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The natural ability of filamentous fungi to synthesize, glycosylate, and secrete high levels of protein products has made them potentially attractive hosts for heterologous protein production. Advances in fungal genetics enabled the expression of several high value proteins in filamentous fungi. Particularly the genus, Aspergillus has proven to be potentially useful for the expression of eukaryotic gene products. This thesis pertains to the optimization of recombinant protein production by the fungal host, Aspergillus niger. The target recombinant protein of interest is hen egg white lysozyme (HEWL). This protein encoded in the genome resulting in relatively stable gene construct; however, it is subject to extracellular protease attack. The objective of the proposed research is the development and application of engineering methodology for the analysis and optimization of a fungal bioprocess for recombinant protein production. The underlying hypothesis is that a significant improvement of target protein productivity is achievable by using appropriate optimization techniques. To accomplish this, during the first phase of this study a statistically based experimental method was used to systematically elucidate the effect of medium components (starch, peptone, ammonium sulfate, yeast extract, and CaCl₂.2H₂O) on hen egg white lysozyme production by Aspergillus niger HEWL WT-13-16. A 2⁵⁻¹ fractional factorial design augmented with center points revealed that peptone, starch, and ammonium sulfate were the most significant factors, whereas the other medium components were not important within the levels tested. Then, the method of steepest ascent was employed to approach the proximity of optimum. This task was followed by a central composite design to develop a response surface for medium optimization. The optimum medium composition for lysozyme production was found to be: starch 34 g/L, peptone 34 g/L, ammonium sulfate 11.9 g/L, yeast extract 0.5 g/L, and CaCl₂.2H₂O 0.5 g/L. This medium was projected to produce theoretically 212 mg/L lysozyme. Using this optimized medium, an experimentally observed maximum lysozyme concentration of 209±18 mg/L verified the applied methodology. A second optimization approach was based on metabolic flux analysis (MFA). A comprehensive metabolic network comprising three intracellular compartments (cytoplasm, mitochondrion and peroxisome) was developed for Aspergillus niger. The metabolic flux network included carbohydrate and amino acid metabolism in both anabolic and catabolic reactions. According to experimental observations, the time course of fermentation was divided into five phases, each with unique physiological properties. The network was used to form a set of linear algebraic equations based on the stoichiometry of the reactions by assuming pseudo-steady state for intracellular metabolites. The metabolic flux model consists of 137 metabolites and 287 processes, of which 181 represent biochemical conversions and 106 represent transport processes between the different compartments and the extracellular environment. In addition, due to the physiological evidence some biochemical reactions considered to be active only in one direction. Linear programming was used for optimizing of the specific growth rate as the objective function in combination with 37 measured input and output fluxes of the key metabolites to evaluate corresponding intracellular flux distributions throughout the batch fermentations. The general applicability of the methodology was evaluated by establishing commonality to optimize recombinant HEWL production. The proposed model was able to predict correctly the specific growth rate, oxygen uptake rate, and carbon dioxide evolution rate with good precision. The results of the metabolic flux and sensitivity analysis were employed for medium design. Growth was biphasic; glucose was utilized initially as the carbon source and was followed by its oxidation product, gluconate, later. Logarithmic sensitivity analysis revealed that the addition of proline, alanine and glutamate benefited growth in defined media. The experimental observations and flux analysis showed that tyrosine was a potential candidate for biomass production improvement. The two amino acids, namely proline and tyrosine benefited biomass production during the initial growth phases. Glutamate and alanine were particularly important during the latter stages of the batch process. A series of growth studies were conducted with the identified amino acids added in the medium. In these preliminary nutritional experiments the contribution to growth enhancement was 46% for proline, 23% for glutamate, and 22% for tyrosine. Model predictions were further verified by conducting batch and fed-batch fermentations in a 7- liter bioreactor. The programmed addition of four amino acids (proline, glutamate, alanine, and tyrosine) according to a predetermined schedule resulted in a 44% improvement in biomass and 41% improvement in recombinant protein production. The experiments also confirmed the model prediction that extra amount of amino acids besides the identified ones would not significantly enhance biomass and the recombinant protein production. A computer-based control system was developed for the on-line monitoring and control of the major state variables (e.g., temperature, pH, and DO) during the time course of fermentation. The graphical programming environment, LabVIEW was used to acquire and integrate these variables in a supervisor computer. The temperature of the bioreactor during sterilization and fermentation was controlled using a cascade methodology. The controller parameters of the master and slave loops were determined experimentally to yield a smooth response with minimum overshoot of both the bioreactor and jacket temperatures. The program scheduled various required steps in an established order during the fermentation. This feature of the software guarantees that every necessary operation will be met. The graphical representation of the process is displayed on the screen and helps the user to follow the process and perform the required adjustments. Furthermore, different variables can be observed simultaneously and saved in text or spreadsheet files for further analysis.

The natural ability of filamentous fungi to synthesize, glycosylate, and secrete high levels of protein products has made them potentially attractive hosts for heterologous protein production. Advances in fungal genetics enabled the expression of several high value proteins in filamentous fungi. Particularly the genus, Aspergillus has proven to be potentially useful for the expression of eukaryotic gene products. This thesis pertains to the optimization of recombinant protein production by the fungal host, Aspergillus niger. The target recombinant protein of interest is hen egg white lysozyme (HEWL). This protein encoded in the genome resulting in relatively stable gene construct; however, it is subject to extracellular protease attack. The objective of the proposed research is the development and application of engineering methodology for the analysis and optimization of a fungal bioprocess for recombinant protein production. The underlying hypothesis is that a significant improvement of target protein productivity is achievable by using appropriate optimization techniques. To accomplish this, during the first phase of this study a statistically based experimental method was used to systematically elucidate the effect of medium components (starch, peptone, ammonium sulfate, yeast extract, and CaCl₂.2H₂O) on hen egg white lysozyme production by Aspergillus niger HEWL WT-13-16. A 2⁵⁻¹ fractional factorial design augmented with center points revealed that peptone, starch, and ammonium sulfate were the most significant factors, whereas the other medium components were not important within the levels tested. Then, the method of steepest ascent was employed to approach the proximity of optimum. This task was followed by a central composite design to develop a response surface for medium optimization. The optimum medium composition for lysozyme production was found to be: starch 34 g/L, peptone 34 g/L, ammonium sulfate 11.9 g/L, yeast extract 0.5 g/L, and CaCl₂.2H₂O 0.5 g/L. This medium was projected to produce theoretically 212 mg/L lysozyme. Using this optimized medium, an experimentally observed maximum lysozyme concentration of 209±18 mg/L verified the applied methodology. A second optimization approach was based on metabolic flux analysis (MFA). A comprehensive metabolic network comprising three intracellular compartments (cytoplasm, mitochondrion and peroxisome) was developed for Aspergillus niger. The metabolic flux network included carbohydrate and amino acid metabolism in both anabolic and catabolic reactions. According to experimental observations, the time course of fermentation was divided into five phases, each with unique physiological properties. The network was used to form a set of linear algebraic equations based on the stoichiometry of the reactions by assuming pseudo-steady state for intracellular metabolites. The metabolic flux model consists of 137 metabolites and 287 processes, of which 181 represent biochemical conversions and 106 represent transport processes between the different compartments and the extracellular environment. In addition, due to the physiological evidence some biochemical reactions considered to be active only in one direction. Linear programming was used for optimizing of the specific growth rate as the objective function in combination with 37 measured input and output fluxes of the key metabolites to evaluate corresponding intracellular flux distributions throughout the batch fermentations. The general applicability of the methodology was evaluated by establishing commonality to optimize recombinant HEWL production. The proposed model was able to predict correctly the specific growth rate, oxygen uptake rate, and carbon dioxide evolution rate with good precision. The results of the metabolic flux and sensitivity analysis were employed for medium design. Growth was biphasic; glucose was utilized initially as the carbon source and was followed by its oxidation product, gluconate, later. Logarithmic sensitivity analysis revealed that the addition of proline, alanine and glutamate benefited growth in defined media. The experimental observations and flux analysis showed that tyrosine was a potential candidate for biomass production improvement. The two amino acids, namely proline and tyrosine benefited biomass production during the initial growth phases. Glutamate and alanine were particularly important during the latter stages of the batch process. A series of growth studies were conducted with the identified amino acids added in the medium. In these preliminary nutritional experiments the contribution to growth enhancement was 46% for proline, 23% for glutamate, and 22% for tyrosine. Model predictions were further verified by conducting batch and fed-batch fermentations in a 7- liter bioreactor. The programmed addition of four amino acids (proline, glutamate, alanine, and tyrosine) according to a predetermined schedule resulted in a 44% improvement in biomass and 41% improvement in recombinant protein production. The experiments also confirmed the model prediction that extra amount of amino acids besides the identified ones would not significantly enhance biomass and the recombinant protein production. A computer-based control system was developed for the on-line monitoring and control of the major state variables (e.g., temperature, pH, and DO) during the time course of fermentation. The graphical programming environment, LabVIEW was used to acquire and integrate these variables in a supervisor computer. The temperature of the bioreactor during sterilization and fermentation was controlled using a cascade methodology. The controller parameters of the master and slave loops were determined experimentally to yield a smooth response with minimum overshoot of both the bioreactor and jacket temperatures. The program scheduled various required steps in an established order during the fermentation. This feature of the software guarantees that every necessary operation will be met. The graphical representation of the process is displayed on the screen and helps the user to follow the process and perform the required adjustments. Furthermore, different variables can be observed simultaneously and saved in text or spreadsheet files for further analysis.

Made available in DSpace on 2016-06-02T19:55:33Z (GMT). No. of bitstreams: 1 4672.pdf: 1519614 bytes, checksum: a835ffbdf3a94ccbfaa789a3611d3aa6 (MD5) Previous issue date: 2012-09-28 / Universidade Federal de Sao Carlos / Biosurfactants are a surface-active chemical compounds synthesized by microorganisms. These compounds have many advantages when compared to their chemically synthesized counterparts as specific action, low toxicity, higher biodegradability, effectiveness at extreme temperatures, pH and strength ionic. They appear as promising candidates to replace chemical surfactants produced from petrochemicals. The use of renewable and low cost substrates such as agro based industrial wastes is one of the attractive strategies for economical large scale biosurfactants production. In this work, it was evaluated glycerol, a co-product of biodiesel production, as carbon source for biosurfactant production. Two microorganisms, Pseudomonas aeruginosa MSCIC02 and Bacillus subtilis LAMI009, both isolated from environmental sources, were used thorough this work. In the first part of the work experiments were carried out in shake flasks using P. aeruginosa. The results showed that the increase in nitrogen source (sodium nitrate) and the decrease in the carbon source (glycerin) favored rhamnolipids production. In the range studied, the maximum biosurfactant concentration obtained was 2.3 g⋅L-1 (C/N ratio 12). The effect of nitrogen concentration on the biosynthesis of rhamnolipids and pH behavior as a function of the nitrate concentration in the cultures indicated that this strain probably carried a denitrification route favoring the production of rhamnolipids. Experimental runs carried out in bioreactor indicated that the integrated process of production and separation/concentration by fractionation in bubble column equipment caused many operation problems, such as the drag cell, and reducing the concentration of rhamnolipids to 0.4 g⋅L-1in the reaction medium. The kinetics of product formation was evaluated by two models. The Luedeking-Piret model was not able to represent the process. The model proposed by MERCIER et. al. (1992) could adequately describe the rhamnolipids production from P. aeruginosa strain. Emulsifying capacity of the cell-free culture medium was assessed by the emulsification index (EI24). The biosurfactant produced was able to emulsify vegetable oils as well as mineral oils. EI24 greater than 55% was reached. In the second part of the work experimental data from Bacillus subtilis LAMI009 cultivated in shake flasks showed that the growth of this strain was dependent on iv the medium supplementation with yeast extract. A change in culture medium was implemented in order to reduce the length of the lag phase. The use of inorganic nitrogen sources showed that both ammonium nitrate and ammonium sulphate reached similar values of surfactin concentration and volumetric productivity. It was obtained 35 mg⋅L-1 and 6.1 mg⋅L-1⋅h-1, respectively. Surface tension of the cell-free culture medium was similar for both nitrogen sources. The minimal value obtained was 29.7 mN⋅m-1. Sodium nitrate was found to be an adequate nitrogen source for cell growth. However, in these assays low productivity and low surface tension reduction were obtained when compared to the other nitrogen sources evaluated. The supplementation of the culture medium with yeast extract improves the surfactin concentration (60.0 mg⋅L-1) and volumetric productivity (5.2 mg⋅L-1⋅h-1). In this assay the surface tension reached 28.1 mN⋅m-1. The inoculum size had a great influence on cell growth and production of surfactin. When 2% (v/v) of inoculum was used the surfactin concentration and volumetric productivity obtained were 148.2 mg⋅L-1 e 14.22 mg⋅L-1⋅h-1, respectively. The search for genes responsible for production of lipopeptides surfactin and iturine indicated the presence of the genes lpa14 and ituD in B. subtilis LAMI009 genome. Analysis of the chromatography profile of methanol extracts of the lipopeptides from culture medium with ammonium nitrate and sodium nitrate as nitrogen source showed characteristic peaks of the surfactin and iturine. Thereby, it is believed that this strain is a co-producer of both surfactin and iturine. Emulsifying capacity of the cell-free culture medium showed higher stability with the media that employed ammonium nitrate and sodium nitrate as nitrogen source. It was obtained EI24 of 65% with n-hexadecane and 45% with kerosene. The acid precipitation of biosurfactant from the cell-free culture medium showed that this prepurification step promoted an increase in the emulsifying capacity of the mixture of lipopeptides synthesized by B. subtilis LAMI009. The aqueous solution of crude biosurfactant was able to emulsify naphthenic oils, vegetable oils, and an aromatic hydrocarbon. Values of EI24 greater than 65% were obtained. Emulsions formed with naphthenic oils were more stable according to droplet-size distribution. The smaller the size of droplets, the more stable was the emulsion. / Biossurfactantes são compostos químicos tensoativos sintetizados por microrganismos. Estes compostos possuem muitas vantagens quando comparados com seus equivalentes sintetizados quimicamente como ação específica, baixa toxicidade, alta biodegradabilidade, efetividade em condições extremas de temperatura, pH e força iônica. Apresentam-se como substitutos promissores aos surfactantes químicos derivados da indústria do petróleo. A utilização de substratos renováveis e de baixo custo, como os resíduos agroindustriais, consiste em um dos fatores mais importantes para a viabilização econômica da produção destes compostos em escala industrial. Neste trabalho avaliou-se o uso da glicerina, um coproduto da produção de biodiesel, como fonte de carbono para produção de biossurfactante. Dois microrganismos, Pseudomonas aeruginosa MSIC02 e Bacillus subtilis LAMI009, ambos isolados a partir de amostras ambientais, foram empregados neste trabalho. Na primeira parte do trabalho experimentos realizados em frascos agitados com a P. aeruginosa mostraram que o aumento da produtividade de ramnolipídeos foi favorecido pelo aumento da concentração da fonte de nitrogênio (nitrato de sódio) e pela redução da concentração da fonte de carbono (glicerina). Na faixa estudada a concentração máxima de biossurfactante obtida foi de 2,3 g⋅L-1 (razão C/N de 12). O efeito da concentração de nitrogênio sobre a biossíntese de ramnolipídeos e o comportamento do pH em função da concentração de nitrato durante os cultivos indicou que esta cepa possivelmente realizou uma rota denitrificante favorecendo a produção de ramnolipídeos. Os cultivos realizados em biorreator indicaram que o processo de produção integrado a extração/concentração por fracionamento em coluna de bolhas acarretou diversos problemas operacionais, como o arraste de células, e a redução da concentração de ramnolipídeos no meio reacional para 0,4 g⋅L-1. Foram avaliados dois modelos cinéticos de formação de produto para os ensaios realizados. O modelo de Luedeking-Piret não apresentou boa representatividade do processo. O modelo proposto por MERCIER et al. (1992) mostrou-se mais adequado para representar a produção de ramnolipídeos pela cepa estudada. A avaliação da capacidade emulsificante do meio de cultivo livre de células mostrou que o biossurfactante produzido pela P. aeruginosa teve um desempenho eficiente, sendo capaz de emulsificar óleos de origem vegetal e mineral e atingir índice de emulsificação (IE24) maior que 55 %. Na segunda parte do trabalho, cultivos realizados em frascos agitados para avaliação da produção de biossurfactantes lipopeptídeos por B. subtilis LAMI009 indicaram que o crescimento desta cepa foi dependente da suplementação do meio com extrato de levedura. Uma adaptação ao meio de fermentação foi necessária para eliminar a extensa fase lag durante o processo fermentativo. A utilização de fontes de nitrogênio inorgânicas mostrou que tanto o nitrato de amônio quanto o sulfato de amônio apresentaram valores de concentração de surfactina e produtividade volumétrica da ordem de 35 mg⋅L-1 e 6,1 mg⋅L-1⋅h-1, respectivamente. A tensão superficial do meio de cultivo livre de células também foi semelhante para ambas fontes de nitrogênio, cujo valor mínimo foi 29,7 mN⋅m-1. O nitrato de sódio foi fonte de nitrogênio adequada para o crescimento celular, entretanto apresentou baixa produtividade quando comparado com as demais fontes de nitrogênio avaliadas. Com a suplementação do meio de cultivo com extrato de levedura ii obteve-se maior concentração de surfactina (60,0 mg⋅L-1) e produtividade volumétrica (5,2 mg⋅L-1⋅h-1) e menor tensão superficial (28,1 mN⋅m-1) relativamente ao meio de cultivo contendo fonte de nitrogênio inorgânica. O tamanho do inóculo exerceu grande influência sobre a concentração de surfactina e a produtividade volumétrica. Quando se utilizou 2% (v/v) de inóculo a concentração de surfactina e a produtividade volumétrica alcançaram valores de 148,2 mg⋅L-1 e 14,22 mg⋅L-1⋅h-1, respectivamente. A pesquisa de genes responsáveis pela produção dos lipopeptídeos surfactina e iturina indicou a presença dos genes lpa14 e ituD no genoma da linhagem B. subtilis LAMI009. A avaliação do perfil cromatográfico dos extratos metanólicos de lipopeptídeos obtidos a partir dos cultivos com as fontes de nitrogênio nitrato de amônio e nitrato de sódio apresentou picos característicos de outro lipopeptídeo além da surfactina, a iturina,. Portanto, acredita-se que esta linhagem é uma co-produtora de surfactina e iturina. A capacidade emulsificante do meio de cultivo livre de células apresentou maior estabilidade com os cultivos com nitrato de amônio e nitrato de sódio, obtendo-se IE24 de 65 % com n-hexadecano e 45 % com querosene. A separação do biossurfactante por precipitação ácida a partir do meio de cultivo livre de células mostrou que esta etapa de pré-purificação promoveu um aumento da capacidade emulsificante da mistura de lipopeptídeos sintetizada por B. subtilis LAMI009. A solução aquosa do biossurfactante bruto foi capaz de emulsificar óleos naftênicos, óleos vegetais e um hidrocarboneto aromático, apresentando IE24 maiores que 65 % com os óleos avaliados. As emulsões formadas com óleos naftênicos, utilizados como base para lubrificantes, foram mais estáveis. Quanto menor o tamanho das gotas mais estável foi a emulsão formada.