Quinolinate phosphoribosyltransferase (QPRTase, EC 2.4.2.19) is an intriguing enzyme which appears to catalyse two distinct chemical reactions; transfer of a phosphoribosyl moiety from 5-phosphoribosyl-1-pyrophosphate to the nitrogen of quinolinic acid and decarboxylation at the 2-position to give nicotinic acid mononucleotide. The chemical mechanism of QPRTase is not fully understood. In particular, enzymatic involvement in the decarboxylation step is yet to be conclusively proven. QPRTase is neurologically important as it degrades the potent neurotoxin, quinolinic acid, implicated in diseases such as Huntington’s disease and AIDS related dementia. Due to its neurological importance and unusual chemistry the mechanism of QPRTase is important. Described here is a mechanistic study on human brain QPRTase. Human brain QPRTase was successfully expressed in E. coli BL21 (DE3) from the pEHISTEV-QPRTase construct and the protein was efficiently purified by nickel affinity chromatography. The crystal structure was solved using multiwavelength methods to a resolution of 1.9 Å. Human brain QPRTase was found to adopt an energetically stable hexameric arrangement. The enzyme was also found to exist as a hexamer during gel filtration under physiological conditions. Kinetic studies allowed the measurement of the kinetic parameters for quinolinic acid. The data gave a Km of 13.4 ± 1.0 μM and a Vmax of 0.92 ± 0.01 μM min-1. There was no evidence for cooperative binding of quinolinic acid to the six subunits of the QPRTase hexamer. The enzyme showed maximum activity at approximately pH 6. The active site of human brain QPRTase is a deep pocket with a highly positive electrostatic surface composed of three arginine residues, two lysine residues and one histidine residue. Mutation of these residues resulted in either complete loss or significant reduction in enzymatic activity showing they are important for binding and/or catalysis. A possible mechanism involving QPRTase in the decarboxylation of quinolinic acid mononucleotide was proposed. A series of quinolinic acid analogues were synthesised and tested as inhibitors of QPRTase. The inhibition studies highlighted some key interactions in the active site.

L'azote est l'un des éléments les plus essentiels dans le monde pour les êtres vivants, car il est essentiel pour la production des éléments de base de la cellule, les acides aminés, les acides nucléiques et les autres constituants cellulaires. L’atmosphère est composé de 78% d'azote gazeux, une source d'azote inutilisable par la plupart des organismes à l'exception de ceux qui possèdent l’enzyme nitrogénase, tels que les bactéries diazotrophique. Ces micro-organismes sont capables de convertir l'azote atmosphérique en ammoniac (NH3), qui est l'une des sources d'azote les plus préférables. Cette réaction exigeant l’ATP, appelée fixation de l'azote, est catalysée par une enzyme, nitrogénase, qui est l'enzyme la plus importante dans le cycle de l'azote. Certaines protéines sont des régulateurs potentiels de la synthèse de la nitrogénase et de son activité; AmtB, DraT, DraG, les protéines PII, etc.. Dans cette thèse, j'ai effectué diverses expériences afin de mieux comprendre leurs rôles détailés dans Rhodobacter capsulatus. La protéine membranaire AmtB, très répandue chez les archaea, les bactéries et les eucaryotes, est un membre de la famille MEP / Amt / Rh. Les protéines AmtB sont des transporteurs d'ammonium, importateurs d'ammonium externe, et ont également été suggéré d’agir comme des senseurs d'ammonium. Il a été montré que l’AmtB de Rhodobacter capsulatus fonctionne comme un capteur pour détecter la présence d'ammonium externe pour réguler la nitrogénase. La nitrogénase est constituée de deux métalloprotéines nommées MoFe-protéine et Fe-protéine. L'addition d'ammoniaque à une culture R. capsulatus conduit à une série de réactions qui mènent à la désactivation de la nitrogénase, appelé "nitrogénase switch-off". Une réaction critique dans ce processus est l’ajout d’un groupe ADP-ribose à la Fe-protéine par DraT. L'entrée de l'ammoniac dans la cellule à travers le pore AmtB est contrôlée par la séquestration de GlnK. GlnK est une protéine PII et les protéines PII sont des protéines centrales dans la régulation du métabolisme de l'azote. Non seulement la séquestration de GlnK par AmtB est importante dans la régulation nitrogénase, mais la liaison de l'ammonium par AmtB ou de son transport partiel est également nécessaire. Les complexes AmtB-GlnK sont supposés de lier DraG, l’enzyme responsable pour enlever l'ADP-ribose ajouté à la nitrogénase par DraT, ainsi formant un complexe ternaire. Dans cette thèse certains détails du mécanisme de transduction du signal et de transport d'ammonium ont été examinés par la génération et la caractérisation d’un mutant dirigé, RCZC, (D335A). La capacité de ce mutant, ainsi que des mutants construits précédemment, RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) et RCIA4 (W237A), d’effectuer le « switch-off » de la nitrogénase a été mesurée par chromatographie en phase gazeuse. Les résultats ont révélé que tous les résidus d'acides aminés ci-dessus ont un rôle essentiel dans la régulation de la nitrogénase. L’immunobuvardage a également été effectués afin de vérifier la présence de la Fe-protéine l'ADP-ribosylée. D335, D388 et W237 semblent être cruciales pour l’ADP-ribosylation, puisque les mutants RCZC, RCIA1 et RCIA4 n'a pas montré de l’ADP-ribosylation de la Fe-protéine. En outre, même si une légère ADP-ribosylation a été observée pour RCIA2 (G344C), nous le considérons comme un résidu d'acide aminé important dans la régulation de la nitrogénase. D’un autre coté, le mutant RCIA3 (H193E) a montré une ADP-ribosylation de la Fe-protéine après un choc d'ammonium, par conséquent, il ne semble pas jouer un rôle important dans l’ADP-ribosylation. Par ailleurs R. capsulatus possède une deuxième Amt appelé AmtY, qui, contrairement à AmtB, ne semble pas avoir des rôles spécifiques. Afin de découvrir ses fonctionnalités, AmtY a été surexprimée dans une souche d’E. coli manquant l’AmtB (GT1001 pRSG1) (réalisée précédemment par d'autres membres du laboratoire) et la formation des complexes AmtY-GlnK en réponse à l'addition d’ammoniac a été examinée. Il a été montré que même si AmtY est en mesure de transporter l'ammoniac lorsqu'il est exprimé dans E. coli, elle ne peut pass’ associer à GlnK en réponse à NH4 +. / Nitrogen is one of the most vital elements in the world for living creatures since it is essential for the production of the basic building blocks of the cell; amino acids, nucleic acids and other cellular constituents. The atmosphere is 78% nitrogen gas (N2), a source of nitrogen unusable by most organisms except for those possessing the enzyme nitrogenase, such as diazotrophic bacteria species. These microorganisms are capable of converting atmospheric nitrogen to ammonia (NH3), which is one of the most preferable nitrogen sources. This ATP demanding reaction, called nitrogen fixation, is catalysed by the nitrogenase enzyme, which is the most important enzyme in the nitrogen cycle. Some proteins are potential regulators of nitrogenase synthesis and activity; AmtB, DraT, DraG, PII proteins and etc. In this thesis I performed various experiments in order to better understand their roles in Rhodobacter capsulatus, in more detail. The membrane protein AmtB, which is widespread among archaea, bacteria and eukaryotes, is a member of the MEP/Amt/Rh family. The AmtB proteins are ammonium transporters, taking up external ammonium, and have also been suggested to sense the presence of ammonium. It has been shown that in Rhodobacter capsulatus AmtB functions as a sensor for the presence of external ammonium in order to regulate nitrogenase. Nitrogenase consists of two metalloprotein components named MoFe-protein and Fe-protein. The addition of ammonium to R. capsulatus culture medium leads to a series of reactions which result in the deactivation of nitrogenase, called “nitrogenase switch-off”. A critical reaction in this process is one in which DraT adds an ADP-ribose group to the Fe-protein of nitrogenase. The entrance of ammonia through the AmtB pore is regulated by GlnK sequestration. GlnK is a PII protein and PII proteins are one of the central proteins in the regulation of nitrogen metabolism. Not only is GlnK-AmtB sequestration important in nitrogenase regulation, but binding of ammonium by AmtB or its partial transport is also necessary. AmtB-GlnK complexes are thought to bind DraG, which is responsible for removing the ADP-ribose that DraT adds to nitrogenase, to form a ternary complex. In this thesis details of the signal transduction mechanism and ammonium transport were examined by generating and characterizing RCZC, a (D335A) site- directed mutant of AmtB. The ability of this mutant, as well as previously constructed mutants RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) and RCIA4 (W237A), to “switch-off” nitrogenase activity was measured by gas chromatography. The results revealed that all the above amino acid residues have critical roles in nitrogenase regulation. Immunoblotting was also carried out to check the presence of ADP-ribosylated Fe-protein. D335, D388 and W237 seem to be crucial for NifH ADP-ribosylation, since their mutants (RCZC, RCIA1 and RCIA4 respectively) didn't show ADP-ribosylation on Fe-protein. In addition, although a slight ADP-ribosylation was observed for RCIA2 (G344C) we still consider it as an important amino acid residue in this matter whereas the remaining mutant RCIA3 (H193E) showed Fe-protein ADP-ribossylation after an ammonium shock, therefore it doesn't seem to be important in NifH ADP-ribosylation. In addition R. capsulatus possesses a second Amt called AmtY, which in contrast to AmtB, doesn't appear to have any specific roles. In order to find out its functionality, AmtY was overexpressed in an E. coli strain lacking AmtB (GT1001 pRSG1) (which was carried out previously by other lab members) and AmtY-GlnK complex formation in response to ammonium addition was examined. It was shown that even though AmtY is able to take up ammonia when expressed in E. coli it fails to associate with GlnK in response to NH4+.

Nitrilases are enzymes which catalyze the hydrolysis of a nitrile into the corresponding carboxylic acid and ammonia. These enzymes are potentially applicable in biocatalysis and bioremediation because of their advantages over the conventional (chemical) methods of nitrile hydrolysis (lower demand for energy, safety, simplicity, high yields, selectivity). In this work, genome mining was used to search for the sequences of hypothetical nitrilases from filamentous fungi. The amino acid sequences of previously characterized fungal nitrilases were used as the templates. Then the new synthetic genes together with other genes from our nitrilase library were expressed in E. coli and the substrate specificities of the enzymes thus produced were compared. Significant attention was focused on the relationships between the sequence of the enzyme and its substrate specificity. The arylacetonitrilases from Arthroderma benhamiae (NitAb) and Nectria haematococca (NitNh) were purified and characterized. Their substrate specificities, kinetic parameters, pH and temperature profiles and subunit and holoenzyme size were assessed. NitAb and NitNh together with other recombinant fungal nitrilases were employed in the hydrolysis of high concentrations of (R,S)-mandelonitrile in a batch or fed-batch mode. Nitrilase from...

A troponina I (TnI) é a sub-unidade inibitória do complexo troponina, responsável pela regulação da contração do músculo esquelético. Foi demonstrado que sua ação inibitória sobre a Mg2+ATPase da actomiosina, deve-se principalmente à região entre os resíduos 96 e 116 (região do peptídeo inibitório). Para estudar o mecanismo de inibição a nível molecular, produzimos três mutantes na região do peptídeo inibitório através de mutações sítio-dirigidas. Substituímos os resíduos lisina 105 por ácido glutâmico (K105E), fenilalanina 106 por tirosina (F106Y) e arginina 113 por ácido glutâmico (R113E). As troponinas I mutantes foram expressas em E.coli, purificadas e ensaiadas em sua atividade inibitória, interações com os outros componentes do complexo regulatório e sua capacidade regulatória. Os resultados obtidos indicam que a mutação na posição 105 alterou a interação da proteína com a tropomiosina, diminuindo sua atividade inibitória e afinidade pela actina-tropomiosina. A substituição na posição 113 alterou a interação da proteína com a actina e com a actina-tropomiosina, também diminuindo a atividade inibitória na presença de tropomiosina e inviabilizando a inibição na ausência de tropomiosina. Já a substituição na posição 106 não produziu alteração detectável. Concluímos que o resíduo 105 faz parte do sítio de ligação da troponina I ao complexo actina-tropomiosina e que o resíduo 113 participa diretamente do mecanismo de inibição. Desta forma, definimos duas interfaces de interação da troponina I com o filamento de actina-tropomiosina, necessárias a ligação da troponina I ao filamento e inibição da ATPase. / Troponin I (TnI) is the inhibitory subunit of the troponin complex, responsible for the regulation of skeletal muscle contraction. It has been demonstrated that TnI\'s inhibitory action on Mg2+ATPase of actomyosin is due principally to the region between residues 96 and 116 (the inhibitory region). To study the inhibitory mechanism at the molecular level, we produced three mutants of the inhibitory region by site-directed mutagenesis. We substituted lysine 105 for glutamic acid (K105E), phenylalanine 106 for tyrosine (F106Y) and arginine 113 for glutamic acid (R113E). The TnI mutants were expressed in E. coli, purified and analyzed for their inhibitory activity, interaction with other components of the regulatory complex and regulatory capacity. The results indicate that the mutation in K105E modified the interaction of TnI with tropomyosin, reduced its inhibitory activity and actin-tropomyosin affinity. The mutant R113E displayed modified interaction with actin and actin-tropomyosin, reduced inhibitory activity in the presence of tropomyosin and essentially no inhibitory activity in the absence of tropomyosin. The mutant F106Y behaved essentially like wild-type TnI. We conclude that residue 105 is part of the site by which troponin I binds to the actin-tropomyosin and that residue 113 participates directly in the inhibitory mechanism. In this way, we have defined two interfaces between troponin I and the actin-tropomyosin which are necessary for binding TnI to the filament and to inhibit the actomyosin ATPase.

A troponina (Tn) regula a contração do músculo estriado esquelético de vertebrados. Ela é composta de três subunidades: troponina I (TnI), troponina C (TnC) e troponina T (TnT). A TnI tem a função inibitória que é neutralizada pela ligação de Ca2+ nos sítios regulatórios do N-domínio da TnC, e a TnT posiciona o complexo no filamento fino. Para monitorar o sinal do Ca2+ sendo transmitido da TnC para a TnI as propriedades espectrais únicas do 5-hidroxitriptofano (5HW) foram utilizadas. O 5HW foi incorporado em mutantes pontuais de TnI com um único códon para triptofano. Foram identificadas duas sondas espectrais intrínsecas na TnI capazes de detectar a ligação de Ca2+ na Tn: as TnIs com 5HW nas posições 100 e 121. Complexos troponina reconstituídos com estes mutantes fluorescentes de TnI, Tn-TnIF100HW e Tn-TnIM121HW, apresentaram respectivamente 12 e 70 % de aumento na intensidade do espectro de emissão devido à ligação de Ca2+ na TnC. Nos complexos binários (TnC-TnI) as TnIs com 5HW nas posições 106 e 121 também captam a ligação do Ca2+ na TnC. A análise da fluorescência destas sondas demonstrou que: 1) as regiões da TnI que respondem ao N-domínio regulatório da TnC ocupado com Ca2+ são a região inibitória da TnI, resíduos 96 até 116, e a região vizinha que inclui a posição 121 da TnI; 2) mutações pontuais e a incorporação de 5HW na TnI podem afetar tanto a afinidade como a cooperatividade da ligação de Ca2+ na TnC, confirmando o papel da TnI em modular a afinidade da TnC por Ca2+; 3) as constantes de dissociação de Ca2+ surpreendentemente altas, Kd ~ 10-8 M, calculadas a partir dos sinais das sondas na região inibitória da TnI, sugerem a possibilidade de que os sítios do domínio N-terminal da TnC sejam os sítios de ligação de Ca2+ de maior afinidade no complexo troponina. / Vertebrate striated muscle contraction is regulated by troponin (Tn). Tn is composed of three subunits: troponin I (TnI), troponin C (TnC) and troponin T (TnT). TnI has an inhibitory role that is neutralized by calcium binding to the regulatory sites in the N-domain of TnC, and TnT positions the troponin complex on the thin filament. In order to follow the Ca2+ induced conformational change that is transmitted from TnC to TnI, the unique spectral properties of 5-hydroxytryptophan (5HW) incorporated as point-mutants of TnI were used. It was possible to identify two new TnI intrinsic spectral probes sensitive to Ca2+ binding to Tn: TnI with single 5HW at positions 100 and 121. Trimeric troponin complexes reconstituted with two fluorescent mutants of TnI, Tn-TnIF100HW and Tn-TnIM121HW, showed respectively 12 and 70 % increase in the emission spectra when Ca2+ bound to TnC. In the binary complexes (TnC-TnI) two TnIs with 5HW at positions 106 and 121 were also sensitive to Ca2+ binding to TnC. Fluorescence analysis of these probes showed: 1) the regions in TnI that respond to Ca2+ binding to the regulatory N-domain of TnC are the inhibitory region of TnI (residues 96 to 116), and a neighbor region that includes position 121; 2) point mutations and incorporation of 5HW in TnI can affect both the affinity and the cooperativity of Ca2+ binding to TnC, confirming the role of TnI as a modulator of the Ca2+ affinity of TnC; 3) the high dissociation constant for sites in the N-terminal domain of TnC (Kd ~ 10-8 M), derived from data using probes in the inhibitory region of TnI suggested the possibility that these sites are the high affinity Ca2+ binding sites in the troponin complex.

Human C-reactive protein (CRP) is the prototypic acute phase protein whose serum concentration increases rapidly during inflammation. CRP is also associated with atherosclerosis; it is deposited at lesion sites where it may interact with modified lipoproteins. There are 2 major questions regarding CRP: 1. How is the serum concentration of CRP regulated? 2. What are the functions of CRP in atherosclerosis? Our first aim was to determine the role of the constitutively expressed transcription factor Oct-1 in regulating CRP gene expression. We found that Oct-1 overexpression inhibited (IL-6+IL-1β)- induced CRP gene expression; maximal inhibition required the binding of Oct-1 to an octamer motif at (-59 to -66) on the CRP promoter. Oct-1 overexpression inhibited both (IL-6+IL-1β)- induced and C/EBPβ-induced CRP gene expression even when the Oct-1 site was deleted. These findings suggest that Oct-1 is a repressor of CRP gene expression that acts via binding to its cognate site on the CRP promoter as well as through indirect interactions with other promoterbound transcription factors. Our second aim was to investigate the interaction of CRP with oxidized low density lipoprotein (ox-LDL). Acidic pH, a hallmark of atherosclerotic lesions, reversibly alters CRP structure and exposes a hidden binding site that enables CRP to bind ox-LDL. Using site-directed mutagenesis we constructed a CRP mutant (E42Q) that showed significant binding to ox-LDL at physiological pH. E42Q CRP required a less acidic pH for maximal binding and bound ox-LDL more efficiently than wild type CRP at any pH. We then examined if reactive oxygen species also induced CRP – ox-LDL interaction. H2O2-treated CRP bound ox-LDL at physiological pH. Like acidic pH, H2O2-treatment induced only a local structural change exposing the ox-LDL binding site. E42Q and H2O2-modified CRP are tools to study the function of CRP in animal models of atherosclerosis, which may not have an inflammatory environment sufficient to modify CRP and induce binding to atherogenic ox-LDL. We conclude that Oct-1 is one of the critical regulators of CRP gene expression, and that CRP can be modified in vitro to convert it into an atherogenic LDL-binding molecule.

Les systèmes bioélectroniques tels que les biopiles enzymatiques nécessitant souvent l'utilisation des assemblages moléculaires complexes comprenant le cofacteur de l'enzyme, des agents de couplage et des médiateurs électrochimiques. Afin de les simplifier, nous avons remplacé ces différents partenaires par 13 analogues simples à synthétiser après identification par criblage in silico. Le noyau aromatique est couplé à un noyau aromatique et puis un médiateur électrochimique est couplé à celui-ci. Les produits sont des poudres de couleurs variées (rose, rouge). Le rendement de la première étape est de 83% avec une pureté d'environ 92%. Le rendement de la seconde étape est compris entre 45% et 65% avec une pureté de 97%. Ces analogues ont été caractérisés chimiquement (RMN, spectrométrie de masse) et électrochimiquement (voltammétrie cyclique et spectroélectrochimie). Les activités de deux enzymes, la formiate déshydrogénase (FDH) et l'alcool déshydrogénase de foie de cheval (HLADH), et d'un catalyseur organométallique, le [Cp*Rh(bpy)(H2O)]2+, ont été évaluées avec ces analogues. De faibles activités ont été observées en présence de l'HLADH avec 4 analogues et en présence de la FDH avec un seul analogue. Au contraire aux enzymes, la réduction d'un médiateur a pu été confirmée en présence du catalyseur [Cp*Rh(bpy)(H2O)]2+ par voltammétrie cyclique. La FDH native n'est pas adaptée à fonctionner avec ces nouveaux substrats solubles dans un LI, le [MMIm][Me2PO4]. Une FDH tolérante (N187S/T321S) au [MMIm][Me2PO4] précédemment obtenue par évolution dirigée a été donc étudiée en isolant les simples mutants N187S et T321S. Le double mutant N187S/T321S et le simple mutant N187S sont 4 fois plus actifs en solution aqueuse et en présence de LI. Des analyses par spectroscopie de fluorescence ont montré que la simple mutation N187S favorise la stabilité du dimère de FDH en modifiant le pKa de l'acide aminé E163. Celui-ci est impliqué dans la thermostabilité et la tolérance des FDHs aux LIs / Bioelectrical systems, such as enzymatic biofuel cells, often require a molecular construction complex comprising the enzyme cofactor, intermediary molecules and electrochemical mediators. In order to simplify them, we have replaced these different partners by 13 analogs that are simple to synthesize after identification by screening in silico. The nicotinamide ring is coupled to an aromatic moiety and an electrochemical mediator is then coupled to it as well, resulting in various colored powders (pink, red). The first step' s yield is around 83% with a purity of approximately 92%. The second step's yield is comprised between 45% and 65% with a purity of 97%. The analogs were characterized chemically (NMR, mass spectrometry) and electrochemically (cyclic voltammetry, spectroelectrochemistry). The activities of two enzymes, the formate dehydrogenase (FDH) and the horse liver alcohol dehydrogenase (HLADH), and an organometallic catalyst, [Cp*Rh(bpy)H2O]2+, were evaluated with these analogs. Weak activities were observed for 4 analogs using the HLADH and 1 analog using the FDH. Unlike the enzymes, the reduction of a conjugated mediator was confirmed with the catalyst [Cp*Rh(bpy)H2O]2+ using cyclic voltammetry. The wild type FDH is not adapted to function with these new substrates, which can be solubilized in an IL such as [MMIm][Me2PO4]. An FDH (N187S/T321S) shown to be tolerant to [MMIm][Me2PO4], and obtained previously by directed evolution, was studied by isolating the two single mutants, N187S and T321S. The double mutant N187S/T321S and the mutant N187S are 4 times more active in aqueous solution and in [MMIm][Me2PO4]. Fluorescence spectroscopy analyses showed that the single mutation N187S favorises FDH dimer stability by modifying the pKa of the amino acid E163. The latter is involved in FDH thermal stability and tolerance in ILs

Tip60 is a 60 kDa nuclear protein which exists in three isoforms, belongs to the MYST/HAT family of proteins and was discovered after its interaction with the Human HIV-1 Tat. As a nuclear protein, Tip60 can act as a coactivator or repressor. To understand the HAT action of Tip60, two possible catalytic models exist; the ping-pong and the ternary complex formation models. In correlation with the exploration of HAT catalytic action, mutations of a Cys to Ala and a Glu to Gln on Esa1 (yeast homolog of Tip60 and MYST/HAT prototype), was reported to show wild type-like and decreased acetylating properties, respectively. In this work, Tip60 HAT action was explored. In Tip60, the Cys in the active site is important for acetylation of the H4(1-20) substrate and the Glu showed semi loss in acetylating the H4(1-20) peptide substrate. These data highlight a unique mechanism of Tip60 catalysis.

The persistence and propagation of bacterial antibiotic resistance presents significant challenges to the treatment of drug resistant bacteria with current antimicrobial chemotherapies, while a dearth in replacements for these drugs persists. The thiopeptide family of antibiotics may represent a potential source for new drugs and thiostrepton, the prototypical member of this antibiotic class, is the primary subject under study in this thesis. Using a facile semi-synthetic approach novel, regioselectively-modified thiostrepton derivatives with improved aqueous solubility were prepared. In vivo assessments found these derivatives to retain significant antibacterial ability which was determined by cell free assays to be due to the inhibition of protein synthesis. Moreover, structure-function studies for these derivatives highlighted structural elements of the thiostrepton molecule that are important for antibacterial activity. Organisms that produce thiostrepton become insensitive to the antibiotic by producing a resistance enzyme that transfers a methyl group from the co-factor S-adenosyl-L-methionine (AdoMet) to an adenosine residue at the thiostrepton binding site on 23S rRNA, thus preventing binding of the antibiotic. Extensive site-directed mutagenesis was performed on this enzyme to generate point mutations at key active site residues. Ensuing biochemical assays and co-factor binding studies on these variants identified amino acid residues in the active site that are essential to the formation of the AdoMet binding pocket and provided direct evidence for the involvement of an active site arginine in the catalytic mechanism of the enzyme. Certain bacteria that produce neither thiostrepton nor the resistance methyltransferase express the thiostrepton binding proteins TIP-AL and TIP-AS, that irreversibly bind to the antibiotic, thereby conferring resistance by sequestration. Here, it was found that the point mutation of the previously identified reactive amino acid in TIP-AS did not affect covalent binding to the antibiotic, which was immediately suggestive of a specific, high affinity non-covalent interaction. This was confirmed in binding studies using chemically synthesized thiostrepton derivatives. These studies further revealed structural features from thiostrepton important in this non-covalent interaction. Together, these results indicate that thiostrepton binding by TIP-AS begins with a specific non-covalent interaction, which is necessary to properly orient the thiostrepton molecule for covalent binding to the protein. Finally, the synthesis of a novel AdoMet analogue is reported. The methyl group of AdoMet was successfully replaced with a trifluoromethyl ketone moiety, however, the hydrated form (germinal diol) of this compound was found to predominate in solution. Nevertheless, the transfer of this trifluoroketone/ trifluoropropane diol group was demonstrated with the thiopurine methyltransferase.

L'azote est l'un des éléments les plus essentiels dans le monde pour les êtres vivants, car il est essentiel pour la production des éléments de base de la cellule, les acides aminés, les acides nucléiques et les autres constituants cellulaires. L’atmosphère est composé de 78% d'azote gazeux, une source d'azote inutilisable par la plupart des organismes à l'exception de ceux qui possèdent l’enzyme nitrogénase, tels que les bactéries diazotrophique. Ces micro-organismes sont capables de convertir l'azote atmosphérique en ammoniac (NH3), qui est l'une des sources d'azote les plus préférables. Cette réaction exigeant l’ATP, appelée fixation de l'azote, est catalysée par une enzyme, nitrogénase, qui est l'enzyme la plus importante dans le cycle de l'azote. Certaines protéines sont des régulateurs potentiels de la synthèse de la nitrogénase et de son activité; AmtB, DraT, DraG, les protéines PII, etc.. Dans cette thèse, j'ai effectué diverses expériences afin de mieux comprendre leurs rôles détailés dans Rhodobacter capsulatus. La protéine membranaire AmtB, très répandue chez les archaea, les bactéries et les eucaryotes, est un membre de la famille MEP / Amt / Rh. Les protéines AmtB sont des transporteurs d'ammonium, importateurs d'ammonium externe, et ont également été suggéré d’agir comme des senseurs d'ammonium. Il a été montré que l’AmtB de Rhodobacter capsulatus fonctionne comme un capteur pour détecter la présence d'ammonium externe pour réguler la nitrogénase. La nitrogénase est constituée de deux métalloprotéines nommées MoFe-protéine et Fe-protéine. L'addition d'ammoniaque à une culture R. capsulatus conduit à une série de réactions qui mènent à la désactivation de la nitrogénase, appelé "nitrogénase switch-off". Une réaction critique dans ce processus est l’ajout d’un groupe ADP-ribose à la Fe-protéine par DraT. L'entrée de l'ammoniac dans la cellule à travers le pore AmtB est contrôlée par la séquestration de GlnK. GlnK est une protéine PII et les protéines PII sont des protéines centrales dans la régulation du métabolisme de l'azote. Non seulement la séquestration de GlnK par AmtB est importante dans la régulation nitrogénase, mais la liaison de l'ammonium par AmtB ou de son transport partiel est également nécessaire. Les complexes AmtB-GlnK sont supposés de lier DraG, l’enzyme responsable pour enlever l'ADP-ribose ajouté à la nitrogénase par DraT, ainsi formant un complexe ternaire. Dans cette thèse certains détails du mécanisme de transduction du signal et de transport d'ammonium ont été examinés par la génération et la caractérisation d’un mutant dirigé, RCZC, (D335A). La capacité de ce mutant, ainsi que des mutants construits précédemment, RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) et RCIA4 (W237A), d’effectuer le « switch-off » de la nitrogénase a été mesurée par chromatographie en phase gazeuse. Les résultats ont révélé que tous les résidus d'acides aminés ci-dessus ont un rôle essentiel dans la régulation de la nitrogénase. L’immunobuvardage a également été effectués afin de vérifier la présence de la Fe-protéine l'ADP-ribosylée. D335, D388 et W237 semblent être cruciales pour l’ADP-ribosylation, puisque les mutants RCZC, RCIA1 et RCIA4 n'a pas montré de l’ADP-ribosylation de la Fe-protéine. En outre, même si une légère ADP-ribosylation a été observée pour RCIA2 (G344C), nous le considérons comme un résidu d'acide aminé important dans la régulation de la nitrogénase. D’un autre coté, le mutant RCIA3 (H193E) a montré une ADP-ribosylation de la Fe-protéine après un choc d'ammonium, par conséquent, il ne semble pas jouer un rôle important dans l’ADP-ribosylation. Par ailleurs R. capsulatus possède une deuxième Amt appelé AmtY, qui, contrairement à AmtB, ne semble pas avoir des rôles spécifiques. Afin de découvrir ses fonctionnalités, AmtY a été surexprimée dans une souche d’E. coli manquant l’AmtB (GT1001 pRSG1) (réalisée précédemment par d'autres membres du laboratoire) et la formation des complexes AmtY-GlnK en réponse à l'addition d’ammoniac a été examinée. Il a été montré que même si AmtY est en mesure de transporter l'ammoniac lorsqu'il est exprimé dans E. coli, elle ne peut pass’ associer à GlnK en réponse à NH4 +. / Nitrogen is one of the most vital elements in the world for living creatures since it is essential for the production of the basic building blocks of the cell; amino acids, nucleic acids and other cellular constituents. The atmosphere is 78% nitrogen gas (N2), a source of nitrogen unusable by most organisms except for those possessing the enzyme nitrogenase, such as diazotrophic bacteria species. These microorganisms are capable of converting atmospheric nitrogen to ammonia (NH3), which is one of the most preferable nitrogen sources. This ATP demanding reaction, called nitrogen fixation, is catalysed by the nitrogenase enzyme, which is the most important enzyme in the nitrogen cycle. Some proteins are potential regulators of nitrogenase synthesis and activity; AmtB, DraT, DraG, PII proteins and etc. In this thesis I performed various experiments in order to better understand their roles in Rhodobacter capsulatus, in more detail. The membrane protein AmtB, which is widespread among archaea, bacteria and eukaryotes, is a member of the MEP/Amt/Rh family. The AmtB proteins are ammonium transporters, taking up external ammonium, and have also been suggested to sense the presence of ammonium. It has been shown that in Rhodobacter capsulatus AmtB functions as a sensor for the presence of external ammonium in order to regulate nitrogenase. Nitrogenase consists of two metalloprotein components named MoFe-protein and Fe-protein. The addition of ammonium to R. capsulatus culture medium leads to a series of reactions which result in the deactivation of nitrogenase, called “nitrogenase switch-off”. A critical reaction in this process is one in which DraT adds an ADP-ribose group to the Fe-protein of nitrogenase. The entrance of ammonia through the AmtB pore is regulated by GlnK sequestration. GlnK is a PII protein and PII proteins are one of the central proteins in the regulation of nitrogen metabolism. Not only is GlnK-AmtB sequestration important in nitrogenase regulation, but binding of ammonium by AmtB or its partial transport is also necessary. AmtB-GlnK complexes are thought to bind DraG, which is responsible for removing the ADP-ribose that DraT adds to nitrogenase, to form a ternary complex. In this thesis details of the signal transduction mechanism and ammonium transport were examined by generating and characterizing RCZC, a (D335A) site- directed mutant of AmtB. The ability of this mutant, as well as previously constructed mutants RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) and RCIA4 (W237A), to “switch-off” nitrogenase activity was measured by gas chromatography. The results revealed that all the above amino acid residues have critical roles in nitrogenase regulation. Immunoblotting was also carried out to check the presence of ADP-ribosylated Fe-protein. D335, D388 and W237 seem to be crucial for NifH ADP-ribosylation, since their mutants (RCZC, RCIA1 and RCIA4 respectively) didn't show ADP-ribosylation on Fe-protein. In addition, although a slight ADP-ribosylation was observed for RCIA2 (G344C) we still consider it as an important amino acid residue in this matter whereas the remaining mutant RCIA3 (H193E) showed Fe-protein ADP-ribossylation after an ammonium shock, therefore it doesn't seem to be important in NifH ADP-ribosylation. In addition R. capsulatus possesses a second Amt called AmtY, which in contrast to AmtB, doesn't appear to have any specific roles. In order to find out its functionality, AmtY was overexpressed in an E. coli strain lacking AmtB (GT1001 pRSG1) (which was carried out previously by other lab members) and AmtY-GlnK complex formation in response to ammonium addition was examined. It was shown that even though AmtY is able to take up ammonia when expressed in E. coli it fails to associate with GlnK in response to NH4+.