Mechanistic and biocatalytic studies of two carboxymethylproline synthases (CMPSs), CarB and ThnE, members of the crotonase superfamily of enzymes, both in isolation and in conjunction with the activity of the crotonyl-CoA carboxylase/reductase (Ccr) the malonyl-CoA synthetase (MatB) and the methylmalonyl-CoA epimerase (MCE) are presented. Protein engineering studies on carboxymethylproline synthases aimed at enabling stereoselective C–C bond formation leading to N-heterocycles via control of trisubstituted enolate intermediates were carried out. Active site substitutions, including at the oxyanion binding site, enabled the production of substituted N-heterocycles in high diastereomeric excesses via stereocontrolled enolate formation and reaction. The biocatalytic promiscuity of malonyl-CoA ligase and the stereoselectivity of crotonyl–CoA carboxylase/reductase were successfully coupled to the selective tri- substituted enolate forming capacity of engineered carboxymethylproline synthases for the preparation of functionalized 5- and 6-membered N-heterocycles substituted with a variety of alkyl side chains at the C-5/C-6 positions at high diastereomeric excess. The effect of methylmalonyl-CoA epimerase on the diastereoselectivity of the carboxymethylproline synthase-catalysed enolated alkylation was also demonstrated. The results illustrate the utility of the crotonase superfamily of enzymes for stereoselective biocatalysis and demonstrate the power of coupled enzyme systems to enhance diastereoselectivity and to expand the range of accepted substrates.

by Wai-keung Leung. / Thesis (M.D.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (p. 217-232). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

Polyketides are a large group of structurally diverse natural products that have shown a variety of biological activities. These molecules are synthesized by polyketide synthases (PKSs). PKSs are classified into three types based on their sequence, primary structure, and catalytic mechanism. Because of the bioactivities of polyketide natural products, this study is focused on the engineering of PKS pathways for efficient production of useful bioactive molecules or structural modification to create new molecules for drug development. One goal of this research is to create an efficient method to produce pharmaceutically important molecules. Seven biosynthetic genes from plants and bacteria were used to establish a variety of complete biosynthetic pathways in Escherichia coli to make valuable plant natural products, including four phenylpropanoid acids, three bioactive natural stilbenoids, and three natural curcuminoids. A curcumin analog dicafferolmethane was synthesized by removing a methyltransferase from the curcumin biosynthetic pathway. Furthermore, introduction of a fungal flavin-dependent halogenase into the resveratrol biosynthetic pathway yielded a novel chlorinated molecule 2-chloro-resveratrol. This demonstrated that biosynthetic enzymes from different sources can be recombined like legos to make various plant natural products, which is more efficient (2-3 days) than traditional extraction from plants (months to years). Phenylalanine ammonia-lyase (PAL) is a key enzyme involved in the first biosynthetic step of some plant phenylpropanoids. Based on the biosynthetic pathway of curcuminoids, a novel and efficient visible reporter assay was established for screening of phenylalanine ammonia-lyase (PAL) efficiency in Escherichia coli. The other goal of this research is to characterize and engineer natural product biosynthetic pathways for new bioactive molecules. The biosynthetic gene cluster of the antibacterial compound dutomycin was discovered from Streptomyces minoensis NRRL B-5482 through genome sequencing. Confirmation of the involvement of this gene cluster in dutomycin biosynthesis and creation of a series of new molecules were successfully conducted by rationally modifying the biosynthetic pathway. More importantly, a new demethylated analog of dutomycin was found to have much higher antibacterial activity against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus.

Pseudouridine synthases are enzymes responsible for modifying uridines to pseudouridines in a site-specific and energy-independent manner. There are 5 families of these synthases, named after the first member of each family to be characterized in Escherichia coli : RluA, RsuA, TruA, TruB and TruD. The 23S ribosomal RNA in E. coli contains 10 pseudouridine modifications made by 6 specific synthases named RluA-RluF. These modifications cluster around important functional regions of the ribosome such as the peptidyl transferase center, the tRNA binding sites, and the inter-subunit bridge regions. My research focuses on understanding the mechanisms of substrate selection by pseudouridine synthases and the roles of these modifications in ribosome biogenesis and function. The main aims of my research were: a) to examine the substrate specificity determinants of RluD, an important E. coli synthase; b) to characterize a mutant strain of E. coli lacking a majority of the pseudouridines on 23S rRNA; and c) to determine the activity of RluA from Vibrio cholerae, which has two closely related RluA paralogs rather than just one, as seen in most organisms. Pseudouridine modifications in the stem-loop of helix 69 (H69) in domain IV of 23S ribosomal RNA are highly conserved in all phyla. The three pseudouridines in H69 in E. coli have been shown to play an important role in 50S subunit assembly and its association with the 30S subunit. These three modifications are made by the pseudouridine synthase, RluD. Previous work showed that RluD is required for normal ribosomal assembly and function, and is the only pseudouridine synthase required for normal growth in E. coli. Here, we show that RluD is far more efficient in modifying H69 in structured 50S subunits, rather than in naked or synthetic 23S rRNA. We suggest that pseudouridine modifications in H69 are made late in the assembly of 23 rRNA into the mature 50S subunit. This is the first reported observation of a pseudouridine synthase being able to modify a structured ribonucleoprotein particle, and may constitute an important late step in the maturation of 50S ribosomal subunits. Deletion of RluD results in aberrant ribosome assembly and impaired translation termination leading to severe growth defects. However, single deletion strains of the remaining five 23S rRNA synthases do not display an altered phenotype. In an effort to identify possible roles for the remaining seven pseudouridines, we constructed a strain (Delta 5 mutant) lacking all 23S rRNA synthases except RluD. Surprisingly, this strain does not exhibit a significant growth defect at 37C in rich or minimal media. However, it does display a slower growth rate at 20C compared to wild-type. When grown in competition with the wild-type strain at 37C, a strong selection against the mutant strain was observed. In order to evaluate the structure of the mutant ribosomes, we determined the effect of various antibiotics that target the 50S subunit. The mutant strain is significantly more sensitive than wild-type to antibiotics targeting the 50S subunit such as chloramphenicol, hygromycin, clindamycin and tiamulin but these effects can be attributed to the loss of the RluC modification at U2504 by itself. In phenotypic microarray tests, we observed that the Delta 5 mutant grew much poorer than wild-type when cultured in a medium containing 6% NaCl. Taken together, the data suggest that these pseudouridines may play an important role in maintaining the structural integrity of the ribosome. In E. coli, the pseudouridine synthase RluA is a dual specificity synthase capable of modifying U746 on 23S rRNA and U32 on 4 cytoplasmic tRNAs. Surprisingly, the Vibrio cholerae genome encodes not one, but two closely related RluA proteins. In order to examine the possible activities of these two proteins, we complemented an rluA deletion in E. coli with plasmid-borne Vibrio rluA1 and rluA2 constructs. Interestingly, only one of these two RluA proteins (Vibrio RluA1) was able to modify E. coli 23S rRNA at U746. In order to determine the structural basis for this difference between the closely related RluA1 and RluA2, we constructed homology models using the structure of E. coli RluA in complex with an RNA stem-loop (PDB ID: 2I82) as a template. These models implicated two possible three amino acid (GVF or FAL) inserts present near the catalytic aspartate in Vibrio RluA2 as the likely cause of the differential activity. We hypothesize that this insert may sterically occlude the binding of substrate RNA to the enzyme, thereby preventing a productive modification reaction.

<p>S-nitrosylation, the prototypic mechanism of redox-based signal transduction, involves the covalent attachment of a nitrogen monoxide group to a Cys-thiol side chain. S-nitrosylation of proteins has been demonstrated to affect a broad range of functional parameters including enzymatic activity, subcellular localization, protein-protein interactions and protein stability. The primary focus of my dissertation was to solve a problem of great importance in the field of S-nitrosylation, which is, to identify denitrosylase(s) i.e., enzymes that remove NO groups from S-nitrosothiols. Recent progress in elucidating the cellular regulation of S-nitrosylation has led to the identification of two physiologically relevant denitrosylating activities that remove the NO group from S-nitrosylated substrates. Thioredoxin/thioredoxin reductase (Trx system) functions as an NADPH-dependent denitrosylase across a broad range of S-nitrosylated proteins (SNO-proteins). S-nitroso-glutathione reductase (GSNOR), which is highly conserved across phylogeny, metabolizes GSNO utilizing NADH as a reducing coenzyme, thereby shifting equilibria between GSNO and SNO-proteins. This dissertation describes the discovery of two novel denitrosylases: one from yeast and the other from mammals. Using technique of column chromatography we have purified these novel denitrosylases to homogeneity and have demonstrated a principal contribution of these enzymes towards S-nitrosothiol metabolism.</p> / Dissertation

In sea urchin development, cell fate specification appears by the 60-cell stage embryo when several embryonic territories are recognized: the small micromeres, the large micromeres which will generate primary mesenchyme cells, the vegetal2 layer that will give rise to pigment cells, immunocytes, and muscle cells, the vegetal1 layer, as well as the oral and aboral ectoderm. A Delta-Notch signaling event is required for the differential specification of mesodermal cells that will give rise to secondary mesenchyme cells (SMCs). SMCs produce four cell types: pigment cells, blastocoelar cells, circumesophageal muscle cells, and coelomic pouch cells. Pigment cells are the first to be specified. During primary invagination at the gastrula stage, eight pigment cell progenitors delaminate from the archenteron into the blastocoel. By the pluteus stage, approximately 30 pigment cells are embedded in the ectoderm. Pigment cells produce echinochrome, a napthoquinone pigment. Previously, several genes in the sea urchin embryo were isolated that are expressed specifically in pigment cell precursors during the blastula stage. The goal of this research was to characterize a subset of these genes, which are highly similar to: the polyketide synthase gene (Pks), a sulfotransferase gene (Sult), three different members of the flavin-containing monooxygenase gene family (Fmo), and the transcription factor glial cells missing (Gcm). Polyketide synthases (PKSs) are a large family of multifunctional proteins mainly found in bacteria, fungi, and plants. They are responsible for the biosynthesis of a variety of polyketide compounds including antibiotics and mycotoxins. In the sea urchin, SpPks is required for echinochrome biosynthesis. Flavin-containing monooxygenases (FMOs) are NADPH-dependent flavoproteins mainly found in bacteria, plants, and higher metazoan. They are responsible for catalyzing the oxidation of several compounds including the detoxification of xenobiotics and activation of numerous metabolites. It is known that SpFmo1 is required for echinochrome biosynthesis. Sulfotransferases are found from bacteria through higher eukaryotes. These enzymes catalyze the sulfate conjugation of several substrates resulting in either compound detoxification or bioactivation.

Tableau d'honneur de la Faculté des études supérieures et postdoctorales, 2011-2012 / Les aminoacyl-ARNt synthetases (aaRS) sont des enzymes essentielles au processus de traduction des acides nucléiques (ADN) en séquences d'acides aminés (protéines). Elles catalysent l'estérification de chacun des 20 acides aminés à leurs ARN de transfert respectifs. Dans une première étape, l'acide aminé est activé pour donner un intermédiaire instable (aa-AMP), lequel réagit avec l'ARNt correspondant dans une seconde étape pour générer l'ARNt aminoacylé (aa-ARNt). Les inhibiteurs synthétisés dans le cas présent sont des analogues de l'intermédiaire instable (chapitres 2, 3 et 4). Les inhibiteurs des aminoacyl-ARNt synthetases ont plusieurs utilités : faciliter la cristallisation des aaRS en vue de déterminer leurs structures par diffraction des rayons-X, étudier les mécanismes réactionnels des aaRS, et à plus long terme, approfondir la recherche sur de nouvelles thérapies antibiotiques. Les aaRS ont évolué de façon divergente entre les procaryotes et les eucaryotes, ce qui rend possible l'inhibition sélective des aaRS bactériennes. Plusieurs bactéries ne possèdent pas la glutamine-ARNt synthetase et utilisent donc une voie indirecte pour le chargement de l'ARNt correspondant (Gln-ARNtGln). En premier lieu, l'acide glutamique est estérifié avec l'ARNt par une glutamyl-ARNt synthetase non discriminante (ND-GluRS). L'ARNtGln incorrectement apparié (Glu-ARNtGln) est par la suite transformé par une aminoacyl-ARNt amidotransférase (AdT) pour donner l'ARNt correctement apparié (Gln-ARNtGln). Ce type de mécanisme existe aussi pour le chargement de l'ARNt correspondant à l'asparagine (transamidation de l'Asp-ARNtAsn). Très peu d'inhibiteurs des aminoacyl-ARNt amidotransférases ont été rapportés jusqu'à maintenant. Pourtant, l'absence de cette enzyme dans le cytoplasme des cellules eucaryotes en fait une cible intéressante pour le développement d'antibiotiques. Le design et la synthèse de nouveaux inhibiteurs ont été réalisés en se basant sur le mécanisme des aminoacyl-ARNt amidotransférases (chapitre 5, 6 et 7).

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Les mécanismes à l'origine de la Bronchopneumopathie Chronique Obstructive (BPCO) et de ses complications cardiovasculaires restent partiellement connus. Le NO est produit par les NO synthases en quantité importante dans le poumon des sujets emphysémateux, mais son rôle dans la maladie n'est pas connu. Une dysfonction endothéliale précoce liée à une diminution de la disponibilité en NO au niveau vasculaire a aussi été observée chez les patients BPCO. Dans un premier travail, nous avons montré que iNOS et eNOS étaient induites de manière diffuse dans le poumon de souris développant un emphysème après une instillation d'élastase. Le recours à des souris iNOS-/- et eNOS -/-, ainsi qu'à un inhibiteur pharmacologique d'iNOS (1400W) ont permis de montrer que l'induction d'iNOS dans le poumon était responsable d'une accumulation de protéines nitratées dans les pneumocytes de type 2 et d'une diminution de l'oxydation protéique. Cependant ni iNOS ni eNOS n'étaient nécessaires au développement de l'emphysème induit par l'élastase. Dans un deuxième travail, nous avons exploré l'effet de la polyglobulie, une complication de la BPCO hypoxique, sur la fonction endothéliale chez 15 patients polyglobuliques et 13 normoglobuliques atteints de BPCO de sévérité égale. La polyglobulie était associée de base à une viscosité sanguine plus élevée et un diamètre artérielbrachial plus important mais avec des forces de cisaillement calculées similaires. L'étude de la vasodilatation en réponse à l'hyperhémie et celle du flux sanguin de l'avant bras mesuré par plethysmographie d'occlusion veineuse en réponse à une perfusion d'acétylcholine (ACh), et de N-monomethyl-L-arginine (L-NMMA) ont permis de montrer que les artères systémiques despatients polyglobuliques ajustent leur diamètre aux forces de cisaillement aigues et chroniques de manière adaptée grâce à une libération adaptée de NO. De plus, nos résultats suggèrent que la polyglobulie modérée n'a pas d'effet délétère sur la fonctionvasculaire chez les patients BPCO. / The mechanisms that lead to COPD and cause its cardiovascular complications are partially known. NO is produced at high levels by NO-synthases in the human lung with emphysema, but its role in this disease is not clear. Interestingly, COPD patients have an endothelial dysfunction linked to the decrease of NO levels in peripheral blood vessels. In a first study, we demonstrated that iNOS and eNOS were diffusely upregulated in the lung of mice with emphysema after elastase instillation. By using iNOS-/- and eNOS -/- mice and a drug-based inhibitor of iNOS (1400W), we demonstrated that the induction of iNOS in the lung was responsible of an increase of protein nitration in alveolar type 2 cells and of an alleviated oxidation of proteins. However, neither iNOS nor eNOS were required for the development of elastase-induced inflammation and emphysema. In a second study, we evaluated the effectsof polycythemia, a common complication of hypoxic lung diseases, on the endothelial function in 15 polycythemic and 13 normocythemic patients with a COPD of equal severity. Polycythemia was associated with higher blood viscosity and a larger diameter of the brachial artery but with a similar calculated wall shear stress (WSS). We studied the flow-mediated brachial arteryvasodilation and the forearm blood-flow responses to endothelium- and non-endothelium-dependent N-monomethyl-L-arginine (LNMMA) infusion by plethysmography. We demonstrated that systemic arteries in polycythemic patients adjust appropriately to chronic or acute WSS elevations by an appropriate basal and stimulated NO release. Overall, our results suggest that moderate polycythemia has no adverse effect on vascular function in COPD.

WGS permet d'analyser et de déchiffrer l'étude de résistances de bactéries multirésistantes(MDR), en comprenant les différents mécanismes de résistance, les annuaires génétiques. Au cours de ma thèse de doctorat, j'ai réalisé: 1 revue de la littérature sur l'utilisation de nouveaux outils de diagnostic contemporains et les capacités dans la détection des foyers dans les maladies infectieuses causées par MDR. L'identification et l'analyse de résistances de bactéries multirésistantes Comme étant des Shewanellalgae, normalement de l'environnement marin, dans notre cas une souche clinique isolée du lavage bronchoalvéolaire d'un patient hospitalis avec pneumonie et Chryseobacteriumin dologenes, isolé d'une fibrose kystique du patient. Dans cette analyse, nous pouvons montrer que les bactéries environnementales telles que les S.algae peuvent être un réservoir de gènes de résistance aux antibiotiques. L'analyse exhaustive de ces bactéries a montré leur capacité à s'adapter à leurs écosystèmes, y compris l'acquisition de nouveaux éléments génétiques par transfert latéral de gènes. La détection des gènes impliqués dans la synthèse de peptides synthetasenon ribosomale et de polycétide synthétase peut avoir un rôle dans leur capacité à survivre dans des environnements hostiles tels que le tractus respiratoire des patients atteints de fibrose kystique ou leur présence chez des patients ayant subi plusieurs antibiotiques. Nous avons réalisé une analyse standardisée «insilico» afin de déterminer la résistance de ces bactéries et la présence de métabolites secondaires associés aux bactériocines et aux NRPS/PKS. L'application du NTS pour le séquençage du génome bactérien de nouvelles espèces bactériennes isolées dans le microbiome humain nous a permis de développer une plateforme capable d'analyser ces nouvelles espèces dans les 48heures. Ce travail permet de mieux comprendre la biodiversité des bactéries isolées dans le microbiome humain. / Theuse of WG Sallows to analyze and to decipherthe study of resistome of Multi Drug Resistant bacteria (MDR), understanding the different resistance mechanisms, genetic directories and their dissemination mechanisms at global level. During them y thesis I have achieved: 1. A literature review on the use of new contemporary diagnostic tools and capabilities in detecting out breaksin infectious diseases caused by MDR. 2: The identification and the analysis of resistome of multidrug resistant bacteria from clinical isolates suchasShewanellaalgae, normally marine environmental, in our case clinical strain isolated from the broncho alveolar lavage of a hospitalized patient with pneumonia and Chryseobacteriumin dologenes, isolated from a patient cysticfibrosis. In this analysis, we can show that environment albacteria suchas S.algae can be a reservoir of antibiotic resistance genes. The exhaustive analysis of these bacteria showed their ability to a dapttotheirecosystemsincludingtheacquisitionofnewgeneticelementsbylateralgenetransfer. The detection of genes in volved in the synthesis of nonribosomal peptide synthetase and polyketide synthases may have a role in their ability to survive in hostile environments suchas therespiratorytractofCFpatients or their presence inpatients having suffered multipleofantibiotic. 3:In this work,through theuse of the NTS onnew bacterial species isolated from human microbiome,we have a chieveda standardized analysis"insilico"to determine there sistome of these bacteria and the presence of secondary metabolites associated bacteriocins and the NRPS/PKS. The application of the NTS for sequenc in go bacterial genome of new bacterial species isolated in the human microbiome, allowe dus to develop a platform capable of analyzing the senew species within 48