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The state of adhesion of bacteria to nanofiber-textured model surfaces is analyzed at single-cell level. The results reveal similarities between the effect of topography on bacteria-surface interactions and vesicle-surface interactions. The results are discussed in the context of controlling bacterial adhesion to surfaces using nanofibrous topographical features. / Master of Science

A strain of Pseudomonas putida that exhibited seedling disease control on cotton was among 5000 strains examined for unique properties that could be used to selectively recover genetically engineered pseudomonads from environmental samples. One isolate (M-17) was found to produce a red halo around single colonies grown on media containing 10 mg/l crystal violet. This decolorization reaction was constitutively produced when the growth medium contained glucose and asparagine, but was inhibited by the substitution of ammonia, nitrate or urea for the amino acid nitrogen source. However, a different medium containing succinic acid and using ammonia as the sole nitrogen source was found to induce the reaction. Factors that did not affect the decolorization reaction included temperature (14-30° C) and pH (3-8). Cultures of M-17 grown in broth containing crystal violet were able to decolorize still broth solutions, but not when incubated on a shaker (150 rpm). Stationary cultures formed a red precipitate. Efforts to characterize the precipitate revealed that it was soluble in polar organic solvents and insoluble in non-polar organic solvents. Thin layer chromatography revealed the presence of six bands that possibly represented various demethylated forms of crystal violet. Chemically derived mutants (cry-) did not produce a red halo but a clear, colorless region surrounding bacterial growth was observed. A greenhouse study demonstrated that strain M-17 provided protection against fungal disease as shown by plant stands on cotton (67% stand) equivalent to the commercial fungicides (70% stand) and significantly improved over the unamended control (38% stand). / Master of Science

Pseudomonas aeruginosa est un pathogène opportuniste responsable des infections pulmonaires chroniques chez les patients atteints de fibrose kystique (FK). L’émergence de nouvelles souches épidémiques hypervirulentes, multi-résistantes aux antibiotiques et possédant une grande capacité de transmission, telles que LESB58, entraîne de grandes difficultés de traitement et une augmentation de la mortalité chez ces patients. Le séquençage complet de LESB58 a révélé un génome à 90% hautement conservé additionné de 455 gènes regroupés sous six prophages (PPs) et cinq îlots génomiques (GIs). Cette étude a pour objectif de déterminer l’implication de ces régions supplémentaires dans la pathogénie de LESB58. Une mutagenèse à étiquette signature (STM) suivie de plusieurs criblages ont permis de sélectionner 162 mutants dont 11 portant une insertion dans un GI ou PP. Des analyses subséquentes ont été réalisées sur ces mutants afin d’évaluer leur niveau de virulence in vivo dans un modèle d’infection pulmonaire chronique chez le rat. Des analyses de génomique ont été effectuées sur deux de ces mutants afin de mieux comprendre leur incapacité à établir l’infection dans le modèle d’infection in vivo. / Pseudomonas aeruginosa is an opportunistic pathogen and causes chronic pulmonary infection to cystic fibrosis (CF) patients. The hypervirulent epidemic strain LESB58 is associated with high transmissibility and is highly resistant to antibiotics causing increased morbidity and mortality. Whole genome sequencing of LESB58 revealed a 90% highly conserved core genome and 455 additional genes grouped in five genomics islands (GIs) and six prophages (PPs). The aim of this study was to determine the implication of the accessory genome in LESB58 virulence. We performed a signature tagged mutagenesis (STM) followed by an in vivo screening of the mutants. From 162 STM mutants defective for in vivo maintenance, we selected 11 harbouring an insertion in GI or PP for further virulence analysis. Two of these mutants were used for genomics analysis in order to better understand their incapacity for in vivo maintenance in the rat model of chronic lung infection.

Chez les procaryotes, FtsZ est reconnu comme étant la protéine clé impliquée dans le contrôle de la septation lors de la division cellulaire. Le gène correspondant, ftsZ, semblait être hautement conservé dans l’évolution chez les bactéries à Gram positif et à Gram négatif. Afin d'amplifier une région génique homologue chez Pseudomonas aeruginosa, deux amorces dirigées contre une région conservée du gène ftsZ ont été conçues à partir de la table d’utilisation des codons riches en GC. Un amplicon de 220 pb a été généré, séquencé et utilisé comme sonde moléculaire afin de cribler une banque génomique de P. aeruginosa PAO dans le vecteur phagique λSE6. Le phage recombinant isolé et cartographié contenait un fragment d’ADN chromosomique de P. aeruginosa de 16.5 kb. L’analyse de la séquence partielle d’un fragment de 4,5 kb BamHl a révélé un arrangement génique ftsA-ftsZ-envA suggérant une organisation similaire à celle observée chez Escherichia coli. L’étude de l’expression protéique in vitro a démontré la présence d’une protéine de 40 kDa. L’alignement des séquences de 8 gènes ftsZ a démontré que ces protéines sont hautement conservées. Une analyse phylogénétique des gènes ftsZ séparant les espèces en deux groupes de bactéries à Gram positif et à Gram négatif semble en accord avec la phylogénie des ARNr de ces espèces. / Québec Université Laval, Bibliothèque 2018 / Ottawa Bibliothèque nationale du Canada, Direction des acquisitions et des services bibliographiques 19 . --

P. aerguinosa is a serious human bacterial pathogen. This thesis describes attempts to use structural biology to identify new starting points for drugs against P. aerguinosa .A number of fragment-based screening techniques were used in order to identify potential inhibitors to P. aerguinosa RmlA protein, the first enzyme in the L-Rhamnose pathway. A 500 “Rule of 3” Fragment Library (Maybridge) was investigated. The first approach was the application of Differential Scanning Fluorimetry (DSF) approach to detect ligands that bind and stabilize RmlA protein. The stabilisation of RmlA was determined by thermal unfolding in the presence of each of the 500 compounds. 21 of those compounds were found to increase the protein stability. The library was then screened by NMR spectroscopy for binding to RmlA. Two techniques were evaluated STD and WaterLOGSY. 106 compounds gave positive results in both NMR experiments. These hits were then tested by a simple STD competition binding with dTTP, a natural RmlA substrate, in order to identify those binding at the active or allosteric site. 21 out of the 106 compounds were observed to compete with dTTP. The results were compared to the results of the DSF screening. Compounds that tested positive in the dTTP competition binding STD experiment and in the DSF screening were tested for their ability to inhibit RmlA in a biological assay. A coupled enzyme assay was used to monitor RmlA activity. Only one compound, 3-pyridin-3-ylaniline, showed significant inhibition of the enzyme activity. The PA1645 protein from P. aerguinosa has been identified as essential. The protein was overexpressed, purified and crystallised. Data were collected at Diamond on beamline IO3 and phases were determined by S-SAD at a wavelength of 1.6Å. Final coordinates have been deposited in the protein data bank under entry code 2XU8. The structure has 3 molecules in the asymmetric unit. There is some ambiguity as to the validity of the proposed trimeric arrangement, with results from solution and crystal disagreeing. Fragment-based screening approach has been applied to RmlA protein, using the DSF technique, a number of ligand-based NMR experiments and a coupled enzyme biological assay. 3-pyridin-3-ylaniline was the only compound that showed significant inhibition of the enzyme activity. The structure of PA1645 from P. aerguinosa has been solved. This work will help to design new drugs to combat multi-drug resistant P. aerguinosa and MTB.

The pyrimidine salvage enzyme, nucleoside hydrolase, is catalyzes the irreversible hydrolysis of nucleosides into the free nucleic acid base and D-ribose. Nucleoside hydrolases have varying degrees of specificity towards purine and pyrimidine nucleosides. In E. coli, three genes were found that encode homologues of several known nucleoside hydrolases in protozoa. All three genes (designated yaaF, yeiK, and ybeK) were amplified by PCR and cloned. Two of the gene products (yeiK and ybeK) encode pyrimidine-specific nucleoside hydrolases, while the third (yaaF) encodes a nonspecific nucleoside hydrolase. All three were expressed at low levels and had different modes of regulation. As a comparative analysis, the homologous genes of Pseudomonas aeruginosa and P. fluorescens (designated nuh) were cloned. Both were determined to encode nonspecific nucleoside hydrolases. The nucleoside hydrolases of the pseudomonads exhibited markedly different modes of regulation. Both have unique promoter structures and genetic organization. Furthermore, both pseudomonad nucleoside hydrolase were found to contain an N-terminal extension of 30-35 amino acids that is shown to act as a periplasmic-signaling sequence. These are the first two nucleoside hydrolases, to date,that have been conclusively demonstrated to be exported to the periplasmic space. The physiological relevance of this is explained.

The regulation of pyrimidine biosynthesis was studied in Pseudomonas putida. The biosynthetic and salvage pathways provide pyrimidine nucleotides for RNA, DNA, cell membrane and cell wall biosynthesis. Pyrimidine metabolism is intensely studied because many of its enzymes are targets for chemotheraphy. Four aspects of pyrimidine regulation are described in this dissertation. Chapter I compares the salvage pathways of Escherichia coli and P. putida. Surprisingly, P. putida lacks several salvage enzymes including nucleoside kinases, uridine phosphorylase and cytidine deaminase. Without a functional nucleoside kinase, it was impossible to feed exogenous uridine to P. putida. To obviate this problem, uridine kinase was transferred to P. putida from E. coli and shown to function in this heterologous host. Chapter II details the enzymology of Pseudomonas aspartate transcarbamoylase (ATCase), its allosteric regulation and how it is assembled. The E. coli ATCase is a dodecamer of two different polypeptides, encoded by pyrBI. Six regulatory (PyrI) and six catalytic (PyrB) polypeptides assemble from two preformed trimers (B3) and three preformed regulatory dimers (I2) in the conserved 2B3:3I2 molecular structure. The Pseudomonas ATCase also assembles from two different polypeptides encoded by pyrBC'. However, a PyrB polypeptide combines with a PyrC. polypeptide to form a PyrB:PyrC. protomer; six of these assemble into a dodecamer of structure 2B3:3C'2. pyrC' encodes an inactive dihydroorotase with pyrB and pyrC' overlapping by 4 bp. Chapter III explores how catabolite repression affects pyrimidine metabolism. The global catabolite repression control protein, Crc, has been shown to affect pyrimidine metabolism in a number of ways. This includes orotate transport for use as pyrimidine, carbon and nitrogen sources. Orotate is important because it interacts with PyrR in repressing the pyr genes. Chapter IV describes PyrR, the positive activator of the pyrimidine pathway. As with other positive activator proteins, when pyrimidine nucleotides are depleted, PyrR binds to DNA thereby enhancing expression of pyrD, pyrE and pyrF genes. When pyrimidine nucleotides are in excess, the PyrR apoprotein binds to orotate, its co-repressor, to shut down all the pyrimidine genes. Like many positive activators, PyrR is subject to autoregulation and has catalytic activity for uracil phosphoribosyltransferase inducible by orotate.

Cyanide is a well known toxicant that arises in the environment from both biological and industrial sources. Bacteria have evolved novel coping mechanisms for cyanide and function as principal agents in the biosphere for cyanide recycling. Some bacteria exhibit the unusual ability of growing on cyanide as the sole nitrogen source. One such organism is Pseudomonas fluorescens NCIMB 11764 (Pf11764) which employs a novel oxidative mechanism for detoxifying and assimilating cyanide. A unique complex of enzymes referred to as cyanide oxygenase (CNO) is responsible for this ability converting cyanide to ammonia which is then assimilated. Because one component of the four member CNO complex was previously shown to act on cyanide independent of the other members, its characterization was sought as a means of gaining a better understanding of the overall catalytic mechanism of the complex. Preliminary studies suggested that the enzyme belonged to a subset of nitrilase enzymes known as cyanide dihydratases (CynD), however, a cynD-like gene in Pf11764 could not be detected by PCR. Instead, a separate nitrilase (Nit) linked to cyanide metabolism was detected. The corresponding nit gene was shown to be one of a conserved set of nit genes traced to a unique cluster in bacteria known as Nit1C. To determine whether the previously described CynD enzyme was instead Nit, efforts were undertaken to isolate the enzyme. This was pursued by cloning and expressing the recombinant enzyme and by attempting to isolate the native enzyme. This thesis is concerned with the latter activity and describes the purification of a Nit-like cyanide-degrading nitrilase (NitCC) from Pf11764 to ~95% homogeneity. Purification was greatly facilitated by the discovery that fumaronitrile, as opposed to cyanide, was the preferred substrate for the enzyme (20 versus 1 U/mg protein, respectively). While cyanide was less effective as a substrate, the specificity for cyanide far outweighed that (10,000 fold) of the recombinant enzyme (NitPG) implying that the native NitCC protein purified in this work is different from that of the cloned recombinant. Further evidence of this was provided by molecular studies indicating that the two proteins differ in mass (34.5 and 38 kDa, respectively) and amino acid sequence. In summary, two different Nit enzymes are encoded by Pf11764. While the two share greater than 50% amino acid sequence identity, the results suggest that the native NitCC enzyme purified in this work functions better as a cyanide-degrading nitrilase and is one of four enzyme components comprising CNO required for Pf11764 cyanide assimilation.