The amino acid proline is unique – within a polypeptide chain, proline adopts either a cis or trans peptide bond conformation while all other amino acids are sterically bound primarily in the trans configuration. In proteins, the isomeric state of a single proline can have dramatic consequences on structure and function. Consequently, cis-trans interconversion confers both barrier and opportunity – on one hand, isomerization is a rate limiting step in de novo protein folding and on the other can be utilized as a post-translational regulatory switch. Peptidyl-prolyl isomerases (PPIs) are a ubiquitous superfamily that catalyzes the interconversion between conformers. Although pervasive, the functions and substrates of most PPIs are unknown. The two largest subfamilies, FKBPs and cyclophilins, are the intracellular receptors of clinically relevant immunosuppressant drugs that also show promise in the treatment of neurodegenerative disorders and cancer. Therefore, narrowing the knowledge gap has significant potential to benefit human health. FKBP25 is a high-affinity binder of the PPI inhibitor rapamycin and is one of few nuclear-localized isomerases. While it has been shown to bind DNA and associate with chromatin, its function has remained largely uncharacterized. I hypothesized that FKBP25 targets prolines in nuclear proteins to regulate chromatin-templated processes. To explore this, I performed high-throughput transcriptomic and proteomic studies followed by detailed molecular characterizations of FKBP25’s function. Here, I discover that FKBP25 is a multifunctional protein required for the maintenance of genomic stability. In Chapter 2, I characterize the unique N-terminal Basic Tilted Helical Bundle (BTHB) domain of FKBP25 as a novel dsRNA binding module that recruits FKBP25’s prolyl isomerase activity to pre-ribosomal particles in the nucleolus. In Chapter 3, I show for the first time that FKBP25 associates with the mitotic spindle apparatus and acts to stabilize the microtubule cytoskeleton. In this chapter, I also present evidence that this function influences the stress response, cell cycle, and chromosomal stability. Additionally, I characterize the regulation of FKBP25’s localization and nucleic acid binding activity throughout the cell cycle. Finally, in Chapter 4, I uncover a role for FKBP25 in the repair of DNA double-stranded breaks. Importantly, this function requires FKBP25’s catalytic activity, identifying for the first time a functional requirement for cis-trans prolyl isomerization by FKBP25. Collectively, this work identifies FBKP25 as a multifunctional protein that is required for the maintenance of genomic stability. The knowledge gained contributes to the exploration of PPIs as important drug targets. / Graduate

This thesis explores localisations and roles of three auxiliary protein factors involved in the biogenesis of Photosystem II (PSII) in the cyanobacterium Synechocystis sp. PCC 6803 and contributes to subcellular localisation of the initial steps of PSII biogenesis and repair-related D1 synthesis. The main results consist in i) identification of a functional interaction of the protein factor Psb27 with a lumenal domain of the Photosystem II subunit CP43, ii) discovery of a novel pigment binding complex formed by the Ycf39 protein and high-light-inducible proteins implicated in photoprotection and delivery of recycled chlorophyll to newly synthesized D1 protein during the PSII reaction centre formation, iii) providing evidence that the early steps of PSII assembly and the repair-related D1 synthesis occur in the thylakoid membrane of Synechocystis, and iv) revealing that the cyanobacterial PsbP orthologue, CyanoP, assists in the early phase of PSII biogenesis as an assembly factor facilitating the association of D2 and D1 assembly modules.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Acute liver failure (ALF) induced by acetaminophen (APAP) is a complex process associated with glutathione (GSH) depletion, energetics metabolism changes and mitochondrial dysfunction, resulting in the impairment of maintenance of tissue normal function. On this matter, organoselenium compounds, such as diphenyl diselenide (PhSe)2, have been highlighted in the last years due to the antioxidant properties and the hepatoprotective effects, however, the (PhSe)2 hepatoprotection mechanism remains unclear. So, this work was aimed to deepen into understanding of the effects of (PhSe)2 on the mitochondrial dysfunction as well as the signaling pathway during the ALF induced by APAP. Firstly, it was performed a comparative study between the organoselenium compound and the classical antidote (N-acetylcysteine, NAC) in the liver homogenate. (PhSe)2 presented similar results to the NAC reducing the oxidative damage markers, maintaining the GSH levels and enhancing the survival after the APAP overdose. The treatment with (PhSe)2 reduced plasmatic levels of transaminases (aspartate and alanine aminotransferase) and the morphological/histological changes. In addition, (PhSe)2 was able to reduce significantly the oxidative damage such as lipid peroxidation, reactive oxygen and nitrogen species generation, mitochondrial protein carbonylation and mitochondrial viability after ALF induced by APAP. In this context, the levels of non enzymatic antioxidants, such as GSH, and enzymatic antioxidants, such as catalase, Mn superoxide dismutase, glutathione peroxidase and glutathione reductase remained to the control levels. In general, the results noticed in this work the probably (PhSe)2 mechanism is closely related with the maintenance of antioxidant defense system and inhibition of mitochondrial transition permeability (MPT) indicated by reduction of mitochondrial swelling, activity preservation of respiratory complexes I, II and ATPase, and maintenance of H+ gradient with the mitochondrial membrane potential (Δψm) generation. It was observed that (PhSe)2 was able to limit the impairment of mitochondrial bioenergetics function with the normalization of oxidative phosphorilation (OXPHOS) and activation of heat shock protein pathway through the enhance of HSP70 levels, which in turn, modulates the MPT protecting the mitochondrial viability. (PhSe)2 treatment was able to maintain the appropriated levels of cytokines associated with the liver recovery, such as tumoral necrosis factor alfa (TNF-α), interleukin 6 (IL-6) and nuclear factor kappa B (NF-κB). Moreover, the integrity of cellular bioenergetic function could be associated with the increase of peroxisome proliferator-activated receptor-γ coactivator (PGC-1α), helping to restore the nuclear respiratory factor 1 (NRF1) levels associated with the mitochondrial biogenesis. Finally, (PhSe)2 could be a useful therapeutic alternative that would contribute to the liver recovery, controlling the quality of mitochondrial function and maintaining homeostasis and cellular health. / A insuficiência hepática aguda (IHA) induzida por paracetamol (APAP) é um processo complexo que envolve depleção de glutationa (GSH), mudanças no metabolismo energético e disfunção mitocondrial, o que resulta na incapacidade de manter o funcionamento adequado do órgão. Neste contexto, a utilização de compostos orgânicos de selênio como o difenil disseleneto (PhSe)2 tem se destacado nos últimos anos, devido as propriedades antioxidantes e efeitos hepatoprotetores, no entanto, o mecanismo pelo qual (PhSe)2 age não está totalmente esclarecido. Assim, este estudo busca aprofundar nossos conhecimentos sobre as ações do (PhSe)2 na disfunção mitocondrial assim como a sinalização intracelular durante a IHA induzida por APAP. Para tanto, estabelecemos primeiramente um parâmetro comparativo entre o composto orgânico de selênio e o antídoto clássico (N-acetil cisteina, NAC), em homogenato. O (PhSe)2 foi tão efetivo quanto NAC reduzindo os marcadores de dano oxidativo, auxiliado na manutenção dos níveis de GSH e aumentando o tempo de sobrevivência após a intoxicação por APAP. O tratamento com (PhSe)2 reduziu alterações morfológica, minimizou o dano quando analisamos histologicamente o tecido hepático e determinou uma redução nos níveis plasmáticos dos indicadores de dano hepatocelular (AST e ALT). Além disso, o (PhSe)2 foi eficaz na redução significativa do dano oxidativo ao limitar a peroxidação lipídica, formação de espécies reativas de oxigênio e nitrogênio, carbonilação de proteínas mitocondriais e viabilidade mitocondrial após a IHA induzida por APAP. Neste contexto, os níveis de antioxidantes não enzimáticos, tais como GSH, e enzimáticos, tais como as enzimas catalase, manganês superoxido dismutase, glutationa peroxidase e glutationa redutase, também foram mantidos semelhantes ao grupo controle. Em geral os resultados observados neste estudo indicam que um importante mecanismo pelo qual o (PhSe)2 exerce os seus efeitos terapêuticos está relacionado a manutenção da atividade do sistema de defesa antioxidante e inibição da transição de permeabilidade mitocondrial (MPT) indicados pela redução do inchaço mitocondrial, preservação da atividade dos complexos respiratórios I, II e ATPase, e manutenção do gradiente de H+ com a formação do potencial de membrana mitocondrial (Δψm). Também observamos que o (PhSe)2 limita a perda do funcionamento bioenergético mitocondrial com a manutenção dos níveis adequados de fosforilação oxidativa (OXPHOS) e ativa a via das proteínas do choque térmico aumentando a expressão de HSP70, a qual apresenta um efeito modulador importante sobre a MPT preservando a viabilidade mitocondrial. O tratamento com (PhSe)2 foi efetivo em preservar níveis apropriados de citocinas envolvidas na recuperação do tecido hepático, tais como fator de necrose tumoral alfa (TNF- α), interleucina 6 (IL-6) e fator nuclear kappa B (NF-κB). Além disso, a manutenção bioenergética celular poderia estar associada com os elevados níveis transcricionais do receptor gama ativado por proliferador de peroxissoma (PGC-1α) que auxilia a restaurar os níveis de fator nuclear respiratório 1 (NRF1) os quais estão envolvidos no processo de biogênese mitocondrial. Por fim, o (PhSe)2 poderia ser uma importante alternativa terapêutica a qual auxiliaria na recuperação do fígado, controle de qualidade mitocondrial e manutenção da homeostase e saúde celular.

Le spermatozoïde est une cellule hautement spécialisée qui doit être capable de réaliser des fonctionsspécifiques pour être capable de féconder un ovocyte. Il doit être capable de réaliser une réactionacrosomique qui consiste en l’exocytose d’une vésicule géante de sécrétion attachée au noyau. Cettevésicule contient des enzymes qui vont permettre au spermatozoïde de traverser la zone pellucide quientoure l’ovocyte. Mon travail a consisté à étudier l’effet d’une des enzymes contenue dansl’acrosome, la sPLA2 de mammifère de groupe X (mGX). C’est la seule phospholipase demammifères parmi les 5 testées qui a un effet d’inhibition sur une population spécifique despermatozoïdes ayant une mobilité diminuée. Mon travail a ainsi confirmé la spécificité de cettephospolipase sur la régulation de la physiologie spermatique. Dans un deuxième temps, j’ai participéà la découverte du gène DPY19L2 impliqué dans une infertilité masculine rare, la globozoospermie.La globozoospermie se caractérise par des spermatozoïdes ayant une tête ronde dépourvued’acrosome. Le gène DPY19L2 est spécifiquement exprimé dans les testicules, il est absent chez80% des patients globozoospermiques. J’ai caractérisé le rôle de cette protéine et montré qu’elle estimpliquée dans l’attachement de l’acrosome au noyau. J’ai pu montrer que cette protéine appartient àla membrane nucléaire interne où elle interagit avec la protéine Sun5, une protéine qui appartientaussi à la membrane nucléaire interne et dont l’expression est spécifique à la spermiogénèse. Sun5est impliquée dans la formation de complexes LINC (Linker of Nucleoskeleton and Cytoskeleton)qui permettent de relier le cytosquelette au nucléosquelette, constitué entre autres par les lamines. Lerôle de DPY19L2 pourrait permettre de stabiliser l’ancrage de la protéine SUN5 afin de transmettreles forces exercées par le cytosquelette au noyau de la spermatide. DPY19L2 appartient à une famillede protéines DPY19L1 à L4 dont les fonctions restent encore peu caractérisées. Une étude récentemontre qu’une diminution de l’expression de Dpy19l1 chez la souris entraîne un défaut de migrationdes neurones glutamatergiques sur la glie radiale. Mon travail a montré l’importance de DPY19L2dans le contrôle des interactions noyau-cytosquelette et devrait permettre de mieux comprendre lerôle des autres protéines de cette famille dans divers organes. / The spermatozoon is a highly specialized cell that must be able to perform specific functions tofertilize the oocyte. It must be able to perform the acrosome reaction, an exocytosis of a giant vesicleof secretion, attached to the nucleus. This vesicle contains enzymes that allow the sperm to penetratethe zona pellucida surrounding the oocyte. The aim of my work was first to study the effect of anenzyme present in the acrosome, the sPLA2 of group X in mouse (mGX). This is the onlymammalian phospholipase among the five tested that has an inhibitory effect on sperm specificpopulation with low mobility. My work has confirmed the specificity of this phospolipase on theregulation of sperm physiology. Second, I participated in the discovery of the gene DPY19L2involved in male infertility, globozoospermia. The globozoospermia is characterized by round headspermatozoa without acrosome. DPY19L2 gene is specifically expressed in the testis and is absent in80% of globozoospermic patients. I then identified the role of this protein, which is involved in theattachment of the acrosome to the nucleus. I showed that this protein belongs to the inner nuclearmembrane where it likely interacts with the protein sun5 which also belongs to the inner nuclearmembrane and whose expression is specific to spermiogenesis. Sun5 is involved in the complexformation, called LINC that connects the cytoskeleton to the nucleoskeleton lamina. The role ofDpy19l2 could help stabilizing the anchoring of protein sun5 in order to transmit the forces exertedby the cytoskeleton to the nucleus of the spermatid during acrosome spreading. Dpy19l2 belongs to aprotein family containing 4 members, Dpy19l1 to l4, which has not been poorly studied so far. Arecent study shows that the knock-down of Dpy19l1 resulted in defective glutamatergics neuronsmigration on the radial glia. The results obtained during my work would improve the knowledge ofCytoskeleton-nucleoskeleton interaction, and give new insight on this new family of proteins.

Le contrôle de l'expression des programmes géniques orchestrant le développement précoce et l'homéostasie des cellules souches fait l'objet de recherches intenses. En effet, les cellules souches embryonnaires (CSE) sont caractérisées par des propriétés comme leur clonogénicité (la capacité à proliférer dans le même état indifférencié) et leur pluripotence (la capacité à se différencier et à former les tissus embryonnaires et adultes). Au niveau moléculaire, l'identité des CSE est orchestrée par le contrôle de l'expression génique aux niveaux épigénétique, transcriptionnel, post- transcriptionnel et traductionnel en réponse à l'activation de voies de signalisation spécifiques. Dans ce contexte, des données récentes suggèrent un rôle de la machinerie traductionnelle les ribosomes et de la régulation de leur biogenèse, dans le maintien de l'homéostasie de cellules souches de différentes espèces. À partir de l'analyse de données transcriptomiques à haut débit (RNAseq), mon équipe d'accueil a ainsi identifié un ensemble de protéines associées aux ribosomes (PaR) significativement enrichies dans les cellules souches embryonnaires murines (CSEm) en comparaison à des lignées cellulaires murines différenciées et à des tissus. Parmi ces candidats, mes travaux de thèse ont consisté à la caractérisation d'une PaR particulièrement enrichie : Rsl24d1. Rsl24d1 est une protéine de biogenèse des ribosomes décrites exclusivement chez la levure. Son profil d'expression dans différentes lignées de CSEm suggère une fonction spécifique: enrichissement au niveau transcriptionnel et protéique dans les CSE à l'état de pluripotence naïf et diminution importante au cours de la différenciation. En effet, des approches de perte d'expression de Rsl24d1 m'ont permis d'établir l'importance de cette PaR dans l'homéostasie des CSEm. Rsl24d1 contribue au maintien de la prolifération cellulaire des CSE, de leur clonogénicité et plus modérément à leur pluripotence. Rsl24d1 semble être une protéine majoritairement nucléaire mais également associée aux sous- unités 60S libres des ribosomes cytoplasmiques. D'autre part, la perte d'expression de Rsl24d1 affecte spécifiquement la biogenèse des particules ribosomiques 60S. Ainsi, comme chez la levure, dans les CSEm, Rsl24d1 est un facteur navette orchestrant la maturation des particules ribosomiques pré-60S. Par ailleurs, Rsl24d1 semble permettre le maintien d'un taux de synthèse protéique élevé permettant notamment le renouvellement des protéines ayant une demi-vie courte parmi lesquels on recense des facteurs de transcription de la pluripotence comme Oct4 (Oct3/4), Nanog et Esrrb. Mes travaux de thèse ont donc permis d'identifier et de caractériser un facteur de biogenèse de la sous-unité 60S, Rsl24d1, impliqué dans l'homéostasie des CSEm / Embryonic stem cells (ESC) possess clonogenic and pluripotency abilities i.e. they are able to self-renew indefinitely in the same developpemental state and to differentiate in all the cell types composing embryonic and adult tissues. ESC homeostasis is coordinated by complex networks which are regulated at different levels of gene expression regulation, including epigenetic, transcriptional and post-transcriptional levels. Furthermore, emerging evidences point out that the translational machinery, ribosomes, are directly implicated in the control of adult and embryonic stem cell homeostasis in different model organisms. Along this line, we have identified Rsl24d1, a ribosomal associated protein (RaP), which is strongly expressed in naïve murine ESCs compared to their differentiated progenies. We demonstrated that Rsl24d1 actively contributes to ESC homeostasis and its expression is essential for ESC proliferation and clonogenic capacities. Finally, we have also demonstrated that Rsl24d1, like Rlp24 its yeast ortholog, is associated to pre-ribosomes in ESCs from the nucleus to the cytoplasm and is required for the biogenesis of the large ribosomal subunit

La biogénèse des ribosomes consiste à assembler les ARN ribosomiques (ARNr) et les protéines ribosomiques de la petite sous unité (RPSs) ou de la grande sous unité (RPLs) afin de former les sous unités 40S et 60S du ribosome. Ce processus est l’un des plus complexes des cellules dont il utilise une grande quantité des ressources. Un taux élevé de biogénèse des ribosomes est une caractéristique de la prolifération cellulaire dans les conditions physiologiques ou pathologiques. L’inhibition de la biogénèse des ribosomes active un checkpoint du cycle cellulaire qui induit un arrêt du cycle cellulaire, et selon le contexte, l’apoptose. L’activation de ce checkpoint est due au facteur suppresseur de tumeur p53 qui s’accumule lorsque la biogénèse des ribosomes est inhibée grâce à l’inhibition de son facteur de dégradation, l’ubiquitine ligase E3 MDM2. Cette inhibition de MDM2 se fait par la fixation d’un complexe formé par les protéines ribosomiques RPL11 et RPL5 et l’ARNr 5S. Des études ont montré le potentiel thérapeutique de l’activation de ce checkpoint dans des cancers caractérisés par une biogenèse ribosomique élevée. Par contre l’activation de p53 semble avoir un rôle pathologique dans les ribosomopathies, un ensemble de pathologies causées par un défaut dans la biogénèse des ribosomes comme l’anémie macrocytaire de Diamond-Blackfan (ABD). p53 est clairement impliqué dans les effets anti-prolifératifs de l’inhibition de la biogénèse des ribosomes, cependant de nombreuses évidences montrent l’existence de mécanismes indépendants de p53 qui affectent l’homéostasie cellulaire. On observe par exemple dans l’ABD, des mutations de RPL11/RPL5 dont la déplétion in-vitro n’induit pas p53. Mon travail de thèse a consisté à élucider les mécanismes mis en place par les cellules pour répondre à l’inhibition de la biogénèse des ribosomes, dans un modèle in-vitro de lignées cellulaires. Dans ces lignées, nous avons inhibé la biogénèse des ribosomes par déplétion des RPs de la grande ou de la petite sous unité, indépendamment de l’induction ou pas de p53, à savoir, RPs6, RPL7a et RPL11. Nous avons mis en évidence des liens entre l’inhibition de la biogénèse des ribosomes et l’homéostasie du réticulum endoplasmique, ou la régulation de l’expression de gènes du métabolisme tels que l’enzyme oncogénique PHGDH. / Ribosome biogenesis is the process that leads to the assembly of ribosomal RNA (rRNA) and ribosomal proteins of the small (RPS) or the large (RPL) subunit into ribosomal 40S and 60S subunits. This is a highly complex process in the cells which uses a large amount of energy and resources. High rate of ribosome biogenesis is a trait of cell proliferation in physiological or pathogenic conditions. Inhibition of ribosome biogenesis activates a cell cycle checkpoint which induces a cell cycle arrest, and apoptosis. Activation of this checkpoint is due to the inhibition of ubiquitin ligase E3 MDM2, which does not anymore address the tumor suppressor factor p53 to proteasome. The p53 tumor suppressor factor then accumulates in cells and blocks the cell cycle progression. The inhibition of MDM2 is caused by the binding of a complex formed by RPL11, RPL5 and rRNA 5S. Few studies reveal that activation of this checkpoint has a therapeutic effect on cancer cells characterized by high rate of ribosome biogenesis. However, p53 activation seems to have pathogenic effects in ribosomopathies, a set of disorders characterized by ribosome biogenesis impairment, like Diamond-Balckfan macrocytic anemia (DBA). It is clear that p53 has anti-proliferative effects when ribosome biogenesis is inhibited, but evidences show that p53independants mechanisms also exist. In DBA for example, mutations in RPL5 and RPL11 that do not lead to p53 activation are observed. The goal of this study was to investigate the cellular mechanisms induced in response to inhibition of ribosome biogenesis. These investigations have been performed in an in-vitro system of cell lines. In those cell lines, ribosome biogenesis has been inhibited by depletion of RPs of the 40S or 60S ribosomal independently of p53 status. We brought out links between inhibition of ribosome biogenesis and endoplasmic reticulum homeostasis, or metabolic genes expression regulation like oncogene PHGDH.

Le complexe Scc2-Scc4 est essentiel pour l’association du complexe cohésine sur l’ADN. Les proteines Cohésine génèrent la cohésion entre les chromatides sœurs, ce qui est essentiel pour la ségrégation des chromosomes. Scc2 (également connu sous le nom NIPBL) est muté chez les patients atteints du syndrome de Cornelia de Lange, une maladie multi-organique caractérisée par des anomalies du développement du visage, de la developpement mental cardiaque et du tractus gastro-intestinal. Comment les mutations localisées au niveau du gène codant pour la proteine Scc2 conduisent à des anomalies du développement chez les patients n’a pas encore été élucidé. Une des hypothèses est que la liaison de Scc2 / cohésine à différentes régions du génome a une incidence sur la transcription. Chez la levure de bière, il a été montre que Scc2 se lie aux genes transcrits par l'ARN Pol III (les ARNt et spliceosomals) , ainsi qu‘aux gènes transcrits par l'ARN Pol II codant pour des petits ARN nucléolaires et nucléaires (snARN et snoARNs ) et des gènes de protéines ribosomiques. Nous rapportons ici que Scc2 est important pour l'expression de ces gènes. Scc2 et le régulateur transcriptionnel Paf1 collaborent pour promouvoir la production de Box H / ACA snoARNs qui guident la pseudouridylation des ARN y compris l'ARN ribosomal. Une mutation de Scc2 a été associée à des défauts dans la production d'ARN ribosomal, la biogenèse des ribosomes, et del’épissage. Alors que le mutant Scc2 n'a pas de défaut général de la synthèse protéique, il montre un déphasage accrue et une réduction de l’utilisation du site interne d'entrée ribosomale (IRES)/ coiffe-indépendante. Ces résultats suggèrent que Scc2 favorise normalement un programme d'expression génétique qui prend en charge la fidélité de la traduction. Nous émettons l'hypothèse que le dysfonctionnement de traduction peut contribuer au syndrome de Cornelia de Lange, qui est causé par des mutations dans Scc2. / The Scc2-Scc4 complex is essential for loading the cohesin complex onto DNA. Cohesin generates cohesion between sister chromatids, which is critical for chromosome segregation. Scc2 (also known as NIPBL) is mutated in patients with Cornelia de Lange syndrome, a multi-organ disease characterized by developmental defects in head, limb, cognition, heart, and the gastrointestinal tract. How mutations in Scc2 lead to developmental defects in patients is yet to be elucidated. One hypothesis is that the binding of Scc2/cohesin to different regions of the genome will affect transcription. In budding yeast, Scc2 has been shown to bind to RNA Pol III transcribed genes (tRNAs, and spliceosomal), as well as RNA Pol II-transcribed genes encoding small nuclear and nucleolar RNAs (snRNAs and snoRNAs) and ribosomal protein genes. Here, we report that Scc2 is important for gene expression. Scc2 and the transcriptional regulator Paf1 collaborate to promote the production of Box H/ACA snoRNAs which guide pseudouridylation of RNAs including ribosomal RNA. Mutation of Scc2 was associated with defects in the production of ribosomal RNA, ribosome biogenesis, and splicing. While the scc2 mutant does not have a general defect in protein synthesis, it shows increased frameshifting and reduced internal ribosomal entry site (IRES) usage/cap-independent translation. These findings suggest Scc2 normally promotes a gene expression program that supports translational fidelity. We hypothesize that translational dysfunction may contribute to the human disorder Cornelia de Lange syndrome, which is caused by mutations in Scc2.

Les mitochondries sont des organites qui remplissent d'importantes fonctions au sein de la cellule eucaryote notamment dans le métabolisme énergétique. En fonction de l'état physiologique (par exemple une variation de la demande énergétique), on peut constater d'importantes variations du contenu mitochondrial cellulaire. Ces variations impliquent une modification de la biogenèse mitochondriale qui est un processus complexe mettant à contribution divers acteurs protéiques ainsi que les génomes nucléaire et mitochondrial. Nous avons étudié la régulation de la biogenèse mitochondriale chez la levure Saccharomyces cerevisiae. Chez cet organisme, un des éléments clés de la biogenèse du compartiment mitochondrial est le facteur de transcription hétéromérique HAP. Ce dernier est constitué de 4 sous-unités dont la sous-unité activatrice est la protéine Hap4p. Nous avons mis en évidence une régulation de la protéine Hap4p par le stress oxydant et l'état rédox du glutathion. Ainsi, un stress oxydatif induit par des molécules pro-oxydantes ou encore un dysfonctionnement de la chaîne respiratoire mitochondriale induit une diminution de la protéine Hap4p. Cette diminution conduit à une diminution de la quantité de marqueurs mitochondriaux tels que les cytochromes et une forte diminution de la vitesse de respiration et de la vitesse de croissance. Nous nous sommes aussi intéressés à la régulation du complexe HAP par la molécule d'hème. Nos résultats sont les premiers à clairement mettre en évidence une régulation positive de la quantité de Hap4p par l'hème et suggèrent aussi une régulation post-traductionnelle de Hap4p par l'état rédox de cette molécule. Tous ces résultats apportent des éléments supplémentaires dans l'étude des mécanismes de la communication mitochondrie-noyau et de la régulation de la biogenèse mitochondriale. / Mitochondria are organelles that play important functions in eukaryotic cell especially in energy metabolism. According to the physiological state (for example energy demand variation), mitochondrial content can vary in large amounts within the cell. These variations involve the modification of mitochondrial biogenesis which is a complex process which depends on many proteins and both nuclear and mitochondrial genomes. We studied the regulation of mitochondrial biogenesis in the yeast Saccharomyces cerevisiae. In this organism, a key component of mitochondrial biogenesis is the heteromeric transcription factor HAP. It is constituted by 4 subunits, Hap4p being the activator subunit. We showed a regulation of Hap4p protein by oxidative stress and the glutathione redox state. Thus, oxidative stress induced by pro-oxidants or by mitochondrial respiratory chain dysfunction leads to a decrease in the Hap4p protein level. This decrease of Hap4p leads to a decrease in mitochondrial markers level such as cytochromes and a decrease of the respiratory and growth rates. We also interested in the regulation of the HAP complex by heme. Our results are the first to clearly show a positive regulation of Hap4p level by heme and also suggest a post-translational regulation of Hap4p by the heme redox state. Altogether, these results represent novel pieces to the study of the mitochondria-nucleus communication and the regulation of mitochondrial biogenesis.

Les cellules cancéreuses produisent une grande quantité de ribosomes afin de synthétiser les protéines nécessaires à leur prolifération rapide. Les mécanismes qui conduisent à cette augmentation de la production de ribosome ne sont que partiellement compris, mais ils semblent intimement liés à l'acquisition du phénotype tumoral. De plus, une nouvelle théorie propose que les ribosomes ne sont pas des effecteurs neutres de la traduction, mais qu'ils jouent un rôle direct dans la régulation de l'expression génique. Cette théorie se base sur l'observation que la composition des ribosomes est hétérogène en fonction des types cellulaires et des conditions environnementales. Dans ce contexte, j'ai étudié les liens entre les altérations des signaux qui contrôlent la biogenèse des ribosomes, tant au niveau quantitatif que qualitatif, et le développement du phénotype tumoral. Ce manuscrit rapporte trois études effectuées au cours de mon travail de thèse. Ces études ont permis d'identifier : i) un nouveau régulateur de la quantité de ribosomes, la LN-Nétrine-1 et ii) des modifications de la composition et de la fonction des ribosomes induites par des altérations génétiques (perte d'activité de p53) et par l'utilisation d'une molécule chimiothérapeutique, le 5- Fluorouracile. Ces perturbations de la quantité et de la fonction des ribosomes modifient le contrôle de la traduction des cellules et la croissance, la prolifération et la survie cellulaire. Il ressort de ces résultats que les ribosomes sont des éléments qui participent au contrôle de l'expression génique et qui jouent un rôle dans la pathologie cancéreuse et la réponse au traitement chimiothérapeutique / Cancer cells produce large amounts of ribosomes to synthesize the proteins required for their rapid proliferation. The mechanisms leading to this increase in ribosome production are only partly understood, but they are related to the acquisition of the tumor phenotype. In addition, a new theory proposes that ribosomes are not neutral effectors of translation, but have a direct role in the regulation of gene expression. This theory is based on the observation that ribosome composition is heterogeneous in different cell types and according to environmental conditions. In this context, I have analyzed the relationships between changes in signals that control ribosome biogenesis, both quantitatively and qualitatively, and the development of the tumor phenotype. This manuscript reports three studies made during this PhD program. These studies identified: i) a novel regulator of the amount of ribosomes, the LN-Netrin-1 and ii) changes in the ribosome composition and function induced by genetic alterations (loss of activity of p53) and by the use of a chemotherapeutic molecule, the 5-Fluorouracil. These perturbations of the amount and the function of ribosomes modify the translation control and cell growth, cell proliferation and cell survival. From these results it can be conclude that ribosomes are elements involved in the regulation of gene expression and play a role in cancer pathology and response to chemotherapy

Most mitochondrial proteins are encoded by nuclear DNA, and synthesised in the cytosol, then imported into the different mitochondrial subcompartments. To reach their destination, mitochondrial inner membrane proteins require import across the outer mitochondrial membrane, and through the intermembrane space. This passage through the IMS is assisted by the small Tim proteins. This family is characterised by conserved cysteine residues arranged in a twin CX3C motif. They can form Tim9-Tim10 and Tim8-Tim13 complexes, while Tim12 appears to form part of a Tim9-Tim10-Tim12 complex that is associated with the inner membrane translocase TIM22 complex. Current models suggest that the biogenesis of small Tim proteins and their assembly into complexes is dependent on the redox states of the proteins. However, the role of the conserved cysteine residues, and the disulphide bonds formed by them, in small Tim biogenesis and complex formation is not clear. As there is no research about the structural characterisation of Tim12 and double cysteine mutants of Tim9, purification of these proteins was attempted using different methods. To investigate how cysteine mutants affect complex formation, the purified double cysteine mutants of Tim9 were studied using in vitro methods. It showed that the double cysteine mutants were partially folded, and they can form complexes with Tim10 with low affinities, suggesting disulphide bonds are important for the structures and complex formation of small Tim proteins. The effect of cysteine mutants on mitochondrial function was addressed using in vivo methods. It showed that cysteines of small Tim proteins were not equally essential for cell viability, and growth defect of the lethal cysteine mutant was caused by low level of protein. Thus, the conclusion of this study is that disulphide bond formation is highly important for correct Tim9- Tim10 complex formation, and yeast can survive with low levels of complex, but it results in instability of the individual proteins.