The Mre11/Rad50 complex has been implicated in the early steps of DNA double-strand break (DSB) repair through homologous recombination in several organisms. However, the enzymatic properties of this complex are incompatible with the generation of 3’ single-stranded DNA for recombinase loading and strand exchange. In thermophilic Archaea, the mre11 and rad50 genes cluster in an operon with genes encoding a bidirectional DNA helicase, HerA, and a 5’ to 3’ exonuclease, NurA, suggesting these four enzymes function in a common pathway. I show that purified Mre11 and Rad50 from Pyrococcus furiosus act cooperatively with HerA and NurA to resect the 5’ strand at a DNA end under physiological conditions in vitro where HerA and NurA alone do not show detectable activity. Furthermore, I demonstrate that HerA and NurA physically interact, and this interaction stimulates both helicase and nuclease activities. The products of HerA/NurA long-range resection are oligonucleotide products and HerA/NurA activity demonstrates both sequence specificity and a preference to cut at a specific distance from the DNA end. I demonstrate a novel activity of Mre11/Rad50 to make an endonucleolytic cut on the 5’ strand, which is consistent with a role for the Mre11 nuclease in the removal of 5’ protein conjugates. I also show that Mre11/Rad50 stimulates HerA/NurA-mediated resection through two different mechanisms. The first involves an initial Mre11 nucleolytic processing event of the DNA to generate a 3’ ssDNA overhang, which is then resected by HerA/NurA in the absence of Mre11/Rad50. The second mechanism likely involves local unwinding of the DNA end in a process dependent on Rad50 ATPase activity. I propose that this unwinding step facilitates binding of HerA/NurA to the DNA end and efficient resection of the break. Furthermore, the binding affinity of NurA for 3’ overhang and unwound DNA end substrates partially explains the efficiency of the two resection mechanisms. Lastly, 3’ single-stranded DNA generated by these enzymes can be used by the Archaeal RecA homolog RadA to catalyze strand exchange. This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in Archaea, and may serve as a model for DSB processing in eukaryotes. / text

This work introduces a database of experimentally verified structures of nucleic acids which were collected from published scientific literature. The database is annotated and the structures are analysed from the perspective of quality and it was found that the experimentally obtained data are not always sufficient - their supporting evidence is often limited and their quality is not convincing. This work also discusses some of the problems, that can be encountered when the structures are experimentally probed. Contents of the database were compared to the RFAM database and despite of its small range it contains 80 new structures. The complete database of 166 structures can be possibly used to optimise software used to predict derived structures of nucleic acids. Furthermore, the work presents several possible ways of improvement of the quality of contained structures.

This thesis summarizes the results of studies on two aspects of nucleic acids. Chemically modified antisense oligonucleotides (AONs) have been evaluated with regards to their suitability for mRNA targeting in an antisense approach (Paper I – III). The chemically modified nucleotidic units 2'-O-Me-T, 2'-O-MOE-T, oxetane-T, LNA-T, azetidine-T, aza-ENA-T, carbocyclic-ENA-T and carbocyclic-LNA-T were incorporated into 15-mer AONs and targeted against a 15-mer RNA chosen from the coding region of SV-40 large T antigen. The comparative study showed that a single modified nucleotide in the AON with North-East locked sugar (oxetane-T and azetidine-T) lowered the affinity for the complementary RNA whereas North locked sugars (LNA-T, aza-ENA-T, carbocyclic-ENA-T, and carbocyclic-LNA-T) significantly improved the affinity. A comparative RNase H digestion study showed that modifications of the same type (North-East type or North type) in different sequences gave rise to similar cleavage patterns. Determination of the Michaelis-Menten parameters by kinetic experiments showed that the modified AONs recruit RNase H resulting in enhanced turnover numbers (kcat) although with weaker enzyme-substrate binding (1/Km) compared to the unmodified AON. The modified AONs were also evaluated with regards to resistance towards snake venom phosphodiesterase and human serum to estimate their stability toward exonucleases. The aza-ENA-T and carbocyclic-ENA-T modified AONs showed improved stability compared to all other modified AONs. In general, the modified AONs with North type nucleotides (except LNA-T) were found to be superior to the North-East type as they showed improved target affinity, comparable RNase H recruitment capability and improved exonuclease stability. The second aspect studied in this thesis is based on physicochemical studies of short RNA molecules utilizing NMR based pH titration and alkaline hydrolysis reactions (Paper IV – V). The NMR based (1H and 31P) pH titration studies revealed the effect of guaninyl ion formation, propagated electrostatically through a single stranded chain in a sequence dependent manner. The non-identical electronic character of the internucleotidic phosphodiesters was further verified by alkaline hydrolysis experiments. The internucleotidic phosphodiesters, which were influenced by guaninyl ion formation, were hydrolyzed at a faster rate than those sequences where such guaninyl ion formation was prevented by replacing G with N1-Me-G.

Der DNA-Verpackungsmechanismus des humanen Cytomegalievirus (HCMV) ist charakteristisch für große DNA-Viren wie Herpesviren und ds-Bakteriophagen. Er beruht auf der Spaltung der konkatemeren DNA durch einen viralen, hetero-oligomeren Proteinkomplex, der Terminase. In der vorliegenden Arbeit konnten die funktionellen Domänen der Terminase-Untereinheit pUL89 in vitro identifiziert und charakterisiert werden. Neben einer Nuklease-Aktivität besitzt pUL89 auch die Fähigkeit dsDNA sequenz-unabhängig zu binden. Durch Nuklease-Untersuchungen konnte gezeigt werden, dass pUL89 sowohl dsDNA, als auch lineare DNA spaltet. PUL89 weist dabei eine größere Spezifität zu dsDNA auf. Des Weiteren konnte nachgewiesen werden, dass die Aminosäure D463 eine zentrale Funktion innerhalb der Nuklease-Aktivität besitzt. Durch kolorimetrische DNA-Bindungsuntersuchungen konnte die Aminosäure R544 als essenziell für die dsDNA-Bindungsfähigkeit von pUL89 identifiziert werden. Basierend auf den in vitro Ergebnissen wurden rekombinanten TB40/E-Virusmutanten mit Mutationen im ORF UL89 durch die En Passant Mutagenese generiert. Mit Hilfe dieser Viren sollte der Einfluss der Mutationen auf die Replikation des Virus charakterisiert werden. Es war möglich nachzuweisen, dass die Aminosäuren E534 und R544 eine essenzielle Aufgabe innerhalb von HCMV erfüllen, da die Mutation einer dieser Aminosäure zu nicht wachstums-fähigen BAC-Mutanten führte. Zur Charakterisierung dieser Konstrukte wurden die Zelllinien HELF Fi301-UL89 und HELF Fi301-vProm-UL89 verwendet. Durch Untersuchungen hinsichtlich der Wachstumseigenschaften, Proteinexpression, DNA-Spaltung, DNA-Bindung sowie elektronenmikroskopischen Aufnahmen, konnte gezeigt werden, dass die wachstums-kompetenten BAC-Mutanten keinen signifikanten Unterschied zum Wildtyp-Virus TB40/E zeigten. Sodass nachgewiesen werden konnte, dass die basischen Aminosäuren H565 und H571 keine essenzielle Funktion in pUL89 erfüllen. / The human cytomegalovirus DNA packaging mechanism is characteristic for large DNA viruses like Herpes viruses and ds bacteriophages. This mechanism is based on the cleavage of concatemeric DNA by the viral heterooligomeric protein complex terminase. This dissertation includes the identification and characterization of functional domains of the HCMV terminase subunit pUL89. PUL89 contain a nuclease activity and the ability to bind dsDNA. This protein shows the property to cut as well dsDNA as linear DNA. The amino acid D463 shows a significant role in this cleavage event. Colorimetric DNA binding experiments show the central role of R544 in DNA binding by pUL89. Based of the in vitro results recombinant TB40/E viruses with mutations in the ORF UL89 were generated. These viruses allow a characterization of the impact of virus replication. It was possible to show that the amino acids E534 and R544 have a functional role in HCMV. The mutation of one of these amino acids was enough to generate a growth deficient mutant. The stable cell lines HELF Fi301-UL89 and HELF Fi301-vProm UL89 were used for the characterization of the growth deficient mutants. The growth competent mutants H656A and H571A show no significant differences in comparison with the wild type TB40/E virus. This was verified by growth kinetics, protein expression characterizations, pulse field gel electrophoresis, DNA binding assays and electron microscopy.

No description available.

This work is dedicated to thorough structural analysis of plant bifunctional nuclease TBN1, the representative of plant nuclease I group. TBN1 along with homologous nucleases from this family plays an important role in plant cell life cycle and also shows considerable anticancerogenic effects. Two variants of TBN1 (wild type and N211D mutant) were studied. Properties of both variants in different solutions were analyzed. Both were successfully crystallized. Structures of both types of TBN1 were solved using X-ray diffraction. The phase problem was solved by Multi-wavelength anomalous dispersion using Zn2+ ions natively present in TBN1. Structural properties of TBN1 such as fold, active site composition, effect of glycosylation and surface electrostatic potential distribution were analyzed. Reaction mechanism of TBN1 was proposed on the basis of structural properties and comparisons with similar structures.

Computationally driven drug design/discovery efforts generally rely on accurate assessment of the forces that guide the molecular recognition process. HINT (Hydropathic INTeraction) is a natural force field, derived from experimentally determined partition coefficients that quantifies all non-bonded interactions in the biological environment, including hydrogen bonding, electrostatic and hydrophobic interactions, and the energy of desolvation. The overall goal of this work is to apply the HINT-based atomic level description of molecular systems to biologically important proteins, to better understand their biochemistry – a key step in exploiting them for therapeutic purposes. This dissertation discusses the results of three diverse projects: i) structural modeling of human sphingosine kinase 2 (SphK2, a novel anticancer target) and binding mode determination of an isoform selective thiazolidine-2,4-dione (TZD) analog; ii) structural modeling of human cytomegalorvirus (HCMV) alkaline nuclease (AN) UL98 (a novel antiviral target) and subsequent virtual screening of its active site; and iii) explicit treatment of interfacial waters during protein-protein docking process using HINT-based computational tools. SphK2 is a key regulator of the sphingosine-rheostat, and its upregulation /overexpression has been associated with cancer development. We report structural modeling studies of a novel TZD-analog that selectively inhibits SphK2, in a HINT analysis that identifies the key structural features of ligand and protein binding site responsible for isoform selectivity. The second aim was to build a three-dimensional structure of a novel HCMV target – AN UL98, to identify its catalytically important residues. HINT analysis of the interaction of 5’ DNA end at its active site is reported. A parallel aim to perform in silico screening with a site-based pharmacophore model, identified several novel hits with potentially desirable chemical features for interaction with UL98 AN. The majority of current protein-protein docking algorithms fail to account for water molecules involved in bridging interactions between partners, mediating and stabilizing their association. HINT is capable of reproducing the physical and chemical properties of such waters, while accounting for their energetic stabilizing contributions. We have designed a solvated protein-protein docking protocol that explicitly models the Relevant bridging waters, and demonstrate that more accurate results are obtained when water is not ignored.

One of the greatest challenges in finfish aquaculture is combating losses caused by infectious bacterial diseases, and a better understanding of the interactions between the host immune system and pathogens is essential for developing new methods to manage infections and outbreaks. Extracellular traps (ETs) are decondensed nuclear chromatin released by neutrophils into the extracellular matrix that can ensnare and kill microbes. Since the discovery of ETs in humans, these innate immune effectors have been characterised across the animal kingdom, including in some fish species, though their existence the salmonids has yet to be confirmed. Therefore, the aim of this thesis was to confirm and characterise the release of ETs in the rainbow trout (Oncorhynchus mykiss) and investigate the interaction of these structures with fish pathogenic bacteria. To do this, a triple-layer Percoll gradient technique was employed to give highly enriched cell suspensions of polymorphonuclear cells (PMNs) derived from head-kidney tissue preparations. Treatment of PMN-enriched cell suspensions with the nucleic-acid-specific stain, SYTOX Green, revealed the presence of ET-like structures that had been released without stimulation. These ET-like structures were confirmed by immunostaining techniques to contain the diagnostic proteinaceous markers of ETs: neutrophil elastase, myeloperoxidase and the H2A histone. Previously characterised inhibitors and inducers of ET release from phagocytic immune cells in other animals confirmed that calcium ionophore (CaI), flagellin, and cytochalasin D shared similar activities for ET-release by rainbow trout PMNs. However, interestingly, as the common ET-inducer phorbol-myristate acetate (PMA) and ET-inhibitor diphenyleneiodonium (DPI) did not exert their expected potency in ET release assays with the PMNs, perhaps indicating that these fish cells are less dependent on NADPH oxidase signalling for ET release compared to mammals and most invertebrate species. The PMN-derived ETs were demonstrated to bind to and trap the extracellular nuclease-deficient bacterial fish pathogen, Vibrio anguillarum (Vib 87) when co-cultured. Finally, extracellular nuclease activity produced by a V. anguillarum isolate (Vib 6) during culture was able to degrade ETs released by rainbow trout PMNs in a dose-dependent manner. Moreover, viable colony counts, fluorescent and phase contrast microscopy demonstrated that V. anguillarum Vib 6 eluded trapping by ETs, while an extracellular nuclease-deficient isolate did not. These observations are consistent with the suggestion that nucleases are a microbial virulence factor during host infection. Confirming the existence and antimicrobial potential of extracellular traps released by rainbow trout PMNs may provide a platform towards the development of novel therapeutics to reduce mortalities in finfish aquaculture caused by infectious microbial pathogens.

La Cytolethal Distending Toxin (CDT) est un facteur de virulence produit par de nombreuses bactéries pathogènes Gram négatives. Sa production est associée à différentes pathologies, dont le développement de cancers. Un lien de causalité a été établi entre dommages à l’ADN, mutagénèse et cancérogenèse. Or, différentes études ont classé CDT dans la famille des génotoxines bactériennes. L’action génotoxique de CDT repose sur l’activité de sa sous-unité catalytique CdtB, connue pour induire des cassures double-brin (CDBs) de l’ADN génomique eucaryote. Cependant, des travaux de l’équipe ont montré qu’à des doses 1000 fois plus faibles que celles utilisées dans la littérature, CDT induit des dommages primaires (probablement de type cassure simple-brin), qui dégénèrent en CDB lors de la phase S. Afin de mieux documenter ce modèle, nous avons étudié ici les systèmes de réparation impliqués dans la réponse aux dommages à l’ADN induits par CDT. Nous avons ainsi confirmé l’importance des voies de réparations des CDBs (Homologous Recombinaison et Non-Homologous End-Joining). Nous avons également montré que le Nucleotide Excision Repair, impliqué dans la réparation des adduits à l’ADN, n’est pas impliqué dans la prise en charge des dommages induits par CDT. En revanche, nous avons démontré, pour la première fois, l’implication de systèmes de réparation de dommages plus précoces, comme le Single-Strand Break Repair et la voie de l’Anémie de Fanconi. Pour finir, afin de mieux caractériser ces dommages et leur induction, nous avons initié des travaux visant à étudier, in vitro, l’activité catalytique de CdtB. Dans ce but, différents mutants catalytiques ont été générés, purifiés, et leur activité nucléase a été testée. Une activité nucléase similaire entre les CdtB sauvages et mutantes a été obtenue lors d’un test in vitro (digestion d’un plasmide super-enroulé). Cependant, un test cellulaire (expression nucléaire en cellules eucaryotes de la sous-unité CdtB sauvage ou mutante) indique bien la perte de l’activité nucléase de la sous-unité mutante. Nos résultats montrent donc l’importance de tester les différentes sous-unités dans différents contextes. En conclusion, notre travail conforte les données selon lesquelles CDT induit des CSB, et non des CDB directes de l’ADN. De plus, notre travail a permis d’éclaircir les processus cellulaires activés dans la cellule hôte, suite aux dommages à l’ADN induits par CDT. / The Cytolethal Distending Toxin (CDT) is a virulence factor produced by many pathogenic gram-negative bacteria, its production being associated to various diseases, including tumorigenesis. A causal relationship has been established between DNA damage, mutagenesis and cancerogenesis. Different studies classified CDT among the bacterial genotoxins. The CDT-related pathogenicity relies on the catalytic subunit CdtB action, shown to induce double-strand breaks (DSB) on the host genomic DNA. Previously, our team showed that, at doses 1000 times lower than those used in the literature, CDT probably induces single-strand breaks that degenerate into DSB during S-phase. To document this model, we studied the repair systems involved in host-cell in response to CDT-induced DNA damage. Since various repair pathways allow cells to respond different type of DNA damage, we speculated that non-DSB repair mechanisms might contribute to the cellular resistance to CDT-mediated genotoxicity. First, we confirm that HR is involved in the management of CDT-induced lesions, but also Non Homologous End Joining, the second major DSB repair mechanism. Next we show that nucleotide excision repair, involved in adducts repair, is not important to take care of CDT-induced DNA damage, whereas base excision repair impairment sensitizes CDT-treated cells, suggesting that CDT induce single-strand breaks. Moreover, we demonstrate for the first time the involvement and the activation of the Fanconi Anemia repair pathway in response to CDT. Finally, to better characterize CDT-induced damage, we initiate experiments to study CdtB nuclease activity in vitro. For this, different CdtB mutants have been generated, purified and their nuclease activity tested. A similar nuclease activity has been obtained for the wt or mutant CdtB in an in vitro assay (digestion of a supercoiled plasmid). However, a cell assay (nuclear expression of CdtB in eukaryotic cells) confirms the loss of activity for the mutant subunit. Our results thus indicate the importance to test the CdtB subunit in different context. To conclude, our work reinforces a model where CDT induces single-strand damage and not direct DSB. This also underlines the importance of cell proliferation to generate DSB and sheds light on the activated host-cell systems, after CDT-induced DNA damage.

No description available.