La Poly(ADP-ribosyl)ation est une modification post-traductionnelle de protéines, impliquée dans un grand nombre de processus biologiques, dont la réparation de l’ADN. Alors que la fonction et le mode d’action de la Poly(ADP-ribose) (PAR) Polymérase 1 (PARP1), activée en réponse aux dommages de l’ADN sont bien compris, on en sait beaucoup moins sur la fonction et la régulation de l’enzyme de dégradation du PAR, la Poly(ADP-ribose) glycohydrolase (PARG). Dans le contexte de ce projet de thèse, nous décrivons de nouvelles lignées U2OS stables, déficientes pour toutes les isoformes de PARG, permettant la complémentation inductible avec chacun des isoformes de PARG. Ces modèles nous ont permis d’évaluer les contributions relatives des isoformes à la réparation de dommages à l’ADN. Nous avons identifié un nouveau partenaire cellulaire de PARG : la protéine-kinase dépendante des dommages à l’ADN (DNA-PK). Nous explorons l’interaction fonctionnelle de ces deux protéines dans le contexte de la réponse cellulaire à la camptothécine (CPT), un agent anticancéreux inhibant la topoisomérase I et provoquant l’activation simultanée de PARP1 et DNA-PK. / Poly (ADP-ribosyl) ation is a post-translational modification of proteins involved in a large number of biological processes, including DNA repair. While the function and mode of action of Poly (ADP-ribose) (PAR) Polymerase 1 (PARP1), activated in response to DNA damage, is well understood, much less is known about the function and regulation the PAR degrading enzyme, Poly (ADP-ribose) glycohydrolase (PARG). In the context of this thesis project, we describe new stable U2OS lines, deficient for all PARG isoforms, allowing the inducible complementation with each of the PARG isoforms. These models allowed us to evaluate the relative contributions of the isoforms to DNA damage repair. We have identified a new cellular partner of PARG: the DNA-dependent protein kinase-dependent kinase (DNA-PK). We explore the functional interaction between these two proteins in the context of the cellular response to camptothecin (CPT), an anticancer drug that inhibits topoisomerase I and induces the simultaneous activation of PARP1 and DNA-PK.

L’altération de l’environnement périnatal peut impacter à long terme l’expression des gènes notamment par le biais de modifications épigénétiques. Une stratégie pour accroitre la thermotolérance des poulets de chair, sensibles à la chaleur en fin d’élevage (J35) est la thermo-manipulation embryonnaire (TM). Lors d’un coup de chaleur à J35, les modifications d’expression de gènes observées chez les poulets TM pourraient être liées à une altération de l’épigénome induite lors de l’embryogenèse et persistante au cours du développement. Cette thèse s’intéresse à deux modifications post-traductionnelles des histones (MPTH) décrites pour être modulées par des variations thermiques : H3K27Me3 et H3K4Me3. Afin d’étudier ces MPTH sans a priori à J35, nous avons mis au point les techniques d’immunoprécipitation de la chromatine suivie de séquençage à haut débit dans deux tissus : l’hypothalamus et le muscle. Nos travaux montrent que le traitement semble impacter principalement l’épigénome de l’hypothalamus, en particulier au niveau de la marque H3K4me3, en modulant des voies liées à la morphogenèse et la réponse hormonale. / Perinatal environment changes may alter gene expression throughout life via epigenetic modifications. A strategy to improve thermal tolerance of heat-sensitive chickens is a thermalmanipulation during embryogenesis (TM). During a heat challenge at the end of the rearing period (D35), modifications of gene expression have been reported in thermally-manipulated chickens. These alterations could be linked to epigenetic modifications induced during the TM that persist throughout life. This work focused on two histone post-translational modifications (HPTM): H3K27me3 and H3K4me3. We adjusted two methods of chromatin immunoprecipitation to conduct a whole genome study of these HPTM at D35, in the hypothalamus and skeletal muscle. We demonstrated that the TM has a major impact in the hypothalamus, especially on H3K4me3. These alterations seem to modulate the hypothalamic morphogenesis and its response to hormones, therefore possibly contributing to better adaptive capacities of TM chickens.

La protéine Tax du virus HTLV-1 a les propriétés d'un oncogène viral et joue un rôle important dans l'induction de la transformation cellulaire menant à l'ATL. L'activité oncogène de Tax résulte d'effets pléiotropes sur divers mécanismes cellulaires y compris l'activation de l'expression de gènes cellulaires spécifiques par la voie NF-&61547;B et la dérégulation de la progression du cycle cellulaire. Dans ce travail, nous avons mis en évidence que Tax est une protéine hautement modifiée dans diverses lignées cellulaires y compris dans les lymphocytes T transformés par HTLV-1. L'ensemble des modifications post-traductionnelles de Tax forment une suite hiérarchisée qui contrôlent la localisation intracellulaire de Tax, sa capacité d'activer les kinases IKK et la voie de signalisation des facteurs NF-&61547;B et sa capacité d'induire un arrêt dans la progression de la mitose. En effet, la phosphorylation de Tax contrôle son ubiquitination et son passage dans le noyau où elle est sumoylée et acétylée. L’ubiquitination et la sumoylation de Tax agissent de manière concertée pour permettre l’activation de l’expression des gènes par la voie NF-& / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

L'unité structurale de la chromatine, nommée nucléosome, est composée d'un double brin d'ADN enroulé autour d'un octamère d'histone, et subit une pléthore de modifications post-traductionnelles. Les conséquences biologiques de l’acétylation des lysines et de l’isomérisation des liaisons peptidyl-prolyl ont été étudiées à travers une analyse à l’échelle atomique par RMN de systèmes d'intérêt reconstitués in vitro. Les liaisons peptidyl-prolyl du domaine N-terminal de l'histone H3 sont substrats in vitro d’une isomérase chez S. cerevisiae nommée Fpr4p, laquelle exerce un contrôle catalyse-dépendant de la transcription. La résolution de la structure du domaine catalytique de Fpr4p, à partir de contraintes géométriques mesurées par RMN, révéla un domaine canonique de la famille FKBP (FK506-binding protein). Grâce à l'analyse de la séquence primaire et aux expériences RMN, nous proposons un modèle structural préliminaire de Fpr4p entière. L'analyse fonctionnelle est réalisée grâce à trois décapeptides construits à partir de la séquence primaire de H3 chez S. cerevisiae. Ils sont tous substrats de Fpr4p et la catalyse est équivalente pour Pro16 et Pro30. La proportion à l'équilibre du conformère cis fut déterminée pour les trois peptides et celle-ci n'est pas affectée par l'activité catalytique de Fpr4p. Les structures en solution des substrats en conformation trans ont été résolues par spectroscopie RMN, et seront utilisées pour des appariements moléculaires in silico sur le domaine catalytique de Fpr4p. Pour étudier le rôle biologique de l'acétylation des histones, une méthodologie de production de protéines acétylées a été développée. Le protocole repose sur la mutation d'une lysine en cystéine d'une protéine recombinante, suivie d'une alkylation contrôlée exploitant la nucléophilie du groupe thiol préalablement introduit. La production de l'agent alkylant adéquat est simple, rapide, réalisable dans un laboratoire de biologie et permet différents marquages isotopiques du groupe acétyle. L'alkylation d'une protéine repliée fut réalisée avec succès en conditions natives. Le dimère d'histone H2A-H2B, un intermédiaire de l'assemblage du nucléosome et siège d'acétylation in vivo, fut reconstruit in vitro. Les déplacements chimiques des domaines N et C-terminaux de H2A sont cohérents avec un état intrinsèquement déstructuré bien que leurs dynamiques moléculaires ne soient pas équivalentes. / The structural unit of chromatin, the nucleosome, is composed of double-stranded DNA wrapped around a histone octamer and is subject to a plethora of post-translational modifications. The biological consequences of peptidyl-prolyl isomerization and lysine acetylation were investigated at atomic scale through analysis of in vitro reconstituted systems by NMR. Peptidyl-prolyl bonds of histone H3 N-terminal domain are substrates in vitro of an isomerase from S. cerevisiae named Fpr4p, which underlies transcriptional control dependent on its catalytic activity. The solution structure of the catalytic domain of Fpr4p was calculated based on restraints from NMR spectroscopy, and reveals a canonical catalytic domain belonging to the FK506-binding protein (FKBP) family. Based on primary sequence analysis and NMR experiments, a preliminary structural model of full length Fpr4p is also presented. Functional analyses were performed with three decapeptides designed from the primary sequence from the N-terminal tail of S. cerevisiae histone H3. All three constitute substrates of Fpr4p, with equivalent catalysis observed for Pro16 and Pro30. The equilibrium proportion of the cis-proline conformer has been determined for all three decapeptides, and these populations are unaffected by Fpr4p catalytic activity. Structural ensembles of the substrates with proline in the trans conformation were determined by using NMR spectroscopy, and will be subsequently used for in silico molecular docking onto Fpr4p. To study a second form of histone regulation, a semi-synthetic method to produce acetylated protein was developed. The protocol relies on the site-specific mutation of lysine to cysteine in recombinant proteins followed by controlled alkylation thanks to nucleophilicity of the introduced thiol. The production of the required alkylation reagent is easy, quick, and suitable for biology laboratory and allows diverse isotopic labeling within the acetyl group. Alkylation of folded proteins has also been achieved in native conditions. As one target of acetylation in vivo, the histone H2A-H2B dimer is an intermediate of nucleosome assembly and was reconstituted in vitro. Chemical shift values of the N- and C-terminal domains of H2A are in agreement with an intrinsically disordered state although they display differences in dynamic mobility.

Indiana University-Purdue University Indianapolis (IUPUI) / Toxoplasma gondii, a single-celled eukaryotic pathogen, has infected one-third of the world’s population and is the causative agent of toxoplasmosis. The disease primarily affects immunocompromised individuals such as AIDS, cancer, and transplant patients. The parasites can infect any nucleated cell in warm-blooded vertebrates, but because they preferentially target CNS, heart, and ocular tissue, manifestations of infection often include encephalitis, myocarditis, and a host of neurological and ocular disorders. Toxoplasma can also be transmitted congenitally by a mother who becomes infected for the first time during pregnancy, which may result in spontaneous abortion or birth defects in the child. Unfortunately, the therapy currently available for treating toxoplasmosis exhibits serious side effects and can cause severe allergic reactions. Therefore, there is a desperate need to identify novel drug targets for developing more effective, less toxic treatments. The regulation of proteins via lysine acetylation, a reversible post-translational modification, has previously been validated as a promising avenue for drug development. Lysine acetyltransferases (KATs) are responsible for the acetylation of hundreds of proteins throughout prokaryotic and eukaryotic cells. In Toxoplasma, we identified a KAT that exhibits homology to Elongator protein 3 (TgElp3), the catalytic component of a transcriptional elongation complex. TgElp3 contains the highly conserved radical S-adenosylmethionine and KAT domains but also possesses a unique C-terminal transmembrane domain (TMD). Interestingly, we found that the TMD anchors TgElp3 in the outer mitochondrial membrane (OMM) such that the catalytic domains are oriented towards the cytosol. Our results uncovered the first tail-anchored mitochondrial KAT reported for any species to date. We also discovered a shortened form of Elp3 present in mouse mitochondria, suggesting that Elp3 functions beyond transcriptional elongation across eukaryotes. Furthermore, we established that TgElp3 is essential for parasite viability and that its OMM localization is important for its function, highlighting its value as a potential target for future drug development.

Indiana University-Purdue University Indianapolis (IUPUI) / Murine double minute (Mdm2) is a highly modified and multi-faceted protein that is overexpressed in numerous human malignancies. It engages in many cellular activities and is essential for development since deletion of mdm2 is lethal in early stages of embryonic development. The most studied function of Mdm2 is as a negative regulator of the tumor suppressor protein p53. Mdm2 achieves this regulation by binding to p53 and inhibiting p53 transcriptional activity. Mdm2 also functions as an E3 ubiquitin ligase that signals p53 for destruction by the proteasome. Interestingly recent evidence has shown that Mdm2 can also function as an E3 neddylating enzyme that can conjugate the ubiquitin-like molecule, nedd8, to p53. This modification results in inhibition of p53 activity, while maintaining p53 protein levels. While the signaling events that regulate Mdm2 E3 ubiquitin ligase activity have been extensively studied, what activates the neddylating activity of Mdm2 has remained elusive. My investigations have centered on understanding whether tyrosine kinase signaling could activate the neddylating activity of Mdm2. I have shown that c-Src, a non-receptor protein tyrosine kinase that is involved in a variety of cellular processes, phosphorylates Mdm2 on tyrosines 281 and 302. This phosphorylation event increases the half-life and neddylating activity of Mdm2 resulting in a neddylation dependent reduction of p53 transcriptional activity. Mdm2 also has many p53-independent cellular functions that are beginning to be linked to its role as an oncogene. There is an emerging role for Mdm2 in tumor metastasis. Metastasis is a process involving tumor cells migrating from a primary site to a distal site and is a major cause of morbidity and mortality in cancer patients. To date, the involvement of Mdm2 in breast cancer metastasis has only been correlative, with no in vivo model to definitively define a role for Mdm2. Here I have shown in vivo that Mdm2 enhances breast to lung metastasis through the up regulation of multiple angiogenic factors, including HIF-1 alpha and VEGF. Taken together my data provide novel insights into important p53-dependent and independent functions of Mdm2 that represent potential new avenues for therapeutic intervention.

<p dir="ltr">This dissertation delves into two research projects that aim to characterize post-translational modifications in two distinct proteins, each originating from a different species – one from the eukaryotic sea slug Aplysia californica and the other from the bacterial pathogen Bordetella bronchiseptica.</p><p dir="ltr">Aplysia have an unusually large neuron and therefore serve as an excellent model for studying cell signaling regulating neuronal chemotaxis. Cortactin is an actin binding protein that is regulated by post-translational modifications, including acetylation and phosphorylation. Studies have shown that Src2 tyrosine kinase phosphorylates cortactin to regulate lamellipodia protrusion and filopodia formation in Aplysia bag cell neurons. However, these in vivo phenotypes have not been tested mechanistically in vitro. To this end, the goal of my thesis work was to validate in vivo observations. The following work describes the methodology we developed to purify homogenous non-phosphorylated proteins. Our collaborative results show that Src2 phosphorylates cortactin at Y499, although Y505 is the preferred site in vitro.</p><p dir="ltr"> Filamentation induced by cAMP (Fic) proteins constitute a recently characterized family of enzymes that are being recognized to regulate diverse cellular processes in bacteria and metazoans. While Fic proteins predominantly utilize adenosine triphosphate (ATP) to post-translationally modify target proteins via a covalent addition of AMP, two Fic proteins have been reported that utilize uridine triphosphate (UTP) and cytidine diphosphate-choline (CDP-choline) to alter the activity of their target. In this dissertation, we report the discovery of the first guanosine triphosphate (GTP) specific Fic protein – BB0907 (BbFic) from Bordetella bronchiseptica. BbFic displays weak to no binding to ATP; instead has a 10-fold increased preferential usage for GTP. We identify key residues involved in GTP recognition. Additionally, sequence similarity network (SSN) analyses reveal that BbFic represents a distinct clade of Fic proteins, highlighting BbFic as a representative new class of guanylyltransferase. Our discovery adds to the functional diversity of the growing Fic protein family and frames the groundwork for understanding Fic-mediated GMPylation as a novel signaling paradigm. </p><p dir="ltr">Taken together, my thesis work provides novel insights into biological consequences of Fic-mediated GMPylation in bacteria and Src-mediated phosphorylation in filopodia formation.</p><p><br></p>

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