The nucleotide sequence at the 5´ end of genes can be specified as the sequence of a promoter associated 5´ untranslated region (UTR) together with the initial coding sequence of a gene. Because this genetic region has been implicated in the control of translation, messenger RNA (mRNA) stability and even transcription, it can be looked at as one of the central control points in gene expression. Both the 5´-UTR and the coding sequence have often been included in optimization strategies targeted to simulate recombinant protein production in E. coli and numerous reports describe various sequence-dependent structural features that can positively influence the overall expression process. Nevertheless, the actual mechanisms by which the regulation of gene expression is exerted at the 5´ end remain obscure. The work reported in this thesis has involved various types of analyses of the functionality of the 5´ end, by using mutations as a major tool. The work can be seen as mainly a detailed empirical analysis of the relation between the specific nucleotide sequences at the 5’ end of genes and the final outcome at the protein production level. The results also indicate that optimizations based on empirical laboratory protocols are currently unlikely to be exceeded by predictions based on bioinformatics software. Sequence mutagenesis of elements in the XylS/Pm - positive regulator/promoter system coupled to high-throughput screening had been previously proven to be a powerful method for increasing the expression of recombinant genes from this expression cassette. At the beginning of this thesis work the effect of introducing random mutations in the DNA sequence of the Pm promoter associated 5´-UTR and two 5´ fusion partners, whose sequences correspond either to a consensus translocation signal peptide or the first 23 codons of a well-expressed celB gene (encoding a cytoplasmic phosphoglucomutase) was investigated. The core of the experimental work was construction of large combinatorial libraries of the different DNA sequences and subsequent selection for improved expression of a reporter gene (either ampicillin or apramycin resistance gene), that was indicated by an increase in antibiotic tolerance of the corresponding E. coli host cells. A shared result of the three individual studies was the establishment of a collection of optimized sequences that generally improved protein production properties of both reporter and industrially relevant heterologous genes. In addition to random mutagenesis, also synonymous mutations were introduced in the DNA sequence of the consensus signal peptide (CSP) and the consequent expression effects were evaluated. As a conclusion, the DNA changes that did not alter the amino acid sequence led to a lesser stimulation of expression of the bla reporter (ampicillin resistance) than when complete sequence randomization was applied. Moreover, similar results were obtained when synonymous codon usage of the first 9 codons of the medically important ifn-α2b gene was optimized by a bioinformatic method, followed by experimental determination of expression levels of several rationally selected ifn-α2b synonymous variants. These results indicated that optimization of the codon usage of the 5´ coding sequence has limited effects, probably due to the sequence intrinsic characteristics. However, the use of optimized 5´ fusion partners or 5´-UTR variants can often overcome such limitations. Besides evaluating the expression at the protein level, the work also addressed how the changes of the 5´ end of a gene influence expression at the level of transcript accumulation and mRNA stability. For that purpose, a non-invasive method for accessing recombinant mRNA stability in bacteria was developed. The procedure was based on the removal of diffusible transcriptional inducers followed by qRT-PCR determination of mRNA levels at consecutive time-points. Among the principal findings was that a 5´ fusion partner (specifically: translocation signals pelB and ompA, together with the celB-based 5´ fusion) contributes to the stimulation of recombinant gene expression by enhancing the stability of the corresponding fusion mRNA. The stimulation of expression caused by specific mutations in the 5´-UTR and adjacent coding sequence (synonymous changes), on the other hand, surprisingly appeared to result from improved rate of mRNA synthesis. Three selected promoter systems (Pm, Ptac and the T7 based) were used in these studies, and part of the work also evaluated how fast each system responds to addition and removal of its inducer, respectively. The expression systems were found to affect both transcript accumulation and decay in a specific way that correlated with the type of transcription regulation each system is subjected to. Finally, a study comparing five bacterial expression systems (XylS/Pm, XylS/Pm ML1-17 (a Pm variant), the bacteriophage T7 RNA polymerase/promoter system, LacI/Ptrc and AraC/PBAD) with respect to their production capacity of five different recombinant proteins was carried out. The comparison revealed many expression system and model gene specific features and that none of the systems was superior in all evaluated aspects; which included system´s adaptability, maximum protein yield, basal expression in the absence of inducer, use of cellular resources and homogeneity of expression. However, particularly because of a large associated collection of optimized genetic elements (such as sequence variants of the Pm promoter, the XylS regulator, 5´-UTR and various translocation signals) and the possibility of simple genetic adjustments that can lead to both higher and lower expression levels, the XylS/Pm system appeared as a good starting point for optimization of various kinds of protein production processes. / A Combinatorial Mutagenesis Approach to Improve Microbial Expression Systems

O sistema de expressão gênica derivado do Semliki Forest Vírus (SFV) vem sendo muito utilizado nos últimos tempos para expressão em grandes quantidades de inúmeras proteínas, quando comparado com outros sistemas. O objetivo desse estudo foi otimizar a capacidade desse vetor viral de expressar proteínas em diferentes linhagens celulares de mamíferos, utilizando como alvo, a glicoproteína do vírus rábico (RVGP). Foram avaliadas formas de obtenção do vetor SFV recombinante, através de diferentes métodos de transfecção, como eletroporação e lipofecção, utilizando um lipossomo comercial chamado Transmessenger (Qiagen, Valencia, CA., U.S.A.). Foi estabelecido, um método rápido e preciso de quantificação das partículas virais, através da técnica de qPCR, para padronizar a relação entre a quantidade de vírus recombinante a ser utilizada em um processo de infecção, visando aumentar os níveis de produção da proteína heteróloga. Diferentes proporções entre vírus e células foram utilizadas em cinco linhagens distintas: BHK-21, Huh-7, VERO, L929 e HEK-293T; sendo avaliados dois tempos de coleta da RVGP após a infecção (24 e 48 h). A proteína gerada foi avaliada através de diferentes métodos como Western Blot, Dot blot e imunofluorescência indireta (IFI), sendo a quantificação da proteína realizada através de ensaio imunoenzimático (ELISA). Esse trabalho contribui para o desenvolvimento de abordagens que utilizam o SFV como vetor de expressão, indicando as melhores metodologias e linhagens celulares, que podem ser utilizadas para aplicação na produção das mais variadas proteínas. / The expression system based on Semliki Forest virus (SFV) is a system which has been widely used in recent times for expression of many proteins in large quantities as compared with other systems. The aim of this study was to optimize the capacity of this vector to express viral proteins in different mammalian cell lines, using as target, the rabies virus glycoprotein (RVGP). We assessed two different methods of transfection to obtain recombinant SFV vector, such as electroporation and liposome commercial Transmessenger (Qiagen, Valencia, CA., U.S.A.). It was established also a fast and accurate quantification of viral particles by qPCR technique, to improve the relation between the amount of recombinant virus to be used in a process of infection, to increase production levels of the heterologous protein. Different proportions between viruses and cells were used in five distinct lineages: BHK-21, Huh-7, Vero, L929 and HEK-293T; being evaluated two sampling times after infection of RVGP (24 e 48 h). The protein was assessed by various methods such as Western blot, Dot blot and indirect immunofluorescence (IIF), and the protein quantification performed by enzyme immunoassay (ELISA). This work contributes to the development of approaches to using the SFV expression vector indicating the best methods and cell lines that can be used for application in the production of various proteins.

O sistema de expressão gênica derivado do Semliki Forest Vírus (SFV) vem sendo muito utilizado nos últimos tempos para expressão em grandes quantidades de inúmeras proteínas, quando comparado com outros sistemas. O objetivo desse estudo foi otimizar a capacidade desse vetor viral de expressar proteínas em diferentes linhagens celulares de mamíferos, utilizando como alvo, a glicoproteína do vírus rábico (RVGP). Foram avaliadas formas de obtenção do vetor SFV recombinante, através de diferentes métodos de transfecção, como eletroporação e lipofecção, utilizando um lipossomo comercial chamado Transmessenger (Qiagen, Valencia, CA., U.S.A.). Foi estabelecido, um método rápido e preciso de quantificação das partículas virais, através da técnica de qPCR, para padronizar a relação entre a quantidade de vírus recombinante a ser utilizada em um processo de infecção, visando aumentar os níveis de produção da proteína heteróloga. Diferentes proporções entre vírus e células foram utilizadas em cinco linhagens distintas: BHK-21, Huh-7, VERO, L929 e HEK-293T; sendo avaliados dois tempos de coleta da RVGP após a infecção (24 e 48 h). A proteína gerada foi avaliada através de diferentes métodos como Western Blot, Dot blot e imunofluorescência indireta (IFI), sendo a quantificação da proteína realizada através de ensaio imunoenzimático (ELISA). Esse trabalho contribui para o desenvolvimento de abordagens que utilizam o SFV como vetor de expressão, indicando as melhores metodologias e linhagens celulares, que podem ser utilizadas para aplicação na produção das mais variadas proteínas. / The expression system based on Semliki Forest virus (SFV) is a system which has been widely used in recent times for expression of many proteins in large quantities as compared with other systems. The aim of this study was to optimize the capacity of this vector to express viral proteins in different mammalian cell lines, using as target, the rabies virus glycoprotein (RVGP). We assessed two different methods of transfection to obtain recombinant SFV vector, such as electroporation and liposome commercial Transmessenger (Qiagen, Valencia, CA., U.S.A.). It was established also a fast and accurate quantification of viral particles by qPCR technique, to improve the relation between the amount of recombinant virus to be used in a process of infection, to increase production levels of the heterologous protein. Different proportions between viruses and cells were used in five distinct lineages: BHK-21, Huh-7, Vero, L929 and HEK-293T; being evaluated two sampling times after infection of RVGP (24 e 48 h). The protein was assessed by various methods such as Western blot, Dot blot and indirect immunofluorescence (IIF), and the protein quantification performed by enzyme immunoassay (ELISA). This work contributes to the development of approaches to using the SFV expression vector indicating the best methods and cell lines that can be used for application in the production of various proteins.

Atualmente, o Brasil encontra-se na privilegiada posição de maior produtor e exportador mundial de carne bovina, tornando a pecuária uma das atividades nacionais mais importantes e rentáveis. Este dado enfatiza a importância de pesquisa e desenvolvimento em reprodução bovina, especialmente em hormônios estimuladores da ovulação, tais como a gonadotrofina coriônica equina (eCG). Os produtos comerciais à base de eCG comercialmente disponíveis são purificados a partir do sangue de éguas gestantes, apresentando variabilidade de lote para lote e presença de contaminantes. Estes fatos, juntamente com a limitação do material de partida (sangue equino), enfatizam a necessidade de haver um sistema de expressão de eCG recombinante passível de ser explorado comercialmente. Neste quesito, as células de mamíferos se mostram um sistema robusto para tal finalidade, visto que são capazes de adicionar modificações pós-traducionais às cadeias polipeptídicas, tais como a glicosilação, o que é essencial para o correto dobramento, maturação e montagem das duas subunidades, além de interferir diretamente com a meia-vida, o reconhecimento do receptor, a solubilidade e a atividade biológica das proteínas. No entanto, mesmo entre os sistemas de expressão heteróloga em células de mamífero, encontra-se muita variabilidade nos padrões de glicosilação adicionado. No presente trabalho, foi realizado um estudo comparativo através da clonagem e expressão de uma forma fusionada de eCG (reCGβα) em duas linhagens celulares diferentes: (1) CHO-DG44, um dos sistemas de expressão mais utilizados pelas indústrias farmacêuticas, capaz de adicionar N-glicanos complexos; e (2) 293T, uma linhagem humana capaz de produzir glicoproteínas carreando oligossacarídeos complexos e sialilados. Os resultados de atividade biológica (in vitro e in vivo) apontam uma maior atividade de reCG produzido por células CHO-DG44. O perfil de N-glicosilação de reCG produzido pelas células CHOD-G44 assemelhou-se mais à eCG selvagem, quando comparado a reCG produzido por células 293T. Por fim, estudos clínicos foram realizados com reCG produzido em meio livre de soro fetal bovino e parcialmente purificado, onde atividade específica de reCG produzido por células CHO-DG44 mostrou-se similar ao produto comercial selvagem. / Brazil is currently the major beef producer and exporter, rendering to livestock one of the country´s most economically relevant activities. This emphasizes the importance of research and development in bovine reproduction, especially at ovulation-stimulatory hormones, such as equine gonadotropin (eCG). The commercially available eCG-based products are purified from blood of pregnant heifers, presenting batch-to-batch variability and the presence of contaminants. These facts, together with the limitation of the bulk material (equine blood), emphasize the need of an eCG expression system able to be commercially explored. In this aspect, mammalian cells are a robust system, capable of add post-translational modifications to polypeptide chains, such as glycosylation, which is essential for the correct folding, maturation and assembly of both eCG subunits. In addition, glycosylation directly interferes with the protein half-life, receptor recognition, solubility and biological activity. In the present work, a comparative study was carried out by cloning and expressing a fusion form of eCG (reCGβα) in two different mammalian cell lines: (1) CHO-DG44, one of the most used by pharmaceutical companies expression systems, capable of add complex-type N-glycans; and (2) 293T, a human cell line capable of produce glycoproteins carrying complex and sialylated oligosaccharides. The in vitro and in vivo biological activity results show a higher potency of reCG produced by CHO-DG44 cells. The N-glycosylation pattern produced by CHO-DG44 cells was more similar to native eCG in comparison to the N-glycosylation produced by 293T cells. Finally, clinical studies were performed with serum absent media produced and partially purified reCG, showing that the specific activity of reCG produced by CHO cells was similar to the commercial wild type product.

Pseudomonas aeruginosa est un pathogène opportuniste responsable de nombreuses maladies nosocomiales chez les patients immunodéprimés ainsi que d'infections graves chez les patients atteints de la mucoviscidose (CF). La colonisation des voies respiratoires des patients CF est souvent mortelle car une fois installée, cette bactérie est difficile à éradiquer et provoque le déclin des fonctions respiratoires des patients. L'antibiothérapie devient inefficace face au développement de souches multi-résistantes et sa capacité à former un biofilm. L'étape cruciale initiant l'infection ou la formation du biofilm est l'adhésion durant laquelle des interactions spécifiques lectines/oligosaccharides permettent la fixation de la bactérie à la surface de la cellule hôte. Bloquer l'adhésion serait un moyen de lutter contre l'infection. Dans l'approche d'une thérapie anti-adhésive, plusieurs lectines impliquées dans l'adhésion et l'élaboration du biofilm sont prises comme cibles. Dans un premier temps, des lectines fimbriales putatives identifiées récemment, CupB6 et CupE6, ont fait l'objet d'une étude. Des essais d'expression, de purification et de cristallisation ont été réalisés dans l'objectif de résoudre leur structure cristallographique. Une étude visant à identifier le ligand naturel de CupB6 a également été entreprise. Puis une étude a été menée pour caractériser le potentiel d'inhibition de plusieurs molécules dérivées du galactose sur la lectine soluble, PA-IL. Certaines de ces molécules pourraient être utilisées comme glycomimétiques offrant une alternative aux antibiotiques. Une étude par microcalorimétrie et cristallographie aux rayons X a permis d'étudier la spécificité d'une lectine de légumineuse, PELa. / P. aeruginosa is an opportunistic pathogenic bacterium responsible for numerous nosocomial infections in immunosuppressed patients. It is the first mortal pathogen in cystic fibrosis (CF) patients. The invasion of the respiratory tract of CF patients by the bacterium is often lethal because it is hard to eradicate and it rapidly impairs the respiratory functions of the patients. None of the current antibiotherapy procedures are efficient against multiresistant, biofilm forming P. aeruginosa. The first step leading to infection or biofilm formation involves the initial adhesion of bacterial cells to the host pulmonary cells via specific lectin/oligosaccharid interactions. Blocking the adhesion would be a way to fight against the infection. The anti-adhesion therapy targets several bacterial lectins involved in adhesiveness and biofilm formation. In this work, the recently identified putative fimbrial lectins CupB6 and CupE6 have been studied. Expression and purification tests followed by crystallization trials have been performed. In parallel, attempts to identify the natural ligand of CupB6 were also carried out. This work also presents a systematic characterization of the inhibitory effects of various galactose-derived molecules on the PA-IL lectin. Some of these molecules could be used as glycomimetic drugs thus offering an interesting alternative to standard antibiotics. Finally, the combination of microcalorimetry together with X-ray crystallography enabled us to gain insights into the ligand specificity of PELa, a legume lectin.

Atualmente, o Brasil encontra-se na privilegiada posição de maior produtor e exportador mundial de carne bovina, tornando a pecuária uma das atividades nacionais mais importantes e rentáveis. Este dado enfatiza a importância de pesquisa e desenvolvimento em reprodução bovina, especialmente em hormônios estimuladores da ovulação, tais como a gonadotrofina coriônica equina (eCG). Os produtos comerciais à base de eCG comercialmente disponíveis são purificados a partir do sangue de éguas gestantes, apresentando variabilidade de lote para lote e presença de contaminantes. Estes fatos, juntamente com a limitação do material de partida (sangue equino), enfatizam a necessidade de haver um sistema de expressão de eCG recombinante passível de ser explorado comercialmente. Neste quesito, as células de mamíferos se mostram um sistema robusto para tal finalidade, visto que são capazes de adicionar modificações pós-traducionais às cadeias polipeptídicas, tais como a glicosilação, o que é essencial para o correto dobramento, maturação e montagem das duas subunidades, além de interferir diretamente com a meia-vida, o reconhecimento do receptor, a solubilidade e a atividade biológica das proteínas. No entanto, mesmo entre os sistemas de expressão heteróloga em células de mamífero, encontra-se muita variabilidade nos padrões de glicosilação adicionado. No presente trabalho, foi realizado um estudo comparativo através da clonagem e expressão de uma forma fusionada de eCG (reCGβα) em duas linhagens celulares diferentes: (1) CHO-DG44, um dos sistemas de expressão mais utilizados pelas indústrias farmacêuticas, capaz de adicionar N-glicanos complexos; e (2) 293T, uma linhagem humana capaz de produzir glicoproteínas carreando oligossacarídeos complexos e sialilados. Os resultados de atividade biológica (in vitro e in vivo) apontam uma maior atividade de reCG produzido por células CHO-DG44. O perfil de N-glicosilação de reCG produzido pelas células CHOD-G44 assemelhou-se mais à eCG selvagem, quando comparado a reCG produzido por células 293T. Por fim, estudos clínicos foram realizados com reCG produzido em meio livre de soro fetal bovino e parcialmente purificado, onde atividade específica de reCG produzido por células CHO-DG44 mostrou-se similar ao produto comercial selvagem. / Brazil is currently the major beef producer and exporter, rendering to livestock one of the country´s most economically relevant activities. This emphasizes the importance of research and development in bovine reproduction, especially at ovulation-stimulatory hormones, such as equine gonadotropin (eCG). The commercially available eCG-based products are purified from blood of pregnant heifers, presenting batch-to-batch variability and the presence of contaminants. These facts, together with the limitation of the bulk material (equine blood), emphasize the need of an eCG expression system able to be commercially explored. In this aspect, mammalian cells are a robust system, capable of add post-translational modifications to polypeptide chains, such as glycosylation, which is essential for the correct folding, maturation and assembly of both eCG subunits. In addition, glycosylation directly interferes with the protein half-life, receptor recognition, solubility and biological activity. In the present work, a comparative study was carried out by cloning and expressing a fusion form of eCG (reCGβα) in two different mammalian cell lines: (1) CHO-DG44, one of the most used by pharmaceutical companies expression systems, capable of add complex-type N-glycans; and (2) 293T, a human cell line capable of produce glycoproteins carrying complex and sialylated oligosaccharides. The in vitro and in vivo biological activity results show a higher potency of reCG produced by CHO-DG44 cells. The N-glycosylation pattern produced by CHO-DG44 cells was more similar to native eCG in comparison to the N-glycosylation produced by 293T cells. Finally, clinical studies were performed with serum absent media produced and partially purified reCG, showing that the specific activity of reCG produced by CHO cells was similar to the commercial wild type product.