In comparison to other Pseudomonas, P. aeruginosa grows poorly in L-lysine as a sole source of nutrient while fast growth mutants can be obtained. The proposed catabolic pathway involves lysine decarboxylation to cadaverine and its subsequent degradation through g-glutamylation pathway to d-aminovalerate and glutarate. The lysine decarboxylase A (ldcA) gene, previously identified as a member of the ArgR regulon of L-arginine metabolism, was found essential for L-lysine catabolism. The ldcA gene encodes a decarboxylase which takes L-lysine but not L-arginine as substrate. Contrarily, the ldcA expression was inducible by L-arginine but not by L-lysine. This peculiar arginine control on lysine utilization was also noted from uptake experiments. The lack of lysine-responsive control on lysine catabolism and its tight connection to arginine regulatory network provided an explanation of lysine as poor nutrient for P. aeruginosa. Catabolism of cadaverine, a product from lysine decarboxylation, was investigated and compared to that of putrescine, another diamine of similar biochemical properties that is derived from arginine and ornithine. While the g-glutamylation pathway was first reported in E. coli for putrescine utilization, an expanded version of this pathway was found in P. aeruginosa with redundant enzymes for polyamine degradation. The PauR protein was identified as a transcriptional repressor of genes for the catabolism of putrescine and cadaverine, as well as their corresponding downstream metabolites, g-aminobutyrate (GABA) and d-aminovalerate (AMV). PauR shows distinct dimer configuration after glutaraldehyde crosslinkage, and possible conformational changes could be triggered by the presence of putrescine and cadaverine, but not GABA. A newly identified ABC transport system, encoded by the agtABCD operon, was found important for the uptake of GABA and AMV; and expression of which is controlled by the AgtSR two-component system. The CbrAB two-component system was proposed to regulate the catabolite repression control protein Crc through a small RNA CrcZ. A consensus CbrB recognition sequence was proposed based on the conserved palindromic nucleotide sequence in the upstream activating sequence of the crcZ promoter. Genetic studies indicated utilization of arginine, lysine and diamines (but not histidine, GABA and AMV) might be under CbrAB regulation through the CbrAB/CrcZ/Crc system in P. aeruginosa.

Metabolically versatile bacteria have evolved diverse strategies to adapt to different environmental niches and respond to fluctuating physico-chemical parameters. In order to survive in soil and water habitats, they employ specific and global regulatory circuits to integrate external and internal signals to counteract stress and optimise their energy status. One strategic endurance mechanism is the ability to choose the most energetically favourable carbon source amongst a number on offer. Pseudomonas putida strains possess large genomes that underlie much of their ability to use diverse carbon sources as growth substrates. Their metabolic potential is frequently expanded by possession of catabolic plasmids to include the ability to grow at the expense of seemingly obnoxious carbon sources such as phenols. However, this ability comes with a metabolic price tag. Carbon source repression is one of the main regulatory networks employed to subvert use of these expensive pathways in favour of alternative sources that provide a higher metabolic gain. This thesis identifies some of the key regulatory elements and factors used by P. putida to supress expression of plasmid-encoded enzymes for degradation of phenols until they are beneficial. I first present evidence for a newly identified DNA and RNA motif within the regulatory region of the gene encoding the master regulator of phenol catabolism – DmpR. The former of these motifs functions to decrease the number of transcripts originating from the dmpR promoter, while the latter mediates a regulatory checkpoint for translational repression by Crc – the carbon repression control protein of P. putida. The ability of Crc to form repressive riboprotein complexes with RNA is shown to be dependent on the RNA chaperone protein Hfq – a co-partnership demonstrated to be required for many previously identified Crc-targets implicated in hierarchical assimilation of different carbon sources in P. putida. Finally, I present evidence for a model in which Crc and Hfq co-target multiple RNA motifs to bring about a two-tiered regulation to subvert catabolism of phenols in the face of preferred substrates – one at the level of the regulator DmpR and another at the level of translation of the catabolic enzymes.

Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The objective of this study was to evaluate the effect of the order of delivery on the efficiency of lactation of pigs. Sixty-six sows with birth orders between 3 and 5 were selected. The weight variation of the females, from calving to weaning, daily feed intake and backfat thickness were evaluated. The variables measured and estimated in the piglets were number of piglets born alive and dead, weight of litters at birth, after homogenization and weekly until weaning. There were no differences (P> 0.05) between the orders of delivery (OP) for the variation of the weight of the sows during lactation. Feed intake and energy intake were not influenced (P> 0.05) by OP. There was no difference (P> 0.05) between POs for birth weight and initial litter weight. OP five sows had litters with energy retention of 1.42 Mcal / d higher than three OP litters. The energy input had no significant difference (P> 0.05) in relation to the OPs. However, the energy output had influence (P <0.05) of the OPs, four OPs and five had higher energy output means than three OPs. OP four and five nuts were more efficient than three OP nuts. The lactate efficiency was 75.08% for OP four and 72.25% for OP five, values higher than OP three, which had efficiency of 53.84%. Labor order three sows show lower lactational efficiency than four and five calving order sows. / O objetivo deste estudo foi avaliar o efeito da ordem de parto na eficiência da lactação de matrizes suínas. Foram selecionadas 60 porcas com ordens de parto entre 3 e 5. Avaliou-se a variação de peso das fêmeas, do parto ao desmame, o consumo diário de ração e espessura de toucinho. As variáveis medidas e estimadas nos leitões foram número de leitões nascidos vivos e mortos, peso das leitegadas ao nascimento, após a homogeneização e semanalmente até o desmame. Não foram encontradas diferenças (P>0,05) entre as ordens de parto (OP) para a variação de peso das porcas durante a lactação. O consumo de ração e a ingestão de energia não foram influenciados (P>0,05) pela OP. Não houve diferença (P>0,05) entre as OP para o peso ao nascimento e peso inicial da leitegada. Porcas de OP cinco apresentaram leitegadas com retenção de energia de 1,42 Mcal/d superior que leitegadas de OP três. A entrada de energia não teve diferença significativa (P>0,05) em relação as ordens de parto. No entanto, a saída de energia teve influência (P<0,05) das OP, porcas de OP quatro e cinco apresentaram médias de saída de energia superior a porcas de OP três. Porcas de OP quatro e cinco foram mais eficientes que porca de OP três. A eficiência lactacional foi de 75,08% para OP quatro e 72,25% para OP cinco, valores superiores as OP três, que teve eficiência de 53,84%. Porcas de ordem de parto três demonstram menor eficiência lactacional que porcas de ordem de parto quatro e cinco.

La morphine constitue l'un des analgésiques les plus utilisés en milieu hospitalier pour soulager les douleurs aiguës et chroniques. Elle exerce ses effets analgésiques en se liant aux récepteurs opioïdes μ (MOR) présents au niveau central et périphérique et possède des effets secondaires, incluant la tolérance, qui limitent son usage à long terme. La première partie de mes travaux avait pour objectif d'étudier le phénomène de tolérance à la morphine et d'en déterminer les mécanismes sous-jacents. A l'heure actuelle, ce phénomène est décrit comme résultant d'une désensibilisation des MOR conduisant à leur endocytose. Nos résultats montrent qu'en cas de tolérance, le catabolisme de la morphine est exacerbé au niveau du système nerveux central. Mes travaux ont également porté sur la caractérisation de la Créatine Kinase (CK) comme étant une protéine liant la morphine à très haute affinité. Nos résultats montrent que la CK possède 2 sites de liaison pour la morphine avec des affinités similaires. En étudiant l'effet potentiel de la CK sur l'analgésie induite par la morphine in vivo, nous avons mis en évidence, que les peptides correspondant aux 2 sites de liaison à la morphine étaient par eux-mêmes analgésiques et que cette analgésie semblait dépendre des récepteurs opioïdes. / Morphine is one of the most used analgesics in hospitals to relieve acute and chronic pain. Morphine exerts its analgesic effects by binding central and peripheral μ opioid receptors (MORs) and has many side effects that limit its long-term use including tolerance. The first part of my thesis was aimed to study the phenomenon of morphine tolerance and to determine the underlying mechanisms. Previously, this phenomenon was explained as resulting !rom MORs desensitization by endocytosis. However, our results show that in case of tolerance, the catabolism of morphine is exacerbated in the central nervous system in particular in astocytes. The second part of my work has focused on the characterization of the Creatine Kinase (CK) as a novel protein that binds morphine with a high affinity. Our results showed that CK has two binding sites with a similar affinity for morphine. Surprisingly, by studying the potential effect of CK on morphine-induced analgesia in vivo, we noticed that the two peptides corresponding to morphine binding sites are analgesics and such analgesia seems to be mediated by opioid receptors.

Amino acids derived from the degradation of casein in cheese serve as precursors for the generation of key flavor compounds. Microbial degradation of tryptophan (Trp) is thought to promote formation of aromatic compounds that impart putrid fecal or unclean flavors in cheese, but pathways for their production have not been established. This study investigated tryptophan catabolism by Lactobacillus casei LC301 and LC202 and Lactobacillus helveticus CNRZ32 and LH212 cheese flavor adjuncts in carbohydrate starvation (pH 6.5, 30 or 37°C, no sugar) and cheese-like conditions (pH 5.2, 4% NaCl, 15°C, no sugar). Enzyme assays of cell-free extracts revealed both species of Lactobacillus catabolized tryptophan to indole lactic acid via indole pyruvic acid through transamination followed by dehydrogenation. Micellar electrokinetic capillary chromatography of culture supernatants showed these enzymes also catalyzed the reverse reactions, i.e., conversion of indole lactic acid to tryptophan. Tryptophan decarboxylase activity was detected in Lactobacillus cell-free extracts, but tryptamine was not detected in culture supernatants. Analysis of culture supernatants showed that tryptophan metabolism in Lactobacillus casei did not differ between the two conditions of incubation as it did in Lactobacillus helveticus LH212 and CNRZ32. Lactobacillus helveticus LH212, for example, did not catabolize Trp in carbohydrate starvation but did in cheese-like conditions. While cells of L. helveticus CNRZ32 did not catabolize Trp in either condition, they catabolized indole pyruvic acid to only Trp in carbohydrate starvation and to both Trp and indole lactic acid in cheese-like conditions. Micellar electrokinetic capillary chromatography of culture supernatants incubated under either starvation or cheese-like conditions showed Lactobacillus casei strains produced more indole lactic acid, and Lactobacillus helveticus strains favored tryptophan anabolic reactions. Based on the results obtained in this study, a putative pathway for the catabolism of tryptophan by lactobacilli in cheese is proposed.

Thesis (PhD (Wine Biotechnology))--University of Stellenbosch, 2011. / Includes bibliography. / ENGLISH ABSTRACT: Alcoholic fermentation, and especially wine fermentation, is one of the most ancient microbiological processes utilized by man. Yeast of the species Saccharomyces cerevisiae are usually responsible for most of the fermentative activity, and many data sets clearly demonstrate the important impact of this species on the quality and character of the final product. However, many aspects of the genetic and metabolic processes that take place during alcoholic fermentation remain poorly understood, including the metabolic processes that impact on aroma and flavour of the fermentation product. To contribute to our understanding of these processes, this study took two approaches: In a first part, the initial aim had been to compare two techniques of transcriptome analysis, DNA oligo-microarrays and Serial Analysis of Gene Expression (SAGE), for their suitability to assess wine fermentation gene expression changes, and in particular to assess their potential to, in combination, provide combined quantitative and qualitative data for mRNA levels. The SAGE methodology however failed to produce conclusive data, and only the results of the microarray data are shown in this dissertation. These results provide a comprehensive overview of the transcriptomic changes during model wine fermentation, and serve as a reference database for the following experiments and for future studies using different fermentation conditions or genetically modified yeast. In a second part of the study, a screen to identify genes that impact on the formation of various important volatile aroma compounds including esters, fatty acids and higher alcohols is presented. Indeed, while the metabolic network that leads to the formation of these compounds is reasonably well mapped, surprisingly little is known about specific enzymes involved in specific reactions, the genetic regulation of the network and the physiological roles of individual pathways within the network. Various factors that directly or indirectly affect and regulate the network have been proposed in the past, but little conclusive evidence has been provided. To gain a better understanding of the regulations and physiological role of this network, we took a functional genomics approach by screening a subset of the EUROSCARF strain deletion library, and in particular genes encoding decarboxylases, dehydrogenases and reductases. Thus, ten genes whose deletion impacted most significantly on the aroma production network and higher alcohol formation were selected. Over-expression and single and multiple deletions of the selected genes were used to genetically assess their contribution to aroma production and to the Ehrlich pathway. The results demonstrate the sensitivity of the pathway to cellular redox homeostasis, strongly suggest direct roles for Thi3p, Aad6p and Hom2p, and highlight the important role of Bat2p in controlling the flux through the pathway. / AFRIKAANSE OPSOMMING: Alkoholiese fermentasie, en veral die maak van wyn, is een van die vroegste mikrobiologiese prosesse wat deur die mensdom ingespan is. Die gisspesie Saccharomyces cerevisiae is gewoonlik grotendeels verantwoordelik vir die fermentasie and verskeie vorige studies het gedemonstreer dat hierdie spesie ‘n baie belangrike rol speel in die uiteindelike kwaliteit en karakter van die voltooide produk. Nieteenstaande die feit is daar steeds baie aspekte van beide die genetiese en metaboliese prosesse wat plaasvind tydens alkoholiese fermentatsie wat nog swak verstaan word, insluitende metaboliese padweë wat ‘n impak het op die smaak en aroma van die fermentasie produk. Om ons kennis van die veld uit te brei het die studie twee aanslae geneem: In die eerste geval is gepoog om twee tegnieke van transkriptoom analiese, nl. DNA oligomikro- arrays en Serial Analysis of Gene Expression (SAGE) te bestudeer vir hul vermoë om geen ekspressie veranderinge tydens wynfermentasie te ondersoek en meer spesifiek om hul potensiaal om ‘n kombinasie van kwantitatiewe sowel as kwalitatiewe data met betreking to mRNA vlakke te produseer. Die SAGE metode kon egter geen betroubare resultate produseer nie en dus word slegs die resultate van die mikro-array eksperimente in die tesis bespreek. Die resultaat is ‘n geheeloorsig oor die geenekspressie veranderinge wat so ‘n wyngis tydens alkoholiese fermentasie ondergaan en dien as ‘n verwysingsraamwerk vir toekomstige studies met geneties gemodifiseerde gis of selfs verskillende fermentasieparameters. Die tweede deel van die studie het gefokus op die identifikasie van gene wat ‘n impak het op die vorming van belangrike, vlugtige aroma komponente, o. a. Esters vetsure en hoër alkohole d.m.v. ‘n siftingseksperiment. Alhoewel daar redelik baie inligting is oor die onderligende metaboliese netwerke wat lei tot die vorming van die verbindings, is daar min kennis van die genetiese regulasie van die netwerk en die fisiologiese rol van individuele padweë wat die netwerk vorm. Verskeie faktore – wat of die netwerk direk of indirek affekteer – is al voorgestel, meer met min konkrete bewyse. Dus het ons gepoog om meer lig op die onderwerp te laat m.b.v. ‘n funksionele genoom aanslag deur ‘n siftingseksperiment te doen op ‘n subgroep (spesifiek gene wat kodeer vir dekarboksilase, dehidrogenase en reduktase ensieme) van die EUROSCARF delesiebiblioteek. Dus is tien gene geïdentifiseer – die delesie waarvan ‘n merkbare effek het op die aroma produksie netwerk en spesifiek die van hoër alkohole. Ooruitdrukkings en enkel en meervoudige delesie rasse van die tien gene is gemaak om d.mv. genetiese analiese, hulle rol in aroma produksie en die Ehrlich padweh uit te pluis. Die resultate toon dat hierdie padweg sensitief is teenoor die sellulêre redoks balans en dui op direkte rolle vir Thi3p, Aad6p en Hom2p, asook dat Bat2p ‘n baie belangrike rol speel in die werking van die padweg.

L’arthrose (OA) est une maladie articulaire dégénérative à l’étiologie complexe et diverse. Les travaux de ces dernières années ont démontré que l’OA est une pathologie affectant tous les tissus de l’articulation incluant le cartilage, la membrane synoviale et l’os sous-chondral. L’OA se traduit par une déstructuration et une perte de fonctionnalité de l’articulation, et est principalement caractérisée par une perte de cartilage articulaire. L’inflammation de la membrane synoviale joue un rôle déterminant dans la progression de l’OA, toutefois elle serait secondaire à la dégradation du cartilage. De plus, l’os sous-chondral est également le siège de nombreuses transformations lors de l’OA. Il est fortement suggéré que ces changements ne correspondent pas seulement à une conséquence, mais pourraient être une cause du développement de l’OA impliquant une communication entre ce tissu et le cartilage. Il est maintenant bien établi que les voies inflammatoires et cataboliques jouent un rôle crucial dans l’OA. C’est pourquoi, nous avons étudié l’implication d’une nouvelle famille de récepteurs membranaires, les PARs, et plus particulièrement le PAR-2 dans les voies physiopathologiques de l’OA. Notre hypothèse est que l’activation de PAR-2 au cours de l’OA est un phénomène majeur du développement/progression de la maladie faisant du récepteur PAR-2 un candidat privilégié pour le développement de nouvelles approches thérapeutiques ciblant non seulement le cartilage mais aussi l’os sous-chondral. Pour cette étude, nous avons travaillé in vitro avec des chondrocytes (Cr) et des ostéoblastes (Ob) OA respectivement du cartilage et de l’os sous-chondral du condyle fémoral humain. Nos résultats ont démontré que PAR-2 était plus exprimé dans les Cr et les Ob OA que dans les cellules normales. Par ailleurs, PAR-2 est régulé positivement par certains facteurs retrouvés au cours de l’OA comme l’IL-1β, le TNF-α et le TGF-β dans les Cr OA, et par l’IL-1β, le TNF-α et la PGE2 dans les Ob OA. De plus, les principaux facteurs cataboliques et inflammatoires, soit la MMP-1, la MMP-13 et la COX-2 sont produits en quantité plus élevée suite à l’activation du récepteur dans le cartilage OA. De même, l’activation de PAR-2 dans les Ob OA conduit à une production accrue de facteurs pro-résorptifs tels que RANKL, l’IL-6, la MMP-1 et la MMP-9, et à l’augmentation de l’activité pro-résorptive de ces cellules. En outre, dans les deux types tissulaires étudiés, l’activation de PAR-2 augmente l’activité de certaines protéines de la famille des MAPKinases comme Erk1/2, p38 et JNK. Finalement, nous avons conclu notre étude en employant un modèle in vivo d’OA induite chez la souris sauvage et déficiente pour le gène PAR-2. Nos résultats ont démontré que l’absence d’expression et de production de PAR-2 influençait le processus inflammatoire et les changements structuraux affectant à la fois le cartilage et l’os sous-chondral, conduisant à un ralentissement du développement de l’OA. Nos travaux de recherche ont donc permis de montrer que le récepteur PAR-2 est un élément majeur du processus OA en agissant sur les voies cataboliques et inflammatoires du cartilage, et sur le remodelage tissulaire de l’os sous-chondral. Mots-clés : Arthrose, chondrocyte, cartilage, ostéoblaste, os sous-chondral, PAR-2, MMPs, COX, ILs, RANKL, résorption osseuse, MAPKinase, catabolisme, inflammation / Osteoarthritis (OA) is a complex degenerative articular disease. Recent studies have shown that OA is a pathology affecting all the tissues of the joint including the cartilage, the synovial membrane and the subchondral bone. OA is regarded as destruction and a loss of functionality of joint, and is mainly characterized by a loss of articular cartilage. The synovial inflammation also plays a key role in the progression of OA; however, it is believed to be secondary to cartilage degradation. In addition, there are also in the subchondral bone numerous changes which occur during the course of the disease. It is strongly suggested that these changes in subchondral bone are not just a consequence but could be a cause of the development of OA, thus involving a cross-talk between this tissue and the cartilage. It is now well established that inflammatory and catabolic pathways play a crucial role during OA. This is why we have engaged the study of the involvement of a new family of membranous receptors, the PARs, and more particularly PAR-2 during the pathophysiological process of OA. Our hypothesis is that PAR-2 activation during OA course is a major phenomenon for the development/progression of the disease, and that PAR-2 seems a suitable candidate for the development of new therapeutic approaches targeting not only the cartilage but also the subchondral bone. Thus, we have performed in vitro studies on OA chondrocyte (Cr) and osteoblasts (Ob) cells issued respectively from human femoral condyle cartilage and subchondral bone. Our results showed that PAR-2 was expressed at a higher level in the OA Cr and Ob compared to normal cells. Moreover, PAR-2 is found to be positively regulated by some factors present during the course of OA, such as IL-1β, TNF-α and TGF-β in the OA Cr, and IL-1β, TNF-α and PGE2 in the OA Ob. In addition, the main catabolic and inflammatory factors including MMP-1, MMP-13 and COX-2 are enhanced following PAR-2 receptor activation in the OA cartilage. Similarly, the activation of PAR-2 in OA Ob lead to an increased production of pro-resorptive factors such as RANKL, IL-6, MMP-1 and MMP-9, and an increased pro-resorptive activity of these cells. In addition, in both tissue types, PAR-2 activation increases the activity of certain protein MAPKinases family such as Erk1/2, p38 and JNK. Finally, we have performed an in vivo study using an OA induced model in wild-type and PAR-2 gene knock-out mice. Our results demonstrated that the absence of PAR-2 expression and production influenced the inflammatory process and structural changes affecting the cartilage and the subchondral bone, leading to a slowing down of OA development. Our research investigation have bring to light that PAR-2 receptor is a key element during OA process by acting on the cartilage catabolic and inflammatory pathways as well as the tissue remodelling of the subchondral bone. Keywords : Osteoarthritis, chondrocyte, cartilage, osteoblast, subchondral bone, PAR-2, MMPs, COX, ILs, RANKL, bone resorption, MAPKinase , catabolism, inflammation

L'arthrose est une maladie articulaire dégénérative, avec une pathogenèse inconnue. Des études récentes suggèrent que l'activation du facteur de transcription du récepteur activateur de la prolifération des peroxysomes (PPAR) gamma est une cible thérapeutique pour ce maladie. Les agonistes du PPARγ inhibent l'inflammation et réduisent la synthèse des produits de dégradation du cartilage in vitro et in vivo. Cependant, des études utilisant des agonistes du PPARγ n’élucident pas les effets exacts médiés par ce gène complexe. En effet, certains de ces agonistes ont la capacité de régulariser d'autres voies de signalisation indépendantes de PPARγ, ainsi entraînant des effets secondaires graves. Afin d'obtenir une efficacité thérapeutique avec potentiellement moins de problèmes de sécurité, il est donc essentiel d'élucider, in vivo, le rôle exact de PPARγ dans la physiopathologie OA. Mon projet de thèse permettra de déterminer, pour la première fois, le rôle spécifique de PPARγ in vivo dans la physiopathologie OA. Les souris utilisées pour l’étude avaient une délétion conditionnelle du gène PPARγ dans le cartilage. Ces dernières ont été générées en employant le système LoxP/Cre. Pour tester cette hypothèse, j'ai généré deux types de souris avec une délétion au PPARγ, (a) une suppression du gène PPARγ spécifiquement dans le cartilage germinale pour l'étude de l'arthrose liée au développement et à l'âge et (b) la suppression inductible du gène PPARγ spécifiquement dans le cartilage chez la souris adulte pour les études OA. L’étude précédente dans notre laboratoire, utilisant ces souris ayant une délétion au gène PPARγ germinales, montre que ces souris présentent des anomalies du développement du cartilage. J'ai également exploré si ces souris qui présentent des défauts précoces du développement ont toutes les modifications phénotypiques dans le cartilage au cours du vieillissement. Mes résultats ont montré que les souris adultes, ayant une délétion au gène PPARγ, ont présenter un phénotype de l'arthrose spontanée associée à une dégradation du cartilage, l’hypocellularité, la fibrose synoviale. Cette étude a montré que PPARγ est un régulateur essentiel pour le cartilage, et c’est le manque (l’absence) de ce dernier qui conduit à un phénotype de l'arthrose spontanée accélérée (American Journal of Pathologie). A partir de ce but de l'étude, on n’a pas pu vérifier si ces souris présentaient l’OA spontanée en raison des défauts de développement ou à la suite de la délétion du gène PPARγ. Pour contourner les défauts de développement, j'ai généré des souris ayant une délétion du gène PPARγ spécifiquement dans le cartilage inductible avec le système Col2rTACre. Ces souris ont été soumises à modèle de la chirurgie OA (DMM: déstabilisation du ménisque médial) et les résultats révèlent que les souris PPARγ KO ont une dégradation accélérée du cartilage, une hypocellularité, une fibrose synoviale et une augmentation de l'expression des marqueurs cataboliques et des marqueurs inflammatoire. La perte de PPAR dans le cartilage articulaire est un évènement critique qui initie la dégradation de cartilage dans OA. Les études récentes suggèrent que le procès d’autophagie, une forme de survie cellulaire programmée, est altéré pendant l’OA et peut contribuer vers une protection diminuée des cellules, résultant la dégradation du cartilage. J’ai donc exploré le rôle de PPARγ dans la protection des cellules en déterminant l’effet de manque de PPARγ dans le cartilage par l’expression de mTOR (régulateur négatif principal d’autophagie) et les gènes d’autophagie durant OA. Mes résultats ont montré que les souris KO PPARγ présentent également une augmentation sur l'expression de mTOR et une diminution sur l’expression des marqueurs autophagiques en comparaison avec les chondrocytes articulaires isolés des souris contrôles OA. J'ai suggéré l'hypothèse que PPARγ contrôle la régulation de la signalisation de mTOR/autophagie, et finalement la mort des chondrocytes et l’expression des facteurs cataboliques et les facteurs inflammatoire. Pour tester cette hypothèse, j’ai fait la transfection des chondrocytes arthrosiques PPARγ-KO avec le vecteur d’expression de PPARγ pour déterminer si la restauration de l'expression de PPARγ peut sauver le phénotype des cellules PPARγ-KO OA. J'ai observé que la restauration de l'expression de PPARγ dans les cellules PPARγ-KO en présence du vecteur d'expression PPARγ, a pu considérablement régulariser négativement l'expression de mTOR et mettre en règle positivement l'expression des gènes autophagiques ainsi que le sauvetage significative de l'expression du collagène de type II et l’aggrecan et de baisser de manière significative l'expression de marqueurs cataboliques critiques et des marqueurs inflammatoires. Pour prouver que l’augmentation de la signalisation de mTOR et la diminution de l'autophagie est responsable du phénotype OA accélérée observée dans les souris PPARγ KO in vivo, j'ai généré les souris doubles KO PPARγ- mTOR inductible spécifique du cartilage en utilisant le système Col2 - rtTA -Cre et soumis ces souris à DMM modèle de l'arthrose. Mes résultants démontrent que les souris avec PPARγ- mTOR doubles KO ont été significativement protégés contre les OA DMM induites associées à une protection significative contre la destruction du cartilage, la perte de protéoglycanes et la perte de chondro-cellularité par rapport aux souris témoins. Considérant que mTOR est un répresseur majeur de l'autophagie, j'ai trouvé que l'expression de deux marqueurs de l'autophagie critiques (ULK1 et LC3B) a été significativement plus élevée dans les chondrocytes extraits les souris doubles KO PPARγ-mTOR par rapport aux souris témoins. En plus, les études de sauvetage in vitro en utilisant le vecteur d'expression PPAR et les études in vivo utilisant les souris doubles KO PPARγ- mTOR montrent que PPARγ est impliqué dans la régulation de la protéine signalant de mTOR/autophagie dans le cartilage articulaire. Ces résultats contournent PPARγ et sa signalisation en aval de mTOR/autophagie en tant que cibles thérapeutiques potentielles pour le traitement de l'arthrose. / Osteoarthritis (OA) is an age related degenerative joint disease with unknown pathogenesis. Recent studies suggest that the activation of the transcription factor Peroxisome Proliferator-Activated Receptor gamma (PPARγ) is a therapeutic target for OA. Agonists of PPARγ inhibit inflammation and reduce the synthesis of cartilage degradation products both in vitro and in vivo. However, studies using agonists of PPARγ do not elucidate the exact effects mediated by this complex gene. Indeed, some of these agonists have the ability to regulate, in vivo, various other signaling pathways independent of PPARγ, resulting in serious side effects. It is therefore vital, in order to achieve therapeutic efficacy with potentially less safety concerns, to elucidate the exact in vivo role of PPARγ in OA pathophysiology. Thus, the aim of my PhD project was to determine the specific in vivo role of PPARγ in OA pathophysiology using cartilage-specific PPARγ knockout (KO) mice and subjecting these mice to surgical model of OA. I generated two separate PPARγ KO mice harboring a (a) constitutive cartilage-specific germ-line deletion of PPARγ gene for developmental and age-related OA study and (b) inducible cartilage-specific deletion of PPARγ in adult mouse specifically for OA studies using LoxP Cre system. Previous study in my laboratory using germ-line PPARγ KO mice shows that these mice exhibit cartilage developmental defects. I further explored if these mice which exhibit early developmental defects have any phenotypic changes in the articular cartilage during ageing. My results showed that adult PPARγ KO mice exhibited a spontaneous OA phenotype associated with enhanced cartilage degradation, hypocellularity, synovial fibrosis, and increased expression of catabolic and inflammatory factors. This study showed that PPARγ is a critical regulator of cartilage health, the lack of which leads to an accelerated spontaneous OA phenotype (Vasheghani et al, 2013; American Journal of Pathology). From this aim of the study, I could not ascertain if cartilage-specific germline PPARγ KO mice exhibited spontaneous OA because of developmental defects or as a result of PPARγ deficiency. To bypass the developmental defects, I then generated inducible cartilage-specific PPARγ KO mice using Col2rTACre system and subjected these mice to destabilization of medial meniscus (DMM) model of OA surgery. My results revealed that PPARγ KO mice showed accelerated cartilage degradation, hypo-cellularity, synovial fibrosis and increased expression of catabolic and inflammatory factors during OA. Loss of chondrocyte cellularity within the articular cartilage is one of the critical events that initiate the degradation of the cartilage during OA. Recent studies suggest that the process of autophagy, a form of programmed cell survival, is impaired during OA and may contribute towards decreased chondro-protection resulting in cartilage degradation. Thus, I further explored the role of PPARγ in chondro-protection by determining the effect of PPARγ deficiency in the cartilage on the expression of mTOR (master negative regulator of autophagy) and autophagy genes during OA. My results revealed that PPARγ-deficient chondrocytes exhibit significantly enhanced expression of mTOR and decreased expression of genes that initiate autophagy process compared to chondrocytes extracted from control OA mice. I then hypothesized that PPARγ controls mTOR/autophagy signaling and ultimately the fate of chondrocytes and the expression of catabolic and inflammatory factors in the articular cartilage. To test this, I transfected PPARγ KO OA chondrocytes with PPARγ expression vector to determine if restoration of PPARγ expression can rescue the phenotype of PPARγ KO OA cells. I observed that restoration of PPARγ expression in PPARγ KO cells significantly down-regulated the expression of mTOR and up-regulate the expression of autophagy genes along with significant rescue in the expression of collagen type II and aggrecan and significant down-regulation in the expression of critical catabolic and inflammatory markers. To validate our in vitro finding that enhanced mTOR signalling and resultant decrease in autophagy is responsible for accelerated OA phenotype observed in PPARγ KO mice, I generated inducible cartilage-specific PPARγ-mTOR double KO mice and subjected these mice to DMM model of OA. My results clearly demonstrate that PPARγ-mTOR double KO mice exhibit significant protection against DMM-induced OA associated with significant protection from cartilage destruction, proteoglycan loss and loss of chondro-cellularity compared with control mice. Since mTOR is a major repressor of autophagy, I found that the expression of two critical autophagy markers (ULK1 and LC3B) was significantly elevated in PPARγ-mTOR double KO mice compared to control mice. My in vitro rescue studies using PPARγ expression vector and in vivo studies using PPARγ- mTOR double KO mice clearly show that PPARγ is involved in the regulation of mTOR/autophagy signalling in the articular cartilage. Therefore, deficiency of PPARγ upregulates mTOR signalling resulting in the suppression of autophagy and decreased chondroprotection and increased catabolic activity leading to accelerated severe OA. This study for the first time provides direct evidence on the role of PPARγ in chondroprotection by modulation of mTOR/autophagy signalling in the articular cartilage. These findings outline PPARγ and its downstream signalling by mTOR/autophagy as potential therapeutic targets for the treatment of OA.

Polihidroxialcanoatos (PHA) são polímeros biodegradáveis, biocompatíveis e podem ser produzidos a partir de matérias primas renováveis. Pseudomonas sp. é capaz de produzir PHA com composição monomérica variada e com teor controlável, o que confere grande variedade de aplicações. Flux Balance Analysis (FBA) foi utilizado no ambiente Matlab pelo uso do software COBRA. Para a análise foi necessário construir um core de Pseudomonas pela modificação dum core de E. coli, e assim fosse possível obter um modelo mais aproximado. Como resultado foi gerada uma rede metabólica viável contendo os genes da via de Weimberg de C. crescentus no core construído. Paralelamente, a Pseudomonas sp. LFM046 foi repicada sucessivas vezes em meio mineral (MM). Testes simples foram feitos para verificar o perfil das colônias isoladas, além de amplificar e sequenciar o gene 16S rDNA. O resultado do BLAST foi uma identidade de 99% com o gene da Pseudomonas sp. IPT 046, confirmando que a bactéria pertence a género Pseudomonas e tem a capacidade de consumir xilose. / Polyhydroxyalkanoates (PHA) are biodegradable, biocompatible polymers and can be produced from renewable raw materials. Pseudomonas sp. is capable of producing PHA with varied monomer composition and with controllable content, which confers a great variety of applications. Flux Balance Analysis (FBA) was used in the Matlab environment by the use of COBRA software. For the analysis, it was necessary to construct a Pseudomonas core by modifying an E. coli core, so that a more approximate model could be obtained. As a result a viable metabolic network was generated containing the C. crescentus Weimberg pathway genes in the constructed core. In parallel, Pseudomonas sp. LFM046 was repeated successively in mineral medium (MM). Simple tests were done to verify the profile of the isolated colonies, in addition to amplifying and sequencing the 16S rDNA gene. The BLAST result was 99% identity with the Pseudomonas sp gene. IPT 046, confirming that the bacterium belongs to the genus Pseudomonas and has the ability to consume xylose.

I formally joined Prof. M. R. N. Murthy’s laboratory at the Molecular Biophysics Unit, Indian institute of Science, on 1st August 2001. During that time, the interest in the laboratory was mainly focused on structural studies on a number of capsid mutants of two plant viruses, sesbania mosaic virus and physalis mottle virus, to gain an insight into the virus structure and its assembly. Besides these two projects, there were a few other collaborative projects running in the lab at that time such as NIa protease from pepper vein banding virus and diaminopropionate ammonia lyase from Escherichia coli with Prof. H. S. Savithri, triosephosphate isomerase from Plasmodium falciparum with Prof. P. Balaram and Prof. H. Balaram and a DNA binding protein (TP2) with Prof. M. R. S. Rao. During my first semester, along with my course work, I was assigned to make an attempt to purify and crystallize recombinant NIa protease and TP2 protein. I started with NIa protease which could be purified using one step Ni-NTA affinity column chromatography. Although the expression and protein yield were reasonably good, protein precipitated with in a couple of hours after purification. Attempts were made to prevent the precipitation of the purified enzyme and towards this end we were successful to some extent. However, during crystallization trials most of the crystallization drops precipitated completely even at low protein oncentration. TP2 protein was purified using three-step chromatographic techniques by one of the project assistant in Prof. M. R. S. Rao’s laboratory. Because of low expression level and three step purification protocol, protein yield was not good enough for complete crystallization screening. Hits obtained from our initial screening could not be confirmed because of low protein yield as well as batch to batch variation. My attempts to crystallize these two proteins remained unsuccessful but in due course I had learnt a great deal about the tips and tricks of expression, purification and mainly crystallization. To overcome the problems faced with these two proteins, we decided to make some changes in the gene construct and try different expression systems. By this time (beginning of 2002), I had finished my first semester and a major part of the course work, so we decided to start a new project focusing on some of the unknown enzymes from a metabolic pathway. Dr. Parthasarathy, who had finished his Ph. D. from the lab, helped me in literature work and in finding targets for structural studies. Finally, we decided to target enzymes involved in the propionate etabolism. The pathways for propionate metabolism in Escherichia coli as well as Salmonella typhimurium were just established and there were no structural information available for most of the enzymes involved in these pathways. Since, propionate metabolic pathways were well described in the case of Salmonella typhimurium, we decided to use this as the model organism. We first started with the enzymes present in the propionate catabolic pathway “2-methylcitrate pathway”, which converts propionate into pyruvate and succinate. 2-methylcitrate pathway resembles the well-studied glyoxylate and TCA cycle. Most of the enzymes involved in 2-methylcitrate pathway were not characterized biochemically as well as structurally. First, we cloned all the four enzymes PrpB, PrpC, PrpD and PrpE present in the prpBCDE operon along with PrpR, a transcription factor, with the help of Dr. P.S. Satheshkumar from Prof. H. S. Savithri’s laboratory. Since these five proteins were cloned with either N- or C-terminal hexa-histidine tag, they could be purified easily using one-step Ni-NTA affinity column chromatography. PrpB, PrpC and PrpD had good expression levels but with PrpE and PrpR, more than 50% of the expressed protein went into insoluble fraction, probably due to the presence of membrane spanning domains in these two enzymes. Around this time, crystallization report for the PrpD from Salmonella was published by Ivan Rayment’s group, so after that we focused only on the remaining four proteins leaving out PrpD. Our initial attempts to crystallize these proteins became successful in case of PrpB, 2-methylisocitrate lyase. We collected a complete diffraction data to a resolution of 2.5 Å which was later on extended to a resolution of 2.1 Å using another crystal. Repeated crystallization trials with PrpC also gave small protein crystals but they were not easy to reproduce and size and diffraction quality always remained a problem. Using one good crystal obtained for PrpC, data to a resolution of 3.5 Å could be collected. Unfortunately, during data collection due to failure of the cryo-system, a complete dataset could not be collected. Further attempts to crystallize this protein made by Nandashree, one of my colleagues in the lab at that time, was also without much success. Attempts to purify and crystallize PrpE and PrpR were made by me as well as one of my colleagues, Anupama. In this case, besides crystallization, low expression and precipitation of the protein after purification were major problems. Our attempt to phase the PrpB data using the closest search model (phosphoenolpyruvate mutase) by molecular replacement technique was unsuccessful,probably because of low sequence identity between them (24%). Further attempts were made to obtain heavy atom derivatives of PrpB crystal. We could obtain a mercury derivative using PCMBS. However, an electron density map based on this single derivative was not nterpretable. Around this time, the structure of 2-methylisocitrate lyase (PrpB) from E. coli was published by Grimm et. al. The structure of Salmonella PrpB could easily be determined using the E. coli PrpB enzyme as the starting model. We also solved the structure of PrpB in complex with pyruvate and Mg2+. Our attempts to crystallize PrpB with other ligands were not successful. Using the structures of PrpB and its complex with pyruvate and Mg2+, we carried out comparative studies with the well-studied structural and functional homologue, isocitrate lyase. These studies provided the plausible rationale for different substrate specificities of these two enzymes. Due to unavailability of PrpB substrate commercially and the extensive biochemical and mutational studies carried out by two different groups made us turn our attention to other enzymes in this metabolic pathway. Since our repeated attempts to obtain good diffraction quality crystals of PrpC, PrpE and PrpR continued to be unsuccessful, we decided to target other enzymes involved in propionate metabolism. We looked into the literature for the metabolic pathways by which propionate is synthesized in the Salmonella typhimurium and finally decided to target enzymes present in the metabolic pathway which converts L-threonine to propionate. Formation of propionate from L-threonine is the most direct route in many organisms. During February 2003, we initiated these studies with the last enzyme of this pathway, propionate kinase (TdcD), and within a couple of months we could obtain a well-diffracting crystal in complex with ADP and with a non-hydrolysable ATP analog, AMPPNP. TdcD structure was solved by molecular replacement using acetate kinase as a search model. Propionate kinase, like acetate kinase, contains a fold with the topology βββαβαβα, identical with that of glycerol kinase, hexokinase, heat shock cognate 70 (Hsc70) and actin, the superfamily of phosphotransferases. Examination of the active site pocket in propionate kinase revealed a plausible structural rationale for the greater specificity of the enzyme towards propionate than acetate. One of the datasets of TdcD obtained in the presence of ATP showed extra continuous density beyond the γ-phosphate. Careful examination of this extra electron density finally allowed us to build diadenosine tetraphosphate (Ap4A) into the active site pocket, which fitted the density very well. Since the data was collected at a synchrotron source to a resolution of 1.98 Å, we could identify the ligand in the active site pocket solely on the basis of difference Fourier map. Later on, co-crystallization trials of TdcD with commercially available Ap4A confirmed its binding to the enzyme. These studies suggested the presence of a novel Ap4A synthetic activity in TdcD, which is further being examined by biochemical experiments using mass-spectrometry as well as thin-layer chromatography experiments. By the end of 2004, we shifted our focus to the first enzyme involved in the anaerobic degradation of L-threonine to propionate, a biodegradative threonine deaminase (TdcB). Sagar Chittori, who had joined the lab as an integrated Ph. D student, helped me in cloning this enzyme. My attempt to crystallize this protein became finally successful and datasets in three different crystal forms were collected. Dataset for TdcB in complex with CMP was collected during a synchrotron trip to SPring8, Japan by my colleague P. Gayathri and Prof. Murthy. TdcB structure was solved by molecular replacement using the N-terminal domain of biosynthetic threonine deaminase as a search model. Structure of TdcB in the native form and in complex with CMP helped us to understand several unanswered questions related to ligand mediated oligomerization and enzyme activation observed in this enzyme. The structural studies carried out on these three enzymes have provided structural as well as functional insights into the catalytic process and revealed many unique features of these metabolic enzymes. All these have been possible mainly due to proper guidance and encouragement from Prof. Murthy and Prof. Savithri. Prof. Murthy’s teaching as well as discussions during the course of investigation has helped me in a great deal to learn and understand crystallography. Collaboration with Prof. Savithri kept me close to biochemistry and molecular biology, the background with which I entered the world of structural biology. The freedom to choose the project and carry forward some of my own ideas has given me enough confidence to enjoy doing research in future.