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Recently, work in ethanol production is exploring the fermentation of syngas (primarily CO, CO2, and H2) following gasification of cellulosic biomass. The syngas fermentation by clostridium microbes utilizes the Wood-Ljungdahl metabolic pathway. Along this pathway, the intermediate Acetyl-CoA typically diverges to produce ethanol, acetic acid, and/or cell mass. To develop strategies for process optimization, a thermodynamic analysis was conducted that provided a detailed understanding of the favorability of the reactions along the metabolic pathway. Thermodynamic analysis provided identification of potentially limiting steps. Once these limiting reactions were identified, further thermodynamic analysis provided additional insights into the ways in which reaction conditions could be adjusted to improve product yield as well as minimize the effect of such bottlenecks. In this way, strategies to enhance product formation were effectively formed. A thermodynamic analysis regarding electron utilization suggested that it would be unlikely that H2 is utilized in favor of CO for electron production when both species are present. Therefore, CO conversion efficiency to products will be sacrificed during syngas fermentation since some of the CO will make electrons at the expense of product and cell mass formation. Furthermore, the analysis showed the thermodynamic difference of ethanol production, acetate production, and acetate to ethanol conversion, at varying reaction conditions, such as at different pH and redox potential levels. These differences were then incorporated into a strategy to optimize production of desired product, improve bioreactor design, and decrease the amount of by-product formed. Based on the thermodynamics analysis, experiments with varying experimental conditions were performed. The results showed that sulfide concentration in the media changed. In order to assess the effects of experimental conditions on syngas fermentation and decrease the experimental variability, experiments with controlled sulfide, redox potential, and pH were designed and the results indicated that these factors play key roles on cell growth, product formation and product distribution. Furthermore, experimental conditions had different effects on fermentation during different phases. For example, cell growth is much better at pH=5.8 than pH=4.5. However, the ethanol production rate at pH=4.5 is better than pH=5.8. A strategy involving controlling the pH and redox potential at different phases was effectively applied to improve ethanol production. This work provided significant insights on how varying experimental conditions can affect the syngas fermentation process.

Tuberculosis, caused by Mycobacterium tuberculosis, still poses a huge global health threat today. During infection, the bacilli are believed to confront with various stresses, including hypoxia. Hypoxia is known to trigger the bacteria to adapt into a nonreplicating dormant state associated with reduced drug susceptibility. In addition to dormancy, mycobacteria, like other bacteria, may switch to sessile biofilm growth that is generally associated with augmented drug and stress tolerance. Bacterial biofilm is physically heterogeneous and may harbor cells displaying distinct metabolic activities. It is therefore likely that some cell populations within an established biofilm are in a nonreplicating dormant state. A better understanding of mycobacterial dormancy establishment and biofilm growth could unveil crucial bacillary survival strategies that will provide insights into a rational design of chemotherapy regimen.The mycobacterial chaperonin 60.1 (Cpn60.1, also known as GroEL1), a probable chaperonin and/or nucleoid associated protein, is necessary for mycobacterial cell wall virulence lipid biosynthesis, which was reported to be enhanced at the early stage of mycobacterial hypoxic adaptation, and for reduced drug susceptibility under aerobic condition. We therefore investigated whether Cpn60.1 was essential for mycobacterial adaptation to hypoxic dormancy using Mycobacterium bovis BCG as the model organism. We found that Cpn60.1, although nonessential for mycobacterial survival, reduced isoniazid (INH) susceptibility under hypoxia. Unexpectedly and interestingly, INH’s bactericidal activity was found to involve electron transport chain perturbation (e.g. enhanced oxygen consumption and increased adenosine triphosphate level) via NADH dehydrogenases, succinate dehydrogenases, cytochrome bc1 and F0F1 ATP synthase. Moreover, respiratory reprogramming to cytochrome bd was observed to protect against INH-induced killing.Intriguingly, we found that Cpn60.1 was required for respiratory and energetic downregulation under excess glycerol as well as in response to drugs (such as Q203 inhibiting cytochrome bc1). Cpn60.1 also played a role in lipidomic adaptation under excess glycerol (e.g. enhanced phthiocerol dimycocerosate and glycerol-based lipids synthesis but repressed trehalose-based lipids synthesis). Defective energetic downregulation in the absence of Cpn60.1 compromised the establishment of the Crabtree effect characterized by respiratory downregulation, glycolytic enhancement and secretion of several metabolites (i.e. pyruvate, succinate, acetate and glutamate). The Crabtree effect was necessary for mycobacterial adaptation to excess glycerol and biofilm growth. Due to a compromised Crabtree effect, a Cpn60.1-deficient Mycobacterium bovis BCG strain, i.e. the Δcpn60.1 strain, suffered from methylglyoxal-induced growth stasis under excess glycerol, leading to the biofilm defect under the standard biofilm medium. Given the essentiality for Cpn60.1 in mycobacterial respiratory adaptation under stresses, it is likely that the enhanced INH susceptibility of the Δcpn60.1 strain under hypoxia was due to a problematic respiratory reprogramming.In summary, Mycobacterium bovis BCG Cpn60.1 is not required for bacillary survival under hypoxic dormancy. However, it participates in various adaptations (e.g. respiratory downregulation) necessary for mycobacterial biofilm growth and for escaping INH’s bactericidal mechanism. / Doctorat en Sciences biomédicales et pharmaceutiques (Pharmacie) / info:eu-repo/semantics/nonPublished

Corantes reativos têxteis podem ser degradados por basidiomicetos, por meio de enzimas oxidativas e hidrolíticas, e compostos de baixa massa molar. Foi avaliada a descoloração de CI Reactive Blue 222 por Peniophora cinerea, Pleurotus ostreatus e Trametes villosa, selecionando condições ótimas para o processo e diferentes vias metabólicas foram observadas. A degradação foi confirmada por cromatografia de camada delgada. Foi sugerido que lacases de P. ostreatus oxidam o grupo cromóforo azo, ligado ao fenol, nas primeiras 24 horas, conjuntamente hidroxilização não enzimática. Lacases de P. cinerea oxidam Mn+2 e quinona, possibilitando a via de Fenton e hidroxilizando assim a molécula do corante, paulatinamente, a partir das ligações mais vulneráveis. T. villosa faz uso prioritariamente da via de Fenton, hidroxilizando gradativamente a molécula do corante. Dessa forma, embora a maioria de estudos associem a produção enzimática à descoloração, a participação dos compostos de baixa massa molar não pode ser negligenciada. / Reactive textile dyes can be degraded by basidiomycetes, by means of hydrolytic and oxidative enzymes, and low molecular weight compounds. Was evaluated the CI Reactive Blue 222 decolorization by Peniophora cinerea, Pleurotus ostreatus, and Trametes villosa, selecting optimal conditions for the process and different metabolic pathways were observed. The degradation was confirmed by thin layer chromatography. It was suggested that P. ostreatus laccases oxidize azo chromophore group attached to the phenol, within 24 hours, together nonenzymatic hydroxylizating. P. cinerea laccases oxidize Mn+2 and quinone, enabling via Fenton and so hidroxylizing the dye molecule, gradually, from the most vulnerable links. T. villosa uses primarily via Fenton, gradually hidroxylizing the dye molecule. Thus, although most studies have linked enzyme production with the decolorization, the share of low molecular weight compounds can not be neglected.

Molecular aspects of nitrogen metabolism in vertebrates is an interesting area of physiology and evolution to explore due to the different ways in which animals excrete nitrogenous waste as they transition from an aquatic to a terrestrial lifestyle. Two main products of nitrogen metabolism in fishes are ammonia and urea. Ammonia is produced during protein catabolism and build up of ammonia is toxic. Some aquatic vertebrates convert ammonia into a less toxic compound urea via de novo synthesis through the ornithine-urea cycle (O-UC). Five enzymes are involved in the O-UC: carbamoyl phosphate synthetase (CPS), ornithine carbamoyl transferase (OCT), argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), and arginase (ARG). An accessory enzyme, glutamine synthetase (GS) also participates in the "fish-type" O-UC. Teleosts excrete ammonia passively over their gills into the aquatic environment. The teleost, Opsanus beta, has been shown to increase urea production after 48 hours of crowding. This thesis explored how crowding stress affected nitrogen metabolite levels of ammonia and urea and O-UC gene expression and enzyme activity in O. beta. Lungfishes while in an aquatic environment avoid ammonia toxicity by releasing excess ammonia across their gills, but when stranded on land they produce urea through the O-UC. Urea production via the O-UC has a metabolic cost of at least four ATP molecules. This thesis explored the response of a lungfish, Protopterus annectens, to six days of aerial exposure and re-immersion conditions by measuring concentrations of O-UC mRNA expression and enzyme activity and nitrogen metabolites ammonia and urea. CPS acts as the entry point to the O-UC and based on enzymatic studies, most aquatic vertebrates utilize one isoform of this enzyme (CPSIII) while terrestrial vertebrates utilize a different isoform of this enzyme (CPSI). Lungfishes are a particularly interesting group of air-breathing fishes, not only because of their link to the origins of tetrapods, but also because CPS I may have originated within this group. Both CPS III and CPS I have been enzymatically described within this group. This thesis uses phylogenetics to investigate how CPS nucleotide sequences in lungfishes evolved compared to other vertebrates.

Frequent use of phenylurea herbicide isoproturon (IPU) in agricultural fields has resulted not only in the contamination of the natural resources including soil and water but also in the adaptation of the soil microflora to its rapid degradation. However, up to now, the mechanisms underlying this microbial adaptation are not well elucidated. The aim of this study was to explore the processes and factors implicated in IPU degradation from the agricultural field to the genes coding for catabolic genes. The study carried out at the experimental field of Epoisses cropped with a winter wheat / barley / rape seed crop rotation indicated that as a result of its periodically repeated use, the soil microflora adapted to IPU mineralization activity. Further analysis using exploratory and geostatistical tools demonstrated the existence of spatial variability in IPU mineralization activity at the field scale which was correlated not only with several soil physico-chemical parameters like organic matter content, CEC and C/N ratio but also with the pesticide application plan over a three year crop rotation. In order to get further insight into underlying mechanisms, an IPU mineralizing bacterial culture and strain Sphingomonas sp. SH were isolated through enrichment cultures performed from two different adapted soils. Both had the catabolic activities highly specific for the mineralization of IPU and its metabolites but none of other structurally related phenylurea herbicides. IPU metabolic activity of both the mixed culture and the strain SH was found to be affected by pH with optimal activity taking place at pH 7.5. Based on the accumulation of different known metabolites during mineralization kinetics, IPU metabolic pathway was proposed to be initiated by two successive demethylations, followed by cleavage of the urea side chain resulting in the accumulation of 4-isopropylaniline, and ultimately the mineralization of the phenyl ring. In order to identify the genes involved in IPU degradation, BAC clone library was established from the genomic DNA of the bacterial culture. Although, the functional screening did not yield in identifying any BAC clone able to degrade IPU or its known metabolites, the PCR based screening led us to identify a cat gene cluster involved in ortho-cleavage of the phenyl ring of catechol through beta-ketoadipate pathway. Based on this finding, it was hypothesized that phenyl ring of 4-isopropylaniline formed during IPU transformation might be mineralized through ortho-cleavage of catechol. This finding allowed us to propose the lower IPU metabolic pathway which was not yet described.

L’usage répété d’isoproturon (IPU) en agriculture pour contrôler développement de plantes adventices dans les cultures céréalières a non seulement abouti à la contamination du sol et des ressources en eaux mais également à l’adaptation de la microflore du sol à la dégradation accélérée de cet herbicide appartenant à la famille des phénylurées. A l’heure actuelle, les mécanismes microbiens impliqués dans cette adaptation ne sont pas encore parfaitement élucidés. Dans ce contexte, l’objectif de cette étude était d’explorer les processus et les facteurs impliqués dans la biodégradation de l’isoproturon, et ce, depuis l’échelle agricole de la parcelle jusqu’à celle des gènes codant cette fonction dans des populations microbienne dégradantes.L’étude réalisée à partir d’une parcelle expérimentale du domaine d’Epoisses, cultivée selon une rotation blé d’hiver/ orge / colza, a montré que, suite à l’usage répété d’IPU, la microflore du sol s’était adaptée à sa minéralisation. Des analyses réalisées à l’aide d’outils statistiques et géostatistiques ont révélé l’existence d’une variabilité spatiale de la minéralisation de l’IPU au sein de la parcelle agricole. Celle-ci s’est révélée être non seulement corrélée avec différents caractéristiques physicochimiques du sol (C/N, CEC, …) mais également avec le plan d’épandage des pesticides au cours de la rotation culturale.Afin de mieux étudier les mécanismes moléculaires responsables de la minéralisation de l’IPU, une culture bactérienne ainsi qu’une souche (Sphingomonas sp. SH) minéralisant l’IPU ont été isolées par enrichissement à partir de deux sols différents, tous deux adaptés à la biodégradation accélérée de l’IPU. La culture bactérienne et la souche pure ont toutes deux montré un métabolisme spécifique pour la dégradation de l’IPU, étant capables de dégrader l’IPU et ses principaux métabolites mais aucun des autres herbicides de la famille des phénylurées. La culture bactérienne et la souche présentaient une activité dégradante optimale à pH7,5 et étaient affectées par des pH inférieurs et supérieurs à cette valeur optimale. Sur la base des métabolites accumulés lors de la dégradation de l’IPU, nous avons proposé que l’IPU serait dégradé par deux déméthylations successives, suivi par la coupure de la chaine urée aboutissant à l’accumulation de 4-isopropylaniline, et finalement la minéralisation du cycle phényl.Afin d’identifier les gènes impliqués dans la minéralisation de l’IPU, une banque de clones BAC a été réalisée à partir de l’ADN génomique purifié de la culture bactérienne. Bien que le crible fonctionnel réalisé n’a pas permis d’identifier de BAC capable de dégrader l’IPU ou l’un de ses métabolites, un criblage moléculaire par PCR ciblant la séquence catA codant la catéchol 1,2-dioxygénase, nous a permis d’identifier trois BACs. Le pyroséquençage des ces 3 BACs et l’agrégation des séquences correspondantes ont permis d’identifier un fragment génomique de 33 kb présentant notamment l’opéron cat impliqué dans le clivage ortho du cycle phényl du catéchol. De ce fait nous avons émis l’hypothèse selon laquelle la 4-isopropylaniline formée lors de la dégradation de l’IPU pourrait être minéralisée par le clivage ortho du catéchol, un intermédiaire clef de la voie des beta-kétoadipates. Ceci nous a donc permis de proposer une voie métabolique pour la voie basse de la dégradation de l’IPU qui, jusqu’alors, n’avait pas encore été décrite. / Frequent use of phenylurea herbicide isoproturon (IPU) in agricultural fields has resulted not only in the contamination of the natural resources including soil and water but also in the adaptation of the soil microflora to its rapid degradation. However, up to now, the mechanisms underlying this microbial adaptation are not well elucidated. The aim of this study was to explore the processes and factors implicated in IPU degradation from the agricultural field to the genes coding for catabolic genes. The study carried out at the experimental field of Epoisses cropped with a winter wheat / barley / rape seed crop rotation indicated that as a result of its periodically repeated use, the soil microflora adapted to IPU mineralization activity. Further analysis using exploratory and geostatistical tools demonstrated the existence of spatial variability in IPU mineralization activity at the field scale which was correlated not only with several soil physico-chemical parameters like organic matter content, CEC and C/N ratio but also with the pesticide application plan over a three year crop rotation. In order to get further insight into underlying mechanisms, an IPU mineralizing bacterial culture and strain Sphingomonas sp. SH were isolated through enrichment cultures performed from two different adapted soils. Both had the catabolic activities highly specific for the mineralization of IPU and its metabolites but none of other structurally related phenylurea herbicides. IPU metabolic activity of both the mixed culture and the strain SH was found to be affected by pH with optimal activity taking place at pH 7.5. Based on the accumulation of different known metabolites during mineralization kinetics, IPU metabolic pathway was proposed to be initiated by two successive demethylations, followed by cleavage of the urea side chain resulting in the accumulation of 4-isopropylaniline, and ultimately the mineralization of the phenyl ring. In order to identify the genes involved in IPU degradation, BAC clone library was established from the genomic DNA of the bacterial culture. Although, the functional screening did not yield in identifying any BAC clone able to degrade IPU or its known metabolites, the PCR based screening led us to identify a cat gene cluster involved in ortho-cleavage of the phenyl ring of catechol through beta-ketoadipate pathway. Based on this finding, it was hypothesized that phenyl ring of 4-isopropylaniline formed during IPU transformation might be mineralized through ortho-cleavage of catechol. This finding allowed us to propose the lower IPU metabolic pathway which was not yet described.

Corantes reativos têxteis podem ser degradados por basidiomicetos, por meio de enzimas oxidativas e hidrolíticas, e compostos de baixa massa molar. Foi avaliada a descoloração de CI Reactive Blue 222 por Peniophora cinerea, Pleurotus ostreatus e Trametes villosa, selecionando condições ótimas para o processo e diferentes vias metabólicas foram observadas. A degradação foi confirmada por cromatografia de camada delgada. Foi sugerido que lacases de P. ostreatus oxidam o grupo cromóforo azo, ligado ao fenol, nas primeiras 24 horas, conjuntamente hidroxilização não enzimática. Lacases de P. cinerea oxidam Mn+2 e quinona, possibilitando a via de Fenton e hidroxilizando assim a molécula do corante, paulatinamente, a partir das ligações mais vulneráveis. T. villosa faz uso prioritariamente da via de Fenton, hidroxilizando gradativamente a molécula do corante. Dessa forma, embora a maioria de estudos associem a produção enzimática à descoloração, a participação dos compostos de baixa massa molar não pode ser negligenciada. / Reactive textile dyes can be degraded by basidiomycetes, by means of hydrolytic and oxidative enzymes, and low molecular weight compounds. Was evaluated the CI Reactive Blue 222 decolorization by Peniophora cinerea, Pleurotus ostreatus, and Trametes villosa, selecting optimal conditions for the process and different metabolic pathways were observed. The degradation was confirmed by thin layer chromatography. It was suggested that P. ostreatus laccases oxidize azo chromophore group attached to the phenol, within 24 hours, together nonenzymatic hydroxylizating. P. cinerea laccases oxidize Mn+2 and quinone, enabling via Fenton and so hidroxylizing the dye molecule, gradually, from the most vulnerable links. T. villosa uses primarily via Fenton, gradually hidroxylizing the dye molecule. Thus, although most studies have linked enzyme production with the decolorization, the share of low molecular weight compounds can not be neglected.

J'ai mis au point une méthodologie pour annoter les superfamilles d'enzymes, en décrire l'histoire et les replacer dans l'évolution de leurs voies métaboliques. J'en ai étudié trois : (1) les amidohydrolases cycliques, dont les DHOases (dihydroorotases, biosynthèse des pyrimidines), pour lesquelles j'ai proposé une nouvelle classification. L'arbre phylogénétique inclut les dihydropyrimidinases (DHPases) et allantoïnases (ALNases) qui ont des réactions similaires dans d'autres voies (dégradation des pyrimidines et des purines respectivement). (2) L'étude de la superfamille des DHODases (qui suivent les DHOases) montre une phylogénie semblable aux DHOases, avec également des enzymes d'autres voies, dont les DHPDases (qui suivent les DHPases). De cette observation est né le concept de module réactionnel, qui correspond à la conservation de l’enchaînement de réactions semblables dans différentes voies métaboliques. Cela a été utilisé lors de (3) l'étude des carbamoyltransférases (TCases) qui incluent les ATCases (précédant les DHOases). J'ai d'abord montré l'existence d'une nouvelle TCase potentiellement impliquée dans la dégradation des purines et lui ai proposé un nouveau rôle en utilisant le concept de module réactionnel (enchaînement avec l'ALNase). Dans ces trois grandes familles j'ai aussi mis en évidence trois groupes de paralogues non identifiés qui se retrouvent pourtant dans un même contexte génétique appelé « Yge » et qui formeraient donc un module réactionnel constitutif d'une nouvelle voie hypothétique. Appliqué à diverses voies, le concept de modules réactionnels refléterait donc les voies métaboliques ancestrales dont ils seraient les éléments de base. / I designed a methodology to annotate enzyme superfamilies, explain their history and describe them in the context of metabolic pathways evolution. Three superfamilies were studied: (1) cyclic amidohydrolases, including DHOases (dihydroorotases, third step of the pyrimidines biosynthesis), for which I proposed a new classification. The phylogenetic tree also includes dihydropyrimidinases (DHPases) and allantoinases (ALNases) which catalyze similar reactions in other pathways (pyrimidine and purine degradation, respectively). (2) The DHODases superfamily (after DHOases) show a similar phylogeny as DHOases, including enzymes from other pathways, DHPDases in particular (after DHPases). This led to the concept of reaction module, i.e. a conserved series of similar reactions in different metabolic pathways. This was used to study (3) the carbamoyltransferases (TCases) which include ATCases (before DHOases). I first isolated a new kind of TCase, potentially involved in the purine degradation, and I proposed a new role for it in the light of reaction modules (linked with ALNase). In those three superfamilies I also found three groups of unidentified paralogs that were remarkably part of the same genetic context called “Yge” which would be a reaction module part of an unidentified pathway. The concept of reactions modules may then reflect the ancestral metabolic pathways for which they would be basic elements.

Les récepteurs à la vasopressine V1bR et à la sérotonine 5HT3R jouent des rôles physiologiques importants dans la détection des signaux extracellulaires, les mécanismes de transmission nerveuse et diverses pathologies dont le cancer, le diabète et des maladies des SNC et SNP. Mes études avaient pour but de générer ou trouver des modulateurs peptidiques de ces deux récepteurs. Pour le V1bR, j’ai développé plusieurs anticorps de type VHH et les ai caractérisés aux plans biochimique et fonctionnel. L’un de ces VHHs agit comme un agoniste allostérique complet et spécifique du V1bR humain (hV1bR). In vitro ce VHH est capable d’activer les voies de signalisation de l’inositol phosphate et des MAP kinases et d’induire l'internalisation du hV1bR. Dans des îlots pancréatiques surexprimant le hV1bR, il induit une augmentation du Ca2+ intracellulaire et une sécrétion d'insuline. Pour le 5HT3R, j’ai criblé par SPR 31 venins de serpents sur des récepteurs recombinants immobilisés et mis en évidence une interaction à partir d’un de ces venins. Suite à purification par chromatographie liquide et identification par spectrométrie de masse, j’ai identifié une toxine préalablement caractérisée comme une enzyme à activité Ca2+-dépendante. Cette toxine interagit avec les 5HT3R A et AB indépendamment du Ca2+ et avec des valeurs de Kd ≤ 10 nM. L’analyse fonctionnelle par électrophysiologie suggère qu’elle agit comme un PAM de l’activité canal du 5HT3R. Des images de ME en coloration négative montrent la toxine fixée sur le domaine extracellulaire du 5HT3R, à distance du site pour la 5HT. Le VHH et la toxine pourraient être utilisés comme outils pharmacologiques et/ou agents thérapeutiques. / The vasopressin V1bR and serotonin 5HT3R receptors play important physiological roles in the detection of extracellular signals, in the mechanisms for neuronal transmission, and in various pathologies including cancer, diabetes, and CNS and PNS diseases. My studies were aimed at generating or finding peptidic modulators of these two receptors. For the V1bR, I developed several antibodies of the VHH type and characterized them biochemically and functionally. One of these VHHs acts as a complete allosteric agonist specific for the human V1bR (hV1bR). In vitro this VHH is able to activate the signaling pathways of inositol phosphate and MAP kinases and to induce the internalization of hV1bR. In pancreatic islets overexpressing hV1bR, it induces an increase in intracellular Ca2+ and a secretion of insulin. For the 5HT3R, using SPR I screened 31 snake venoms on immobilized recombinant receptors and for one of these venoms, evidenced an interaction. Following purification by liquid chromatography and identification by mass spectrometry, I identified a toxin previously characterized as an enzyme with Ca2+-dependent activity. This toxin interacts with the 5HT3R A and AB independently of Ca2+ and with Kd values ≤ 10 nM. Functional analysis by electrophysiology suggests that it acts as a PAM of the 5HT3R channel activity. Images recorded by negative staining EM show that the toxin binds to the 5HT3R extracellular domain, at a distance from the 5HT binding site. Both this VHH and this toxin could be used as pharmacological tools and / or therapeutic agents.