A análise de fluxos metabólicos para a produção de PHAMCL por Pseudomonas sp. LFM046 revelou que a baixa eficiência de conversão de carboidratos em PHA (60-70% do valor máximo teórico) deve estar associada à utilização principal da via das pentoses (VP) para o metabolismo de carboidratos. Eficiências significativamente maiores poderiam ser obtidas se uma parcela maior da glicose fosse metabolizada pela via Entner-Doudoroff (ED). Assim, neste trabalho foi realizada a análise de fluxos metabólicos utilizando glicose marcada (C13) e o melhoramento genético de Pseudomonas sp. LFM046 utilizando estratégia de engenharia metabólica. Experimentos com glicose marcada confirmaram um maior fluxo de carboidratos pela VP em relação a ED. A superexpressão de genes específicos de ED em Pseudomonas sp. LFM046 demonstrou apenas pequenos aumentos na eficiência de conversão de carboidratos em PHA pelas linhagens recombinantes. / The metabolic flux analysis for PHAMCL production by Pseudomonas sp. LFM046 revealed that the low efficiency of carbohydrates conversion into PHA (60-70% of the maximum theoretical value) should be associated with the main use of pentose phosphate pathway (PP) for the carbohydrate metabolism. Significantly higher efficiencies could be obtained if a larger portion of the glucose was metabolized via the Entner-Doudoroff (ED). Therefore, the metabolic fluxes analysis was performed in this work using labeled glucose (13C) and the genetic improvement of Pseudomonas sp. LFM046 by using metabolic engineering approach. Experiments with labeled glucose confirmed an increased flow of carbohydrates by PP compared to ED. The overexpression of specific genes from ED in Pseudomonas sp. LFM046 showed only small increases in the efficiency of carbohydrates conversion into PHA by recombinant strains.

by Woo Yiu Ho, Anthony. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 162-171). / Abstract also in Chinese. / Abstract --- p.i / Acknowledgements --- p.iii / Table of Contents --- p.iv / List of Figures --- p.ix / List of Tables --- p.xi / List of Abbreviations --- p.xii / Chapter 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Bacterial Adhesion and Aggregation --- p.1 / Chapter 1.1.1 --- Significance of Bacterial Adhesion Studies --- p.1 / Chapter 1.1.2 --- Definitions --- p.4 / Chapter 1.1.3 --- Colonization Process --- p.7 / Chapter 1.1.4 --- Specific and Nonspecific Interactions --- p.8 / Chapter 1.1.5 --- Models of Bacterial Adhesion and Aggregation Processes --- p.14 / Chapter 1.1.6 --- Experimental Systems in Adhesion Research --- p.16 / Chapter 1.1.7 --- Experimental Systems in Aggregation Research --- p.19 / Chapter 1.2 --- Pseudomonas aeruginosa --- p.21 / Chapter 1.2.1 --- General Description and Clinical Significance --- p.21 / Chapter 1.2.2 --- Adhesins of Pseudomonas aeruginosa --- p.22 / Chapter 1.2.3 --- "Alginate, Mucoidity, Biofilm Formation and Cystic Fibrosis" --- p.23 / Chapter 1.2.4 --- Lipopolysaccharides --- p.26 / Chapter 1.2.5 --- Pili --- p.29 / Chapter 1.2.6 --- Flagella --- p.30 / Chapter 1.2.7 --- Lectins --- p.31 / Chapter 1.2.8 --- Other Adhesins --- p.31 / Chapter 1.2.9 --- Rhamnolipids --- p.32 / Chapter 1.3 --- Current Study --- p.33 / Chapter 2 --- MATERIALS AND EQUIPMENT --- p.35 / Chapter 2.1 --- Bacterial Strain --- p.35 / Chapter 2.2 --- Solid Surfaces --- p.35 / Chapter 2.3 --- Chemicals --- p.36 / Chapter 2.4 --- Recipes --- p.38 / Chapter 2.5 --- Equipment --- p.38 / Chapter 3 --- METHODS --- p.40 / Chapter 3.1 --- Maintenance and Culturation --- p.40 / Chapter 3.1.1 --- Maintenance of Bacterial Strains --- p.40 / Chapter 3.1.2 --- Seed Culture Preparation --- p.40 / Chapter 3.1.3 --- Culturation in Defined Growth Media --- p.40 / Chapter 3.2 --- Bacterial Adhesion and Aggregation Assay Methods --- p.41 / Chapter 3.2.1 --- Bacterial Adhesion on Glass Assay --- p.41 / Chapter 3.2.2 --- Bacterial Adhesion on Plastic Assay --- p.44 / Chapter 3.2.3 --- Bacterial Adhesion under Shear Assay --- p.44 / Chapter 3.2.4 --- Bacterial Aggregation Examination by Adhesion on Glass Assay --- p.45 / Chapter 3.2.5 --- Bacterial Aggregation Examination by Top-agar Assay --- p.45 / Chapter 3.2.6 --- Bacterial Aggregation Examination by Epi-fluorescence Microscopy --- p.46 / Chapter 3.2.7 --- Bacterial Aggregation Screening Test --- p.46 / Chapter 3.3 --- Determination of the Effects of Various Factors on Adhesion and Aggregation --- p.47 / Chapter 3.3.1 --- Culturation Period --- p.47 / Chapter 3.3.2 --- Osmotic Shock during the Washing Procedure --- p.47 / Chapter 3.3.3 --- Growth Media --- p.48 / Chapter 3.3.4 --- Assay Conditions --- p.48 / Chapter 3.3.5 --- Cell Pretreatments --- p.48 / Chapter 3.4 --- Isolation of Aggregation-deficient Mutants --- p.49 / Chapter 3.5 --- Outer Membrane Protein Profiles --- p.50 / Chapter 3.5.1 --- Isolation of Outer Membrane Fraction --- p.50 / Chapter 3.5.2 --- Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis --- p.51 / Chapter 3.6 --- Determination of the Mobility of the Bacteria on Surfaces --- p.52 / Chapter 3.6.1 --- Subsurface Twitching Assay --- p.52 / Chapter 3.6.2 --- Soft-agar Swarm Assay --- p.53 / Chapter 3.7 --- Detection of Alginate Production --- p.53 / Chapter 3.7.1 --- Extraction of Alginate from Spent Growth Medium --- p.53 / Chapter 3.7.2 --- Releasing Cell Surface-associated Alginate --- p.54 / Chapter 3.8 --- Other Assay Methods --- p.55 / Chapter 3.8.1 --- Protein Assay --- p.55 / Chapter 3.8.2 --- Carbohydrate Determination --- p.55 / Chapter 3.8.3 --- Alginate Determination --- p.55 / Chapter 4 --- RESULTS --- p.57 / Chapter 4.1 --- Standardization of the Assays for Bacterial Adhesion and Aggregation --- p.57 / Chapter 4.1.1 --- Effects of Cell Density and Exposure Time on the Number of Adhered Bacteria Detected in Bacterial Adhesion on Glass Assay --- p.57 / Chapter 4.1.2 --- Characterization of Bacterial Aggregation by Different Examination Methods --- p.62 / Chapter 4.1.3 --- Effects of Culturation Period on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.67 / Chapter 4.1.4 --- Effects of Osmotic Shock during Washing on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.70 / Chapter 4.1.5 --- Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 as a Function of Time under the Standard Assay Condition --- p.71 / Chapter 4.1.6 --- Consistency of Bacterial Adhesion on Glass Assay --- p.74 / Chapter 4.2 --- Effects of Growth Media on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.77 / Chapter 4.3 --- Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 in Different Assay Media --- p.77 / Chapter 4.3.1 --- Effects of Various Buffers on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.77 / Chapter 4.3.2 --- Effects of pH on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.78 / Chapter 4.3.3 --- Effects of Various Electrolytes on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.81 / Chapter 4.3.4 --- Concentration Effects of Monovalent and Divalent Cations on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.88 / Chapter 4.3.5 --- Concentration Effects of Phosphate Buffers on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.93 / Chapter 4.3.6 --- Concentration Effects of Ammonium Sulfate and Cyclohexylammonium Sulfate on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.96 / Chapter 4.3.7 --- Effects of Cation Chelation on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.99 / Chapter 4.3.8 --- Effects of Sugars on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.100 / Chapter 4.3.9 --- Effects of Amino Acids on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.101 / Chapter 4.4 --- Adhesion and Aggregation after Pretreatments of the Cells --- p.103 / Chapter 4.4.1 --- Effects of Protease Treatments on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.103 / Chapter 4.4.2 --- Effects of Externally Added Proteins on Adhesion and Aggregation of Pronase-treated Cells --- p.107 / Chapter 4.4.3 --- Effects of Acid or Base Treatments on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.108 / Chapter 4.4.4 --- Effects of Heat Treatment on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.108 / Chapter 4.4.5 --- Effects of Extensive Washing on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.110 / Chapter 4.5 --- Isolation and Growth Characteristics of Aggregation-deficient Mutants --- p.111 / Chapter 4.6 --- Comparisons of the Adhesion and Aggregation Characters of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 --- p.115 / Chapter 4.6.1 --- Under Standard Condition --- p.115 / Chapter 4.6.2 --- On Different Surfaces and in Different Electrolytes --- p.115 / Chapter 4.6.3 --- Under Shear --- p.118 / Chapter 4.6.4 --- Adhesion and Aggregation of Combined Suspensions of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 --- p.122 / Chapter 4.7 --- Characterization of the Cell Surface Properties of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 --- p.125 / Chapter 4.7.1 --- Outer Membrane Protein Profiles --- p.125 / Chapter 4.7.2 --- Pili-elicited Twitching Mobility --- p.125 / Chapter 4.7.3 --- Mobility Due to Flagella --- p.128 / Chapter 4.7.4 --- Production of Alginate --- p.128 / Chapter 5 --- DISCUSSIONS --- p.130 / Chapter 5.1 --- Choice of the Materials --- p.130 / Chapter 5.2 --- Development of the Assay Methods --- p.130 / Chapter 5.2.1 --- Development of the Procedures for Bacterial Adhesion Assays --- p.130 / Chapter 5.2.2 --- Development of the Assay Methods for Bacterial Aggregation --- p.132 / Chapter 5.2.3 --- Standardization of the Assays --- p.133 / Chapter 5.2.4 --- Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 as a Function of Time under the Standard Assay Condition --- p.134 / Chapter 5.2.5 --- Consistency of Bacterial Adhesion on Glass Assay --- p.135 / Chapter 5.2.6 --- Limits of Bacterial Adhesion on Glass Assay --- p.135 / Chapter 5.3 --- Effects of Growth Media on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.135 / Chapter 5.4 --- Effects of Various Chemicals in the Assay Media on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.136 / Chapter 5.4.1 --- Effects of Electrolytes on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.137 / Chapter 5.4.2 --- Effects of Aggregation on Adhesion --- p.140 / Chapter 5.4.3 --- Effects of Cyclohexylammonium Sulfate and Ammonium Sulfate on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.141 / Chapter 5.4.4 --- Effects of Sugars and Amino Acids on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.143 / Chapter 5.5 --- Effects of Various Cell-surface Modifications on Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 --- p.144 / Chapter 5.6 --- Isolation and Growth Characteristics of Aggregation-deficient Mutants --- p.146 / Chapter 5.7 --- Comparisons of the Adhesion and Aggregation Characters of Pseudonomas aeruginosa ATCC 10145 and Mutant 9 --- p.147 / Chapter 5.7.1 --- Adhesion and Aggregation of Pseudonomas aeruginosa ATCC 10145 and Mutant 9 on Different Surfaces In Different Electrolytes --- p.147 / Chapter 5.7.2 --- Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 Under Shear --- p.147 / Chapter 5.7.3 --- Adhesion and Aggregation of Combined Suspensions of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 --- p.148 / Chapter 5.8 --- Characterization of the Cell Surface Properties of Pseudomonas aeruginosa ATCC 10145 and Mutant 9 --- p.148 / Chapter 5.9 --- General Discussions --- p.151 / Chapter 6 --- APPENDIX --- p.154 / Chapter 6.1 --- Visual Examination of Adhesion and Aggregation of Pseudomonas aeruginosa ATCC 10145 on Glass --- p.154 / Chapter 6.2 --- Fractal Analysis of Bacterial Aggregates --- p.154 / Chapter 7 --- REFERENCES --- p.162

Le Pseudomonas aeruginosa est un pathogène nosocomial majeur. Le clone ST235 est le plus prévalent des clones internationaux dits à hautris que. Ce clone est très fréquemment multi résistant aux antibiotiques, ce qui complique la prise en charge des infections dont il est à l’origine.Malgré son importance clinique, la base moléculaire Du succès du clone ST235 n’est pas comprise.Dans ce travail, nous avons cherché à comprendre l’origine spacio temporelle de ce clone et les bases moléculaires de son succès. A l’aide d’outils bio informatiques existants ,nous avons trouvé que le clone ST235 a émergé en Europe en 1984 et que tous les isolates ST235 produisent l’exotoxine ExoU. Nous avons également identifié 22 gènes Contigus spécifiques de ce clone et impliqués dans l’efflux transmembranaire, dans le traitement de l’ADN et dans la transformation bactérienne. Cette combinaison unique de gènes a pu contribuer à la gravité des infections dues à ce clone et à sa capacité à acquérir des gènes de résistance aux antibiotiques. Ainsi, la diffusion mondiale de ce clone a probablement été favorisée par l’utilisation extensive des fluoroquinolones, puis il est de venu localement résistant aux amino glycosides, aux β-lactamines, et aux carbapénèmes par mutation et acquisition d’éléments de résistance. Nous avons majoritairement utilisé des outils existants,mais avons découvert que les programmes de détection des séquences d’insertions (IS, ayant un rôle important dans l’évolution des génomes bactériens) ne sont pas adaptés aux données dont nous disposions. Nous avons ainsi mis au point un outil (appelé panISa) qui détecte de façon précise et sensible les IS à partir de données brutes de séquençage de génomes bactériens. / Pseudomonas aeruginosa is a major nosocomial pathogen with ST235 being the most prevalent of the so-called ‘international’ or ‘high-risk’ clones. This clone is associated with poor clinical outcomes in part due to multi- and high-level antibiotic resistance. Despite its clinical importance, the molecular basis for the success of the ST235 clone is poorly understood. Thus this thesis aimed to understand the origin of ST235 and the molecular basis for its success, including the design of bioinformatics tools for finding insertion sequences (IS) of bacterial genomes.To fulfill these objectives, this thesis was divided into 2 parts.First, the genomes of 79 P. aeruginosa ST235 isolates collected worldwide over a 27-year period were examined. A phylogenetic network was built using Hamming distance-based method, namely the NeighborNet. Then we have found the Time to the Most Recent Common Ancestor (TMRCA) by applying a Bayesian approach. Additionally, we have identified antibiotic resistance determinants, CRISPR-Cas systems, and ST235-specific genes profiles. The results suggested that the ST235 sublineage emerged in Europe around 1984, coinciding with the introduction of fluoroquinolones as an antipseudomonal treatment. The ST235 sublineage seemingly spreads from Europe via two independent clones. ST235 isolates then appeared to acquire resistance determinants to aminoglycosides, β-lactams, and carbapenems locally. Additionally, all the ST235 genomes contained the exoU-encoded exotoxin and identified 22 ST235-specific genes clustering in blocks and implicated in transmembrane efflux, DNA processing and bacterial transformation. These unique genes may have contributed to the poor outcome associated with P. aeruginosa ST235 infections and increased the ability of this international clone to acquire mobile resistance elements.The second part was to design a new Insertion Sequence (IS) searching tool on next-generation sequencing data, named panISa. This tool identifies the IS position, direct target repeats (DR) and inverted repeats (IR) from short read data (.bam/.sam) by investigating only the reference genome (without any IS database). To validate our proposal, we used simulated reads from 5 species: Escherichia coli, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus, and Vibrio cholerae with 30 random ISs. The experiment set is constituted by reads of various lengths (100, 150, and 300 nucleotides) and coverage of simulated reads at 20x, 40x, 60x, 80x, and 100x. We performed sensitivity and precision analyses to evaluate panISa and found that the sensitivity of IS position is not significantly different when the read length is changed, while the modifications become significant depending on species and read coverage. When focusing on the different read coverage, we found a significant difference only at 20x. For the other situations (40x-100x) we obtained a very good mean of sensitivity equal to 98% (95%CI: 97.9%-98.2%). Similarly, the mean of DR sensitivity of DR identification is high: 99.98% (95%CI: 99.957%-99.998%), but the mean of IR sensitivity is 73.99% (95%CI: 71.162%-76.826%), which should be improved. Focusing on precision instead of sensibility, the precision of IS position is significantly different when changing the species, read coverage, or read length. However, the mean of each precision value is larger than 95%, which is very good.In conclusion, P. aeruginosa ST235 (i) has become prevalent across the globe potentially due to the selective pressure of fluoroquinolones and (ii) readily became resistant to aminoglycosides, β-lactams, and carbapenems through mutation and acquisition of resistance elements among local populations. Concerning the second point, our panISa proposal is a sensitive and highly precise tool for identifying insertion sequences from short reads of bacterial data, which will be useful to study the epidemiology or bacterial evolution.

Bactérias aclimatadas a cobre foram isoladas a partir de amostras de solo e água coletadas na região da Mina de Sossego (Vale, Carajás, PA). Pseudomonas putida sp. foi escolhida, pois, apresentou a maior capacidade sortiva de Cu2+, Q = 40 mg/g. O cultivo em regime de batelada, meio mineral, com glicerol como fonte de carbono, resultou fator de conversão de glicerol a células, YX/S, de 0,49 g/g e velocidade específica máxima de crescimento, mmax, de 0,11 h-1. Alta concentração celular, 90 g/L, foi alcançada em cultivos em regime de batelada alimentada. Promoveu-se sorção de cobre pelas células, por meio de adição contínua ou em pulsos, de solução de CuSO4. A maior sorção específica de cobre, Q, de 30 (mg de Cu2+/g de células), foi verificada na adição por pulsos. Fotos de MET da bactéria na ausência e presença de Cu2+ mostram acúmulo de cobre na membrana e internamente, caracterizando biossorção e bioacumulação. / Bacteria acclimated to copper were isolated from soil and water samples collected in Mina de Sossego (Vale, Carajás, PA). Pseudomonas putida sp. was chosen as it had the highest sorptive capacity for Cu2+, Q = 40 mg/g. The fed-batch culture in mineral medium with glycerol as the carbon source resulted in a glycerol-to-cell conversion factor, YX/S of 0.49 g/g and maximum specific growth rate, mmax of 0.11 h-1. High cell concentration, 90 g/L, was achieved in cultures in fed-batch regimen. Cooper sorption by cells was promoted, by continuous or pulse addition of CuSO4 solution. The highest specific copper sorption, Q, 30 (mg Cu+2/g of cells) was seen with the addition by pulses. TEM photos of the bacteria in the absence and presence of Cu+2 show copper accumulation in the membrane and internally, featuring biosorption and bioaccumulation.

Pseudomonas aeruginosa é uma gamma-proteobacteria ubíqua, sendo a principal causa de infecção hospitalar dentre todos os patógenos relacionados com pneumonia em UTI. A defesa do hospedeiro se dá por vários mecanismos como a liberação, por fagócitos, de espécies reativas de oxigênio, como o ânion superóxido (O2?-), peróxido de hidrogênio (H2O2) e o radical hidroxila (OH?) para combater o patógeno. LsfA pertence à família das peroxirredoxinas (Prx) e ao sub-grupo de Prxs que contém somente uma cisteína catalítica (denominadas 1-Cys Prx). Prxs são enzimas capazes de remover peróxidos (incluindo peroxinitrito) em velocidades muito elevadas. Além disso, LsfA está relacionada a patogenicidade de P. aeruginosa. Dentro desse contexto, o objetivo do presente trabalho é a caracterização bioquímica e estrutural de LsfA; que pode possibilitar a identificação de inibidores dessa enzima antioxidante. Por outro lado, caracterizando cineticamente reações de oxido-redução de LsfA e caracterizando seus mecanismos de ação, podemos identificar seus substratos biológicos. Dessa maneira, utilizando diferentes técnicas, determinamos as constantes de segunda ordem de LsfA com H2O2 (na ordem de 107 M -1.s -1); para terc-butilhidroperóxido (na ordem de 106 M-1.s-1) e peroxinitrito (na ordem de 107 M-1.s-1). A redução de LsfA por ascorbato foi descrita previamente por nosso grupo (na ordem de 103 M-1.s-1); e aqui apresentamos dados preliminares sobre a redução dessa 1-Cys Prx por GSH. Além disso, fomos capazes de determinar a estrutura cristalográfica de LsfA em sua forma oxidada e superoxidada, com resolução de 2.6 e 2.0 ? respectivamente; que, como esperado, se apresentou no estado dimérico, em ambos os casos. Descrevemos aqui características sobre a estrutura do sítio ativo de LsfA, que apresenta mais eletronegativo, com a cisteína peroxidásica desprotonada, e mais hidrofóbico. Na estrutura de LsfA superoxidada, observamos a co-cristalização dessa enzima com uma molécula de polietileno glicol que pode estar mimetizando um substrato. Portanto, esses estudos levantaram importantes informações estruturais e bioquímicas de uma enzima antioxidante envolvida com a virulência de P. aeruginosa / Pseudomonas aeruginosa is a ubiquous gamma-proteobacteria that is the main cause of hospitalar infections among all pathogens related with pneumonia. Host defenses against pathogens are mainly by phagocytes, which releases reactive oxygen species, such as superoxide (O2?-), hydrogen peroxide (H2O2) and hydroxyl radical (OH?) to fight against pathogen. LsfA belongs to peroxiredoxins (Prx) family; and to the 1-Cys Prx sub-group (Prx6 sub-family) that possess only one catalytic cysteine. Prx are enzymes can remove peroxides with extremely high efficiency. LsfA was already related with P. aeruginosa virulence. So, the aim of the present work is the structural and biochemical characterization of LsfA, which may enable the discovery of inhibitors. Furthermore, the investigation of the kinetics and the mechanism of catalysis of LsfA may give insights on the chemical nature of its biological substrates. Therefore, using different techniques; the second order rate constants of LsfA with H2O2 (107 M -1.s -1), tert-butylhydroperoxide (106 M -1.s -1) and peroxynitrite (107 M -1.s -1) were determined. Our group has already determined the rate constant between ascorbate and LsfA (103 M -1.s -1) and preliminary data on the reduction of this 1-Cys Prx by glutathione is described. Furthermore, two crystallographic structures of LsfA were elucidated in distinct oxidative states (sulfenic and sulfonic acid in the CP), both in the dimeric state; at 2.6 and 2.0 ? resolution respectively. Features in the LsfA active site are also described here, such as poor exposure to the solvent. In the LsfA crystal structure where Cp is hyperoxidized to sulfinic acid, we observed the presence of an electronic density compatible with a PEG molecule that might be mimicking one of the possible substrates. Therefore, relevant structural and biochemical information were gained with our studies about an antioxidant enzyme involved with P aeruginosa virulence

Nos últimos anos, um estilo de vida celular vem ganhando destaque no mundo científico: o biofilme. O biofilme é uma comunidade celular em que as células permanecem aderidas a um substrato e envoltas em uma matriz de biopolímeros. Bactérias no estado de biofilme possuem algumas características alteradas, como o aumento da resistência a antibióticos e a facilidade de troca de genes de resistência, sendo um grande inconveniente na área médica e industrial. O patógeno humano Pseudomonas aeruginosa é uma bactéria gram-negativa causadora de infecções associadas a pacientes que apresentam o sistema imune debilitado, sendo muito comum em casos de fibrose cística. Além disso, P. aeruginosa é um organismo modelo no estudo de formação de biofilme, podendo produzir três tipos distintos de exopolissacarídeos: alginato, PSL e PEL. Devido ao pouco conhecimento do polissacarídeo PEL, a cepa P. aeruginosa PA14 vem sendo amplamente estudada, uma vez que essa é a única cepa em que PEL é o principal polímero responsável pela estabilidade da matriz de polissacarídeos. No processo de produção e exportação de PEL, sete proteínas são necessárias: Pel(A-G). Segundo predições computacionais e comparações com outros tipos de complexos biossintéticos de exopolissacarídeos, um modelo de arranjo molecular das proteínas Pel foi proposto, embora algumas proteínas não possuam uma função bem determinada no processo de síntese de PEL. Nesse contexto, o trabalho buscou estudar as proteínas envolvidas na formação de PEL para a melhor elucidação do mecanismo de ativação, produção e exportação desse polissacarídeo, com destaque para a enzima glicosiltransferase PelF e a investigação de uma possível interação de PelF com a proteína reguladora de produção do polissacarídeo, PelD, e a transportadora de membrana interna, PelG. Foram realizados diversos testes de interação entre PelF, PelG e construções solúveis de PelD por cromatografia de exclusão molecular, crosslinking e pull-down que não apresentaram interações entre tais construções, indicando que frações de membrana de PelD ou outros parceiros de interação podem ser necessários para a formação do complexo de síntese e exportação de PEL da membrana interna. Adicionalmente, mutantes de PelD sítio-dirigidos foram construídos em P. aeruginosa PA14 e tiveram sua capacidade de formação de biofilme avaliadas para investigação do mecanismo de ativação de PelD. A diminuição da formação de biofilme de mutantes de algumas regiões de PelD como a hélice S (resíduos 158-176), o core hidrofóbico ocupado pela hélice S e resíduos que estabilizam a ligação de c-di-GMP nos levou a propor um mecanismo de ativação desse importante regulador proteico de formação de biofilme em P. aeruginosa nunca descrito anteriormente. / In the last years, a cellular lifestyle has been in the spotlight in the scientific world: the biofilm. Biofilm is a cellular community in which cells are attached to a substrate and surrounded by a biopolymeric matrix. Bacteria in a biofilm lifestyle has some altered characteristics, as a higher antibiotics tolerance and facility in resistance genes exchange, turning them into a big problem in medical and industrial fields. The human pathogen Pseudomonas aeruginosa is a gram-negative bacterium which causes infections associated to patients with an impaired immune system, as frequently found in patients with cystic fibrosis. Moreover, P. aeruginosa is a model organism in biofilm formation studies, producing three distinct types of exopolysaccharides: alginate, PSL and PEL. Since there is few information about PEL polysaccharide, the strain PA14 has been broadly studied because this is the unique strain in which PEL is the main polymer that gives stability of the polysaccharide matrix. In the process of PEL production and exportation, seven proteins are required: Pel(A-G). Computational predictions and comparison with other similar exopolysaccharides biosynthetic complexes led to a model of molecular complex of Pel proteins, though some proteins do not have a clear role in the PEL synthesis process. In this context, the work aimed to study the proteins related to PEL synthesis for a better understanding of the mechanism of production and exportation of this polysaccharide, focusing on the glycosyltransferase PelF and the investigation of its possible interaction with PelD, the regulatory protein of the polysaccharide production, and PelG, the putative inner membrane transporter. Several interaction assays were performed with PelF, PelG and soluble constructs of PelD using size exclusion chromatography, crosslinking and pull-down. No interaction was detected, showing that membrane fractions of PelD or other interaction partners can be required to the inner membrane complex of synthesis and export of PEL. Additionally, site-directed mutants of PelD in P. aeruginosa PA14 were constructed to evaluate their biofilm formation ability and investigate PelD activation mechanism. Mutants in regions as S-helix (residues 158-176), hydrophobic core occupied by the S-helix and residues of c-di-GMP stabilization presented a decrease of biofilm formation compared to the wild type strain. Those results allowed us to propose an activation mechanism of this important regulator of biofilm formation in P. aeruginosa never described before.

Ramnolipídios (RHLs) são biossurfactantes produzidos por Pseudomonas. O objetivo deste trabalho foi avaliar o potencial de produção de ramnolipídios por isolados de Pseudomonas considerando os efeitos das fontes de carbono ou nitrogênio tanto na concentração de ramnolipídios produzida como na composição deste. De 47 isolados bacterianos, cinco foram selecionados qualitativamente para avaliação da produção de ramnolipídios, analisando 48 combinações diferentes de meio mineral. A produção de polihidroxialcanoatos (PHAs) também foi avaliada. Glicose e óleos de canola e linhaça foram as fontes de carbono que promoveram a maior formação de RHLs. Nitrato de sódio se mostrou a melhor fonte de nitrogênio para produção desse tensoativo. A análise do PHA e do RHL purificados revelou a presença de 3-hidroxi-6-dodecenoato (3HDd<font face=\"Symbol\">D6), um composto proveniente exclusivamente da <font face=\"Symbol\">b-oxidação do ácido linoleico. Esses resultados indicam que a <font face=\"Symbol\">b-oxidação de ácidos graxos também contribui com intermediários metabólicos para a biossíntese de RHLs, ao contrário ao reportado na literatura. / Ramnolipids (RHLs) are biosurfactants produced by Pseudomonas. The aim of this study was to evaluate the production of rhamnolipids by Pseudomonas isolates, considering the effects of carbon and nitrogen sources on their concentration and composition. From 47 bacterial isolates, five were selected qualitatively for to evaluate the RHLs production, analyzing 48 different combinations of mineral medium. The production of polyhydroxyalkanoates (PHAs) was also evaluated. Linseed oil, canola oil and glucose were the carbon sources that promoted formation the largest amounts of RHLs. From plant oils, sodium nitrate proved to be the best nitrogen source for RHLs production. The analysis of purified PHA and RHL revealed the presence of the 3-hydroxy-6-dodecenoate, a compound derived exclusively from <font face=\"Symbol\">b-oxidation of linoleic acid. These results indicate that the <font face=\"Symbol\">b-oxidation of fat acids, contributes with intermediates for the biosynthesis of RHLs, unlike literature reports.

Copies of author's previously published articles inserted. Bibliography :leaves 65-80 Ice nucleation active (INA) bacteria were detected in a pea field in South Australia. They were identified as strains of Pseudomonas syringae and Pseudomonas flourescens biotype 1. Some chemical agents were tested on the two ice nucleating species, as cryoprotectants.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 86-98).

Το γένος Pseudomonas ανήκει στην οικογένεια Pseudomonadaceae και περιλαμβάνει πολλά είδη. Το συχνότερο είδος ψευδομονάδας που προκαλεί νόσο στον άνθρωπο είναι η Pseudomonas aeruginosa. Η P.aeruginosa είναι ένα Gram αρνητικό, αυστηρά αερόβιο βακτηρίδιο, το οποίο αναπτύσσεται στους 37-42οC και καλλιεργείται σχετικά εύκολα σε κοινά θρεπτικά υλικά. Η P. aeruginosa έχει χαρακτηριστεί ως ένα από τα σημαντικότερα και σοβαρότερα ευκαιριακά παθογόνα βακτηρία, τα οποία είναι υπεύθυνα για νοσοκομειακές λοιμώξεις σε διάφορες ειδικές ομάδες ασθενών όπως ανοσοκατασταλμένα άτομα, άτομα με κυστική ίνωση (cystic fibrosis), ασθενείς με νεοπλασίες, κ.α. Οι λοιμώξεις που προκαλεί η P. aeruginosa χαρακτηρίζονται σοβαρές και επικίνδυνες αφενός μεν γιατί προκαλεί νόσο σε άτομα ήδη επιβεβαρυμένα από άλλες καταστάσεις, αφετέρου δε γιατί εμφανίζει ανθεκτικότητα στα περισσότερα αντιβιοτικά. Ο τρόπος με τον οποίο η P. aeruginosa ασκεί την παθογόνο δράση της είναι πολύπλοκος και δεν έχει διευκρινισθεί επακριβώς. Διάφοροι κυτταρικοί παράγοντες αλλά και εξωκυττάρια προϊόντα θεωρούνται υπεύθυνα για την έκφραση της παθογόνου δράσης του μικροοργανισμού. Οι πιο σημαντικοί κυτταρικοί παράγοντες είναι: ο λιποπολυσακχαρίτης, οι φίμπριες, οι πρωτεΐνες της εξωκυττάριας μεμβράνης, ο εξωκυττάριος πολυσακχαρίτης (Slime), καθώς επίσης και ο βλεννώδης πολυσακχαρίτης (αλγινικό οξύ) που σχετίζεται με τα βλεννώδη στελέχη. Επίσης διάφορα εξωκυττάρια προϊόντα-παράγοντες τα οποία θεωρούνται υπεύθυνα για τη λοιμογόνο δράση του βακτηρίου, είναι διάφορα ένζυμα και κυρίως το Εξωένζυμο-S και η Εξωτοξίνη-A. Στους μηχανισμούς άμυνας του ξενιστή έναντι της P. aeruginosa τα μακροφάγα που προσελκύονται στην εστία της λοίμωξης παίζουν το σπουδαιότερο ρόλο. Οι κυτταροκίνες που παράγονται από τα ενεργοποιημένα μακροφάγα καθορίζουν την έκταση της βλάβης και την έκβαση της λοίμωξης. Σε πειραματικά μοντέλα σήψης από P. aeruginosa η παραγωγή του παράγοντα νεκρώσεως όγκου (TNF-α) σε μικρά ποσά έχει συσχετισθεί με προστασία σε σοβαρές λοιμώξεις, ενώ η υπερπαραγωγή του οδηγεί σε σηπτικό σοκ. Η ρύθμιση της παραγωγής του TNF-α αντικατοπτρίζει τη ρύθμιση της ενεργοποίησης του μακροφάγου. Διαφορετικοί υποδοχείς επιφανείας όπως οι TLR’s, συμβάλουν στην αναγνώριση του μικροβίου και την επακόλουθη ενεργοποίηση του μακροφάγου. Τα ενδοκυττάρια γεγονότα που σχετίζονται με τη μετάδοση του σήματος ενεργοποίησης στα μακροφάγα δεν είναι απόλυτα αποσαφηνισμένα. Πρώιμα συμβάντα ενεργοποίησης των μακροφαγων που ρυθμίζουν την παραγωγή του TNF-α, είναι η ενεργοποίηση των MAP κινασών. Η οικογένεια των MAPK’s περιλαμβάνει 3 κινάσες: την p38, την Erk1,2 και την JNK, που έχουν ταυτοποιηθεί ως πιθανοί θεραπευτικοί στόχοι σε πειραματικά μοντέλα σήψης. Η διαδοχική φωσφορυλίωση υποστρωμάτων ενεργοποιεί διάφορους μεταγραφικούς παράγοντες, χαρακτηριστικότεροι των οποίων είναι ο NF-κΒ και ο AP-1, ο οποίοι συμμετέχουν στη μεταγραφή των γονιδίων των κυτταροκινών που εκφράζονται στη διάρκεια της σηπτικής καταπληξίας. Σημαντικότερη από αυτές είναι ο TNF-α. Η ρύθμιση της παραγωγής του TNF-α είναι αντιπροσωπευτικός στόχος μελέτης των μηχανισμών που διέπουν την ενεργοποίηση των μακροφάγων. Αυτή η ρύθμιση γίνεται τόσο στο επίπεδο μεταγραφής του γονιδίου όσο και στο μετά-μεταγραφικό και μεταφραστικό επίπεδο. Συνεργασία μεταξύ των πρωτεϊνών μεταγραφής και αυτών που δεσμεύονται στη 3-UTR περιοχή του mRNA του TNF-α συμβάλουν στην εκλεκτική ρύθμιση της παραγωγής του από τα μακροφάγα. Οι μηχανισμοί που ενέχονται στην ενεργοποίηση των μακροφάγων από την P. aeruginosa δεν έχουν πλήρως μελετηθεί. Ταυτοποίηση των συγκεκριμένων μορίων-στόχων στη μετάδοση του σήματος ενεργοποίησης στα μακροφάγα συμβάλει στην κατανόηση των μηχανισμών ελέγχου της σηπτικής καταπληξίας. Σκοπός της παρούσας διατριβής είναι η αποσαφήνιση της δράσης της P. aeruginosa στα διάφορα στάδια ενεργοποίησης των μακροφάγων όπως: α) το επίπεδο της φωσφορυλίωσης-ενεργοποίησης διαφόρων πρωτεϊνικών κινασών (π.χ. MAPK’s), β) την ενεργοποίηση-δράση μεταγραφικών παραγόντων με αντιπροσωπευτικότερους τον NF-κΒ και AP-1, και τέλος, γ) την διερεύνηση των υποδοχέων επιφανείας όπως οι Toll-like υποδοχείς στη μετάδοση του σήματος ενεργοποίησης, αλλά και σύνδεση αυτών με την ενεργοποίηση των MAPK’s. Σε επίπεδο παραγωγής TNF-α πρωτεΐνης και ενεργοποίησης μεταγραφικών παραγόντων, τα αποτελέσματά μας έδειξαν ότι: α) Το Slime-GLP είναι ισχυρότερος διεγέρτης από τον LPS P. aeruginosa για την παραγωγή TNF-α σε υπερκείμενα μονοκυτταρικών καλλιεργειών. β) Αυτή η διαφορετική ρύθμιση της παραγωγής πρωτεϊνικού TNF-α, αντικατοπτρίζεται και σε επίπεδο ενεργοποίησης μεταγραφικών παραγόντων. Συγκεκριμένα, το Slime-GLP μπορεί και επάγει περισσότερο την ενεργοποίηση του NF-κΒ από ότι ο LPS της P. aeruginosa και αυτή η ενεργοποίηση είναι σχεδόν ίση με αυτή που προκαλεί ολόκληρο το ζωντανό κύτταρο της P. aeruginosa. γ) Ο NF-κΒ που ενεργοποιείται με Slime-GLP αποτελείται από το ετεροδιμερές p50/p65. δ) Ο μεταγραφικός παράγοντας AP-1 ενεργοποιείται σχετικά πιο καθυστερημένα από ότι ο NF-κΒ, αλλά και σε αυτή την περίπτωση το Slime-GLP φαίνεται να είναι ισχυρότερος διεγέρτης από τον LPS P. aeruginosa. Σε επίπεδο ενεργοποίησης των MAP κινασών τα αποτελέσματά μας έδειξαν ότι η διαφορετική ρύθμιση της παραγωγής του TNF-α, σε επίπεδο πρωτεΐνης, μετά από διέγερση με LPS ή Slime-GLP αντικατοπτρίζεται και σε επίπεδο ενεργοποίησης των διαφορετικών MAP κινασών. Συγκεκριμένα το Slime-GLP ενεργοποιεί τις p38 και Εrk1,2 σε μεγαλύτερο βαθμό από ότι ο LPS της P. aeruginosa. Η ενεργοποίηση των p38 και Erk1,2 που αποτυπώνεται με αύξηση των επιπέδων φωσφορυλίωσής τους, αντιστοιχεί και με αύξηση της ενεργότητάς τους. Η χρήση ειδικών αναστολέων έναντι των p38 (SB203580) και Erk1,2 (PD98059) μπορεί και αναστέλλει σημαντικά την παραγωγή του πρωτεϊνικού TNF-α κατά 80-95% και 60-80% αντίστοιχα. Το Slime- GLP διαφέρει από τον ομόλογο LPS της P. aeruginosa μόνο στο βαθμό της ενεργοποίησης των MAP κινασών, δηλαδή μπορεί και επάγει ισχυρότερα τις MAP κινάσες από ότι ο ομόλογος LPS. Η συμμετοχή των Toll-like υποδοχέων στη μετάδοση του σήματος αυτής της διαφορετικής ενεργοποίησης των MAP κινασών από τους LPS και Slime-GLP της P. aeruginosa, μελετήθηκε με τη χρήση ειδικών μονοκλωνικών αντισωμάτων (anti-TLR2) και (anti-TLR4). Συγκεκριμένα, η ενεργοποίηση της p38, μετά από διέγερση με Slime-GLP, μειώνεται σημαντικά παρουσία του anti-TLR2, ενώ παρουσία του anti-TLR4 η μείωση της ενεργοποίησης της p38 δεν είναι τόσο προφανής. Αντίθετα, μείωση της ενεργοποίησης της p38, όταν αυτή επάγεται από τον LPS της P. aeruginosa, παρατηρούμε μόνο στην περίπτωση που αδρανοποιούμε τον TLR4. Τα αποτελέσματά μας υποδεικνύουν έναν μοριακό μηχανισμό με τον οποίο ο LPS και ο εξωκυττάριος πολυσακχαρίτης Slime-GLP της P. aeruginosa, χρησιμοποιούν διαφορετικούς υποδοχείς στην επιφάνεια των μακροφάγων για την διαφορετική ενεργοποίηση των MAP κινασών και τη ρύθμιση της παραγωγής του TNF-α στα ανθρώπινα μακροφάγα κύτταρα / Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that is associated with severe infections of immunocompromized or critically ill patients. P. aeruginosa infections both chronic and acute, are associated with high incidence of morbidity and mortality. Many gene products of the bacterium, involving lipolysaccharide (LPS), extracellular slime glycolipoprotein (Slime-GLP), exotoxin- A, and exoenzyme-S, contribute to the pathophysiology of P. aeruginosa infection, by stimulating different cell types of the immune system. Macrophages play a key role in execution of the innate and adaptive arms of the immune response to Pseudomonas infection. Activated macrophages exert their effects by producing several types of cytokines and/or other mediators. TNF-α an early proinflammatory cytokine produced by activated macrophages is probably the most important mediator of systemic toxicity. TNF-α production primarily by cells of monocytic lineage is a crucial event in the course of these infections. During in vivo infections with P. aeruginosa, both LPS and Slime-GLP produced by mucoid and non-mucoid strains are being released. Extracellular Slime-GLP causes systemic toxicity when administered in vivo. Signal transduction pathways and early activation intracellular events that mediate induction of TNF-α by human monocytes have been the subject of great interest by many investigators. A key component of many intracellular signaling pathways are the mitogen-activated protein (MAP) kinases. This superfamily includes the extracellular signal response kinases (ERK’s), c-jun N-terminal kinases and the p38 family of kinases. A wide range of bacterial compounds including LPS of Gram-negative bacteria, LTA and peptidoglycan of Gram-positive bacteria and Treponema components differentially activate the MAP kinase family members. Recently it has been shown that cell surface Toll-like receptor (TLR) proteins participate in the ability of the host to discriminate different LPS structural features, and/or other components of the bacterial cell. Although it is now clear that the TLR family of membrane proteins is linked to the activation of MAP kinase family members by different microbial components the subsequent pathways that lead to inflammatory mediator production are still being elucidated. The aim of our study was to delineate the molecular mechanisms leading to differential TNF-α induction by P. aeruginosa LPS and Slime-GLP, specifically theIdentification of specific molecular targets of P. aeruginosa Slime-GLP in human monocytes-macrophages may have important therapeutic implications for P. aeruginosa mediated systemic toxicity.