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Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand polymerase structure with a unique and large 369 amino acid insertion within the polymerase domain (thumb region) homologous to E. coli RNase T. The goal of this study was to evaluate whether the polymerase domain is necessary for the essential replicative role of POLIB. To study the structure-function relationship, an RNAi-complementation system was designed to ectopically express POLIB variants in T. brucei that has endogenous POLIB silenced by RNAi.Control experiments expressing an ectopic copy of POLIB wildtype (IBWTPTP) or polymerase domain mutant (IBPol-PTP) in the absence of RNAi did not impact fitness in procyclic cells despite protein levels being 5 - 8.5 fold higher than endogenous POLIB levels. Immunofluorescence detection of the tagged variants indicated homogenous expression of the variants in a population of cells and negligible changes in kDNA morphology. Lastly, Southern blot analyses of cells expressing the IBWTPTP or IBPol-PTP variants indicated no changes in free minicircle species. A dually inducible RNAi complementation system was designed and tested with the IBWTPTP and IBPol-PTP variants. Inductions of POLIB RNAi accompanied by ectopic expression of either variant using the standard 1 mg/ml tetracycline resulted in low protein levels of both variants while knockdown of the endogenous POLIB mRNA was greater than 85%. Increasing the tetracycline concentration to 4 mg/ml improved expression levels of both variants. However, levels of the ectopically expressed variants never exceeded that of endogenous POLIB. Using the 4 mg/ml induction conditions, complementation with IBWTPTP resulted in a partial rescue of the POLIB RNAi phenotype based on fitness curves, quantification of kDNA content and Southern blot analysis of free minicircles. IBWTPTP complementation resulted in gradual increase of IBWTPTP protein levels over the 10 day induction, and a small kDNA phenotype instead of the progressive loss of kDNA normally associated with POLIB RNAi. Additionally, the loss of free minicircles was delayed. Complementation with the IBPol-PTP variant produced more consistent levels of IBPol-PTP protein although still below endogenous POLIB levels. Loss of fitness was similar to POLIB RNAi alone. However, a small kDNA phenotype emerged early after just four days of complementation and persisted for the remainder of the induction. The majority of the IBRNAi + IBPol-PTP population (70%) contained small kDNA compared to the parental POLIB RNAi or IBWTPTP complementation that had only 45% and 50% small kDNA, respectively. Lastly, the pattern of free minicircle loss closely resembled POLIB RNAi alone. Together, these data suggest that the dually inducible system results in a partial rescue with the IBWTPTP variant. Rescue with IBPol-PTP variant results in a noticeably different phenotype from either POLIB RNAi alone or IBWTPTP complementation indicating that the POLIB polymerase domain is likely essential for the in vivo role of POLIB during kDNA replication.

Les papillomavirus sont des virus à ADN qui infectent la peau et les muqueuses. Ils causent des verrues et peuvent aussi mener au développement de cancers, dont le cancer du col de l’utérus. La réplication de leur génome nécessite deux protéines virales : l’hélicase E1 et le facteur de transcription E2, qui recrute E1 à l’origine de réplication virale. Pour faciliter l’étude de la réplication du génome viral, un essai quantitatif et à haut débit basé sur l’expression de la luciférase a été développé. Parallèlement, un domaine de transactivation a été identifié dans la région régulatrice N-terminale de la protéine E1. La caractérisation de ce domaine a montré que son intégrité est importante pour la réplication de l’ADN. Cette étude suggère que le domaine de transactivation de E1 est une région protéique intrinsèquement désordonnée qui permet la régulation de la réplication du génome viral par son interaction avec diverses protéines. / Papillomaviruses are small DNA viruses that infect skin and mucosa. They cause warts and can also lead to the development of cancers, including cervical cancer. Replication of their genome requires two viral proteins: the E1 helicase and the E2 transcription factor, which recruits E1 to the viral origin of replication. To facilitate the study of viral genome replication, a quantitative and high-throughput assay based on luciferase expression has been developed. In parallel, a transactivation domain has been identified in the N-terminal regulatory region of the E1 protein. Characterization of this domain showed that its integrity is important for DNA replication. This study suggests that the E1 transactivation domain is an intrinsically unstructured protein region that allows regulation of viral genome replication by its interaction with diverse proteins.

La leucémie lymphoïde représente environ 30% des cas de cancer chez l’enfant. Elle est souvent causée par des réarrangements chromosomiques impliquant des gènes encodant des facteurs de transcription, qui contrôlent des programmes génétiques complexes. Par exemple, LMO2 (LIM-only 2) est un facteur de transcription oncogénique fréquemment exprimé de façon aberrante dans les leucémies lymphoblastiques aigues des cellules T (T-ALL). Dans l’hématopoïèse normale, LMO2 est essentiel à la génération des cellules souches hématopoïétiques à l’origine de toutes les cellules sanguines. D’ailleurs, certaines cellules leucémiques possèdent des propriétés normalement réservées aux cellules souches hématopoïétiques. Ainsi, l’étude de la fonction de LMO2 dans les cellules souches hématopoïétiques peut être pertinente autant dans le contexte hématopoïétique normal que leucémique. Afin de mettre en évidence de nouvelles fonctions moléculaires pour LMO2, j’ai choisi d’identifier les protéines qui s’y associent. En plus de ses partenaires connus, j’ai identifié plusieurs protéines de transcription/remodelage de la chromatine, en accord avec son rôle transcriptionnel. Plusieurs nouvelles fonctions potentielles ont été révélées, indiquant que cette protéine adaptatrice pourrait faire partie de complexes non transcriptionnels, régulant d’autres processus cellulaires. Les oncogènes comme LMO2 pourraient être des régulateurs à large spectre. Particulièrement, j’ai identifié des interactions entre LMO2 et des protéines de réplication de l’ADN. J’ai montré que LMO2 contrôle la réplication de l’ADN dans les cellules hématopoïétiques, et possiblement durant la leucémogenèse, indépendamment de son rôle transcriptionnel. Ensemble, ces études ont donc permis de révéler de nouvelles fonctions pour LMO2, et pourraient servir de paradigme pour d’autres facteurs de transcription oncogéniques, particulièrement aux autres protéines de la famille LMO, qui sont aussi des oncogènes puissants. / Lymphoid leukemia represents about 30% of childhood cancer cases. It is often caused by chromosomal rearrangements involving genes coding for transcription factors, controlling complex genetic programs. As an example, the oncogenic transcription factor LMO2 (LIM-only 2) is often aberrantly expressed in T cell acute lymphoblastic leukemia (T-ALL). In normal hematopoiesis, LMO2 is essential for the generation of hematopoietic stem cells that give rise to all blood cells. Moreover, some leukemic cells possess properties normally reserved to hematopoietic stem cells. Thus, studying the role of LMO2 in hematopoietic stem cells could be relevant to the contexts of normal hematopoiesis and leukemogenesis. To reveal new molecular functions for LMO2, I chose to identify its associated proteins. In addition to its known protein partners, I identified many proteins involved in transcription/chromatin remodeling, in agreement with its transcriptional role. In addition, several new potential functions have been revealed, indicating that this scaffold protein could be part of non-transcriptional protein complexes, regulating different cell processes. Oncogenes like LMO2 could be master regulators in normal hematopoietic and leukemic cells. Particularly, I identified protein-protein interactions between LMO2 and DNA replication proteins. I demonstrated that LMO2 controls S phase progression in hematopoietic cells, independently of its association in transcriptional complexes. LMO2 overexpression in mice induces T-ALL and affects specifically the cell cycle status of thymocyte progenitors, which are targets of transformation by LMO2. Thus, LMO2 promotes DNA replication in hematopoietic cells, and possibly in leukemogenesis. Together, these studies allowed to reveal new functions for LMO2, and could serve as a paradigm for other oncogenic transcription factors, especially for other LMO proteins which are all potent oncogenes.

Le virus du papillome humain (VPH) est l’agent étiologique du cancer du col utérin, ainsi que d’autre néoplasies anogénitales et des voies aérodigestives supérieures. La réplication de son génome d’ADN double brin est assurée par les protéines virales E1 et E2, de concert avec la machinerie cellulaire de réplication. E1 assure le déroulement de l’ADN en aval de la fourche de réplication, grâce à son activité hélicase, et orchestre la duplication du génome viral. Nos travaux antérieurs ont démontré que le domaine N-terminal de E1 contient un motif de liaison à la protéine cellulaire p80/UAF1 qui est hautement conservé chez tous les VPH anogénitaux. L’intégrité de ce motif est essentielle au maintien de l’épisome viral. Les travaux présentés dans cette thèse ont d’abord déterminé que le motif de liaison à UAF1 n’est pas requis pour l’assemblage du pré-réplisome viral, mais important pour la réplication subséquente de l’ADN du VPH. Nous avons constaté qu’en présence de E1 et E2, UAF1 est relocalisé dans des foyers nucléaires typiques de sites de réplication du virus et qu’en outre, UAF1 s’associe physiquement à l’origine de réplication du VPH. Nous avons aussi déterminé que l’inhibition du recrutement de UAF1 par la surexpression d’un peptide dérivé de E1 (N40) contenant le motif de liaison à UAF1 réduit la réplication de l’ADN viral. Cette observation soutient le modèle selon lequel UAF1 est relocalisé par E1 au réplisome pour promouvoir la réplication de l’ADN viral. UAF1 est une protéine à domaine WD40 n’encodant aucune activité enzymatique et présumée exploiter des interactions protéine-protéine pour accomplir sa fonction. Nous avons donc investigué les protéines associées à UAF1 dans des cellules du col utérin et avons détecté des interactions avec les enzymes de déubiquitination USP1, USP12 et USP46, ainsi qu’avec la phosphatase PHLPP1. Nous avons établi que E1 forme un complexe ternaire avec UAF1 et n’importe laquelle des USP associés : USP1, USP12 ou USP46. Ces USP sont relocalisés au noyau par E1 et s’associent à l’ADN viral. De plus, l’activité enzymatique des USP est essentielle à la réplication optimale du génome viral. Au contraire, PHLPP1 ne forme pas de complexe avec E1, puisque leurs interactions respectives avec UAF1 sont mutuellement exclusives. PHLPP1 contient un peptide de liaison à UAF1 homologue à celui de E1. Ce peptide dérivé de PHLPP1 (P1) interagit avec le complexe UAF1-USP et, similairement au peptide N40, antagonise l’interaction E1-UAF1. Incidemment, la surexpression du peptide P1 inhibe la réplication de l’ADN viral. La génération de protéines chimériques entre P1 et des variants de E1 (E1Δ) défectifs pour l’interaction avec UAF1 restaure la capacité de E1Δ à interagir avec UAF1 et USP46, ainsi qu’à relocaliser UAF1 dans les foyers nucléaires contenant E1 et E2. Ce recrutement artificiel de UAF1 et des USP promeut la réplication de l’ADN viral, un phénotype dépendant de l’activité déubiquitinase du complexe. Globalement, nos travaux suggèrent que la protéine E1 du VPH interagit avec UAF1 afin de recruter au réplisome un complexe de déubiquitination dont l’activité est importante pour la réplication de l’ADN viral. / Human papillomaviruses (HPVs) are the etiological agents of cervical cancers, as well as multiple other anogenital and oropharyngeal neoplesias. The viral proteins E1 and E2, in concert with the host DNA replication machinery, mediate the replication of the double-stranded DNA genome of HPV. E1 exploits its helicase activity to unwind DNA ahead of the replication fork and orchestrates synthesis of the viral genome. Our previous work demonstrated that E1 contains in its N-terminus a binding motif for the host protein p80/UAF1, a domain that is highly conserved amongst anogenital HPVs. The integrity of this region was essential for the maintenance of the viral episome. The research presented here first demonstrated that the UAF1-binding motif is not required for the assembly of the E1-E2-Origin pre-replisome, but important for the following viral DNA replication. We have determined that UAF1 is relocalized, in presence of E1 and E2, in nuclear foci reminiscent of viral DNA synthesis sites. UAF1 also physically interacted, through E1-binding, with the viral origin of replication. Moreover, we have shown that inhibition of E1-UAF1 interaction through the overexpression of an E1-derived and UAF1-binding peptide, N40, interferes with HPV DNA replication. This is in agreement with the model according to which E1 recruits UAF1 to the replisome to promote viral DNA replication. UAF1 is a WD40-containing protein with no enzymatic activity and presumed to function through interactions with other cellular factors. We have investigated the UAF1 interaction network in cervical cells and discovered that UAF1 associates with the deubiquitinating enzymes USP1, USP12 and USP46, as well as with the phosphatase PHLPP1. E1 was found to assemble as a ternary complex with UAF1 and any of the associated USPs: USP1, USP12 or USP46. These USPs were also relocalized by E1 to the nucleus and they associated with the viral origin in presence of E2. Moreover, their enzymatic function was essential for optimal viral genome replication. In contrast, PHLPP1 did not associate with E1, and the interactions of the latter proteins with UAF1 were shown to be mutually exclusive. PHLPP1 contains a UAF1-binding motif homologous to the one encoded within E1. This PHLPP1-derived peptide, P1, interacts with the UAF1-USP complex and, similarly to N40, competes with E1-UAF1 interaction. Accordingly, P1 overexpression leads to inhibition of HPV DNA replication. The fusion of the peptide P1 to an E1 protein (E1Δ) defective for UAF1-binding restored its capacity to interact with UAF1 and USP46, as well as to relocalize UAF1 into E1-E2-containing nuclear foci. This artificial recruitment of UAF1 and of the associated USPs increased viral DNA replication, a process that involved the enzymatic activity of the USPs. Collectively, our work suggests that HPV E1 interacts with UAF1 in order to recruit to the replisome a deubiquitinating complex whose activity is required for optimal viral DNA replication.

Currently, pupils' interest in science continues to decline, although this area of education is very important in every day life (medicine, environment, etc.) and there is high demand for science professions on the labor market. Molecular biology curriculum concerning DNA and the transfer of genetic information is abstract and difficult topic for pupils to imagine, and for teachers to explain. There are many ways to teach this topic. Very popular are iquiry and laboratory practise. But not all schools have their own laboratories, and can teach molecular practical effectivelly. Inquiry based teaching is time consuming to prepare, and not every topic is appropriate to be taught this way. Another possibilities how to visualize "invisible" molecules and processes are computer software and animations or 3D physical model. In my thesis, I examined the effect of using computers and animations to teach abou DNA compared to using a 3D physical model on students' knowledge. I laso tested the possible influence of gender and pupils' preferences on their achieved score on knowledge tests. The research was performed in five classes at three high schools in Prague. Students in year 12 were on different types of high school and some of them took special biology class, their age was between 15 and 18 years. The...