Genetic modification of plastids in the model plant tobacco (Nicotiana tabacum) has demonstrated that numerous foreign gene products can accumulate to high levels in this setting. Plastid biotechnology is maturing to encompass the improvement of food and feed species and the production of biopharmaceutical proteins for oral delivery necessitating development of stable transplastomic edible plants. In the interest of establishing an edible platform we have investigated the use of native and foreign regulatory elements in relation to foreign gene expression in plastids. Multiple sequence alignments of intergenic regions for 20 species of angiosperm showed that despite 95% identity in the coding region, identity in the psbA upstream region is 59% across all taxa examined, other gene coding regions displayed sequence identity of 80-97%, whereas the non-coding regions were 45-79% suggesting that our physical data can be extrapolated beyond the model presented. We found that by exchanging psbA untranslated regions (UTRs) between N. tabacum and lettuce (Lactuca sativa), the expression of the CTB-proinsulin (CTB-Pins) monocistronic transcript declined by 84% and foreign protein accumulation was reduced by as much as 97% in mature leaves. Polyribosome association assays suggest that ribosome-free transgenic transcripts are stabilized where the native UTR is employed. RNA EMSA revealed that binding proteins interacted with psbA 5' UTRs in a species specific manner and the half life of the L. sativa 5'UTR-CTB-Pins mRNA was reduced by 3.7 fold in N. tabacum stromal extracts. Our data indicate that the use of species-specific regulatory elements could lead to establishment of reproducible plastid transformation in desirable target species such as L. sativa. Using transplastomic L. sativa for oral delivery of bioencapsulated CTB-Pins we delayed the onset of diabetes in NOD mice when retinyl acetate supplement was provided compared to untouched mice. In this 30 week study we monitored blood glucose levels and evaluated the in vitro suppressive capacity of regulatory T cells isolated from diabetic mice. Whether delay or prevention was achieved appeared to be a function of antigen dose as high dose resulted in a nine week delay of onset while low dose reduced the incidence of diabetes by 36%. In addition we have evaluated metabolic engineering in the N. tabacum model where we generated cis-genic lines expressing nucleus-encoded methionine pathway enzymes in plastids. Transplastomic expression of Cystathionine gamma-Synthase led to a three-fold increase in enzyme activity and a doubling of methionine content in leaves without a deleterious phenotype. In exploring molecular mechanisms supporting gene expression in plastids and applying transplastomic technology to real human problems this work seeks address the potential of plastid biotechnology for improvement of commodity crops and production of biopharmaceuticals.

Amino acids are necessary for protein synthesis and specialized metabolism in plants. Yet very little is known about how plants sense and regulate when and where to allocate amino acids to meet the demand for nitrogen in growing tissues. In particular, while characterized in yeast and mammals, no amino acid sensor has been identified in plants. Amino Acid Permease 1 (AAP1) has been previously characterized and was shown to mediate amino acid uptake from the soil. aap1 knockout plants and several EMS mutants affected in AAP1 sequence display enhanced tolerance to toxic concentrations of amino acids. Yet, two of the corresponding variant proteins appear to be functional transporters, effectively dissociating amino acid transport and phenotype. To understand this apparent discrepancy, I precisely studied AAP1 localization of expression at the plant and cellular level, and in specific tissue types of the root where AAP1 function is required for the tolerance phenotype and the amino acid uptake activity. I showed that AAP1 protein is present in the endoplasmic reticulum of the cortex in wild type plants Yet, its ectopic expression in root tip and phloem increased amino acid uptake, while expression in cortex could not. This and other of my results do not support the current model of AAP1 functioning in amino acid uptake by the root. I propose that the main effect of mutations in AAP1 is a disturbance in amino acid metabolism, possibly triggered by altered amino acid sensing. In this new model, AAP1 would be necessary for sensing amino acid status of cortex cells, possibly in the endoplasmic reticulum, and adjust amino acid metabolic activity and uptake to current availability. In effect, disruption of the sensing function, either by complete loss of AAP1 function (knockout) or by uncoupling the transport and sensing function (EMS mutants), would lead to the various characteristics of the phenotype of the aap1 mutants I observed. My main hypothesis is that AAP1 is a transporter endowed with sensing function, i.e., an amino acid transceptor. / Doctor of Philosophy / Changing environments create challenges for plants to grow under harsher, nutrient limiting conditions. Nitrogen is an essential nutrient for plant growth, used for the synthesis of amino acids and other nitrogen-containing metabolites. Amino acids are necessary for protein synthesis and other specialized metabolism – being targets for manipulation for improving agronomic traits. Protein content is a complex trait that involves many genes, possibly including amino acid transporters. In addition, the amount of nitrogen needed by and available to the plant increases or decreases depending on the environment conditions. How plants control nitrogen need and use at the molecular level is not well understood. The data presented here challenge a current model and I report how a protein (AAP1) involved in the acquisition of amino acids from the soil provides regulatory control over these processes. . This valuable information is useful for better understanding how plants use nitrogen and more precise breeding methods can be used to improve traits, such as protein content in agronomically important crops.

Os herbicidas são aplicados em lavouras com o objetivo de eliminar plantas daninhas presentes, mas os efeitos sobre as culturas muitas vezes não são perceptíveis ou não são amplamente considerados. As plantas sob condições de estresse, podem reagir ao elicitor manifestando reações oxidativas durante as quais espécies reativas de oxigênio (EROs) são geradas. O herbicida glifosato atua como um inibidor competitivo da 5-enolpiruvil xiquimato-3- fosfato sintase da via do xiquimato e o seu efeito herbicida imediato é a inibição da síntese de aminoácidos aromáticos e metabólitos secundários derivados dos fenilpropanoides. A geração de espécies ativas de oxigênio e mecanismos de resposta a estresse oxidativo não são freqüentes no estudo do herbicida glifosato, portanto o presente trabalho objetivou estudar e avaliar parâmetros bioquímicos que poderiam ser afetados pelo herbicida glifosato em variedades suscetíveis e resistentes (transgênicos) dando ênfase na resposta de enzimas antioxidantes e no balanço de aminoácidos. Foram desenvolvidos dois experimentos onde em um deles foi avaliado o efeito da concentração de glifosato em plantas crescidas em hidroponia e no outro foi avaliada a resposta de plântulas de soja de quatro variedades de soja duas resistentes e duas susceptíveis. O perfil de aminoácidos mostrou estar alterado entre variedades susceptíveis e resistentes. O aumento de asparagina, glutamato, histidina e isoleucina de folha assim como o conteúdo total de aminoácidos de folha foram menores e/ou não significativo nas variedades resistentes. A tendência de aumento de atividade de algumas enzimas antioxidantes analisadas como a catalase na raiz, peroxidases na folha ou a glutationa redutase de folha indicou que existem mecanismos ativados para defesa frente a espécies ativas de oxigênio. No entanto, os níveis de peroxidação lipídica não variaram em nenhuma das variedades utilizadas neste estudo. Embora hajam sido apresentadas evidencias que o glifosato gera estresse oxidativo é de se considerar que o modo de ação deste herbicida não é exercido através de mecanismos geradores de radicais livres, porém estes mecanismos parecem estar mascarados pela grande proliferação de aminoácidos livres que podem atuar como antioxidantes. / Herbicides are applied in cultures with the objective to eliminate weeds, but the effects over the plants sometimes are not perceptible or are not widely considered. Plants under stress conditions can react to the elicitor with oxidative manifestations where reactive oxygen species (ROS) are generating. Glyphosate acts as a competitive inhibitor of enolpiruvyl shiquimate-3- phosphate synthase in the shikimate metabolic pathway and its immediately effect is the inhibition of aromatic aminoacids synthesis and secondaries metabolites derived for phenylpropanoids components. ROS generation and response mechanisms to the oxidative stress is not frequently studied in glyphosate applications, although the present work objectives are study and evaluate biochemistry parameters that could be affect by glyphosate herbicide in susceptible and resistant (transgenic) "varieties" giving emphasis in the antioxidant enzymes response and amino acids balance. Two experiments were set up to evaluate the effect of glyphosate in plants of two soybean lines growing under hydroponic conditions and the second experiment evaluated the time effect after application of glyphosate in four soybean lines, susceptible and two resistant (transgenic). Enhancement of asparagine, glutamate, hystidine and isoleucine in leaves, and the total contents of soluble amino acids were lower in resistant lines. This tendency to the increase of antioxidant enzymes like catalase in roots, peroxidases and gluthatione reductase in leaves indicates defense mechanisms activated against ROS. Nevertheless, lipid peroxidation levels were not changed in all lines. The present work shows evidences for oxidative stress generating by glyphosate but it is necessary to consider that the glyphosate action mode does not occur through the EROs generating mechanisms. These mechanisms could be masked by enhancement of amino acid.

Os herbicidas são aplicados em lavouras com o objetivo de eliminar plantas daninhas presentes, mas os efeitos sobre as culturas muitas vezes não são perceptíveis ou não são amplamente considerados. As plantas sob condições de estresse, podem reagir ao elicitor manifestando reações oxidativas durante as quais espécies reativas de oxigênio (EROs) são geradas. O herbicida glifosato atua como um inibidor competitivo da 5-enolpiruvil xiquimato-3- fosfato sintase da via do xiquimato e o seu efeito herbicida imediato é a inibição da síntese de aminoácidos aromáticos e metabólitos secundários derivados dos fenilpropanoides. A geração de espécies ativas de oxigênio e mecanismos de resposta a estresse oxidativo não são freqüentes no estudo do herbicida glifosato, portanto o presente trabalho objetivou estudar e avaliar parâmetros bioquímicos que poderiam ser afetados pelo herbicida glifosato em variedades suscetíveis e resistentes (transgênicos) dando ênfase na resposta de enzimas antioxidantes e no balanço de aminoácidos. Foram desenvolvidos dois experimentos onde em um deles foi avaliado o efeito da concentração de glifosato em plantas crescidas em hidroponia e no outro foi avaliada a resposta de plântulas de soja de quatro variedades de soja duas resistentes e duas susceptíveis. O perfil de aminoácidos mostrou estar alterado entre variedades susceptíveis e resistentes. O aumento de asparagina, glutamato, histidina e isoleucina de folha assim como o conteúdo total de aminoácidos de folha foram menores e/ou não significativo nas variedades resistentes. A tendência de aumento de atividade de algumas enzimas antioxidantes analisadas como a catalase na raiz, peroxidases na folha ou a glutationa redutase de folha indicou que existem mecanismos ativados para defesa frente a espécies ativas de oxigênio. No entanto, os níveis de peroxidação lipídica não variaram em nenhuma das variedades utilizadas neste estudo. Embora hajam sido apresentadas evidencias que o glifosato gera estresse oxidativo é de se considerar que o modo de ação deste herbicida não é exercido através de mecanismos geradores de radicais livres, porém estes mecanismos parecem estar mascarados pela grande proliferação de aminoácidos livres que podem atuar como antioxidantes. / Herbicides are applied in cultures with the objective to eliminate weeds, but the effects over the plants sometimes are not perceptible or are not widely considered. Plants under stress conditions can react to the elicitor with oxidative manifestations where reactive oxygen species (ROS) are generating. Glyphosate acts as a competitive inhibitor of enolpiruvyl shiquimate-3- phosphate synthase in the shikimate metabolic pathway and its immediately effect is the inhibition of aromatic aminoacids synthesis and secondaries metabolites derived for phenylpropanoids components. ROS generation and response mechanisms to the oxidative stress is not frequently studied in glyphosate applications, although the present work objectives are study and evaluate biochemistry parameters that could be affect by glyphosate herbicide in susceptible and resistant (transgenic) "varieties" giving emphasis in the antioxidant enzymes response and amino acids balance. Two experiments were set up to evaluate the effect of glyphosate in plants of two soybean lines growing under hydroponic conditions and the second experiment evaluated the time effect after application of glyphosate in four soybean lines, susceptible and two resistant (transgenic). Enhancement of asparagine, glutamate, hystidine and isoleucine in leaves, and the total contents of soluble amino acids were lower in resistant lines. This tendency to the increase of antioxidant enzymes like catalase in roots, peroxidases and gluthatione reductase in leaves indicates defense mechanisms activated against ROS. Nevertheless, lipid peroxidation levels were not changed in all lines. The present work shows evidences for oxidative stress generating by glyphosate but it is necessary to consider that the glyphosate action mode does not occur through the EROs generating mechanisms. These mechanisms could be masked by enhancement of amino acid.

Amino acid availability plays an important role in modulating the activity of T-cells. One of the pathways employed by T-cells to sense nutrient levels is the “mammalian target of rapamycin” (mTOR) pathway that is inhibited in response to nutrient depletion. Indoleamine 2,3-dioxygenase (IDO) is the first and rate-limiting enzyme along the tryptophan catabolising kynurenine pathway. T-cells are very sensitive to lack of this essential amino acid in their microenvironment and this confers strong immunomodulatory properties to cells expressing active IDO. It therefore has a significant physiological role as a homeostatic mechanism used in mammalian organisms to dampen excessive activation of the immune system but is also used as an immune evasion mechanism by many cancers. In this study, we investigated the IDO inhibitory properties and mechanism of action of the tryptophan metabolite 3-hydroxyanthranilic acid (3-HAA) that potentially forms a negative feedback loop in the kynurenine pathway. We studied the molecule in enzymatic assays, in live cells and discovered that it inhibits IDO in an indirect way via the formation of hydrogen peroxide. Secondly, we looked at the effects of tryptophan and its metabolites on T-cell proliferation and mTOR activity, and discovered a metabolite that inhibits T-cell proliferation. Lastly we examined mechanisms of T-cell suppression employed by myeloid derived suppressor cells (MDSCs), focusing on their ability to deplete amino acids from their microenvironment. We were able to exclude tryptophan consumption as a suppressive mechanism and established that by manipulating extracellular concentrations of several amino acids other than arginine and cysteine – that are known to be utilised by MDSCs - we were able to reduce their inhibitory properties. In summary, we have described in detail how 3-HAA inhibits IDO in in vitro assays, outlined how some tryptophan metabolites can inhibit T-cell proliferation, and clarified aspects of suppressive mechanism employed by MDSCs.

A restrição calórica (RC) é uma intervenção dietética capaz de estender a longevidade de vários organismos. O modelo para RC em Saccharomyces cerevisiae consiste da diminuição da concentração de glicose no meio de cultura e mostra um aumentado tanto do tempo de vida cronológico quanto replicativo. Nosso objetivo foi investigar experimentalmente a ação da RC, focando principalmente nas causas e consequências das modificações de geração de EROs mitocondriais e como estas estão associadas ao processo de envelhecimento. Em um primeiro período de estudos, verificamos quais as fontes mitocondriais de EROs, e comprovamos que uma quantidade significativa se origina de proteínas da matriz mitocondrial, e não da cadeia de transporte de elétrons. Nós estudamos a participação de glicose e de outras fontes de carbono sobre o tempo de vida cronológico em leveduras e mostramos que o aumento da longevidade promovida pela RC está associado à uma mudança de metabolismo fermentativo para respiratório, com participação da via de sinalização de glicose. No estágio realizado no laboratório do Professor Francis Sluse na Université de Liegè, Bélgica, estudamos a ação da RC em leveduras focando nas consequências das modificações no proteoma mitocondrial. Em nosso estudo proteômico, encontramos grandes modificações em proteínas envolvidas com o metabolismo de aminoácidos. Monitoramos a atividade de enzimas relacionadas ao metabolismo de aminoácidos e o tempo de vida cronológico de S. cerevisiae e as mutantes nulas bat2Δ, gdh1Δ, gdh2Δ e gdh3Δ, que codificam a aminotransferase de aminoácidos de cadeia ramificada citosólica, NADP glutamato desidrogenase citosólica, a NAD glutamato desidrogenase mitocondrial, e a NADP glutamato desidrogenase mitocondrial, respectivamente. A atividade da NAD glutamato desidrogenase é aumentada em RC, mas a de NADP glutamato desidrogenase decresce em células controle. Aumentos do tempo de vida cronológico foram observados nas mutantes bat2Δ e gdh1Δ devido a RC, mas nenhuma diferença significativa foi encontrada nas mutantes nulas para Gdh2p e Gdh3p em fase estacionária, indicando que essas proteínas são essenciais para os efeitos benéficos da RC. Nessas células WT crescidas em condições normais e as mutantes nulas apresentam iguais longevidades. Juntos, nossos resultados indicam que o aumento da longevidade em S. cerevisiae promovida pela RC depende da interação entre o sinal de glicose e o metabolismo de aminoácidos. / Calorie restriction (CR) is a dietary intervention capable of extending lifespans in a wide range of organisms. A yeast model of CR has been developed in which limiting the concentration of glucose in growth media of Saccharomyces cerevisiae leads to enhanced chronological and replicative life spans. Our aim was to experimentally investigate the effects of CR, focusing mainly on the causes and consequences of changes in mitochondrial reactive oxygen species (ROS) generation and how these are associated with the aging process. Initially, we looked for sources of mitochondrial ROS, and found that a significant amount of ROS comes from mitochondrial matrix enzymes and not from the electron transport chain. We studied the participation of glucose and other carbon sources in chronological lifespan and show that increased longevity promoted by CR is associated with a metabolism change from fermentation to respiration, with participation of glucose repression pathway. During studies performed in the laboratory of Professor Francis Sluse at the Université de Liège, Belgium, we studied the effect of CR in yeast with focus on the consequences of changes in the mitochondrial proteome. We found large proteomic changes in proteins involved in amino acid metabolism. We monitored the activity of enzymes related to amino acid metabolism and chronological life span of S. cerevisiae null mutants bat2Δ, gdh1Δ, gdh2Δ, and gdh3Δ, which encode for the cytosolic branched-chain amino acid aminotransferase, cytosolic NADP glutamate dehydrogenase, mitochondrial NAD glutamate dehydrogenase and mitochondrial NADP glutamate dehydrogenase, respectively. The activity of NAD glutamate dehydrogenase is increased in CR, but NADP glutamate dehydrogenase decreases in control cells. Increases in chronological life span due to RC were observed in bat2Δ and gdh1Δ mutants, but no significant difference was found in Gdh2p and Gdh3p null mutants in the stationary phase, indicating that these proteins are essential for the beneficial effects of CR. In rich medium, WT cells and null mutants have similar life spans. Together, our results indicate that longevity enhancement by CR in S. cerevisiae depends on the interaction between glucose signals and amino acid metabolism

In this work an intersection between optimization methods and animal cell culture modeling is considered. We present optimization based methods for analyzing and building models of cell culture; models that could be used when designing the environment cells are cultivated in, i.e., medium. Since both the medium and cell line considered are complex, designing a good medium is not straightforward. Developing a model of cell metabolism is a step in facilitating medium design. In order to develop a model of the metabolism the methods presented in this work make use of an underlying metabolic reaction network and extracellular measurements. External substrates and products are connected via the relevant elementary flux modes (EFMs). Modeling from EFMs is generally limited to small networks, because the number of EFMs explodes when the underlying network size increases. The aim of this work is to enable modeling with more complex networks by presenting methods that dynamically identify a subset of the EFMs. In papers A and B we consider a model consisting of the EFMs along with the flux over each mode. In paper A we present how such a model can be decided by an optimization technique named column generation. In paper B the robustness of such a model with respect to measurement errors is considered. We show that a robust version of the underlying optimization problem in paper A can be formed and column generation applied to identify EFMs dynamically. In papers C and D a kinetic macroscopic model is considered. In paper C we show how a kinetic macroscopic model can be constructed from the EFMs. This macroscopic model is created by assuming that the flux along each EFM behaves according to Michaelis-Menten type kinetics. This modeling method has the ability to capture cell behavior in varied types of media, however the size of the underlying network is a limitation. In paper D this limitation is countered by developing an approximation algorithm, that can dynamically identify EFMs for a kinetic model. / I denna avhandling betraktar vi korsningen mellan optimeringsmetoder och modellering av djurcellodling.Vi presenterar optimeringsbaserade metoder för att analysera och bygga modeller av cellkulturer. Dessa modeller kan användas vid konstruktionen av den miljö som cellerna ska odlas i, dvs, medium.Eftersom både mediet och cellinjen är komplexa är det inte okomplicerat att utforma ett bra medium. Att utveckla en modell av cellernas ämnesomsättning är ett steg för att underlätta designen av mediet. För att utveckla en modell av metabolismen kommer de metoder som används i detta arbete att utnyttja ett underliggande metaboliskt reaktions\-nätverk och extracellulära mätningar. Externa substrat och produkter är sammankopplade via de relevanta elementära metaboliska vägarna (EFM).Modellering med hjälp av EFM är i allmänhet begränsad till små nätverk eftersom antalet EFM exploderar när de underliggande nätverket ökar i storlek. Målet med detta arbete är att möjliggöra modellering med mer komplexa nätverk genom att presentera metoder som dynamiskt identifierar en delmängd av EFM. I artikel A och B betraktar vi en modell som består av EFM och ett flöde över varje EFM.I artikel A presenterar vi hur en sådan modell kan bestämmas med hjälp av en optimeringsteknik som kallas kolumngenerering.I artikel A undersöker vi hur robust en sådan modell är med avseende till mätfel. Vi visar att en robust version av det underliggande optimeringsproblemet i artikel A kan konstrueras samt att kolumngenerering kan appliceras för att identifiera EFM dynamiskt. Artikel C och D behandlar en kinetisk makroskopisk modell. Vi visar i artikel C hur en sådan modell kan konstrueras från EFM.Denna makroskopiska modell är skapad genom att anta att flödet genom varje EFM beter sig enligt Michaelis-Menten-typ av kinetik. Denna modelleringsmetod har förmågan att fånga cellernas beteende i olika typer av media, men storleken på nätverket är en begränsning.I artikel D hanterar vi denna begränsing genom att utveckla en approximationsalgoritm som identifierar EFM dynamiskt för en kinetisk modell. / <p>QC 20150827</p>

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-08-10T17:18:30Z No. of bitstreams: 2 Tese - Leandro Nascimento da Silva Rodrigues - 2014.pdf: 2636013 bytes, checksum: 332020037e85516d843bbcbfc5e4da75 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-08-15T13:41:26Z (GMT) No. of bitstreams: 2 Tese - Leandro Nascimento da Silva Rodrigues - 2014.pdf: 2636013 bytes, checksum: 332020037e85516d843bbcbfc5e4da75 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-08-15T13:41:26Z (GMT). No. of bitstreams: 2 Tese - Leandro Nascimento da Silva Rodrigues - 2014.pdf: 2636013 bytes, checksum: 332020037e85516d843bbcbfc5e4da75 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-11-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The dimorphic fungus Paracoccidioides is the etiological agent of paracoccidioidomycosis, a systemic mycosis with high relevance for the public health in Brazil and other Latin American countries such as Colombia and Venezuela. Generally, microorganisms require responses to stress conditions to survive in response to environmental changes and pathogenic organisms, particularly, require an effective response even higher to react against host defences. Osmotic stress has been used as a model to study signal transduction and seems to cause many cellular adaptations, which include signal transduction pathways modification, protein expression alteration and cellular volume and size regulation. In this work we have evaluated the proteomic profile of yeast cells of Paracoccidioides sp. (Pb01) obtained in osmotic stress condition. Data describe an osmoadaptative response of this fungus when subjected to this treatment. Proteins involved in the synthesis of the cell wall components were modulated, evidencing a remodelling of the cell wall. In addition, it was also observed alterations on the energy metabolism, given that proteins of the pentose phosphate pathway were abundant while proteins of the glycolysis were less abundant under osmotic stress condition. In addition changes in amino acid metabolism were also observed; more clearly the degradation of amino acids such as leucine, isoleucine and valine was induced during osmotic stress. Hereupon, our study suggests that Paracoccidioides sp. (Pb01) present a vast osmoadaptative repertoire; comprising different proteins which act complementarily and that this response could be able to minimize the effects caused by osmotic stress. / O fungo dimórfico Paracoccidioides é o agente etiológico da paracoccidioidomicose, uma micose sistêmica com grande relevância na saúde pública no Brasil e em outros países da América Latina, como Colômbia e Venezuela. Microrganismos, em geral, requerem respostas às condições de estresse para sobreviver às mudanças ambientais e patógenos, em particular, necessitam de uma resposta efetiva ainda maior para reagir às defesas do hospedeiro. O estresse osmótico é usado como um modelo para estudos de transdução de sinais e parece causar muitas adaptações celulares, as quais incluem alterações nas vias de transdução de sinais, expressão de proteínas e regulação do volume e tamanho celulares. Neste trabalho foi avaliado o perfil proteômico das células leveduriformes de Paracoccidioides sp. (Pb01) obtidas sob condições de estresse osmótico. Os dados evidenciam uma resposta osmoadaptativa deste fungo, quando submetido a este tipo de estresse. Proteínas envolvidas na biossíntese de componentes de parede celular foram moduladas, evidenciando um remodelamento de parede. Também foram observadas prováveis alterações no metabolismo de energia, tendo em vista que proteínas da via das pentoses fosfato mostraram-se abundantes, enquanto proteínas da via glicolítica mostraram-se em menor abundância frente às condições de estresse osmótico. Adicionalmente alterações no metabolismo de aminoácidos também foram observadas; de forma mais evidente a degradação de aminoácidos como leucina, valina e isoleucina foi induzida durante o estresse osmótico. Neste sentido, nosso estudo sugere que Paracoccidioides sp. (Pb01) possui um amplo repertório osmoadaptativo, composto por diferentes proteínas que atuam de maneira complementar e que devem atuar promovendo a minimização dos efeitos causados pelo estresse osmótico.

A restrição calórica (RC) é uma intervenção dietética capaz de estender a longevidade de vários organismos. O modelo para RC em Saccharomyces cerevisiae consiste da diminuição da concentração de glicose no meio de cultura e mostra um aumentado tanto do tempo de vida cronológico quanto replicativo. Nosso objetivo foi investigar experimentalmente a ação da RC, focando principalmente nas causas e consequências das modificações de geração de EROs mitocondriais e como estas estão associadas ao processo de envelhecimento. Em um primeiro período de estudos, verificamos quais as fontes mitocondriais de EROs, e comprovamos que uma quantidade significativa se origina de proteínas da matriz mitocondrial, e não da cadeia de transporte de elétrons. Nós estudamos a participação de glicose e de outras fontes de carbono sobre o tempo de vida cronológico em leveduras e mostramos que o aumento da longevidade promovida pela RC está associado à uma mudança de metabolismo fermentativo para respiratório, com participação da via de sinalização de glicose. No estágio realizado no laboratório do Professor Francis Sluse na Université de Liegè, Bélgica, estudamos a ação da RC em leveduras focando nas consequências das modificações no proteoma mitocondrial. Em nosso estudo proteômico, encontramos grandes modificações em proteínas envolvidas com o metabolismo de aminoácidos. Monitoramos a atividade de enzimas relacionadas ao metabolismo de aminoácidos e o tempo de vida cronológico de S. cerevisiae e as mutantes nulas bat2&#916;, gdh1&#916;, gdh2&#916; e gdh3&#916;, que codificam a aminotransferase de aminoácidos de cadeia ramificada citosólica, NADP glutamato desidrogenase citosólica, a NAD glutamato desidrogenase mitocondrial, e a NADP glutamato desidrogenase mitocondrial, respectivamente. A atividade da NAD glutamato desidrogenase é aumentada em RC, mas a de NADP glutamato desidrogenase decresce em células controle. Aumentos do tempo de vida cronológico foram observados nas mutantes bat2&#916; e gdh1&#916; devido a RC, mas nenhuma diferença significativa foi encontrada nas mutantes nulas para Gdh2p e Gdh3p em fase estacionária, indicando que essas proteínas são essenciais para os efeitos benéficos da RC. Nessas células WT crescidas em condições normais e as mutantes nulas apresentam iguais longevidades. Juntos, nossos resultados indicam que o aumento da longevidade em S. cerevisiae promovida pela RC depende da interação entre o sinal de glicose e o metabolismo de aminoácidos. / Calorie restriction (CR) is a dietary intervention capable of extending lifespans in a wide range of organisms. A yeast model of CR has been developed in which limiting the concentration of glucose in growth media of Saccharomyces cerevisiae leads to enhanced chronological and replicative life spans. Our aim was to experimentally investigate the effects of CR, focusing mainly on the causes and consequences of changes in mitochondrial reactive oxygen species (ROS) generation and how these are associated with the aging process. Initially, we looked for sources of mitochondrial ROS, and found that a significant amount of ROS comes from mitochondrial matrix enzymes and not from the electron transport chain. We studied the participation of glucose and other carbon sources in chronological lifespan and show that increased longevity promoted by CR is associated with a metabolism change from fermentation to respiration, with participation of glucose repression pathway. During studies performed in the laboratory of Professor Francis Sluse at the Université de Liège, Belgium, we studied the effect of CR in yeast with focus on the consequences of changes in the mitochondrial proteome. We found large proteomic changes in proteins involved in amino acid metabolism. We monitored the activity of enzymes related to amino acid metabolism and chronological life span of S. cerevisiae null mutants bat2&#916;, gdh1&#916;, gdh2&#916;, and gdh3&#916;, which encode for the cytosolic branched-chain amino acid aminotransferase, cytosolic NADP glutamate dehydrogenase, mitochondrial NAD glutamate dehydrogenase and mitochondrial NADP glutamate dehydrogenase, respectively. The activity of NAD glutamate dehydrogenase is increased in CR, but NADP glutamate dehydrogenase decreases in control cells. Increases in chronological life span due to RC were observed in bat2&#916; and gdh1&#916; mutants, but no significant difference was found in Gdh2p and Gdh3p null mutants in the stationary phase, indicating that these proteins are essential for the beneficial effects of CR. In rich medium, WT cells and null mutants have similar life spans. Together, our results indicate that longevity enhancement by CR in S. cerevisiae depends on the interaction between glucose signals and amino acid metabolism

Si les différentes composantes du syndrome métabolique (SM) sont susceptibles d’affecter le métabolisme protéique et des acides aminés (AA), les données disponibles sont peu nombreuses et souvent contradictoires, du fait de l’hétérogénéité de présentation de ce syndrome et des limites des approches classiques d’investigation du métabolisme azoté. Ce travail de thèse met à profit une nouvelle approche isotopomique, s’appuyant sur la mesure de l’abondance naturelle des isotopes stables de l’azote (δ15N) et du carbone (δ13C) dans les protéines et AA tissulaires pour identifier les altérations du métabolisme protéique survenant lors de l’induction nutritionnelle d’un SM chez le rat. Nos résultats permettent dans un premier temps de valider expérimentalement les prédictions d’un modèle multi-compartimental développé dans le laboratoire et montrant que les δ15N reflètent l’orientation différentielle des AA entre les voies anaboliques (protéosynthèse) et cataboliques (oxydation). Nous avons également montré que sous certaines conditions, les δ13C permettent d’estimer la part des carbones des AA et protéines tissulaires provenant respectivement des protéines, glucides et lipides alimentaires, renseignant ainsi sur la flexibilité métabolique des individus. Les mesures de δ15N et δ13C dans les protéines et AA, seules ou combinées à la mesure des taux de synthèse protéique après administration d’eau deutérée, nous ont ensuite permis de mettre en évidence les modifications du métabolisme protéique et des AA survenant lors de l’exposition périnatale et post-sevrage à un régime gras et sucré, ainsi que celles associées à des différences de sensibilité individuelles à l’induction d’un syndrome métabolique par ce même type de régime. Ces altérations sont tissu-spécifiques et diffèrent selon qu’elles proviennent uniquement de différences de sensibilité individuelle au régime ou qu’elles sont également attribuables à des différences d’équilibre glucido-lipidique dans l’alimentation. L’ensemble de nos résultats montrent que l’apparition d’un SM est associée à des réorientations du métabolisme des AA entre les voies anaboliques et d’oxydation, affectant de façon différente le foie, le muscle, l’intestin et le tissu adipeux, et à une altération de la flexibilité métabolique dans le muscle. Ces travaux ouvrent la voie à des études chez l’Homme, s’appuyant sur les mesures de δ15N et δ13C dans des pools accessibles. / Although the different components of the metabolic syndrome (MS) are likely to affect protein and amino acid (AA) metabolism, the available data are few and often contradictory, due to the heterogeneity of presentation of this syndrome and the limitations of classical approaches to investigate nitrogen metabolism. The present thesis work uses a novel isotopomic approach, based on the measurement of the natural abundance of stable isotopes of nitrogen (δ15N) and carbon (δ13C) in tissue proteins and AA to identify alterations in protein metabolism occurring during the nutritional induction of MS in rats. Our results allow to validate experimentally the predictions of a multi-compartimental model developed in the laboratory and showing that the δ15N reflects the differential orientation of AA between anabolic (proteosynthesis) and catabolic (oxidation) pathways. We have also shown that under certain conditions, the δ13C can allow to estimate the proportion of carbons in AA and tissue proteins issuing from dietary proteins, carbohydrates and lipids respectively, thus providing information on the metabolic flexibility of individuals. The measurements of δ15N and δ13C in proteins and AA, alone or combined with the measurement of protein synthesis rates after administration of deuterated water, then allowed us to highlight the changes in protein and AA metabolism occurring during perinatal and post-weaning exposure to a high-fat high-sugar diet, as well as those associated with individual differences in sensitivity to the induction of a MS by the same kind of diet. These alterations are tissuespecific and differ according to whether they result solely from differences in individual sensitivity to diet or whether they are also attributable to differences in the carbohydrate/lipid balance of the diet. Altogether, our results show that the development of MS is associated with changes in AA metabolic partitioning between the anabolic and oxidative pathways, differently affecting the liver, muscle, intestine and adipose tissue, and with an altered metabolic flexibility in muscle. This work opens the way to human studies, based on the measurements of δ15N and δ 13C in accessible pools.