Open reading frame (ORF) sso0433 from the archaeon Sulfolobus solfataricus encodes a protein kinase, SsoPK5 that exhibits 33% sequence identity to p53 related protein kinase (PRPK) from Homo sapiens and 26% sequence identity to piD261/Bud32 from Saccharomyces cerevisiae. Given this high degree of similarity, the objectives of this thesis were to (a) clone and purify recombinant SsoPK5, (b) examine its commonalities and differences with its eukaryotic homologues, and (c) determine if it was regulated by nucleotides or related compounds. Substantial progress was achieved on each objective. After successful cloning of ORF sso0433 and purification of its protein product, SsoPK5, it was determined that SsoPK5 was cold labile and incubation at 4ºC for an extended period of time rendered SsoPK5 incapable of phosphotransferase activity. When stored at room temperature, SsoPK5 was capable of transferring the γ-phosphate from ATP to casein, reduced carboxyamidomethylated and maleylated (RCM) lysozyme,and p53. SsoPK5 phosphotransferase activity required a divalent metal cofactor; like pid261/Bud32, SsoPK5 preferred Mn²⁺ over the more commonly preferred Mg²⁺. SsoPK5 was shown to phosphorylate itself on threonine and serine residues; one of the specific amino acid residues modified is threonine-151. Recombinant SsoPK5 is activated by ADP-ribose and 5′-AMP. Activation was observed when SsoPK5 was stabilized by ATP or a nonhydrolytic analogue, such as β,γ- methylene adenosine 5′-triphosphate (AMP-PCP). Activation was not a result of phosphoryl transfer nor hydrolytic breakdown of ATP or 5′-AMP. This was deduced by the lack of ³²P radioactivity incorporated into SsoPK5 during pre-incubation with [γ-³²P] ATP for 60 min at 65ºC, and activation by adenosine 5′-O-thiomonophosphate (AMPS), a hydrolysis-resistant analog of AMP. These results may indicate that ADP-ribose acts as a pseudochaperone for SsoPK5 thereby facilitating maximal activity. / Ph. D.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 4 uppsatser.

ADP-ribose polymer metabolism has been studied in human cells derived from a patient with Glutamyl Ribose Phosphate Storage Disease (GRPSD) and in mouse C3H1OT1/2 cells following oxidative stress induced by hydrogen peroxide (H202 ). It has been postulated that GRPSD resulted from an abnormality in ADP-ribose polymer metabolism. This study has shown that these cells exhibit reduced poly(ADP ribose) polymerase activity which is proposed to result from modification of the enzyme with ribose phosphate groups. The modification in the polymerase is proposed to be secondary to a defect in either ADP-ribosyl proteinlyase or an overproduction of a cellular phosphodiesterase. The metabolism of ADP-ribose polymers was rapidly altered by H202 and there were independent effects on adenine nucleotide pools. The results suggest that ADP-ribose polymer metabolism is involved in cellular defenses to oxidative stress.

The NTPDase1 enzymatic activity (E.C.3.6.1.5, Apyrase, ecto-ATP-diphosphohydrolase, CD39) which hydrolyses ATP and ADP, was analyzed in peripheral lymphocytes from patients with B chronic lymphocytic leukemia (B-CLL) which the main characteristic is the accumulation of monoclonal mature B-lymphocyte. The sample was composed by 23 patients with B-CLL whose were diagnosed according to the clinical and laboratorial criteria and also by the immunophenotypic characteristics. The patients were divided, according to the Binet staging system, in 4 groups: stage A (early), stage B (intermediate), stage C (advanced) and control group. The results demonstrated a significant increase in ATP hydrolysis (F(29,3)=26.79 p<0.001) for all the stages of the disease and related to the control as a function of length of disease advance with higher activity in stage C. ADP hydrolysis (F(29,3)=23.76 p<0.001) was also enhanced according to ATP results. Besides this it was found a great correlation between the activity of NTPDase-1 and the total absolute white cells count in peripheral blood. The alteration in NTPDase-1activity in lymphocytes from patients with B-CLL at the different stages, contributes to confirm the ectonucleotidases role in regulate the ATP and ADP levels, which actuates like signalling molecules in many blood cells like the lymphocytes. Therefore more studies need to be done so that we can elucidate such enzymatic system in the nucleotides and its role in the B-CLL. / A atividade da enzima NTPDase1 (E.C.3.6.1.5, Apyrase, ecto-ATP-difosfoidrolase,CD39) que hidrolisa ATP e ADP, foi analisada em linfócitos periféricos de pacientes com leucemia linfocítica crônica (LLC-B), doença que possui como característica principal o acúmulo de linfócitos B maduros. A amostra foi composta por 23 pacientes com LLC-B, diagnosticados de acordo com critérios clínicos, laboratoriais e resultados de imunofenotipagem. Os pacientes foram divididos, conforme o sistema de classificação de Binet, em 4 grupos: estágio A (inicial), estágio B (intermediário), estágio C (avançado) e um grupo controle. Os resultados demonstraram que a hidrólise do ATP foi significativamente aumentada (F(29,3)=26.79 p<0.001) em todos os estágios da doença e em relação ao controle e esse aumento é compatível com o avanço da doença mostrando a maior hidrólise no estágio C. A hidrólise do ADP acompanhou os resultados do ATP e também estava aumentada (F(29,3)= 23.76 p<0.001). Além disso, verificou-se uma forte correlação entre a atividade da enzima NTPDase1 e a contagem absoluta de glóbulos brancos do sangue periférico. A alteração na atividade da enzima NTPDase1 em linfócitos de pacientes com LLC-B em seus diferentes estágios, vem confirmar o importante papel das ecto-nucleotidases na regulação dos níveis de ATP e ADP, os quais atuam como moléculas sinalizadores em várias células sangüíneas como os linfócitos. Entretanto, mais estudos são necessários para melhor elucidar as funções desse sistema enzimático no controle de nucleotídeos e o seu papel na LLC-B.

Adenosine diphosphate (ADP) ribosylation is a post-translational modification dependent on the transfer of ADPr units from nicotinamide adenine dinucleotide (NAD+) on to a plethora of biomolecules (i.e., proteins, DNA, RNA, etc.) in response to physiological stressors (i.e., nutrient deprivation, oxidative stress, DNA strand breaks). Poly-ADP-ribosylation (PARylation) is primarily mediated by the family of poly(ADP-ribose) polymerases (PARPs) and enzymatically degraded (dePARylation) by hydrolases such as poly(ADP-ribose) glycohydrolase (PARG). This thesis characterizes the role of poly(ADP-ribose) polymerase 1 (PARP1) and PARG in the skeletal muscle of healthy mature mice under normal physiological conditions. Specifically, we validate the deletion of Parp1 and Parg in inducible skeletal muscle-specific KO mouse models followed by performing general phenotyping of both male and female mice. The thesis concludes that under normal physiological conditions the activity of Parp1 or Parg in (de)PARylation is dispensable for maintaining skeletal muscle mass, function, and homeostasis in healthy mature mice.

Aging is a complicated and multifactorial phenomenon. Model systems involving the induction of replicative senescence in cultured cells have been indispensable in elucidating some of the mechanisms underlying this complex process. An understanding of how and why cellular senescence occurs is thus critical to the field of aging research. While there is much correlative evidence to suggest a connection between poly(ADP-ribose) (PAR) and mammalian longevity, no studies have been done to explore a possible role for PARP-1 — the enzyme responsible for synthesis of 90% of cellular PAR — in mechanisms of senescence. Furthermore, many techniques currently used for analysis of protein poly(ADP-ribosyl)ation are fraught with imprecision. We therefore sought to address these issues both by developing methods for the unambiguous analysis of poly(ADP-ribosyl)ation by mass spectrometry, and by exploring the role of PARP-1 in nicotinamide-mediated cellular lifespan extension. Due to the challenges introduced by PAR's biochemical characteristics, successful mass spectrometric analysis of poly(ADP-ribosylation) will require the use of techniques to reduce the mass, charge, and heterogeneity of the polymer, as well as methods to enrich for poly(ADP- ribosyl)ated protein. To this end, we evaluated the effectiveness of several approaches, including ammonium sulfate fractionation, boronate affinity chromatography, snake venom phosphodiesterase digestion, manipulation of PARP-1 reaction conditions, and immobilized metal affinity chromatography (IMAC) for the preparation of poly(ADP-ribosyl)ated protein samples prior to MS analysis using both MALDI-TOF and Q-TRAP LC-MS. Based on this work, we developed a three-tiered scheme that may provide the first ever identification of poly(ADP- ribosyl)ated peptides from full-length wild-type PARP-1 by mass spectrometry. Past work in our laboratory has demonstrated that nicotinamide (NAM), a component of vitamin B3, significantly extends the replicative lifespan of human fibroblasts. In order to help elucidate the role of PARP-1 in cellular senescence, we then analyzed the poly(ADP-ribosyl)ation response of aging cells undergoing NAM-mediated lifespan extension. While NAM is a known PARP-1 inhibitor, we found that oxidative stress-induced poly(ADP- ribosyl)ation is increased, not decreased, in NAM-treated cells. We propose that supplemented NAM is taken up by the NAD salvage pathway, ultimately leading to increased cellular NAD and extending replicative lifespan by both preventing PARP-mediated NAD depletion and upregulating SIRT1. We further propose that the demonstrated protective effects of NAM treatment in a number of disease models are due not to PARP-1 inhibition as is commonly assumed, but to upregulation of NAD salvage. / Ph. D.

Poly(ADP-ribosyl)ation, a covalent modification of proteins catalyzed by poly(ADP-ribose) polymerases (PARPs), plays a crucial role in regulating DNA repair, DNA replication, and cell death. Poly(ADP-ribose) Polymerase-1 (PARP-1) is a nuclear zinc-finger DNA-binding protein that is the most extensively studied member of the PARP family. The activation of PARP-1 depends on the N-terminal DNA-binding domain, which consists of two unusually long zinc finger-like motifs (termed FI and FII) of the form CX₂CX₂₈/₃₀HX₂C and a newly discovered zinc-ribbon motif (FIII). Though zinc is indispensible for PARP-1 activity, the metal binding affinities of the unusual zinc fingers of PARP-1 is not yet known. In this dissertation, the second zinc finger of PARP-1 was used as a model peptide to study the binding properties of several divalent metal ions (Co²⁺, Cd²⁺, Zn²⁺, and Pb²⁺). Metal-induced protein folding was investigated by circular dichroism, and the effects of the metal ions on PARP-1 activity were investigated by poly(ADP-ribosyl)ation activity assays. This study represents the first detailed biochemical characterization of the PARP zinc fingers. The functional role of each zinc finger in DNA damage recognition is critical for understanding how PARP-1 is involved in DNA repair. Thus, we constructed a series of PARP-1 zinc finger variant proteins and investigated their DNA binding properties and their effects on PARP activity. Using a combination of southwestern blotting and activity assays, we demonstrated that FII is more important for DNA binding, while FI and FIII seem to facilitate PARP activity. The DNA sequence-independent binding properties of PARP-1 were further characterized using DNA probes bearing defined secondary structures. Together, our results indicate that the zinc fingers help position the enzyme at specific DNA damage sites, and also help to activate the catalytic domain upon DNA binding. PARP-1 is involved in caspase-independent apoptosis, and the translocation of apoptosis inducing factor (AIF) out of the mitochondrial matrix has been shown to require PARP-1 activity. However, it is not readily apparent how the catalytic activity of PARP-1 (a nuclear protein) triggers the release of AIF from the mitochondrial matrix. In an attempt to understand the relationship between PARP-1 activity and caspase-independent apoptosis, we demonstrate here that AIF is an in vitro protein substrate for PARP-1. The possible implications of this finding will be discussed. / text

L’ADN contient l’information génétique essentielle au développement et au bon fonctionnement de tout organisme vivant. Cependant, l’ADN peut être endommagé ou modifié par une exposition régulière à différents facteurs tels que la lumière du soleil, la pollution, la radiation, etc. La cellule a ainsi développé des mécanismes de réparation très efficaces puisqu’un ADN sain est essentiel pour la santé d’un organisme. La protéine humaine PARP1 est une enzyme clé de la réparation de l’ADN. PARP1 détecte rapidement les dommages à l’ADN en s’y liant, ce qui stimule son activité catalytique. PARP1 catalyse la formation de chaînes d’ADP-ribose qui sont ajoutées à PARP1, ainsi que d’autres protéines, en tant que modification post-traductionnelle. Les chaînes d’ADP- ribose permettent la décondensation de la chromatine ainsi que le recrutement de facteurs de réparation à l’ADN endommagé. PARP1 possède plusieurs domaines régulateurs en plus de son domaine catalytique, le domaine catalytique lui-même se divisant en un domaine hélicoïdal (HD) ainsi qu’un domaine ADP- ribosyltransférase. L’augmentation de l’activité catalytique de PARP1, à la suite de sa liaison à l’ADN endommagé, implique qu’un signal allostérique se transmette à travers ses différents domaines. Le HD joue un rôle essentiel dans le relais de cette communication allostérique puisque c’est ultimement un changement de conformation du HD (i.e « ouverture ») qui révèle le site actif et active l’enzyme. De plus, il a été démontré que les inhibiteurs de PARP1 peuvent moduler l’affinité de l’enzyme pour l’ADN endommagé. Certains inhibiteurs peuvent ainsi provoquer la « capture » de l’ADN par PARP1, un phénomène qui requiert la présence du HD et qui est particulièrement toxique pour les cellules cancéreuses présentant des défauts de réparation de l’ADN. Pour cette raison, la mort cellulaire induite par les inhibiteurs de PARP1 est un traitement prometteur et quatre inhibiteurs sont déjà utilisés pour traiter le cancer des ovaires et du sein. Cependant, le mécanisme précis derrière la capture de l’ADN par PARP1 est encore nébuleux et nécessite de plus amples recherches. Puisque la capture de l’ADN par PARP1 requiert le relais d’un signal allostérique par le HD, et que l’ouverture du HD participe à cette communication, il est donc essentiel de comprendre les changements de conformations effectués par ce domaine. Nous avons ainsi obtenu pour la première fois une structure atomique de PARP1 en conformation active. Celle-ci montre que l’ouverture du HD amène la formation d’une interface additionnelle entre ce domaine et les autres domaines régulateurs de PARP1. Ainsi, entraver la formation de cette nouvelle interaction, par des mutations ponctuelles, diminue grandement l’activité catalytique de PARP1 lié à l’ADN, ce qui suggère que l’interface participe à la communication allostérique de l’enzyme. Tel que mentionné plus haut, les inhibiteurs de PARP1 peuvent moduler de manières différentes l’affinité de PARP1 pour les dommages à l’ADN et ainsi influencer distinctement la communication allostérique de l’enzyme. Nous avons caractérisé une nouvelle série d’inhibiteurs de PARP1 et évalué leur capacité à moduler l’affinité de PARP1 pour l’ADN endommagé. Nos travaux démontrent qu’un inhibiteur volumineux occupant le site actif n’augmentera pas nécessairement l’affinité de PARP1 pour les dommages à l’ADN. Leur capacité à favoriser la capture de l’ADN dépend plutôt de leur interaction avec la région du HD voisine au site actif. En résumé, nos travaux participent à l’amélioration des connaissances concernant l’activation catalytique de PARP1 et la communication allostérique. Une meilleure compréhension de l’allostérie de PARP1 permettra la conception de médicaments ayant la toxicité désirée pour tuer les cellules cancéreuses. / DNA contains the genetic instructions for the development and proper function of all living organisms. However, DNA can be broken and modified in harmful ways through daily exposures to exterior stresses such as sun light, pollution, radiation, etc. Since stable and undamaged DNA is essential for the health of an organism, cells have developed repair mechanisms to ensure that DNA damage is taken care of efficiently. The human protein PARP1 is a key enzyme that contributes to DNA repair. PARP1 rapidly detects DNA lesions which greatly stimulates its catalytic activity. PARP1 catalyzes the formation of chains of ADP-ribose that are attached covalently to PARP1 itself, or other target proteins, as a posttranslational modification. The chains of ADP-ribose allow for the recruitment of chromatin remodelling factors and repair factors to process the DNA lesions. PARP1 carries multiple regulatory domains in addition to its catalytic domain, with the catalytic domain itself composed of the helical domain (HD) and the ADP-ribosyltransferase fold. DNA damage binding greatly stimulates PARP1 catalytic activity, which requires that an allosteric signal is relayed across the enzyme’s domains. Interestingly, the HD has been found to play an essential role in the PARP1 allostery. The HD undergoes a change of conformation (i.e. opening) following PARP1 DNA damage binding which reveals the active site. Additionally, inhibitors binding the active site of the enzyme can modulate PARP1 DNA binding affinity. Some inhibitors can induce PARP1 DNA “trapping”, a phenomenon that requires the HD and appears particularly toxic to cancer cells bearing DNA repair deficiencies. Cell death induced by PARP1 inhibitors is a promising cancer treatment and four inhibitors have approval for clinical use against ovarian and breast cancers. However, the precise mechanism underlying PARP1 trapping on DNA is still unclear and requires further research. Since PARP1 trapping requires the presence of the HD, and that the HD opening is involved in relaying the allosteric signal, it remains essential to characterize its change of conformation. We have obtained for the first time atomic structures of PARP1 in a catalytically active state. Crystal structures show that the HD in open conformation forms an additional interdomain interface. Mutating this interface prevents PARP1 strong catalytic activation following DNA damage binding, suggesting that the allosteric communication is impaired. Additionally, these structures reveal how the HD active conformation leads to the reveal of the active site in the ART domain. As mentioned above, PARP1 inhibitors can modulate the enzyme’s DNA binding affinity and therefore impact its allosteric communication. We have characterized a series of novel inhibitors and tested their propensity to increase PARP1 DNA binding affinity. Our work highlights that bulky inhibitors that fill the active site will not necessarily promote PARP1 affinity for DNA lesions. Rather, it appears that inhibitors may trigger DNA trapping via their interaction with a neighboring region of the HD. Overall, our work deepens our understanding of PARP1 catalytic activation and allosteric communication. Properly understanding how PARP1 trapping occurs will help the design of specific drugs with the desired toxicity to kill cancer cells.

published_or_final_version / abstract / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Physiology / Doctoral / Doctor of Philosophy