of the putative -35 and -10 promoter elements indicating the involvement of supercoiling for the optimal alignment during the transcription. Moreover, upon genome relaxation, the occupancy of RNA polymerase was decreased on the promoter region of topoI gene implicating the role of DNA topology in the Supercoiling Sensitive Transcription (SST) of TopoI gene from mycobacteria. The involvement of intrinsic promoter elements in such regulation has been proposed. In Chapter 4, the importance of TopoI for the Mtb growth and survival has been validated. Mtb contains only one Type IA topoisomerase (Rv3646c), a sole DNA relaxase in the cell, and hence a candidate drug target. To validate the essentiality of Mtb topoisomerase I for bacterial growth and survival, conditionally regulated strain of topoI in Mtb was generated. The conditional knockdown mutant exhibited delayed growth on agar plate and in liquid culture the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the Mtb growth and open up new avenues for targeting the enzyme. In Chapter 5, the influence of perturbation of TopoI activity on the Msm growth and physiology has been studied. Notably, Msm contains an additional DNA relaxation enzyme– an atypical Type II topoisomerase TopoNM. The TopoI depleted strain exhibited slow growth and drastic change in phenotypic characters. Moreover, the genome architecture was disturbed upon depletion of TopoI. Further, the proteomic and transcript analysis indicated the altered expression of the genes involved in central metabolic pathways and core DNA transaction processes in the mutant. The study suggests the importance of TopoI in the maintenance of cellular phenotype and growth characteristics of fast growing mycobacteria having additional topoisomerases. In Chapter 6, the ChIP-Seq method is used to decipher the genome wide distribution of the DNA gyrase, topoisomerase I (TopoI) and RNA polymerase (RNAP). Analysis of the ChIP-Seq data revealed the genome wide distribution of topoisomerases along with RNAP. Importantly, the signals of topoisomerases and RNAP was found to be co-localized on the genome suggesting their functional association in the twin supercoiled domain model, originally proposed by J. C. Wang. Closer inspection of the occupancy profile of topoisomerases and RNAP on transcription units (TUs) revealed their co-existence validating the topoisomerases occupancy within the twin supercoiled domains. On the genomic scale, the distribution of topoisomerases was found to be more at the ori domains compared to the ter domain which appeared to be an attribute of higher torsional stress at ori. The reappearance of gyrase binding at the ter domain (and the lack of it in the ter domain of E. coli) suggests a role for Mtb gyrase in the decatenation of the daughter chromosomes at the end of replication.

碩士
國立交通大學
生物科技研究所
86
LacZ operon is regulated by DNA supercoiling which expression increases on the negative supercoiling template. In previously study, we found that lacZ expression was growth rate-dependent in Escherichia coli . The intracellular ATP/ATP ratio has been proved directly related to DNA supercoiling because gyrase activity is ATP dependent. Therefore, the growth rate control of lacZ expression might be dependent on the intracellular ATP/ADP ratio and DNA superhelicity changes. In this study, we determined the pla We also examined the total cAMP concentration during exponential growth of Escherichia coli on different carbon medium and at different growth rate in chemostat cultures. The cAMP concentration decreased with increasing cell growth rate. Further introduction of cya mutant into lacZ fusion strain, we found that growth rate-dependent regulation of lacZ expression pattern was changed. Therefore, we proposed that growth rate control of lacZ expression is cAMP dependent .

碩士
國立交通大學
生物科技研究所
84
We determined the plasmid pBR322 superhelicity at different cell growth rate in Escherichia coli and found that DNA supercoiling was growth rate depedent. The DNA supercoiling of plasmid pBR322 was more negitive when the cell growth rate increassed. Since the expression of lac promoter increased with increasing superhelical density and gyrA promoter was a reciprocalresponse to changes in superhelical density; therefore, we also examined theexpression of lac and gyrA promoters during expontial growth of Escherichia coli on different medium and at different growth rate in chemostat cultures.The expression of lac promoter decreased monotonically with increasing cell growth rate, gyrA promoter expression showed a reciprocal response. When theDNA supercoiling was perturbed by topA10 mutant or gyrA inhibitor novobiocin,the effect of cell growth rate on lacZ operon expression pattern was changed.In the topA10 mutant, the lacZ operon expression did not regulate by cell growth rate when the specific growth rate was lower than 0.72 1/hr. If mediumcontained 25 ug/ml novobiocin and the specific growth rate is higher than 0.61/hr, the lac promoter expression became growth rate independent. Thus, changesin cell growth rate affected the DNA supercoiling of Escherichia coli as well as the growth rate depent genes, lacZ and gyrA, expression.

A steady state level of negative supercoiling is essential for chromosome condensation, initiation of replication and subsequent elongation step. DNA gyrase, found in every eubacteria, serves the essential housekeeping function of maintenance of the negative supercoiling status of the genome. The functional holoenzyme is a heterotetramer, comprising of two GyrA and two GyrB subunits. DNA gyrase is an indispensable enzyme and serves as a readily susceptible target for natural antibacterial agents. The enzymatic steps of topoisomerisation by gyrase involve transient double strand break and rejoining of the strands after intact duplex transfer. Corruption of its catalytic cycle can lead to the generation of cytotoxic double-strand DNA breaks. Most of the anti-gyrase agents achieve their objective by targeting the vulnerable step of the reaction cycle i.e. DNA cleavage step. Bacteria on their part must have evolved and adopted strategies to counter the action of external agents and prevent the generation of double strand breaks thereby safeguarding their genome. In the present thesis, attempts have been made to understand the role of three endogenous gyrase interacting proteins in gyrase modulation and cellular defense against anti-gyrase agents. The thesis is divided into six chapters. Chapter 1 introduces the wonder enzymes “DNA topoisomerases” starting with a brief classification of these enzymes and their physiological functions. In the next section, DNA gyrase has been discussed in greater detail. The structural aspects as well as the mechanism of the topoisomerisation reaction catalyzed by gyrase have been discussed. Final section gives an overview of different gyrase modulators known till date focusing on their source, structure and mode of action. The scope and objectives of the present study is presented at the end of this chapter. In Chapter 2 is aimed at understanding the physiological role of GyrI. GyrI, originally identified in Escherichia coli as an inhibitor of DNA gyrase, has been previously shown in the laboratory to render protection against gyrase poisons and also various other DNA damaging agents (mitomycin C, MNNG). Abolishing GyrI expression renders the cell hypersensitive to these cytotoxic agents. Interestingly, GyrI exhibits contrasting behavior towards two plasmid encoded proteinaceous poisons of DNA gyrase. It reduces microcin B17-mediated double-strand breaks in vivo, imparting protection to the cells against the toxin. However, a positive cooperation between GyrI and F plasmid encoded toxin CcdB, results in enhanced DNA damage and cell death. These results suggest a more complex functional interplay and physiological role for GyrI. Search for other chromosomally encoded gyrase inhibitors led to YacG, a small zinc finger protein (7.3kDa) from E. coli, shown to be a member of DNA gyrase interactome, in a protein-protein interaction network described recently. Chapter 3 deals with the detailed characterization of YacG. It is shown that YacG inhibits DNA gyrase by binding to GyrB subunit and preventing DNA binding activity of the enzyme. More importantly, it protects against the cytotoxic effects of other gyrase inhibitors like ciprofloxacin, novobiocin, microcin B17 and CcdB. Further investigations revealed that YacG and its homologues are found only in proteobacteria. Hence, it appears to be a defense strategy developed by gram-negative bacteria to fight against the gyrase targeting cytotoxic agents. Inhibition by YacG appears to be specific to E. coli gyrase as mycobacterial enzyme is refractile to YacG action. GyrB, only in gram-negative organisms, possesses extra stretch of 165 amino acids, indispensable for DNA binding. Biochemical experiments with the truncated GyrB lacking the extra stretch reveal the importance of this stretch for stable YacG-GyrB interaction. E. coli topoisomerase IV is also resistant to YacG mediated inhibition, probably due to the absence of the extra stretch in ParE subunit, which is otherwise highly similar to GyrB. Further, YacG homologues from other proteobacterial members (Sinorhizobium meliloti and Haemophilus influenzae homologues sharing 35% and 63 % identity with E. coli YacG respectively ) also inhibits E. coli DNA gyrase at comparable levels. YacG thus emerges as a proteobacteria specific inhibitor of DNA gyrase. The occurrence of both YacG and the gyrase extra stretch only in proteobacteria, suggest co-evolution of interacting partners in proteobacteria. In Chapter 4, the study of endogenous gyrase modulators is extended to Mycobacterium sp. glutamate racemase (MurI) from E. coli has been shown earlier to be an inhibitor of DNA gyrase. However, nothing much was known about its mode of action. MurI is an important enzyme in the cell wall biosynthesis pathway, which catalyses the conversion of L-glutamate to D-glutamate, an integral component of the bacterial cell wall. In this chapter, it is demonstrated that M. tuberculosis MurI inhibits DNA gyrase activity, in addition to its precursor independent racemization function. The inhibition is not species specific as E. coli gyrase is also inhibited. However, it is gyrase specific as topoisomerase I activity remains unaltered. The mechanism of inhibition by MurI has been elucidated for the first time and it is shown that MurI binds to GyrA subunit of the enzyme leading to a decrease in DNA binding of the holoenzyme. The sequestration of the gyrase by MurI results in inhibition of all reactions catalyzed by DNA gyrase. Chapter 5 is the extension of the studies on glutamate racemase into another species, i.e. Mycobacterium smegmatis. DNA gyrase inhibition seems to be an additional attribute of some of the glutamate racemases, but not all, as Glr isozyme from B. subtilis has no effect on gyrase activity in spite of sharing a high degree of similarity with the gyrase inhibitory glutamate racemases. It is shown that like the M. tuberculosis MurI, M. smegmatis enzyme is also a bifunctional enzyme. It inhibits DNA gyrase in addition to its racemization activity. Further, overexpression of the enzyme in M. smegmatis provides protection to the organism against fluoroquinolones. DNA gyrase inhibitory property thus appears to be a typical characteristic of these MurI and seems to have evolved to either modulate the function of the essential housekeeping enzyme or to provide protection to gyrase against gyrase inhibitors, which cause double strand breaks in the genome. In the above chapters, it is shown that besides its crucial role in cell wall biosynthesis, mycobacterial MurI moon lights as DNA gyrase inhibitor. That the two activities exhibited by M. tuberculosis MurI are unlinked and independent of each other is demonstrated in Chapter 6. Racemization function of MurI is not essential for its gyrase inhibitory property as mutants compromised in racemization activity retain gyrase inhibition property. MurI- DNA gyrase interaction influences gyrase activity but has no effect on racemization activity of MurI. MurI expression in mycobacterial cells provides protection against the action of ciprofloxacin, thereby suggesting a role of MurI in countering external agents targeting DNA gyrase. Further M. tuberculosis MurI overexpressed in near homologous expression system of M. smegmatis yields highly soluble enzyme which can be further used for structural and functional studies. In conclusion, the studies reveal that the endogenous inhibitors essentially influence the enzyme activity by sequestering the enzyme away from DNA. None of them cause cytotoxicity, which usually arises as a result of DNA damage caused by accumulation of gyrase-DNA covalent intermediate. On the contrary they provide protection against such gyrase poisons. Comparative analysis of these proteinaceous inhibitors, however, does not reveal a common motif or structural fold, required for their ability to inhibit DNA gyrase. Based on these studies, it can be proposed that these endogenous proteins exist to serve as cellular defense strategies against external abuse and also to modulate the intracellular activity of DNA gyrase as and when required, for accurate division, functioning and survival of the cells.

Packaging of genomic DNA by proteins and super coiling into chromatin and chromatin-like structures (in bacteria) influences nearly all nuclear process such as replication, transcription, repair, and recombination. A ubiquitous class of enzymes termed “DNA topoisomerases” pay key roles during these process. The reactions catalyzed by the members of the DNA topoisomerases family share a common chemistry, which involves phosphodiester bond breakage and re-joining, to bring about a change in the linking number of DNA. Nevertheless, the underlying mechanisms used by these enzymes differ significantly from another. Consequently, DNA topoisomerases are divided into type I and type II enzymes. The mechanism(s) by which DNA topoisomerases perform their functions, and act as targets for anti-bacterial and anti-neoplastic drugs, has attracted considerable interest. Based on these and other finding, I have chosen DNA gyrase from mycobacteria as the subject of my Ph.D. theses investigation. The prokaryotic enzyme, DNA gyrase, is unique amongst all topoisomerases being the only enzyme capable of introducing negative super coils in to duplex DNA. Since no equivalent enzymatic activity has been reported in humans, this essential enzyme has been exploited as a during target against many microbial infections including tuberculosis.DNA gyrase is a tetrameric protein, comprised of two pairs of subunits, encoded by gyrA and gyrB. Inhibitors of DNA gyrase know till date target either of the two subunits and are categorized broadly in to two class, viz. coumarins and quinolones. With the emergence of multiple-drug resistant strains of pathogenic bacteria such as Mycobacterium tuberculosis, which is a leading cause of death world-wide, there is a need to develops new lead molecules with novel mechanisms of inhibition. Towards this end, a new approach to inhibit the mycobacterial DNA gyrase using single-chain antibody has been explore in the present study. In addition to this, the differences in the catalytic properties of the subunits and assembly of the Mycobacterium smegmatis enzyme vis-à-vis Escherichia coli DNA gyrase have been examined. Further, the in vivo relationship of DNA gyrase with the transcription machinery of the cell has also been investigated, with an emphasis on the biology of mycobacteria.

Yes
Topoisomerase inhibitors are in common use as chemotherapeutic agents although they can display reduced efficacy in chemotherapy-resistant tumours, which have inactivated DNA damage response (DDR) genes, such as ATM and TP53. Here, we characterise the cellular response to the dual-acting agent, Alchemix (ALX), which is a modified anthraquinone that functions as a topoisomerase inhibitor as well as an alkylating agent. We show that ALX induces a robust DDR at nano-molar concentrations and this is mediated primarily through ATR- and DNA-PK- but not ATM-dependent pathways, despite DNA double strand breaks being generated after prolonged exposure to the drug. Interestingly, exposure of epithelial tumour cell lines to ALX in vitro resulted in potent activation of the G2/M checkpoint, which after a prolonged arrest, was bypassed allowing cells to progress into mitosis where they ultimately died by mitotic catastrophe. We also observed effective killing of lymphoid tumour cell lines in vitro following exposure to ALX, although, in contrast, this tended to occur via activation of a p53-independent apoptotic pathway. Lastly, we validate the effectiveness of ALX as a chemotherapeutic agent in vivo by demonstrating its ability to cause a significant reduction in tumour cell growth, irrespective of TP53 status, using a mouse leukaemia xenograft model. Taken together, these data demonstrate that ALX, through its dual action as an alkylating agent and topoisomerase inhibitor, represents a novel anti-cancer agent that could be potentially used clinically to treat refractory or relapsed tumours, particularly those harbouring mutations in DDR genes.

Indiana University-Purdue University Indianapolis (IUPUI)
The Cre/loxP system is a tool for targeted recombination of DNA. For applying Cre recombinase-mediated genome modifications, there is a requirement for reliable, high-fidelity, and specific transgenic expression of the Cre recombinase. This study focuses on the reliability of different bone cell specific Cre models in the Cre/loxP system. In this study, DMP1-Cre transgenic mouse which has a transgene driven by DMP1 promotor that allows Cre-expression only in late stage osteoblasts and osteocytes was used. Ctsk-Cre mouse with a driven by Ctsk promoter was used so that only osteoclasts would undergo Cre-mediated recombination. E2A-Cre mouse where the Cre recombinase is driven by a global promoter E2A was also included in this study as a control line to test the Cre reporter line Ai9. Dmp1-Cre, Ctsk-Cre and E2A-Cre mice were crossed to the fluorescent Cre-reporter line—Ai9, which harbors a floxed stop codon, followed by the fluorophoremTomato, inserted into the Rosa26 locus. This construct is expected to give red fluorescence when it recombines with Cre-expressing mouse cells and no fluorescence in non-recombinant mouse cells. Double positive (Ai9+/Cre+) offspring selected by PCR were perfused, and 5mu-m thick section of bone and soft tissues were examined for red fluorescent expression. Cre positive cells were quantitated using ‘ImageJ’ software program. The DMP1-vi Cre mouse results showed significant expression in the targeted osteocytes and osteoblasts. In addition, skeletal muscle tissue also showed significant Cre- expression. Ctsk-Cre mice showed significant expression in targeted osteoclasts. But brain tissue was positive in Cre-expression. Bone-Cre mouse models are expected to express Cre recombinase only in their respective bone cells and they have been used for gene deletion studies in bone cells. However, this study has revealed that the bone cell specific Cre mouse models DMP1-Cre and Ctsk-Cre have unexpected expression in muscle and brain respectively. In order to use these models for targeted gene deletion in bone cells, further testing and studies have to be conducted.

The budding yeast Saccharomyces cerevisiae exhibits exquisite control of cellular size in response to the nutritional composition of its environment. Size control is mediated at the G1/S phase transition, termed Start: passage through Start represents an irreversible commitment to cell division and is contingent on achieving a critical size. When nutrients are plentiful, yeast increase their critical size set-point resulting in larger cells; in contrast, in poor nutrients, yeast pass Start at a smaller size. The genetic basis for nutrient-dependent size control and the means by which yeast sense their size remain elusive. One measure of growth potential is ribosome biogenesis, the rate of which correlates with cell size. I characterized a G-patch domain containing protein, Pfa1, which has been shown to activate the helicase activity of the pre-rRNA processing factor Prp43. Intriguingly, Pfa1 is multiply phosphorylated in response to inhibition of the TOR kinase, the central player in growth regulation. This phosphorylation occurs in a region required for Pfa1 function in ribosome biogenesis, independent of its role as a helicase activator. Consistently, phosphorylation correlates with loss of physical interactions with ribosome biogenesis and altered interactions with the ribosome. Mutation of these phosphorylation sites eliminates TOR-dependent phospho-regulation, and confers sensitivity to TOR inhibition. I propose a model wherein Pfa1 is phosphorylated in response to nutrient stress, leading to relocalization of essential processing factors, and inhibition of both ribosome biogenesis and tRNA maturation. Further, I constructed and verified a non-covalent short oligonucleotide barcode microarray platform, and applied it to genome-scale parallel analyses of both the DNA damage response and cell size control in S. cerevisiae. Through these studies, I uncovered novel connections between size control and numerous cellular processes including: the large subunit of the ribosome; the mitochondrial pH gradient; and proteins involved in oxidant-induced cell cycle arrest.

碩士
國立交通大學
生物科技系所
92
To understand the expression of ATP generation and cell division genes in different carbon sources, we individually used acetate, glucose, glycerol or succinate as a sole carbon for energy source. The results of this study showed that the expression of ATP generating genes in metabolic pathway varied with carbon sources and ATP concentration increased with cell growth rate. Comparision with the wild-type strain and relA spoT double mutant, the growth rate and ATP yields were changed, but ATP/ADP ratio remained at the same level. DNA supercoiling was dependent on ATP/ADP ratio. Whereas ppGpp did not change DNA supercoiling. Under various growth conditions, fast-growing E. coli cells were larger than slowly growing ones. Starvation of the cells resulted in filamentous morphology. In addition, the results clearly showed that relA spoT double mutant had more filamentous than wild-type cells regardless acetate or glucose as carbon substrates. It was also notable that the filamentous features provided the phenotypic clues for ppGpp function. However, the morphology raised the possibility of indirect, rather than direct, effects of ppGpp. It indicated that a link between the levels of ppGpp and cell division, which ppGpp could act as a positive regulator of the expression of ftsZ gene. Deficiency of ppGpp (relA spoT double mutant) drastically reduced the expression of minC and minD. These results also suggested that ppGpp was important factor involved in the regulation of cell cycle of E. coli under starvation condition.

博士
國立臺灣大學
微生物研究所
87
Epstein-Barr virus (EBV) encodes an alkaline deoxyribonuclease (DNase), which possesses both endonuclease and exonuclease activities and utilizes both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) as substrates. Previously, studies of EBV DNase have been focused on the detection of anti-DNase antibodies in the patients with EBV associated diseases, the biochemical properties and the relationship between function and structure of the enzyme. In this dissertation, one monoclonal antibody (mAb) to EBV DNase was generated and the relationship of function and structure of EBV DNase including DNA binding domains and nuclear localization signals (NLSs) was further investigated and the effect of EBV DNase on the cell growth was examined. A mAb to EBV DNase, designated 311H, was obtained and the mAb can recognize the EBV DNase protein specifically. The antigenic epitope of 311H was located to a.a. 1-152 of EBV DNase. This mAb is useful for following studies of EBV DNase. To map regions of EBV DNase responsible for DNA binding activity, a series of mutant DNase polypeptides was expressed using an in vitro transcription/translation system and their DNA binding activities to DNA cellulose were determined. The results indicated that the C-terminus of EBV DNase, residues 450-460, is essential for nuclease activity but dispensable for DNA binding. However, deletion of residues 441-470 resulted in the loss of both nuclease and DNA binding activities. In the N-terminus, deletion of residues 23-28 and residues 7-61 re sulted in the loss of nuclease activity but the DNA binding activities of the trucated enzymes were intermediate and low, respectively. Mutation of Leu23 to Gly showed drastically reduced nuclease activity but its DNA binding ability was not affected. DNA binding and nuclease activities of all six internal deletion mutants were abolished, except that mutant ID2, with deletion of residues 138-152, retained an intermediate ability to bind DNA. These data indicate that since mutations at distinct regions within EBV DNase resulted in the loss of nuclease and/or DNA binding activities, it is suggested that these distinct regions are required for maintenance of intact and highly ordered structure(s) for both activities. It has been reported that EBV DNase may be detected in the nucleus and/or cytoplasm of infected cells. In this study, using cell-fractionation and immunoblotting to determine the distribution of EBV DNase in Akata cells stimulated with anti-human immunoglobulin G antibody (anti-IgG), the DNase was found to be located predominantly in the nucleus. To map the signals in DNase which mediate its nuclear localization, we monitored the nuclear transport of fusion proteins consisting of various fragments of EBV DNase linked to a cytoplasmic protein, beta-galactosidase (-Gal). The results demonstr ated that two regions of the DNase with NLS activity, designated NLS-A (amino acids 239-266) and NLS-B (amino acids 291-306), were able independently to localize the -Gal to the nuclei of HEp-2 cells. Five basic residues (R or K) were found in each NLS and distributed differently in primary structure. The basic domains and flanking residues of NLS-A and NLS-B are 250YKRPCKRSFIRFI262 and 294LKDVRKRKLGPGH306, respectively. Further examination of these sequences revealed that NLS-A contains bulky aromatic amino acids (Y and F) which may diminish its capacity to act as a strong NLS. In NLS-B, the histidine residue at amino acid 306 is required for NLS-B activity. In addition, two hydrophobic regions within the DNase were found to inhibit the function of NLS-A but not NLS-B, suggesting that these two domains are different types of NLSs and differ in their sensitivity to hydrophobic regions in the context of protein structure. EBV DNase was expresed under inducible control of lactose operon to investigate its effects on cells. Induction of DNase expression with IPTG in Raj i cells caused DNA strand breaks, which were examined by using a comet assay. In addition, the expression of DNase resulted in decreased growth of Raji cells with cell cycle arrest at G1 and accumulation of cyclin E and p27Kip1. The results imply that EBV-DNase-induced DNA strand breaks may be associated with the chromosomal instability of cells.

Indiana University-Purdue University Indianapolis (IUPUI)
The epigenetic state of any cell is, in part, regulated by the interaction of DNA with nuclear histones. Histone tails can be modified in a number of ways that impact on the availability of DNA to interact with transcriptional complexes, including methylation, acetylation, phosphorylation, ubiquituination, and sumoylation. Histones are acetylated by a large family of enzymes, histone acetyl transferases (HATs), and deacetylated by the histone deacetylases (HDACs). Acetylated histones are generally considered markers of genomic regions that are actively being transcribed, whereas deacetylated and methylated histones are generally markers of regions that are inactive. The goal of the present study was to 1) study the epigenetic state with regard to the presence of euchromatin and heterochromatin in the developing chick and murine retina, 2) study and compare the localization patterns of the classical HDACs in the developing chick and murine retina with respect retinal progenitors and early differentiated cell types 3) to test the hypothesis that overall HDAC activity is required for dividing retinal progenitors to leave the cell cycle and differentiate. Our results showed that the classical HDACs were ubiquitously expressed in the developing chick and murine retinas. Species specific differences as well as stage dependent variations were observed in the localization of the HDACs in the cell types that were studied in the chick and murine retina. Our preliminary results also showed that HDAC inhibition may lead to the inability of the cell types to leave the cell cycle and a subsequent increase in the number of progenitor cells present in the developing chick retina.

The area of systems biology evolved in an attempt to introduce mathematical systems theory principles in biology. Although we believe that all biological processes are essentially chemical reactions, describing those using precise mathematical rules is not easy, primarily due to the complexity and enormity of biological systems. Here we introduce a formal approach for modeling biological dynamical relationships and diseases such as cancer. The immediate motivation behind this research is the urgency to find a practicable cure of cancer, the emperor of all maladies. Unlike other deadly endemic diseases such as plague, dengue and AIDS, cancer is characteristically heterogenic and hence requires a closer look into the genesis of the disease. The actual cause of cancer lies within our physiology. The process of cell division holds the clue to unravel the mysteries surrounding this disease. In normal scenario, all control mechanisms work in tandem and cell divides only when the division is required, for instance, to heal a wound platelet derived growth factor triggers cell division. The control mechanism is tightly regulated by several biochemical interactions commonly known as signal transduction pathways. However, from mathematical point of view, these pathways are marginal in nature and unable to cope with the multi-variability of a heterogenic disease like cancer. The present research is possibly one first attempt towards unraveling the mysteries surrounding the dynamics of a proliferating cell. A novel yet simple methodology is developed to bring all the marginal knowledge of the signaling pathways together to form the simplest mathematical abstract known as the Boolean Network. The malfunctioning in the cell by genetic mutations is formally modeled as stuck-at faults in the underlying Network. Finally a mathematical methodology is discovered to optimally find out the possible best combination drug therapy which can drive the cell from an undesirable condition of proliferation to a desirable condition of quiescence or apoptosis. Although, the complete biological validation was beyond the scope of the current research, the process of in-vitro validation has been already initiated by our collaborators. Once validated, this research will lead to a bright future in the field on personalized cancer therapy.