Neointimal proliferation is a key process underlying many cardiovascular diseases such as atherosclerosis and angioplasty-induced restenosis. Vascular smooth muscle cells (SMC) are significant contributors to the development and stability of the neointimal lesion. This is due, in part, to their capacity to be phenotypically modulated, facilitating SMC proliferation in response to mechanical injury, their subsequent migration, and deposition of extracellular matrix. The aim of this thesis was to characterize the function of two genes identified in our laboratory to be upregulated shortly after mechanical injury of vascular SMC and their exposure to fibroblast growth factor (FGF)-2, an injury-induced cytokine. The first is activation transcription factor (ATF) 4, which is upregulated by FGF-2 and mechanical injury in vascular SMC in vitro, and by balloon-injury in the artery wall. The induction of ATF4 by FGF-2 was shown to be mediated through the PI3K pathway, and preceded by phoshorylation of eIF2alpha, a known upstream effector of ATF4 activation. Knock-down of ATF4 expression inhibited balloon-injury induced neointimal hyperplasia, suggesting that ATF4 is a key player in the SMC response to injury. Furthermore, microarray analysis identified several genes whose transcription in response to FGF-2 may be regulated by ATF4. In particular, this work demonstrates that ATF4 is necessary for VEGF-A upregulation in SMC in response to FGF-2 and mechanical injury in vitro and in the artery wall following balloon-injury. The second is a translation factor, YrdC203. Using confocal fluorescence microscopy, YrdC203 was found to localize partially to the ER, and with RPL12, a component of the 60S ribosomal subunit. Immunoprecipitation studies demonstrate that YrdC203 also interacts with an initiation factor, eIF5B. Mutation of an initiation factor’s signature on the exterior of YrdC203 perturbed its interaction with RPL12 and eIF5B, and inhibited the increase in protein synthesis observed with overexpression of YrdC203. This implicates YrdC203 as a translation factor responsible for ensuring protein synthesis in vascular SMC in response to injury. The present work provides evidence for new molecular mechanisms, transcriptional and translational, regulating the response of vascular SMC to injury. This would provide leads for future therapeutic targets.

Neointimal proliferation is a key process underlying many cardiovascular diseases such as atherosclerosis and angioplasty-induced restenosis. Vascular smooth muscle cells (SMC) are significant contributors to the development and stability of the neointimal lesion. This is due, in part, to their capacity to be phenotypically modulated, facilitating SMC proliferation in response to mechanical injury, their subsequent migration, and deposition of extracellular matrix. The aim of this thesis was to characterize the function of two genes identified in our laboratory to be upregulated shortly after mechanical injury of vascular SMC and their exposure to fibroblast growth factor (FGF)-2, an injury-induced cytokine. The first is activation transcription factor (ATF) 4, which is upregulated by FGF-2 and mechanical injury in vascular SMC in vitro, and by balloon-injury in the artery wall. The induction of ATF4 by FGF-2 was shown to be mediated through the PI3K pathway, and preceded by phoshorylation of eIF2alpha, a known upstream effector of ATF4 activation. Knock-down of ATF4 expression inhibited balloon-injury induced neointimal hyperplasia, suggesting that ATF4 is a key player in the SMC response to injury. Furthermore, microarray analysis identified several genes whose transcription in response to FGF-2 may be regulated by ATF4. In particular, this work demonstrates that ATF4 is necessary for VEGF-A upregulation in SMC in response to FGF-2 and mechanical injury in vitro and in the artery wall following balloon-injury. The second is a translation factor, YrdC203. Using confocal fluorescence microscopy, YrdC203 was found to localize partially to the ER, and with RPL12, a component of the 60S ribosomal subunit. Immunoprecipitation studies demonstrate that YrdC203 also interacts with an initiation factor, eIF5B. Mutation of an initiation factor’s signature on the exterior of YrdC203 perturbed its interaction with RPL12 and eIF5B, and inhibited the increase in protein synthesis observed with overexpression of YrdC203. This implicates YrdC203 as a translation factor responsible for ensuring protein synthesis in vascular SMC in response to injury. The present work provides evidence for new molecular mechanisms, transcriptional and translational, regulating the response of vascular SMC to injury. This would provide leads for future therapeutic targets.

Structure, fonction et évolution de la famille universelle Sua5/YrdC impliquée dans la synthèse du nucléoside modifié t6ALa t6A est universellement présente au sein des ARNt décodant les codons ANN et est essentielle pour la fidélité de traduction. Sa synthèse se déroule en deux étapes, dont la première implique la formation de l’intermédiaire de réaction Thréonyl-Carbamoyl-AMP (TC-AMP) par la famille Sua5/YrdC. Cette famille est retrouvée chez tous les organismes et était donc vraisemblablement présente chez le dernier ancêtre commun universel (LUCA). Elle est composée de deux variants distincts, YrdC et Sua5, qui partagent un domaine catalytique orthologue. A la différence du variant YrdC qui est composé d’un domaine unique, le variant Sua5 possède un domaine C-terminal additionnel nommé SUA5, de fonction inconnue. La plupart des espèces code pour un seul variant et les deux variants sont présents dans les trois domaines du vivant, Eucaryote, Archée et Bactérie. Afin d’identifier le rôle du domaine SUA5 et du linker inter-domaine, nous avons étudié la protéine Sua5 de l’archée Pyrococcus abyssi. Nos résultats montrent que ces deux régions sont importantes pour l’activité de Sua5. Le linker est capable de contrôler le passage des ligands en changeant de conformation tandis que le domaine SUA5 agit comme une plateforme d’ancrage pour le linker. Afin de comprendre l’histoire évolutive de la famille Sua5/YrdC, nous avons ensuite étudié la distribution des variants et nous avons utilisé des approches in silico et in vitro afin de déterminer les différences fonctionnelles entre YrdC et Sua5. L’ensemble de ces données nous permet de proposer que LUCA possédait une protéine Sua5 et qu’YrdC serait apparu suite à une perte de domaine dans certains lignées lors de l’évolution. / Structure, function and evolution of the universal Sua5/YrdC family involved in the modified nucleoside t6A synthesist6A is universally found in tRNAs that read ANN codons and is essential for translation fidelity. Its synthesis takes place in two stages, the first one involving the formation of the reaction intermediate Threonyl-Carbamoyl-AMP (TC-AMP) by the Sua5/YrdC family. This family is found in all organisms and was thus presumably presents in the Last Universal Common Ancestor (LUCA). It’s composed of two distinct variants, YrdC and Sua5, which share an orthologous catalytic domain. While YrdC is a single domain protein, Sua5 has an additional C-terminal domain of unknown function named SUA5. Most species encode for either variant and both variants are found in the three domains of life, Eukarya, Archaea and Bacteria. To discover the role of the SUA5 domain and the inter-domain linker, we studied the Sua5 protein from the archaeon Pyrococcus abyssi. We found that they are both important for the activity of Sua5. The linker is able to control the entry and exit of ligands by changing conformation while the SUA5 domain acts as an anchoring platform for the linker. To understand the evolutionary history of the Sua5/YrdC family, we then studied the distribution of Sua5 and YrdC across the tree of life and we used in silico and in vitro approaches to identify functional differences between YrdC and Sua5. Taken together, our work allows us to propose that LUCA encoded a Sua5 protein and that YrdC emerged after domain loss in some lineages during evolution.

La plupart de ARN de transfert (tRNA) subissent des modifications post-transcriptionnelle nécessaires à leur fonction. La modification t6A (N6-threonylcarbamoyladenosine) présente en position 37 des ARNt spécifiques des codons ANN, joue un rôle primordial dans la fidélité de la traduction (appariement correct avec le codon AUG initiateur ; prévention des décalages de phase de lecture etc.). La modification t6A est catalysée en deux étapes par les protéines de la famille Sua5 /YrdC (aboutissant à la synthèse d’un intermédiaire TCA : threonylcarbamoyladenylate) puis transfert de l’entité Carbamoylthreonine du TCA sur l’ARNt via les protéines du complexe KEOPS chez les eucaryotes et archae ou des protéines YgjD, YeaZ et YjeE chez les bactéries ou encore de la protéine Qri7 dans les mitochondries de levures. Le complexe KEOPS comprend les 4 sous-unités suivantes : Kae1, Bud32, Cgi121 et Pcc1 auxquelles s’ajoutent une 5ème sous-unité (Gon7) retrouvée uniquement chez la levure. Alors que YgjD est l’homologue bactérien de la protéine Kae1, YeaZ et YjeE n’ont pas d’homologue chez les eucaryotes ni les archées. Jusqu’à présent, les mécanismes catalytiques responsables de la modification t6A restent peu connus.Nous présentons dans cette thèse une série d’études structure-fonction de plusieurs protéines impliquées dans la biosynthèse de la modification t6A : Sua5 de P. Abyssi ; les sous-complexes Bud32-Cgi121 et Gon7-Pcc1 de S. cerevisiae ainsi que le sous-complexe YgjD-YeaZ de E. coli. Les principaux résultats confirment que Sua5/YrdC est l’acteur majeur de la synthèse de l’intermédiaire TCA via son activité pyrophosphatase. Dans la levure, la protéine Gon7, empêche l’homodimérisation de Pcc1 qui ne peut plus induire de dimérisation du complexe entier (alors que c’est le cas chez les archées pour lesquelles Gon7 est absente). La structure du sous-complexe Bud32-Cgi121 de levure fournit des informations essentielles quant à son rôle de Kinase et d’ATPase au sein du complexe KEOPS. Ensemble, ces deux structures Bud32-Cgi121 et Gon7-Pcc1 nous permettent de proposer un modèle pentamérique du complexe KEOPS. Enfin, concernant les protéines bactériennes, nous montrons que l’activité ATPase de YjeE est stimulée par son association au complexe YgjD-YeaZ et que la formation du complexe ternaire YgjD-YeaZ-YjeE a lieu en présence d’ATP. Nous proposons un modèle structural de ce complexe ternaire pouvant expliquer les rôles des protéines YeaZ et YjeE dans la modification t6A.L’ensemble des études structurales abordées dans cette thèse permet donc de mieux comprendre le mécanisme catalytique de la modification t6A essentielle et ubiquitaire dans les 3 royaumes de la vie. / Most tRNAs undergo chemical modifications during their maturation after the transcription. N6-threonylcarbamoyladenosine (t6A) is universally present at position 37 of tRNAs that recognize ANN-codons. tRNA t6A plays an essential role in translational fidelity through enhancing the codon-anticodon interaction. Recently, the tRNA t6A-modifying enzymes have been identified and characterized in bacteria, archaea and yeast. The biosynthesis of tRNA t6A proceeds in two main steps: first, the biosynthesis of an unstable intermediate threonylcarbamoyladenylate (TCA) by Sua5/YrdC family protein, using ATP, L-threonine, bicarbonate as substrates; second, the transfer of threonylcarbamoyl-moiety from TCA onto A37 of cognate tRNAs by a set of other proteins that use Kae1/Qri7/YgjD family proteins as a catalytic component. Though the biosynthesis of tRNA t6A could be accomplished by Sua5 and Qri7 in yeast mitochondria, the t6A biosynthesis in archaea and yeast cytoplasm requires Sua5 and KEOPS protein complex, which consists of Kae1, Bud32, Cgi121, Pcc1 in archaea, and a fifth Gon7 in yeast. In bacteria, it requires YrdC, YgjD, YeaZ and YjeE, of which YeaZ and YjeE are not related to any KEOPS subunits. Presently, the molecular mechanism of Sua5/YrdC in catalyzing the TCA biosynthesis is not well understood; How the KEOPS subunits assembly and cooperatively transfer threonylcarbamoyl-moiety from TCA to tRNA is not known; The contribution of YeaZ and YjeE in t6A biosynthesis in bacteria still remains to be probed.In this study, we report crystal structures of P. abyssi Sua5, S. cerevisiae Gon7/Pcc1 and Bud32/Cgi121 binary complexes, and E. coli YgjD-YeaZ heterodimer. Based on the information revealed by the crystal structures, advanced biochemical characterizations were carried out to validate the hypotheses. We confirm first that Sua5/YrdC is capable of catalyzing the TCA biosynthesis using substrates of ATP, L-threonine, and bicarbonate. The structure of P. abyssi Sua5 in complex with pyrophosphate provides a basis for its ATP-pyrophosphatase activity. Second, the structure of Gon7 reveals that it functions as a structural mimic of Pcc1 and therefore prevents the formation of Pcc1 homodimer, which mediates the formation of a dimer of tetrameric KEOPS from archaea. The structure of Bud32-Cgi121 in complex with ADP provides a basis in support of the dual kinase and ATPase activities of Bud32. We present a structural model of yeast KEOPS that exists as a heteropentamer. Third, we discovered that the weak intrinsic ATPase activity of YjeE is activated by YgjD-YeaZ heterodimer. YgjD, YeaZ and YjeE associate and form a ternary complex that is regulated by both the formation of YgjD-YeaZ heterodimer and the binding of ATP to YjeE. The model of YgjD-YeaZ-YjeE ternary complex provides structural insight into the essential role of YeaZ and YjeE in t6A biosynthesis in bacteria. This work provides structural insights into understanding the biosynthesis of tRNA t6A that is essential and ubiquitous in all three domains of life.

Cardiovascular disease, which involves the cardiac, cerebrovascular and peripheral vascular system, is the major cause of morbidity and mortality in the western world. Changes in the vascular microenvironment trigger cascades of molecular events involving altered signaling, transcription and translation of a gene. The aim of this thesis was to increase our understanding on the molecular regulation of activated vascular smooth muscle cells. The first study looking at PDGF-D expression provides new insights into the regulatory mechanisms controlling the phosphorylation of Sp1. Studies performed identified three amino acids in Sp1 (Thr668, Ser670 and Thr681) that is phosphorylated by PKC-zeta activated by AngII. In the second study, the translational regulatory role of a novel gene YrdC induced by injury was investigated. Current knowledge of translational regulators controlling altered gene expression is little and studies in this thesis shows a splice variant of YrdC playing an important role in controlling mRNA translation and thus protein synthesis in the context of injury. The final study investigated in this study was the increased expression of the apoptotic FasL by the activation of GATA6. Although FasL has been extensively studied over the years, this is the first study linking a GATA factor with FasL in any cell type and provides key insights into the transcriptional events underpinning FasL-dependent SMC apoptosis following exposure to AngII.