La poly(ADP-ribosyl)ation est une modification post-traductionnelle créée par l'ajout successif d'unités ADP-ribose sur une protéine acceptrice pour former un polymère (pADPr) hétérogène branché. La caractérisation biochimique de tous les membres de la famille des PARPs est incomplète mais un constat important peut être dégagé par l'analyse de cette famille élargie : les PARPs présentent une grande diversité de domaines protéiques fonctionnels. Conséquemment, il est logique de croire que cette étonnante diversité sera responsable de fonctions variées dans plusieurs sentiers de signalisation ou événements cellulaires. La poly(ADP-ribosyl)ation, bien qu'étant une modification cruciale impliquée dans la régulation de l'intégrité génomique et la survie cellulaire, ne se limite plus aux seules fonctions nucléaires mais se présente de plus en plus comme un événement pouvant se dérouler dans un contexte physiologique extra-nucléaire. De plus, la liaison noncovalente de plusieurs protéines au pADPr libre ou à d'autres protéines poly(ADP-ribosyl)ées est un phénomène dont nous commençons à mieux mesurer les impacts fonctionnels. Contrairement aux PARPs, lesquelles sont exprimées par une superfamille de gènes apparentés, la majorité de l'activité de dégradation du pADPr est attribuable à l'expression d'un seul gène chez les mammifères : la poly(ADP-ribose) glycohydrolase (PARG). Un volet important de mon projet de recherche visait à identifier des partenaires de la PARG dans le but de reconnaître les sentiers biochimiques qui pourraient inclure une composante de poly(ADP-ribosylation) dans leur régulation et définir des interactions fonctionnellement pertinentes. Dans une optique complémentaire, les protéines associées au pADPr, que ce soit de manière covalente, noncovalente ou en association avec des complexes protéiques, ont été ciblées par des approches protéomiques. Enfin, des études protéomiques ont permis d'aborder l'état de phosphorylation de la PARP-1 et de la PARG

Thèse (M.Sc.)--Université Laval, 2003. / Bibliogr.: f. 77-93. Publié aussi en version électronique.

La poly(ADP-ribose) polymerases consistant en une population hétérogène de polymères formés à partir du NAD. La poly(ADP-ribose) glycohydrolase est responsable de la dégradation du poly(ADP-ribose). Les activités enzymatiques de ces enzymes constituent un système de régulation pour différents sentiers métaboliques. En effet, l'interaction démontrée entre le pADPr et de multiples protéines a permis de confirmer un rôle de modulateur de nombreuses voies de signalisation tel que la réparation de l'ADN, apoptose, cycle cellulaire, surveillance de l'intégrité du génome, transcription et modulation de la chromatine. Ainsi, nous avons formulé l'hypothèse que le pADPr pourrait coordonner la réparation des lésions à l'ADN et la progression du cycle cellulaire avec la signalisation d'événement apoptotiques. Une approche efficace constituerait à identifier et caractériser les protéines (intermédiaires) associées au pADPr selon une logique temporelle. Les diverses actions du pADPr sur les processus biologiques dépendent (dans le cas de la majorité du pADPr, soit celui métabolisé par PARP-1) de la gravité des dommages induits à l'ADN. Par conséquent, il existe probablement des points de seuil faisant basculer les voies de signalisation de la réparation vers la mort cellulaire. Une approche réductionniste, dans ce type de problème, ne peut apporter des réponses satisfaisantes. L'utilisation de la protéomique quantitative semble être une approche plus appropriée. Un volet du travail présenté dans cette thèse visait à identifier des partenaires des PARP-1, PARP-2 et PARG dans le but de reconnaître les sentiers biochimiques qui pourraient inclure une composante de poly(ADP-ribosylation) dans leur régulation et définir des interactions fonctionnellement pertinentes. Par la suite, nous avons établi un réseau dynamique des complexes associés au pADPr en fonction du temps suivant un dommage alkylant induit par un stress génotoxique. Ainsi, certains événements modulés par le pADPr ont été analysés et cartographies. De plus, nous avons caractérisé un rôle novateur du pADPr dans la formation des granules de stress suite à un stress génotoxique. En conséquence, nos résultats ont permis d'édifier les premières bases pour la biologie des systèmes de la poly(ADP-ribosyl)ation en fournissant un répertoire d'interactions protéique exhaustif.

Poly(ADP-ribosyl)ation is a reversible post-translational modification of histones and nuclear proteins rapidly stimulated by DNA damage. Its homeostasis is a dynamic process regulated by the synthesizing enzymes poly(ADP-ribose) polymerases (PARPs) and the degrading enzyme poly(ADP-ribose) glycohydrolase (PARG). PARP-1, the first-discovered and major PARP, has been the focus of many studies aimed at clarifying the biological function of poly(ADP-ribose) (PAR). This abundant nuclear enzyme plays key roles in a variety of cellular processes, including the regulation of chromatin structure, transcription and genomic integrity. Its multifunctionality has made it an attractive and potential target for therapy, as evidenced by the numerous PARP-1 inhibitors currently undergoing clinical trials. The transient nature of PAR, explained by the close coordination between PARP-1 and PARG, has also highlighted the potential of targeting PARG for diseases of inappropriate cell death. A number of obstacles, however, have prevented PARG from being studied as extensively as PARP-1. The extreme sensitivity of PARG to proteases and its insolubility at high concentrations have limited structure-activity relationship analyses and structural studies of PARG, and the unavailability of high-throughput activity assays has stalled the discovery and development of specific and cell permeable PARG inhibitors, subsequently slowing down the validation of PARG as a therapeutic target. The work presented in this dissertation describes in detail strategies devised to overcome these difficulties. First, a novel colorimetric high-throughput assay for PARG was evaluated and its sensitivity and precision were compared to a widely-used radiolabelling assay. Second, several expression and purification systems were constructed in order to obtain high quantities of soluble human PARG protein adequate for in vitrostructural studies. The efficacy of these strategies was demonstrated in structure-activity analyses of PARG which led to the identification of a regulatory segment far removed linearly from the catalytic site of PARG. This region, necessary for catalytic activity, corresponds with a recently identified mitochondrial targeting sequence (MTS) and was thus named the ‘regulatory segment/MTS’ (REG/MTS). Finally, based on structural data obtained, secondary structure predictions were made to provide insight into the molecular composition of the different domains of PARG, whose structures still remain to be determined.

Polymers of ADP-ribose (PAR) are rapidly synthesized by poly(ADPribose) polymerases (PARPs) and rapidly degraded by poly(ADP-ribose) glycohydrolase (PARG) following genotoxic stress. Since PAR metabolism plays an important role in cell fate determination following genotoxic stress, enzymes involved in PAR metabolism potentially represent promising therapeutic targets for modulating diseases of inappropriate cell proliferation or death. PARP-1 has been well validated and several PARP-1 inhibitors are currently being evaluated in clinical trials for cancer and ischemia treatment. In contrast, the biological function of PARG is still poorly understood. Due to low abundance of protein levels in mammalian cells and its unique substrate, PARG potentially represents another attractive target for pathological conditions mentioned above. PARG-Δ2,3 cells derived from homozygous PARG-Δ2,3 mice with targeted disruption of exons 2 and 3 of the PARG gene are used in this dissertation. The nuclear isoform PARG60 in PARG-Δ2,3 cells lacks the putative regulatory domain A compared to the nuclear isoform PARG110 in wild type cells. We report in this dissertation that PARG-Δ2,3 cells accumulate less PAR in spite of more rapid depletion of NAD following treatment with N-methyl- N’- Nitro-N-Nitrosoguanidine (MNNG). The estimation of PARP and PARG activity in intact cells shows increased activity of both enzymes in PARG-Δ2,3 cells following MNNG treatment, indicating the important role of domain A in the regulation of PARG and PARP activity under these conditions. Following MNNG treatment, PARG-Δ2,3 cells show reduced formation of XRCC1 foci, decreased H2AX phosphorylation, decreased DNA break intermediates during repair, and increased cell death. The altered PAR metabolism and defective cellular responses related to DNA repair in PARG-Δ2,3 cells may contribute to increased sensitivity of these cells to MNNG. Studies presented in this dissertation clearly demonstrate the important role of PARG110 in PAR metabolism and cellular responses to genotoxic stress, and thus provide supportive data for the validation of PARG as a promising potential therapeutic target.

Poly(ADP-ribose) polymerase-1 (PARP-1) is an abundant nuclear protein that catalyzes the cleavage of NAD⁺ into nicotinamide and ADP-ribose moiety, the latter of which may be covalently attached as a branched polymer of poly(ADP-ribose) to PARP-1 itself (automodification) or to other nuclear acceptor proteins (transmodification). PARP-1 plays pivotal roles in many fundamental biological processes, including DNA repair, gene expression, cell death and cell cycle regulation. The multiple functions of PARP-1 in various cellular events correlate well to its roles in carcinogenesis, inflammatory response, neural function, and aging. PARP-1 has a modular organization comprising six independent domains (domain A-F). Each domain has its own characteristic function in PARP-1 enzymatic catalysis. In this dissertation, the solution structure of domain C was determined by multi-dimensional NMR spectroscopy. To complement the structural results, the requirement of domain C for PARP-1 catalysis was demonstrated using activity assays. This structure-function relationship study will help to unveil the mechanism of the PARP-1 reaction, and should provide valuable information for the design of more potent and selective PARP-1 inhibitors. The determination of poly(ADP-ribosyl)ation sites is critical for understanding the biological roles of this modification. However, the identification of poly(ADPribosyl)ation sites has countered some daunting technical limitations due to the difficulties resulting from the heterogenous nature of this modification. In this dissertation, a methodology based on mass spectrometry is developed and used to identify ADP-ribosylation sites within the automodification domain (domain D) of PARP-1. Using this method, we were able to unambiguously localize three ADPribosylation sites on domain D. This method can be readily applied to study the transmodification of other substrates as well as PARP-1 automodification. As many as seventeen PARP homologues exist in the human proteome. The functional redundancy of the multiple PARP proteins has complicated the analysis of mammalian PARP-1 function in vivo. We have probed the biological roles of PARP-1 using an artificial PARP-1 pathway in yeast, an organism lacking the endogenous PARP-1. Our data suggest the heterologously expressed human PARP-1 in yeast retains some similar functions as it does in mammalian cells. Furthermore, a new function of PARP-1 in ribosome biogenesis was proposed. / text

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Thèse (Ph. D.) -- Université Laval, 1998. / Bibliogr.: f. 195-232. Publié aussi en version électronique.

Thèse (M.Sc.) -- Universoté Laval, 1997. / Bibliogr.: f. 79-85. Publié aussi en version électronique.

Changes in the synthesis and activity of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) are associated with myocardial remodeling. Here we measured the expression and activity of MMPs and TIMPs, and tested the hypothesis that increased MMP activity plays a proapoptotic role in β-adrenergic receptor (β-AR)-stimulated apoptosis of adult rat ventricular myocytes (ARVMs). β-AR stimulation (isoproterenol, 24 h) increased mRNA levels of MMP-2 and TIMP-1 while it decreased TIMP-2 mRNA levels as analyzed by real-time PCR. Western blot analysis, immunocytochemical analysis, in-gel zymography, and MMP-2 activity assay confirmed β-AR-stimulated increases in MMP-2 protein-levels and activity. Inhibition of MMPs using GM-6001 (a broad-spectrum inhibitor of MMPs), SB3CT (inhibitor of MMP-2), and purified TIMP-2 inhibited β-AR-stimulated apoptosis as determined by TdT-mediated dUTP nick end labeling staining. Treatment with active MMP-2 alone increased the number of apoptotic cells. This increase in MMP-2-mediated apoptosis was inhibited by GM-6001 and SB3CT pretreatment. Coimmunoprecipitation studies indicated increased physical association of MMP-2 with β1-integrins after β-AR stimulation. Inhibition of MMP-2 using SB3CT or stimulation of β1-integrin signaling using laminin inhibited the increased association of MMP-2 with β1- integrins. β-AR stimulation increased poly-ADP-ribose-polymerase cleavage, which was inhibited by inhibition of MMP-2. These data suggest the following: 1) β-AR stimulation increases MMP-2 expression and activity and inhibits TIMP-2 expression; 2) inhibition of MMPs, most likely MMP-2, inhibits β-AR-stimulated apoptosis; and 3) the apoptotic effects of MMP-2 may be mediated, at least in part, via its interaction with β1 integrins and poly-ADP-ribose-polymerase cleavage.