Les membres de la famille SMC (Structural Maintenance of Chromosomes), présents dans tous les domaines de la vie, sont impliqués dans des processus allant de la cohésion des chromatides-sœurs jusqu’à la réparation de l’ADN. Chacun des membres de cette famille, composée de 6 membres (Smc1 à Smc6), s’associe avec un autre membre ainsi qu’à des sous-unités non-SMC pour former 3 complexes : cohésine, condensine et Smc5-6. L’implication du complexe Smc5-6 dans plusieurs aspects du maintien de l’intégrité génomique est bien démontrée. Néanmoins, une question fondamentale concernant ce complexe demeure encore sans réponse: comment peut-il être impliqué dans autant d’aspects de la vie d’une cellule? Encore à ce jour, il est difficile de répondre à cette question en raison du manque d’information disponible au sujet des activités biochimiques de ce complexe. C’est pourquoi l’objectif de ce travail consiste en la caractérisation biochimique du complexe Smc5-6. La biochimie de cohésine et condensine suggère diverses possibilités en ce qui a trait aux activités biochimiques du complexe Smc5-6. La première étape de mon projet fut donc d’élaborer une procédure pour la purification de Smc5 et Smc6 après surexpression en levure. Après plusieurs expériences, il apparut clair que les deux protéines possèdent une activité de liaison à l’ADN simple brin (ADNsb) ainsi qu’à l’ADN double brins (ADNdb) et que, même si les protéines peuvent se lier aux deux types d’ADN, elles possèdent une plus grande affinité pour l’ADNsb. De plus, ces expériences permirent de démontrer que l’interaction entre Smc5 ou Smc6 et l’ADNsb est très stable, alors que l’interaction avec l’ADNdb ne l’est pas. Suite à l’obtention de ces résultats, la seconde étape fut la détermination de la ou des partie(s) de Smc5 et Smc6 permettant la liaison à l’ADN. Pour répondre à cette question, une dissection moléculaire fut réalisée, suivi d’une caractérisation des différents domaines constituants Smc5 et Smc6. De cette façon, il fut possible de démontrer qu’il existe deux sites de liaison à l’ADN sur Smc5 et Smc6 ; le premier site se trouvant dans le domaine «hinge» ainsi que dans la région adjacente du domaine «coiled-coil» et le second au niveau de la tête ATPase des deux protéines. Bien que les deux domaines puissent lier l’ADNsb, il fut démontré qu’une différence majeure existe au niveau de leur affinité pour ce type d’ADN. En effet, le domaine «hinge» possède une affinité plus forte pour l’ADNsb que la tête ATPase. De plus, cette dernière est incapable de lier l’ADNdb alors que le domaine «hinge» le peut. L’identification des sites de liaison à l’ADN sur Smc5 et Smc6 permettra de créer de nouveaux mutants possédant un défaut dans la liaison à l’ADN. Ainsi, l’étude du complexe Smc5-6 durant la réparation de l’ADN in vivo sera facilité. / The Smc5-6 complex is part of the SMC (Structural Maintenance of Chromosomes) family and is involved in the maintenance of genome integrity. This complex is required for the replication and repair of DNA. Unfortunately, the DNA substrates recognized by the Smc5-6 complex are still unknown. To address this gap, I used a biochemical approach to purify and functionally characterize the core of the Smc5-6 complex represented by the two SMC proteins. Subsequently, I wanted to understand which part(s) of Smc5 or Smc6 mediate their binding to DNA. I show here that Smc5 and Smc6 bind to all types of DNA tested. Despite this ability to associate with several types of nucleic acids, they have a clear preference for single-stranded DNA (ssDNA). The ability of Smc5 and Smc6 to link DNA independently of each other suggests that both SMC proteins have the potential to target the Smc5-6 complex to its DNA substrates in vivo. Furthermore, the minimal length of ssDNA required for the binding of Smc5 or Smc6 is between 45 to 75 nucleotides. This length of ssDNA is shorter than the size of ssDNA intermediates created during DNA repair or replication reactions. In addition to having a preference for ssDNA, the binding of both SMC proteins to this type of DNA is stronger than their binding to double-stranded DNA (dsDNA). Finally, the molecular dissection of SMC proteins into functional domains revealed that there are two independent DNA-binding sites on each molecule of Smc5 or Smc6. The first region is located in the hinge domain, while the second region is located in the ATPase head of the protein. The affinity and selectivity of independent domains towards DNA substrates suggest a functional differentiation between the two DNA-binding sites of SMC molecules. Indeed, the hinge domain has a greater affinity for ssDNA than the ATPase head. In terms of selectivity, the hinge domain is capable of binding to dsDNA whereas the ATPase head cannot. Taken together, our identification of the DNA-binding domains on Smc5 and Smc6 will enable the creation of new mutants with a defect in their DNA-binding activity. Thus, the study of the Smc5-6 complex during DNA repair, in vivo, will be facilitated.

Fanconi anemia is an autosomal recessive disorder caused by mutation in one of Fanconi genes and it is manifested by developmental abnormalities, bone marrow failure, predisposition to cancer, cellular sensitivity to cross-linking agents and many other symptoms. Proteins encoded by Fanconi genes and some other proteins are part of Fanconi anemia pathway (FA pathway), which is responsible for DNA repair of an interstrand cross-link (ICL). The repair by this pathway requires monoubiquitination of FANCD2, which is induced and regulated by ATR dependent FANCI phosphorylation. The FANCI phosphorylation initiates the FA pathway but the molecular mechanism of this initialization is not known. Furthermore the proper function of entire pathway requires both: sequence of phosphorylation events of FANCI and monoubiquitination of FANCI:FANCD2 complex . The principle of this work was to study molecular mechanism of initiation and regulation of FA pathway by FANCI phosphorylation. Therefore phosphomimetic mutants of FANCI have been created to investigate their role in processes leading to FANCD2 monoubiquitination. The main aim was to reveal how the phosphorylation of FANCI affects DNA binding and also DNA binding of FANCI:FANCD2 complex. Since both DNA and FANCI phosphorylation are required for proper FANCD2...

Das Immediate-Early Protein 2 (IE2) des humanen Zytomegalievirus ist ein essentieller Regulationsfaktor des lytischen Infektionszyklus. Es aktiviert verschiedene early Promotoren, autoreprimiert seine eigene Expression und besitzt darüber hinaus auch zellzyklusregulatorische Aktivitäten. Um einzelne Funktionen des IE2 Proteins gezielt analysieren zu können, ist eine genaue Kenntnis seiner regulatorischen Domänen unabdingbar. Im Rahmen dieser Arbeit wurde daher eine Struktur-Funktionsanalyse des IE2 Proteins durchgeführt mit dem Ziel, seine funktionellen Domänen genauer zu charakterisieren. Hierfür wurden verschiedene IE2-Mutanten hergestellt und ihre Aktivität im Hinblick auf Transaktivierung, Autorepression und DNA-Bindung sowie Zellzylusarrestinduktion bestimmt. Die Untersuchungen ergaben, dass innerhalb einer Core-Region im C-Terminus des Proteins (AS 450-544) die regulatorischen Domänen der untersuchten Funktionen überlappen und hier schon kleinere Mutationen zu einem Funktionsverlust führen. Im Gegensatz dazu ist der Bereich N-terminal des Core deutlich weniger sensitiv gegenüber Mutationen. Hier konnten Sequenzen identifiziert werden, die spezifisch für einzelne Funktionen wie die Transaktivierung oder die Zellzyklusarrestinduktion erforderlich sind. Darüber hinaus hat sich gezeigt, dass eine im bisherigen Verständnis essentielle putative Zinkfingerdomäne außerhalb des Core liegt und für die Funktionalität des Proteins, vor allem für seine DNA-Bindung, nicht benötigt wird. Somit ist der Bereich, in dem die regulatorischen Domänen der untersuchten Funktionen überlappen, deutlich kleiner, als bisher angenommen. Vor diesem Hintergrund lässt sich eine Strategie für die Erstellung von diskriminierenden Virusmutanten ableiten, bei der Einzelfunktionen von IE2 im Viruskontext eliminiert und somit im Sinne ihrer physiologischen Relevanz analysierbar werden. / The Immediate Early Protein 2 (IE2) of human cytomegalovirus is an essential regulatory factor of the viral replicative cycle. It fulfills several functions including transactivation, negative autoregulation and cell cycle regulation. In order to analyse the physiological significance of each of the IE2 functions a precise knowledge of the regulatory protein domains is needed. Therefore, a structure-function analysis of the IE2 protein was performed in this work. Different sets of IE2 mutants were tested in parallel with regard to transactivation, DNA-binding, autoregulation and cell cycle regulation. We found the IE2 protein to contain an unexpectedly clear-cut core domain (amino acids (aa) 450-544) that is defined by its absolute sensitivity to any kind of mutation. In contrast, the region adjacent to the core (aa 290-449) generally displays greater tolerance towards mutations. Although specific sequences correlate with distinct IE2 activities none of the mutations analysed completely abolished any particular function. The core is separated from the adjacent region by the putative zinc finger (428-452) which was found to be entirely dispensable for any function tested. Our work supports the view that the 100 amino acids of the core domain hold the key to most functions of IE2. A systematic, high-density mutational analysis of this region may identify informative mutants which discriminate between various IE2 functions. Such mutants could then be tested in a viral background.

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Abstract not available

The first chapter will provide an introduction to the physiology, pathogenesis and biology of mycobacteria. Host-pathogen interactions, different modes of resistance of the bacteria, adaptations for survival under nutrient and oxygen depleted conditions has been discussed. This is followed by a general discussion on gene expression and regulation in the microbe. The physiology of bacteria under stresses from the view of the transcriptional regulation of specific genes has also been discussed. The scope and objective of the present study in M. smegmatis covered in the thesis has been considered at the end. The next chapter discusses the characterization of msdps promoter in vivo with the help of reporter gene assay technologies. With the advent of promoterless E. coli-mycobacterium shuttle vectors, activity assays can be easily performed to characterize unknown upstream putative promoter sequences of genes. Both the 1 kb upstream as well as a 200bp upstream region of msdps gene has been characterized by. Primer extension analysis and subsequent site directed mutagenesis studies reveal +1 transcription start site and the promoter consensus sequence for the msdps gene respectively. Next chapter comprises of the method of constructing heterologous in vitro transcription machinery in mycobacteria. It is followed by characterization of transcription initiation at two dps promoters of M. smegmatis. A novel pull-down assay has been designed which enabled us to identify the sigma factors in the reconstituted RNA polymerases to be associated with the respective dps promoters and to compare the regulation of the two genes at transcription level. Further characterization through single round in vitro transcription at mycobacterial promoters has been attempted. The following two chapters provide some newer insights into the structure-function relationship of the first Dps molecule, MsDps (MsDps1) with respect to its DNA binding activity. The DNA binding activity is associated with the higher oligomeric form only. With the help of time resolved anisotropy and Förster Resonance Energy Transfer (FRET) experiments, we have monitored the nature of Dps dodecamer-DNA complex and mapped the distance between the N and C169 position in the absence and the presence of DNA. A new computational programme, Maximum Entropy Method (MEM) has been applied successfully to analyze data obtained from phase-modulation (Phi-M) lifetime experiments in order to get distribution of lifetime. In the last chapter a new method is adopted to predict amino acids important for stabilizing the interface in a trimeric structure. Subsequently, single and double amino acid mutants of the native MsDps protein has been constructed through site directed mutagenesis and are scored for the ability of the mutants to oligomerize under conditions similar to that of the native protein. This helped us to propose a hypothetical model of the overall mechanism of the protein oligomerization process in solution.

Photo sensitizers showing visible light induced DNA cleavage activity are of current importance for medicinal applications related to photodynamic therapy (PTD) considering greater skin penetration of light near 700 nm. While organic molecules and complexes of 4d-5d metal ions are extensively studied for their DNA photo-damage properties in UV and visible light, the chemistry of 3D metal complexes showing visible light-induced DNA cleavage activity is relatively unexplored efforts have been made in this thesis work to design new ternary copper (II) complexes having a-amino acids Such copper (II) complexes with tunable coordination geometry could find potential applications in PDT. Ternary Copper (II) complexes containing L-methionine, S-methy1-L-cysteine and phenanthroline bases are prepared and characterized. They display DNA binding and visible light induced DNA cleavage activity. An enhancement of the DNA cleavage activity is observed for analogous ternary copper (II) complexes contained L-lysine with a pendant cationic amine moiety as a photo-induced DNA Cleavage activity using binary and ternary copper (II) complexes of L-arginine and phenanthroline bases. We have observed AT selective DNA binding and visible light –induced DNA cleavage activity. The crescent-shaped bis-arginine Copper (II) complex mimics the natural antiviral antibiotic netropsin. T o investigate the role of the pendant groups of the amino acids, we have explored the DNA binding and DNA cleavage activity of analogues L-glutamine and L-asparagine complexes. We have prepared ternary copper (II) complexes containing two photosensitizers, viz., L-tryptophan (L-trp) and dipyridoquininoxaline/dipyridophenazine to achieve double strand breaks forming linear DNA. Complex [Cu(L-trp)(dppz)(H2O)+ shows a stacking arrangement of the indole and dppz rings giving a separation that fits with the base pair separation of ds-DNA. Photosensitizes in these complexes approach two different complementary stands of the ds-DNA, leading to double strand breaks and formation of linear DNA. Mechanistic studies on the DNA photocleavage reactions reveal the formation of singlet oxygen(1O2)species by a type-II pathway in preference to the hydroxyl radical generation. A process leading to an efficient DNA cleavage activity on visible light irradiation. The observation of sequence selectivity and double strand DNA cleavage on red light exposure by national design of the complexes is significant considering importance of the results in the chemistry of photodynamic therapy of cancer. The results of this dissertation open up new avenues for designing and developing 3d metal-based photosensitizers with potential utility in nulcleic acid chemistry.

SMC1 and SMC3 form a high-affinity heterodimer, which provides an open backbone of the cohesin ring, to be closed by a kleisin protein. RNAi mediated knock-down of either one heterodimer partner, SMC1 or SMC3, is expected to cause very similar if not identical phenotypes. However, we observed highly distinct, protein-specific phenotypes. Upon knock-down of human SMC1, much of SMC3 remains stable, accumulates in the cytoplasm and does not associate with other cohesin proteins. Most of the excess nuclear SMC3 is highly mobile and not or only weakly chromosome-associated. In contrast, human SMC3 knock-down rendered SMC1 instable without cytoplasmic accumulation. As observed by differential protein extraction and in FRAP experiments the remaining SMC1 or SMC3 proteins in the respective SMC1 or SMC3 knock-down experiments constituted a cohesin pool, which is associated with chromatin with highest affinity, likely the least expendable. Expression of bovine EGFP-SMC1 or mouse EGFP-SMC3 in human cells under conditions of human SMC1 or SMC3 knock-down rescued the respective phenotypes, but in untreated cells over-expressed exogenous SMC proteins mis-localized. Paucity of either one of the SMC proteins causes RAD21 degradation. These results argue for great caution in interpreting SMC1 and SMC3 RNAi or over-expression experiments. Under challenged conditions these two proteins unexpectedly behave differently, which may have biological consequences for regulation of cohesin-associated functions and for human cohesin pathologies.

Self-assembly processes were used to construct supramolecular architectures based on metal-ligand interactions. The structures formed strongly depend on the used metal ion, the ligand type, the chosen counter ion and solvent as well as on the experimental conditions. The focus of the studies was the design of multifunctional N-donor ligands and the characterization of their complexing and structural properties. This work was divided into three distinct main parts: The bis(2-pyridylimine), the bis(2-hydroxyaryl) imine and the tripodal imine / amine ligand approach. In the first part a series of bis(2-pyridylimine) derivatives having different linking elements were employed as building blocks for novel supramolecular architectures. Reaction of individual d-block metal salts with these ligands has led to the isolation of coordination polymers, a metallamacrocycle, double-stranded helicates, triple-stranded helicates as well as of circular meso-helicates. The nature of the spacer in the Schiff base ligands, the noncovalent weak interactions, such as hydrogen bond, face-to-face π-π and edge-to-face CH-π interactions, are all important factors influencing the architecture of the final products. Topological control of the assembly process of the hexanuclear meso-helicates is clearly associated with the bidentate coordination of the sulfate anion which directs the formation of a double- rather than a triple-stranded helicate around the octahedrally coordinated Cu(II). Surprisingly, the variation of the linker function in the ligands, which significantly changes the linking angle of the pyridylimine strands, has only a little influence of the resulting structure. Also the use of a mixture of ligands does not influence the meso-helicate topology; the result is the symmetrically mixed meso-helicate. The new iron(II) triple helicate [Fe2(L5)3](PF6)4 14 {L5 = bis[4-(2-pyridylmethyleneimino)phenyl]-1,1-cyclohexane} in its chloride form binds strongly to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the helicate. The induced CD spectrum gives some evidence that [Fe2(L5)3]4+ interacts with the DNA in a single binding mode, which is consistent with major groove binding. The cytotoxicity of the new iron(II) triple helicate 14 was evaluated on human lung cancer A549 cells and compared with that of cisplatin and that of the previously reported iron(II) triple helicate [Fe2(L1)3]4+{L1 = bis[4-(2-pyridylmethyleneimino)phenyl]methane}. The first results show some distinguishing features for 14 obviously caused by the existing structural differences of the complexes. In the second part of the thesis, novel uranyl complexes of the bis(2-hydroxyaryl) imine ligands have been synthesized and characterized. 1D coordination polymers and mononuclear structures were formed. In all complexes a distorted hexagonal bipyramidal coordination geometry around the uranyl centre is observed. The imine nitrogen atoms of the ligands do not bind to the metal centre but interact strongly with the hydroxy group via H-bonding. DFT calculations made with L8 ( α,α’-Bis(salicylimino)-m-xylene) are in good agreement with the X-ray crystal structure data. Liquid-liquid extraction studies involving selected ligands and Eu(III) or U(VI) indicate remarkably high selectivity for U(VI) over Eu(III) at weak acidic pH conditions. We believe that the study made opens up new possibilities for uranyl ion extraction which could be interesting in view of the treatment of nuclear waste. In the third part of the thesis, a series of multifunctional tripodal ligands with different N-donor centres were used for U(VI) and lanthanide, Nd(III), Eu(III) and Yb(III), binding and extraction. Reaction of these metal ions with selected tripodal ligands afforded complexes which were characterized by ESI mass spectroscopy. The complex composition was found to be 1:1 in all cases. The extraction behaviour of the tripodal ligands towards Eu(III) and U(VI) was studied both in the absence and presence of octanoic acid as co-ligand using the extraction system Eu(NO3)3 or UO2(NO3)2–buffer–H2O/ ligand–CHCl3. These separation systems show a remarkably high selectivity for U(VI) over Eu(III). It is interesting to note that the addition of the octanoic acid to the extraction system leads to high synergistic effects. A series of Eu(III) extraction experiments were done to clarify the composition of the extracted complexes. The results clearly point to the formation of various species with changing composition.

This PhD aimed to elucidate the mechanisms by which polymorphisms may alter androgen-induced transactivation of androgen receptor (AR) target genes which may be important in prostate cancer aetiology. The second aspect of this PhD focused on identifying and characterising functional polymorphisms that may have utility as predictive risk indicators for prostate cancer and which may aid in earlier therapeutic intervention and better disease management. Analyses were carried out on the kallikrein-related peptidase 3 (KLK3), also known as the prostate specific antigen (PSA), gene and the kallikrein-related peptidase 4 (KLK4) gene. The PSA and KLK4 genes are part of the serine protease family that have trypsin or chymotrypsin like activity and are thought to play a role in the development of hormone-dependent cancers in tissues such as those in the prostate, breast, endometrium and ovaries. In the prostate, PSA is regulated by androgens and three androgen response elements (AREs) have been described in the promoter and upstream enhancer region. The PSA ARE I harbours a polymorphism at -158 bp from the transcription initiation site (TIS) that results in a G to A transition (G-158A). This PhD investigated the functional significance of the PSA G-158A polymorphism which has been reported to be associated with prostate cancer risk. Electromobility shift assays (EMSAs) investigating the interaction of ARE I variants with the AR DNA binding domain (AR-DBD) demonstrated that the A allele had a two-fold increased binding affinity for the AR-DBD when compared with the G allele. This was confirmed with endogenous AR in limited proteolysis-EMSA experiments. The limited proteolysis-EMSA experiments also demonstrated differential sensitivities of PSA ARE I alleles to trypsin digestion, which suggests that the G-158A polymorphism has an allosteric effect on the AR that alters AR/ARE I complex stability. Furthermore, Chromatin Immunoprecipitation (ChIP) assays suggest that the A allele more readily recruited the AR in vivo when compared with the G allele and is consistent with the in vitro binding data. Luciferase reporter assays carried out in both LNCaP and 22Rv1 prostate cancer cells, and using the natural (dihydrotestosterone; DHT) ligand demonstrated that the A allele was more responsive to androgens in LNCaP cells. Hence, this study has elucidated the potential mechanisms by which the G-158A polymorphism may differentially regulate PSA expression (of which up-regulation of PSA is thought to be important in prostate cancer development and progression). KLK4 has similar tissue-restricted expression as PSA and is up-regulated by steroid hormones in many endocrine cells including those in the prostate. A putative ARE (KLK4-pARE) located at -1,005 to -1019 relative to the more predominantly used transcription initiation site, TIS3, was initially found in supershift assays using AR antibodies to interact with endogenous AR. However, subsequent EMSA analysis using purified AR-DBD suggest that KLK4-pARE may be interacting with the AR indirectly. To investigate this hypothesis, a tandem construct of KLK4-pARE was cloned into the pGL3-Promoter vector for hormone-induced reporter assays. However, reporter assays did not demonstrate any responsiveness of KLK4-pARE to androgens, estradiol or progestins. Consequently, Real-Time PCR was carried out to reassess the hormonal regulation of KLK4 at the mRNA level. Consistent with the literature, data from this study suggests that KLK4 may be up-regulated by androgens, progestins and estradiol in a cyclical manner. Hormone-induced luciferase reporter assays were then carried out on seven promoter constructs that span 2.8 kb of the KLK4 promoter from TIS3. However, none of the seven promoter constructs demonstrated any significant responsiveness to androgens, estradiol or progestins. This study suggests that hormone response elements (HREs) that may drive the hormonal regulation of KLK4 in prostate cancer may be located further upstream from the promoter region investigated in this PhD, or alternatively, may lie 3' of TIS3. The characterisation of KLK4 promoter polymorphisms and their flanking sequences were also carried out in parallel to the functional work with the intent to assess the functional significance of any polymorphisms that may be located within HREs. In total 19 polymorphisms were identified from the public databases and from direct sequencing within 2.8 kb of the KLK4 promoter from TIS3. However, the functional and clinical significance of these 19 polymorphisms were not further pursued given the negative findings from the functional work. The PSA AR enhancer region was also assessed for potential polymorphisms that may be associated with prostate cancer risk. A total of 12 polymorphisms were identified in the PSA enhancer of which two (A-4643G and T-5412C) have been reported to alter functionality of the enhancer region and thus, prioritised for further analysis. Association analysis for prostate cancer risk was then carried out on these PSA enhancer polymorphisms as none of the KLK4 promoter polymorphisms were found in functional HREs. No significant association for either the A-4643G or T-5412C polymorphism with prostate cancer risk was found at the P = 0.05 level. However, under an age-adjusted dominant model a 1.22- (95% CI = 1.16-1.26) and 1.23-fold (95% CI = 1.17-1.29) increased risk for prostate cancer was found for the A-4643G or T-5412C polymorphisms, respectively. Both polymorphisms were also assessed for association with tumour grade and stage and PSA levels. Genotypes were significantly different for the A-4643G and T-5412C polymorphisms with tumour stage and PSA levels, respectively. However, these results are likely to be biased by the case population which consist primarily of men who presented with incidental (pT1) and organ-confined (pT2) tumours. To summarise, the A-4643G and T-5412C polymorphisms are unlikely to be associated with prostate cancer risk, PSA levels or stage/grade of disease. However, further analyses in a larger cohort is warranted given that these polymorphisms alter androgen responsiveness of the PSA enhancer and that elevated PSA levels are indicative of men with prostate cancer. To summarise, this PhD has elucidated the functional significance of the PSA G-158A polymorphism in prostate cancer and which may be important in prostate cancer patho-physiology. This PhD has also furthered the understanding of the hormonal regulation of KLK4 in prostate cancer cells. Finally, this PhD has carried out a pilot study on two functional PSA enhancer polymorphisms (A-4643G and T-5412C) with prostate cancer risk.