Cette étude porte sur l'évaluation de la performance d'un procédé biologique visant â réduire la concentration en sulfure d'hydrogène (H[indice inférieur2]S) présent dans le biogaz. De l'air est injecté dans la phase gazeuse d'un bioréacteur de digestion anaérobie (ratio volumique air/biogaz=1/20) de telle sorte à assurer à la surface du liquide, une zone en micro-aérobie.Cette recherche s'intéresse spécifiquement aux boues anaérobies psychrophiles (25[degrés celsius]), acclimatées à du lisier bovin ou porcin. Une première expérience vise à évaluer le potentiel de biotransformation des boues non alimentées en lisier et soumises à une charge connue en H[indice inférieur 2]S (entre 0,68 et 2,19 mg H[indice inférieur 2]S L[indice supérieur -1] boues h[indice supérieur -1]) injectée dans la phase liquide à la base du bioréacteur. Un taux maximal de biotransformation de 1,27 mg H[indice inférieur 2]S L[indice supérieur -1] boues h[indice supérieur -1] a été obtenu pour un taux de réduction du H[indice inférieur 2]S de 96,9%, une capacité 6,7 fois supérieure au taux maximal obtenu pour un bioréacteur alimenté avec du lisier bovin (0,19 mg H[indice inférieur 2]S L[indice supérieur -1] boues h[indice supérieur -1]). Une deuxième expérience consiste à évaluer l'impact d'un tel procédé sur le rendement en méthane et la stabilité d'un bioréacteur en opération. Deux bioréacteurs psychrophiles sont opérés en mode semi-batch et alimentés de manière identique avec du lisier bovin. Un seul des deux bioréacteurs est opéré en micro-aérobie. Ce bioréacteur a présenté des concentrations en H[indice inférieur 2]S indétectables (<50 ppm), sauf les journées où le ratio volumique air/biogaz était entre 0 et 0,056. Des concentrations variant entre 0 et 3500 ppm étaient mesurées dans l'effluent gazeux du bioréacteur sans injection d'air. Le bioréacteur en micro-aérobie a présenté un rendement spécifique en méthane 6,5% plus faible que le bioréacteur témoin, mais cet écart a diminué jusqu'à 0,87% pour les 4 derniers cycles de l'expérience durant lesquels le débit d'air a été réduit et maintenu à 4 ml/min.

Essential genes are involved in control of the basic metabolism of their host. These genes encode elements involved is such crucial processes as DNA replication, transcription, translation or biosynthesis of important molecules. What makes essential genes unique is the fact that they cannot be lost from the genome. If any of them becomes inactivated it would result in inevitable death of an organism. Because of their role they can be efficiently used to control the survival of genetically modified organisms. Specific regulatory mechanisms can be applied to modulate the activity of essential genes, which prevents an organism from growing at determined conditions. Such mechanisms are called “kill switches” and have been developed in recent years as a response to significant development in the field of molecular biology. Proteins encoded by psychrophilic organisms are characterized by decreased resistance to thermal denaturation. This is believed to be a result of adaptation to low-temperature environment, where mutations that destabilize the protein structure are not selected against. For these reasons they often cannot perform their functions at moderate temperatures, which are typical for mesophilic organisms. At the same time psychrophilic proteins do not display any inhibition at permissive conditions. Use of psychrophilic alleles of essential genes has been proposed as a method of rendering modified organisms incapable of surviving at elevated temperatures. This allows generation of attenuated strains of pathogenic bacteria or generally safe versions of laboratory organisms. A temperature-sensitive organism can be created by substituting a single essential gene in mesophilic organism with its psychrophilic homologue. This can be facilitated by using the host’s native recombination system or through the use of plasmid based allele shuffling mechanisms. The objective of this work was to analyze a number of psychrophilic alleles of various essential genes for their ability to cause temperature-sensitive phenotype in mesophilic bacterium Francisella novicida. The special attention has been placed on investigating psychrophilic alleles of bacterial DNA ligase. Furthermore a selected psychrophilic strain has been characterized as a potential source of multiple temperature-sensitive alleles of essential genes. Finally the secondary focus was to develop a simple and robust mechanism allowing efficient exchange of alleles of essential genes in the mesophilic host. / Graduate

F. tularensis is a Gram-negative bacterial pathogen and it is the causative agent of tularemia. It has the ability to replicate to high numbers within a variety of host cells, including macrophages. Little is known of its virulence mechanisms; however, all species of Francisella contain a cluster of virulence genes known as the Francisella Pathogenicity Island (FPI), which is thought to encode a type 6 secretion system. While 14 of the 18 FPI genes encode products required for intracellular growth in macrophages, the functions of most of these proteins remain to be determined. Therefore, further work is required to understand the role played by the FPI in Francisella pathogenesis. In this thesis, the localization of the core FPI proteins IglA, IglB, IglC and IglD, was examined in order to further elucidate of the structure and activities of the FPI-encoded secretion system. Deletion mutagenesis of pdpA was performed to determine how host intracellular signalling might be affected by secretion of the putative FPI effector protein PdpA. In addition, variations in virulence between different biotypes of Francisella were investigated with respect to the role played by the FPI protein PdpD. Considering the highly infectious nature of Francisella and the absence of a quality vaccine, it is clear that this organism represents an excellent model for proof of principle investigations focussing on new vaccine technologies for intracellular pathogens. The second half of this thesis describes the construction and characterization of live attenuated temperature-sensitive vaccines. These vaccines were created in the intracellular pathogen F. novicida through allelic replacement of essential genes with naturally-occurring, cold-adapted, thermolabile homologues isolated from Arctic bacteria. Thus, the objectives of this work were twofold: to provide further characterization of the structural components and effector proteins associated with the FPI-encoded secretion system, and to develop a new and effective vaccine technology for use against intracellular bacteria. / Graduate

Very little is known about the hydrophobic proteins of psychrophiles and their roles in cold adaptation. In light of this situation, methods were developed to analyse the hydrophobic proteome (HPP) of the model psychrophilic archaeon Methanococcoides burtonii. Central to this analysis was a novel differential solubility fractionation procedure, which resulted in a significant increase in the efficiency of resolving the HPP. Over 50% of the detected proteins were not identified in previous whole cell extract analyses, and these underwent an intensive manual annotation process producing high quality functional assignments. Utilising the functional assignments, biological context analysis of the HPP was performed, revealing novel and often unique biology. The analysis acted as a platform for differential proteomics of the organism???s response to both temperature and substrate using stable isotope labelling. The results of which revealed that low temperature growth was associated with an increase in the abundance of surface and secreted proteins, and translation apparatus. Conversely, growth at a higher temperature was associated with an increase in the abundance of general protein folding machinery and indications of an oxidative stress response, emphasising that the temperature for maximum growth rate is stressful. Through investigation of the response of M. burtonii to substrate it was found that growth on methanol was stressful, and its low energy yield resulted in an increase in the abundance of energy conserving systems. The extracellular polymeric substance (EPS) and morphology of M. burtonii was also investigated with respect to both temperature and substrate, using a number of techniques in microscopy. It was found that the EPS was comprised of proteins, sugars and RNA, and that growth at different temperatures resulted in the production of EPS that displayed significantly different properties on dehydration, thus indicating compositional variation. When cells were grown on methanol they took on highly irregular shapes and had electron transparent inclusions. The observations from the ultrastructural analysis were contemplated with respect to the proteomic findings, revealing novel avenues of research. This study has highlighted the roles of hydrophobic proteins in cold adaptation biology, and the value of comprehensive proteomics for the examination of adaptation in microorganisms

No description available.

abstract: Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed. / Dissertation/Thesis / M.S. Molecular and Cellular Biology 2011

No description available.

Les organismes vivants sont soumis à diverses pressions de sélection qui n'agissent pas seulement au niveau du phénotype global mais à chaque niveau de l'organisation de la cellule.<br />Nous avons analysé la composition globale en acides aminés de l'ensemble les protéines de chaque protéomes étudiés à l'aide, entres autres, de l'Analyse Factorielle des Correspondances et d'un outil de partitionnement, les nuées dynamiques.<br />Ont été étudiés<br />(i) les modèles microbiens les mieux connus E. coli, B. subtilis et M. jannaschii,<br />(ii) un échantillon représentatif du monde procaryote de 28 organismes aux caractéristiques les plus diverses,<br />(iii) la pathogénicité de P. luminescens,<br />(iv) la qualité psychrophile de la bactérie P. haloplanktis, dont la vie à basse température est caractérisée par des<br />protéines fortement biaisées en asparagine et<br />(v) une perspective d'application aux eucaryotes simples est évoquée au regard des travaux préliminaires sur l'usage<br />des codons de P. marneffei, un chamipgnon dimorphique et pathogène.

La protéine humaine EED appartient à la famille des «Polycomb». Elle intervient dans la régulation génique. Elle jouerait aussi un rôle dans le cycle du virus de l'immunodéficience humaine (VIH-1) en participant au transport du complexe de préintégration et en facilitant la réaction d'intégration. EED a été surproduite afin d'être cristallisée seule et en complexe avec les protéines virales IN, MA et Nef. Un modèle de EED a été construit par homologie structurale. D'après nos expériences de « phage display », les régions susceptibles d'interagir avec les partenaires viraux se situent sur des boucles de ce modèle.<br />La bactérie psychrophile P. haloplanktis produit la cellulase Cel5G. Les structures de cette cellulase seule et en complexe avec le cellobiose, ont été déterminées à haute résolution par remplacement moléculaire. La cellulase Cel5A de la bactérie mésophile E. chrysanthemi a été utilisée comme modèle. Nos résultats permettent de mieux comprendre les déterminants structuraux responsables de l'adaptation des enzymes aux basses températures.

Cette thèse porte sur deux aspects complémentaires, le développement et l’implémentation de nouvelles approches de cristallisation et de cristallographie sérielle ainsi que leur mise en œuvre dans l’étude structurale de complexes enzymes : ARNt. La cristallographie est la méthode la plus employée en biologie structurale, mais elle présente encore des points délicats. Plusieurs méthodes avancées ont été déployées dans ce travail pour y pallier qui ont conduit à la résolution de la structure de l’ARNt nucléotidyltransférase du psychrophile Planococcus halocryophilus et à l’étude de son adaptation structurale au froid ; des puces microfluidiques de cristallisation qui ont servi à la résolution de plusieurs structures à température ambiante par cristallographie sérielle ; enfin le Xtal Controller utilisé pour l’étude d’évènements de nucléation et de croissance cristalline dans un but de préparation d’échantillons pour analyse sous rayonnement XFEL. Entre autres systèmes biologiques, cette thèse présente la caractérisation de deux familles d’inhibiteurs visant les aspartyl-ARNt synthétases, notamment du pathogène Pseudomonas aeruginosa. / This thesis focuses on two complementary aspects, the development and implementation of new approaches of crystallization and of serial crystallography as well as their use in the structural study of enzymes/tRNA complexes. Crystallography is the most used method in structural biology, but it presents delicate points. Different methods were implemented in this work to overcome these points, which led to the resolution of the structure of the CCA-adding enzyme of the psychrophilic organism Planococcus halocryophilus and to the study of its structural adaptation to the cold; novel microfluidic crystallization chips that have been used for the resolution of several structures by serial crystallography at room-temperature; finally the Xtal Controller used for the study of nucleation and crystal growth events with the purpose of preparing samples for analysis under XFEL radiation. Among other biological systems, this thesis presents the study and characterization of two families of inhibitors targeting aspartyl-tRNA synthetases, including the one of the pathogenic organism Pseudomonas aeruginosa.