Foram estudados a composição e o pH do meio de cultivo para a produção do fragmento de anticorpo (scFv) anti-LDL(-), expresso em Pichia pastoris recombinante. Os experimentos que definiram a composição e pH do meio assim como a concentração inicial de células na fase de indução foram realizados em agitador orbital a 250 rpm, com temperatura de 30 ºC na fase de crescimento e 20 ºC na fase de indução, durante 72 horas, com adição diária de 1% (v/v) de metanol. Para modificação do meio foi realizado um planejamento experimental empregando como variáveis independentes: extrato de soja, casaminoácidos e ureia, os quais substituíram o YNB e a biotina presentes no meio padrão (BMMY). Apesar de haver maior produção no meio com extrato de soja, o meio contendo 10 g.L-1 de casaminoácidos foi selecionado, uma vez que este favoreceu a etapa de purificação. A partir da faixa de pH estudada entre 3,0 e 8,0, determinou-se que o pH 8,0 no início da fase de indução favorece a maior produção. Finalmente, o meio BMMY-CA (pH 8,0) foi utilizado para cultivo em biorreator com volume de trabalho de 10L e a partir deste cultivo foram calculados os parâmetro cinéticos (velocidades de crescimento, de consumo de substrato e de produção, bem como produtividade). Diante do conjunto de experimentos realizados, foi possível otimizar a composição do meio de cultivo e as condições operacionais, que possibilitaram um aumento do rendimento bem como aumento do volume de produção do scFv anti-LDL(-) em biorreator. / Composition and pH culture medium for the production of anti- LDL(-) antibody fragment (scFv) were studied in recombinant yeast Pichia pastoris. The experiments that defined medium composition, pH and the initial cell concentration in the induction phase were carried out in baffled shaker flasks at 250 rpm, with temperature at 30°C for growth phase and 20°C for induction phase, during 72 hours with daily addition of 1% (v/v) methanol. A design of experiments employing for medium modification with independent variables: soy extract, casamino acids and urea, which replaced the YNB and biotin present in the standard medium (BMMY) was conducted for medium formulation. Even though, there was an increase in medium production with soy extract, the medium containing 10 g.L-1 casamino acids was selected since it favors the purification step. Through a pH range study (3.0 to 8.0), it was determined that pH 8.0 during induction phase offered higher levels. Then, the best results from shaker flask cultivation (BMMY-CA with casamino acids and pH 8.0) were carried out in 1L bioreactor, showing a biomass and a scFv production increase compared to the standard, BMMY (pH 6.0). Finally, the medium BMMY-CA (pH 8,0) was submitted to a volume scale-up into a 10L bioreactor, which was also used to evaluate kinetic parameters (rates of growth, substrate consumption and production as well as productivity). In conclusion, by optimizing culture medium and operating conditions it was possible to increase yield and scale-up the production of scFv anti-LDL(-) in bioreactor.

No description available.

Upland soils are a significant sink of atmospheric methane, but the organisms responsible for methane consumption have yet to be identified. The ecology of methanotrophs was investigated in a beech forest soil which exhibited atmospheric-methane-uptake. Maximal methane-oxidation was observed in the upper mineral layer between the organic and inorganic horizons at a rate of 3.1 +/- 0.3 nmoles CH 4 g [fresh wt soil]-1 d-1. A clone bank of the methanotroph pmoA gene was constructed by PCR amplification from soil DNA extracts. The PCR primers used coamplify the related amoA gene of ammonia-oxidizers. The clones recovered grouped into three clusters: Nitrosospira-like sequences, a group somewhat related to alpha-Proteobacteria methanotrophs and previously referred to as the RA14 group, and a cluster which could not be characterized as either amoA or pmoA sequences. No pmoA genes closely related to genera of cultured methanotrophs were obtained. The 16S rDNA was also targeted using eubacterial and methanotroph-specific primers. 16S rDNA sequence analysis revealed the presence of organisms distantly related to known methanotrophs. Methanotroph enrichment cultures were established by inoculating mineral salts medium with soil and incubating under an atmosphere of 10% methane in air. Gene sequencing from the enrichments indicated the presence of organisms belonging to the genera Methylosinus and Methylocystis. The results suggest that the dominant methanotrophs in the forest soil are not related to known organisms and do not grow under conditions typically used to isolate methanotrophs.

Resumo: O gene GPD2 de Saccharomyces cerevisiae, que codifica a enzima glicerol-3- fosfato desidrogenase (G3PDH; EC 1.1.1.8; NAD+: oxidoredutase) foi clonado na levedura Pichia pastoris para expressar extracelularmente a enzima em meio de cultura. Essa enzima apresenta aplicação prática em diversos sistemas acoplados para determinação quantitativa de triacilglicerol, glicerol, ácido fosfatídico e outros fosfolipidios também podendo ser usada para medir atividades enzimáticas em diversos tipos de amostras. Para que a atividade extracelular fosse suficiente em ensaios industriais e biológicos, um estudo de indução da expressão da enzima foi realizado no presente trabalho, que consistiu em escolher o clone que melhor secreta a enzima e estudar o meio de crescimento (BMGY), a densidade inicial celular (0,05 mg/mL), o meio de indução enzimática (BMMY), a natureza do tampão (tampão fosfato), o pH (6,0), o tempo de produção da proteína (4 dias), a concentração da enzima através de membrana filtrante (120 vezes), a melhor fonte de peptona (Acumédia), o estudo de pré-indução celular por estresse osmótico (atividade de 0,477 ± 0,0 U/mL em 24 horas com NaCl 0,35M). O processo de produção da G3PDH mostrou que a máxima produtividade enzimática (795 U/mL e atividade específica de 44,49 U/mg) e biomassa final de 17,75 mg/mL foi obtida com as seguintes condições experimentais: 48 horas de indução com meio BMMY, utilizando 1% de metanol, 1% de glicerol, densidade inicial celular de 0,05 mg/mL, pH 5,0 e sobrenadante concentrado 120 vezes em membrana filtrante. / Abstract: The GPD2 gene from Saccharomyces cerevisiae, which encodes the enzyme glycerol-3-phosphate dehydrogenase (G3PDH, EC 1.1.1.8, NAD +: oxidoredutase) was cloned in the yeast Pichia pastoris to express the enzyme extracellularly in the culture medium. The enzyme G3PDH has practical application in various systems coupled to quantitative determination of triacylglycerol, glycerol, phosphatidic acid and other phospholipids. It can also be used to measure the enzymatic activities in diverse types of samples. For the application of the enzyme extracellular in industrial and biological tests, a study of induction of expression of the enzyme was accomplished in the present work, that consisted of to choose of clone that more expressing the enzyme, the growth medium (BMGY), the cellular initial density (0.05 mg/mL), the medium of enzymatic induction (BMMY), the buffer nature (phosphate potassium), pH (6.0), the time of production of the protein (4 days), the concentration of the protein (120-fold), the peptone source (Acumédia), the study of pre-induction cellular for osmotic stress (activity of 0.477 ± 0.0 U/mL in 24 hours with NaCl 0.35M). The study of the variable determinative in the process of production of the G3PDH it showed that the maximum enzymatic productivity (0.795 U/mL and 44.49 U/mg of specific activity) and final biomass of 17.75 mg/mL was obtained with the following experimental conditions: 48 hours of induction with medium BMMY, using 1% methanol, 1% glycerol, cellular initial density of 0.05mg/mL, pH 5.0 and the supernatant concentrated 120-fold in filter menbrane. / Orientador: Edwil Aparecida de Lucca Gattás / Coorientador: Maristela de Freitas Sanches Peres / Banca: Edwil Aparecida de Lucca Gattás / Banca: José Roberto Ernandes / Banca: Luiz Henrique Souza Guimarães / Mestre

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24665号 / 農博第2548号 / 新制||農||1098(附属図書館) / 学位論文||R5||N5446(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 阪井 康能, 教授 木岡 紀幸, 教授 井上 善晴 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(農学) / 甲第23251号 / 農博第2458号 / 新制||農||1085(附属図書館) / 学位論文||R3||N5341(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 阪井 康能, 教授 小川 順, 教授 井上 善晴 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Made available in DSpace on 2014-06-11T19:23:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-06-18Bitstream added on 2014-06-13T18:50:48Z : No. of bitstreams: 1 silva_vc_me_arafcf.pdf: 335369 bytes, checksum: 08eedc270c2e51ba9d6a9688bf400044 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O gene GPD2 de Saccharomyces cerevisiae, que codifica a enzima glicerol-3- fosfato desidrogenase (G3PDH; EC 1.1.1.8; NAD+: oxidoredutase) foi clonado na levedura Pichia pastoris para expressar extracelularmente a enzima em meio de cultura. Essa enzima apresenta aplicação prática em diversos sistemas acoplados para determinação quantitativa de triacilglicerol, glicerol, ácido fosfatídico e outros fosfolipidios também podendo ser usada para medir atividades enzimáticas em diversos tipos de amostras. Para que a atividade extracelular fosse suficiente em ensaios industriais e biológicos, um estudo de indução da expressão da enzima foi realizado no presente trabalho, que consistiu em escolher o clone que melhor secreta a enzima e estudar o meio de crescimento (BMGY), a densidade inicial celular (0,05 mg/mL), o meio de indução enzimática (BMMY), a natureza do tampão (tampão fosfato), o pH (6,0), o tempo de produção da proteína (4 dias), a concentração da enzima através de membrana filtrante (120 vezes), a melhor fonte de peptona (Acumédia), o estudo de pré-indução celular por estresse osmótico (atividade de 0,477 ± 0,0 U/mL em 24 horas com NaCl 0,35M). O processo de produção da G3PDH mostrou que a máxima produtividade enzimática (795 U/mL e atividade específica de 44,49 U/mg) e biomassa final de 17,75 mg/mL foi obtida com as seguintes condições experimentais: 48 horas de indução com meio BMMY, utilizando 1% de metanol, 1% de glicerol, densidade inicial celular de 0,05 mg/mL, pH 5,0 e sobrenadante concentrado 120 vezes em membrana filtrante. / The GPD2 gene from Saccharomyces cerevisiae, which encodes the enzyme glycerol-3-phosphate dehydrogenase (G3PDH, EC 1.1.1.8, NAD +: oxidoredutase) was cloned in the yeast Pichia pastoris to express the enzyme extracellularly in the culture medium. The enzyme G3PDH has practical application in various systems coupled to quantitative determination of triacylglycerol, glycerol, phosphatidic acid and other phospholipids. It can also be used to measure the enzymatic activities in diverse types of samples. For the application of the enzyme extracellular in industrial and biological tests, a study of induction of expression of the enzyme was accomplished in the present work, that consisted of to choose of clone that more expressing the enzyme, the growth medium (BMGY), the cellular initial density (0.05 mg/mL), the medium of enzymatic induction (BMMY), the buffer nature (phosphate potassium), pH (6.0), the time of production of the protein (4 days), the concentration of the protein (120-fold), the peptone source (Acumédia), the study of pre-induction cellular for osmotic stress (activity of 0.477 ± 0.0 U/mL in 24 hours with NaCl 0.35M). The study of the variable determinative in the process of production of the G3PDH it showed that the maximum enzymatic productivity (0.795 U/mL and 44.49 U/mg of specific activity) and final biomass of 17.75 mg/mL was obtained with the following experimental conditions: 48 hours of induction with medium BMMY, using 1% methanol, 1% glycerol, cellular initial density of 0.05mg/mL, pH 5.0 and the supernatant concentrated 120-fold in filter menbrane.

Chloromethane is the most abundant halocarbon in the environment, and responsible for substantial ozone destruction in the stratosphere. Sources and sinks of chloromethane are still poorly constrained. Although synthesized and used industrially, chloromethane is mainly produced naturally, with major emissions from vegetation and especially the phyllosphere, i.e. the aerial parts of plants. Some phyllosphere epiphytes are methylotrophic bacteria which can use single carbon compounds such as methanol and chloromethane as the sole source of carbon and energy for growth. Most chloromethane-degrading strains isolated so far utilize the cmu pathway for growth with chloromethane which was characterized by the team. The main objective of this work was to investigate whether epiphytes may act as filters for plant emissions of chloromethane, by using a laboratory bipartite system consisting of the model plant Arabidopsis thaliana, known to produce chloromethane mainly by way of the HOL1 gene, and the reference chloromethane-degrading bacterial strain Methylobacterium extorquens CM4, possessing the cmu pathway and of known genome sequence. Three A. thaliana Col-0 variants with different levels of expression of HOL1, i.e. the wild-type strain, its homozygous HOL1 knockout mutant hol1 and an HOL1-OX HOL1 overexpressor, were selected using PCR and qRT-PCR. Chloromethane-degrading strains were isolated from the A. thaliana phyllosphere, and shown to contain the cmu pathway. A plasmid-based bacterial bioreporter for chloromethane was constructed which exploits the promoter region of the conserved chloromethane dehalogenase gene cmuA of strain CM4. It yields rapid, highly sensitive, specific and methyl halide concentration-dependent fluorescence. Application of the bioreporter to the three A. thaliana variants differing in expression of HOL1 investigated in this work suggested that they indeed synthesize different levels of chloromethane. Analysis by qPCR and qRT-PCR of metagenomic DNA from the leaf surface of these variants showed that the relative proportion and expression of cmuA in this environment paralleled HOL1 gene expression. Taken together, the results obtained indicate that even minor amounts of chloromethane produced by A. thaliana in the face of large emissions of methanol may provide a selective advantage for chloromethane-degrading methylotrophic bacteria in the phyllosphere environment. This suggests that chloromethane-degrading epiphytes may indeed act as filters for emissions of chloromethane from plants. Further experiments are envisaged to further assess the adaptation mechanisms of chloromethane-degrading bacteria in the phyllosphere, building upon the comparative genomic analysis of chloromethane-degrading strains which was also performed in this work, and on the preliminary investigations using high-throughput sequencing that were initiated.

O gênero Methylobacterium é composto por bactérias de coloração rósea, metilotróficas e que podem colonizar endofiticamente a planta. Algumas espécies deste gênero são capazes de promover o crescimento vegetal e reduzir o ataque de fitopatógenos. A linhagem de M. mesophilicum SR1.6/6 foi isolada de ramos de citros e devido a sua interação com a planta hospedeira e com patógenos associados a planta, tem sido foco vários trabalhos. Os sistemas de secreção e as bombas de efluxo podem estar envolvidos na modulação das interações de bactérias endofíticas com seus ambientes. Assim, neste estudo foi analisada a composição dos exsudatos produzidos pelas plantas de milho e citros na interação com a SR1.6/6 por GC-MS, foi realizada a reanotação de genes relacionados ao sistema de secreção e bombas de efluxo e foi avaliada a expressão de alguns genes destes sistemas na interação com Zea mays e Citrus sinensis por qPCR. Foram encontrados sistemas de secreção tipo I, II e V, vias SEC e TAT e bombas de efluxo, principalmente super-expressos durante a interação com a planta hospedeira. / Methylobacterium genus is composed by pink-pigmented facultative methylotrophic bacteria. Some species of this genus are able to promote plant growth and reduce the incidence of pathogens. The SR1.6/6 strain of Methylobacterium mesophilicum is a bacterium isolated from citrus and due to its interaction with the plant has been the focus of several studies. Multidrug efflux pumps and secretion system can be involved modulating the interactions of bacteria with their environments. In this work was analised the root exsudates composition from two host plants citrus and corn interacting with SR1.6/6 by GC-MS technique, additionally was searched and reannotated genes related to secretion system and some multidrug efflux pumps and finally evaluated the gene expression of some of this genes during the interaction with Zea mays and Citrus sinensis by qPCR. Type I, II and V secretion system, SEC and TAT pathway and some multidrug efllux pumps were found in this strain according gene expression. This systems were up-regulated mainly during interaction with host plant.

Le chlorométhane est le plus abondant des composés organo-halogénés dans l’atmosphère et il est impliqué dans la destruction de l’ozone dans la stratosphère. Les sources et les puits de chlorométhane restent mal évalués. Bien que synthétisé et utilisé de manière industrielle, il est principalement produit naturellement, avec comme sources majeures les émissions provenant des végétaux et plus particulièrement de la phyllosphère, qui correspond aux parties aériennes des plantes. Certaines bactéries épiphytes de la phyllosphère sont des méthylotrophes capables d’utiliser des composés organiques sans liaison carbone-carbone comme le méthanol et le chlorométhane comme unique source de carbone et d’énergie pour leur croissance. La plupart des bactéries chlorométhane-dégradantes isolées jusqu’à présent utilisent une voie métabolique pour leur croissance sur chlorométhane appelée voie cmu (pour chloromethane utilisation), caractérisée par l’équipe. L’objectif principal de cette thèse a été de déterminer si des bactéries de la phyllosphère peuvent jouer le rôle de filtre pour l’émission de chlorométhane par les plantes. Dans ce but, un modèle de laboratoire a été mis en place, constitué de la plante Arabidopsis thaliana connue pour produire du chlorométhane par une réaction impliquant le gène HOL1, et la bactérie Methylobacterium extorquens CM4, souche de référence pour l’étude du métabolisme de dégradation du chlorométhane, qui possède la voie cmu et dont le génome complet a été séquencé et analysé. Des variants d’A. thaliana avec différents niveaux d’expression du gène HOL1 (le type sauvage, le mutant homozygote « knock-out » hol1 et un variant HOL1-OX avec surexpression) ont été sélectionnés par PCR et qPCR. Des souches bactériennes chlorométhane-dégradantes ont été isolées à partir de la phyllosphère d’A. thaliana, dont il a été montré qu’elles possèdent la voie cmu. Un bio-rapporteur bactérien pour le chlorométhane a été construit à l’aide d’un plasmide exploitant la région promotrice du gène conservé de la déshalogénase (cmuA) de la souche M. extorquens CM4. Il présente une réponse fluorescente rapide, sensible, et spécifique aux méthyl-halogénés de manière concentration-dépendante. L’application du bio-rapporteur aux trois variants d’A. thaliana étudiés suggère des niveaux d’émissions de chlorométhane différents. L’analyse, par qPCR et qRT-PCR, de l’ADN métagénomique extrait de la surface des feuilles a montré une corrélation entre la proportion relative de bactéries portant le gène cmuA et l’exprimant dans cet environnement, et l’expression du gène HOL1. Ces résultats indiquent qu’une production de chlorométhane, même très modeste par rapport aux fortes émissions de méthanol par A. thaliana, confère un avantage sélectif pour les bactéries épiphytes chlorométhane-dégradantes. Ces dernières pourraient ainsi bien jouer un rôle de filtre pour les émissions de chlorométhane de la phyllosphère vers l’atmosphère. En perspective, de nouvelles expériences complémentaires, basées sur l’analyse par génomique comparative des souches chlorométhane-dégradantes également effectuée dans le cadre du projet et sur une analyse par séquençage à haut-débit initiée dans ce travail, sont proposées pour améliorer la compréhension des mécanismes d’adaptation des bactéries chlorométhane-dégradantes dans la phyllosphère. / Chloromethane is the most abundant halocarbon in the environment, and responsible for substantial ozone destruction in the stratosphere. Sources and sinks of chloromethane are still poorly constrained. Although synthesized and used industrially, chloromethane is mainly produced naturally, with major emissions from vegetation and especially the phyllosphere, i.e. the aerial parts of plants. Some phyllosphere epiphytes are methylotrophic bacteria which can use single carbon compounds such as methanol and chloromethane as the sole source of carbon and energy for growth. Most chloromethane-degrading strains isolated so far utilize the cmu pathway for growth with chloromethane which was characterized by the team. The main objective of this work was to investigate whether epiphytes may act as filters for plant emissions of chloromethane, by using a laboratory bipartite system consisting of the model plant Arabidopsis thaliana, known to produce chloromethane mainly by way of the HOL1 gene, and the reference chloromethane-degrading bacterial strain Methylobacterium extorquens CM4, possessing the cmu pathway and of known genome sequence. Three A. thaliana Col-0 variants with different levels of expression of HOL1, i.e. the wild-type strain, its homozygous HOL1 knockout mutant hol1 and an HOL1-OX HOL1 overexpressor, were selected using PCR and qRT-PCR. Chloromethane-degrading strains were isolated from the A. thaliana phyllosphere, and shown to contain the cmu pathway. A plasmid-based bacterial bioreporter for chloromethane was constructed which exploits the promoter region of the conserved chloromethane dehalogenase gene cmuA of strain CM4. It yields rapid, highly sensitive, specific and methyl halide concentration-dependent fluorescence. Application of the bioreporter to the three A. thaliana variants differing in expression of HOL1 investigated in this work suggested that they indeed synthesize different levels of chloromethane. Analysis by qPCR and qRT-PCR of metagenomic DNA from the leaf surface of these variants showed that the relative proportion and expression of cmuA in this environment paralleled HOL1 gene expression. Taken together, the results obtained indicate that even minor amounts of chloromethane produced by A. thaliana in the face of large emissions of methanol may provide a selective advantage for chloromethane-degrading methylotrophic bacteria in the phyllosphere environment. This suggests that chloromethane-degrading epiphytes may indeed act as filters for emissions of chloromethane from plants. Further experiments are envisaged to further assess the adaptation mechanisms of chloromethane-degrading bacteria in the phyllosphere, building upon the comparative genomic analysis of chloromethane-degrading strains which was also performed in this work, and on the preliminary investigations using high-throughput sequencing that were initiated.