DNA replication is a fundamental process in all living organisms. It is a semi- discontinuous process in which the leading strand is synthesized continuously and the lagging strand is synthesized discontinuously as short Okazaki fragments (OF). The initiation of DNA synthesis requires DNA polymerase α (Pol α/primase) in complex with the primase to form a complex of four subunits. Pol α/primase is the only enzyme that can perform de novo DNA synthesis on single-stranded DNA. The catalytic subunit of the primase (PRIM1) synthesizes RNA primers that are approximately nine nucleotides long. The synthesized RNA primers are then passed intramolecularly to the polymerase active site (POLA1), which is thought to be mediated by the C-terminal domain of the primase large subunit (PRIM2-C) to synthesize dNTPs of approximately 20 nucleotides. The aim of this project was to optimize the expression and purification of Pol α/primase. The insect codon optimized POLA1 was C-terminally Strep tagged and transposed into the baculovirus genome. The other subunits of Pol α/primase, POLA2, PRIM1 and PRIM2 were cloned and expressed in E. coli cells. The cell lysates from Sf9 insect cells and E. coli cells were then mixed and purified by immunoaffinity chromatography and size-exclusion chromatography. This helped us achieve a pure Pol α/primase containing all the four subunits with a good total yield. The identity of all the protein bands were verified by mass spectroscopy. Furthermore, the protein demonstrated primer extension activity on multiple primer/template substrates. We also characterized the effect of the human replication protein A (RPA) on the DNA polymerization activity of Pol α/primase.

Le cytomégalovirus humain (CMVH) est un pathogène opportuniste majeur en cas d’immunodépression et représente la principale cause d’infection congénitale d’origine virale. Bien qu’efficaces, l’utilisation des molécules conventionnelles est limitée par l’émergence de résistance et leur toxicité. Il devient alors nécessaire de développer de nouveaux traitements.L’étude des nouvelles mutations émergeant sous traitement antiviral demeure donc essentielle. L’introduction de ces nouvelles mutations, par mutagénèse « en passant », dans un chromosome bactérien artificiel contenant le génome viral nous permet, après transfection en cellules humaines, de tester la sensibilité de la souche recombinantes aux antiviraux.Différentes mutations de résistances ont ainsi été caractérisées. Afin de mettre en évidence de nouvelles cibles antivirales, des analyses bio-informatiques et la production de virus recombinants ont permis d’identifier de potentiels motifs fonctionnels essentiels à la réplication au sein du complexe terminase et hélicase-primase. Ainsi, nous avons montré quela sous-unité pUL56 du complexe terminase appartient à la famille des LAGLIDADG Homing Endonuclease. En effet, pUL56 contient un motif LATLNDIERFL et un motif de liaison à l’ADN. La technologie Alpha utilisant des protéines purifiées a permis de valider le caractère essentiel du fragment WMVVKYMGFF de pUL56 pour l’interaction avec pUL89. Enfin, nous avons mis en évidence les résidus impliqués dans la fixation de l’ATP au sein de l’hélicase et dans la stabilisation du zinc de la primase. Ainsi, la compréhension de la structure de ces protéines pourrait permettent de mieux appréhender leur fonctionnement au sein du processus de réplication du CMVH et le développement de nouvelles thérapies ciblant ces domaines. / Human cytomegalovirus (HCMV) is an important opportunistic pathogen for immunecompromised patients and is the leading cause of congenital viral infection. Although they are effective, using of conventional molecules is limited by the emergence of resistance and their toxicity. Then it becomes necessary to develop new treatments. Study of new mutationsemerging under antiviral treatment is therefore essential. Introduction of these new mutations, by « en passant » mutagenesis, into an artificial bacterial chromosome containing the viral genome allows us, after transfection into human cells, testing antivirals sensitivity of the recombinant. Different mutations of resistances have been characterized. In order tohighlight new antiviral targets, bioinformatics and recombinant viruses production allowed to identify potential functional patterns essential for viral replication within terminase and helicase-primase complex. Thus, we have shown that pUL56 subunit of the terminase complex belongs to the LAGLIDADG Homing Endonuclease family. Indeed, pUL56 contains aLATLNDIERFL motif and a DNA binding motif. Alpha technology using purified proteins allowed to validate the essential character of the WMVVKYMGFF fragment of pUL56 for the interaction with pUL89. Finally, we highlighted the residues involved in ATP binding within the helicase and in the stabilization of zinc within the primase. Thus, understanding of these proteins structure could allow us to better understand their role within the viral replication process and the development of new therapies targeting these domains.

Le virus Epstein-Barr (EBV) est un gamma herpèsvirus humain infectant plus de 95 % de la population mondiale. Lorsque la primo-infection a lieu pendant l'adolescence ou à l'âge adulte, elle peut induire la mononucléose infectieuse (MNI), cette maladie est le plus souvent bénigne. EBV est aussi associé à un certain nombre de cancers de type lymphome (lymphomes de Burkitt et d'Hodgkin) et de type carcinome (carcinomes gastriques et indifférenciés du rhinopharynx). L'importance des protéines de latence du virus dans l'apparition des tumeurs a été très étudiée. Des études récentes montrent que les protéines lytiques d'EBV sont aussi très importantes pour l'apparition et le développement des tumeurs. Le complexe Hélicase-Primase (H-P) du virus herpès simplex 1 (HSV-1, alpha herpèsvirus) est la cible de nouveaux antiviraux. Les activités ATPase, hélicase et primase du complexe d'HSV-1 ont été largement étudiées, mais aucune information structurale du complexe H-P n'est disponible actuellement pour un membre des herpèsvirus humains. Nous avons entrepris l'étude du complexe H-P d'EBV (BBLF4 : hélicase, BSLF1 : primase et BBLF2/3 : sous-unité accessoire) afin de caractériser sa structure et les activités qu'il porte. Nous avons pu établir les conditions d'expression et de purification du complexe et débuter des études structurales et enzymatiques préliminaires. Nous avons pu observer une activité ATPase basale du complexe indépendante de la présence d'un substrat ADN simple brin. Nous observons deux formes solubles du complexe lors des purifications, une présentant probablement une stœchiométrie proche de 1/1/1 et une seconde forme ayant surement un excès de la protéine Hélicase (BBLF4). Ces premiers résultats apportent des informations nouvelles pour le complexe H-P d'EBV et doivent être poursuivis afin de les confirmer et de pouvoir les comparer avec ceux déjà connus pour le complexe H-P d'HSV-1. / Epstein-Barr Virus (EBV) is a human herpesvirus largely present worldwide. When primary infection occurs during adolescence or adulthood, it could cause infectious mononucleosis (IM). This disease is most of the time minor. EBV is also associated with several cancers like lymphomas (Burkitt's lymphoma and Hodgkin's lymphoma) or carcinomas (gastric carcinoma and nasopharyngeal carcinoma). Latent proteins of the virus are largely studied and are important for apparition of tumors. Recent studies show that lytic proteins are also important for tumor apparition and progression. The Helicase-Primase complex (H-P) of herpes simplex 1 (HSV-1), a well-known herpèsvirus, is a target for new antiviral drugs. ATPase, helicase and primase activities of HSV-1 complex are well studied, but no information is available for the structure of the H-P complex of human herpesvirus. We studied the H-P complex of EBV (BBLF4: helicase, BSLF1: primase and BBLF2/3: accessory subunit) to characterize its structure and enzymatic activities. We describe the expression and purification conditions and begin preliminary studies on structure and activities of the H-P complex. We show a basal ATPase activity that is DNA single strand independent. We were able to purify two forms of the H-P complex, the first has a stoichiometry close to 1/1/1 and the second one has an excess of helicase protein (BBLF4). These preliminary results on H-P complex of EBV have to be validated with other experiments before being compared to information already known for the HSV-1 complex. Key words : EBV, Helicase-Primase complex, BBLF4, BSLF1, BBLF2/3, ATPase, stoichiometry.

Mitochondrion is an organelle found in the eukaryotic cell. It is responsible for essential metabolic processes as well as ATP production via oxidative phosphorylation (OXPHOS). The mitochondrion contains DNA that encodes for several subunits in the OXPHOS system as well as rRNA and tRNA for translation. It also has its own replication, transcription and translation machinery. Proper maintenance of the mitochondrial DNA is critical for the cell’s health. Saccharomyces cerevisiae mitochondrial transcription system has been a great model system for its ease of genetic manipulation as well as having conserved RNA polymerases across species. The polymerases are homologues to T7 RNA polymerase, but have longer N-terminal domain and require transcription factor(s). The reason for the extra domain as well as the need for an accessory factor is still unclear. This study reveals the role of Rpo41 N-terminal domain (NTD) as well as clarifies the role of Mtf1, the transcription factor, in transcription initiation. Rpo41 is the 153 kDa catalytic subunit, and Mtf1 is 40 kDa, the transcription factor of the yeast mitochondria. We have shown that Mtf1 is required for correct promoter sequence recognition as well as inhibition of incorrect initiation. Although it was thought that Rpo41 has intrinsic promoter recognition capability, we have shown that Rpo41 can initiate transcription on a pre-melted DNA, even if it is not the consensus promoter sequence. N-terminal truncation mutant studies showed that the NTD of Rpo41 is also required for correct transcription initiation. On linear duplex DNA, N-terminal truncation of 321 amino acids has little effect when Mtf1 is present. On pre-melted DNA, it shows opposite trend from the wild-type. 160 N-terminal amino acid residue truncation shows little activity, whereas Mtf1 increases activity, even on non-promoter initiation sites. We further investigated properties of Rpo41 in replication. A link between mitochondrial transcription and replication has been suggested before, where Rpo41 functions as the leading strand primase. Our studies show that Rpo41 can indeed function as the leading and lagging strand primase, and explains why Rpo41 is able to initiate transcription on non-promoter sites. N-terminal truncation resulted in loss of primase activity, which shows that NTD is required for replication. / text

The phage-derived Lambda Red recombination system utilizes exogenous DNA in order to generate precise insertion, deletion, and point mutations in Escherichia coli and other bacteria. Due to its convenience, it is a frequently-used tool in genetics and molecular biology, as well as in larger-scale genome engineering projects. However, limited recombination frequency constrains the usefulness of Lambda Red for several important applications. In this work, I utilize a mechanism-guided approach in order to improve the power and utility of Lambda Red recombination.

München, Techn. Univ., Diss., 2003.

Les archées hyperthermophiles ont une température optimale de croissance supérieure à 80°C.Les cellules exposées à un stress thermique subissent une augmentation de la sensibilité aux agents induisant des cassures double brin de l’ADN. Les études sur les eucaryotes et bactéries ont démontré que la recombinaison homologue joue un rôle essentiel non seulement dans la réparation de l’ADN, mais aussi dans le redémarrage des arrêts de la fourche de réplication. Les enzymes associées aux étapes initiales de la recombinaison homologue chez les archées sont homologues à celles des eucaryotes, et différentes des analogues bactériens. De plus, plusieurs études ont démontré que les protéines impliquées dans la recombinaison homologue sont essentielles chez les archées hyperthermophiles, soulignant l’importance biologique de cette voie de réparation chez ces organismes particuliers. Le rôle de la recombinaison homologue pour la stabilité génomique a été bien étudié chez les eucaryotes et les bactéries, cependant, peu de ses propriétés fonctionnelles ont été étudiées chez les archées hyperthermophiles. Pour mieux comprendre le mécanisme de recombinaison homologue impliquée au niveau de la maintenance génomique chez les archées, un réseau d’interactions protéine-protéines a été révélé précédemment au laboratoire à partir des protéines de Pyrococcus abyssi. Ces travaux ont démontré de nouvelles interactions où interviennent les protéines de la réplication et les protéines de la recombinaison de l’ADN. L’objet de cette étude de thèse est de présenter deux interactions : PCNA/Mre11-rad50 (MR) complexe et Primase/RadA. Pour la première fois chez P. furiosus, une interaction physique et fonctionnelle a été démontrée entre le PCNA et le complexe MR (l’initiateur de HR). Un motif, situé en position Cterminale de Mre11, permet l’interaction avec PCNA.PCNA stimule l’activité endonucléase du complexe MR à distance proche de l’extrémité 5’ d’une cassure double brin. Cette propriété est en accord avec l’intervention ultérieure des enzymes assurant la suite du mécanisme de réparation par recombinaison homologue. Par ailleurs, les protéines RadA, Primase et P41 ont été produites et purifiées. Leurs fonctions enzymatiques ont été confirmées. Cependant, nous n’avons pas pu caractériser la fonction de l’association de RadA/Primase. / Hyperthermophilic archaea (HA) are found in high-temperature environments and grow optimally above 80°C. Usually, cells exposed to heat stress display an increased sensitivity to agents inducing double-stranded DNA breaks (DSBs). Studies in Eukaryotes and Bacteria have revealed that homologous recombination (HR) plays a crucial role not only in DNA DSBs repair, but also in the collapsed/stalled DNA replication fork restart.Recombinase and various HR-associated enzymes in archaea specifically resemble the eukaryotic homologues, rather than bacterial homologues.Furthermore, several studies have demonstrated the necessity of HR proteins in HA, suggesting that, HR is an important mechanism in HA. HR influencing genome stability has been well studied in Eukaryotes andBacteria, however, few of its functional properties have been studied in HA.To better understand how HR mechanism is involved in the archaeal genome maintenance process, a previous work proposed a protein-protein interaction network based on Pyrococcus abyssi proteins. Through the network, new interactions involving proteins from DNA replication and DNA recombination were highlighted. The targets of the study presented here for two protein interaction are: PCNA/Mre11-rad50 complex (MR complex) and Primase/RadA. For the first time in P. furiosus, we showed both physical and functional interactions between PCNA (Maestro in DNA replication) and MR complex (initiator of HR). We have identified a PCNA-interaction motif (PIP) located in the C-terminal of Mre11, and shown that PCNA stimulated MR complex endonuclease cleavage proximal to the s’ strand of DNA DSBs at physiological ionic strength. For the second interaction, we have purified the proteins PabRadA/PfuRadA, PabPrimase and PabP41, and confirmed its enzymatic functions. However, we were not able to characterize the function of Primase/RadA association.

Aspergillus fumigatus is a foodborne and airborne human pathogen which produces mycotoxins such as gliotoxin, helvolic acid, fumigallin, and fumigaclavin. The most common disease caused by A. fumigatus is aspergillosis, which is often fatal, especially among AIDS, cancer, and organ-transplant patients. In this study, random cDNA cloning was performed from a cDNA library of A. fumigatus (IMI 385708) constructed on &amp / #955 / ZAP Express. Some of these clones were selected according to their insert sizes and were further subjected to sequence analysis. The sequences were then analyzed by a BLAST search (NCBI Genome Database) to determine the possible functions of these genes. Two of the clones were identified as the primase and 60S ribosomal protein L1-b genes. These genes and a third gene corresponding to the antigenic cell wall galactomannoprotein gene of A. fumigatus were used for the design of three distinct primer pairs. For the primer design, a software was written to differentiate nonconserved regions by multiple sequence alignment. Designed primers were employed in PCR experiments against genomic DNAs of different Aspergillus species. Unique bands were obtained only against A. fumigatus genomic DNA. It was concluded that this PCR-based detection method can be further developed for the rapid detection of A. fumigatus spores from air and food samples.

Le virus Epstein-Barr (EBV) est un gamma herpèsvirus humain infectant plus de 95 % de la population mondiale. Lorsque la primo-infection a lieu pendant l'adolescence ou à l'âge adulte, elle peut induire la mononucléose infectieuse (MNI), cette maladie est le plus souvent bénigne. EBV est aussi associé à un certain nombre de cancers de type lymphome (lymphomes de Burkitt et d'Hodgkin) et de type carcinome (carcinomes gastriques et indifférenciés du rhinopharynx). L'importance des protéines de latence du virus dans l'apparition des tumeurs a été très étudiée. Des études récentes montrent que les protéines lytiques d'EBV sont aussi très importantes pour l'apparition et le développement des tumeurs. Le complexe Hélicase-Primase (H-P) du virus herpès simplex 1 (HSV-1, alpha herpèsvirus) est la cible de nouveaux antiviraux. Les activités ATPase, hélicase et primase du complexe d'HSV-1 ont été largement étudiées, mais aucune information structurale du complexe H-P n'est disponible actuellement pour un membre des herpèsvirus humains. Nous avons entrepris l'étude du complexe H-P d'EBV (BBLF4 : hélicase, BSLF1 : primase et BBLF2/3 : sous-unité accessoire) afin de caractériser sa structure et les activités qu'il porte. Nous avons pu établir les conditions d'expression et de purification du complexe et débuter des études structurales et enzymatiques préliminaires. Nous avons pu observer une activité ATPase basale du complexe indépendante de la présence d'un substrat ADN simple brin. Nous observons deux formes solubles du complexe lors des purifications, une présentant probablement une stœchiométrie proche de 1/1/1 et une seconde forme ayant surement un excès de la protéine Hélicase (BBLF4). Ces premiers résultats apportent des informations nouvelles pour le complexe H-P d'EBV et doivent être poursuivis afin de les confirmer et de pouvoir les comparer avec ceux déjà connus pour le complexe H-P d'HSV-1.

Plants maintain organelle genomes that are descended from ancient microbes. Ages ago, these ancient microbes were engulfed by larger cells, beginning a process of co-evolution we now call the endo-symbiotic theory. Over time, DNA from the engulfed microbe was transferred to the genome of the larger engulfing cell, eventually losing the ability to be free-living, and establishing a permanent residency in the larger cell. Similarly, the larger cell came to rely so much on the microbe it had engulfed, that it too lost its ability to survive without it. Thus, mitochondria and plastids were born. Nearly all multicellular eukaryotes possess mitochondria; however, different evolutionary pressures have created drastically different genomes in plants versus animals. For one, animals have very compact, efficient mitochondrial genomes, with about 97% of the DNA coding for genes. These genomes are very consistent in size across different animal species. Plants, on the other hand, have mitochondrial genomes 10 to more than 100 times as large as animal mitochondrial genomes. Plants also use a variety of mechanisms to replicate and maintain their DNA. Central to these mechanisms are nuclear-encoded, organelle targeted replication proteins. To date, there are two DNA polymerases that have been identified in plant mitochondria and chloroplasts, Pol1A and Pol1B. There is also a DNA helicase-primase that localizes to mitochondria and chloroplasts called Twinkle, which has similarities to the gp4 protein from T7 phage. In this dissertation, we discuss the roles of the polymerases and the effects of mutating the Pol1A and Pol1B genes respectively. We show that organelle genome copy number decreases slightly and over time but with little effect on plant development. We also detail the interactions between Twinkle and Pol1A or Pol1B. Plants possess the same organellar proteins found in animal mitochondria, which are homologs to T7 phage DNA replication proteins. We show that similar to animals and some phage, plants utilize the same proteins in similar interactions to form the basis of a DNA replisome. However, we also show that plants mutated for Twinkle protein show no discernable growth defects, suggesting there are alternative replication mechanisms available to plant mitochondria that are not accessible in animals.