To study the regulation of gene expression, a good reporter system is very useful. The lack of a good reporter system for the solvent-producing clostridia hindered the progress of research in this area. The objective of this study was to develop a reporter system to facilitate the elucidation of the control mechanism for the expression of solvent-producing genes. A potential reporter gene was found in Clostridium beijerinckii NRRL B593, which contains an adh gene encoding a primary-secondary alcohol dehydrogenase and this adh gene is not present in Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NRRL B592. The adh gene was cloned into the E. coli -Clostridium shuttle vectors to generate plasmids. An electro-transformation procedure was developed for C. beijerinckii NRRL B592. Shuttle plasmids were transformed into C. beijerinckii NRRL B592 or C. acetobutylicum ATCC 824. The copy number of the plasmids in C. beijerinckii was 4. Isopropanol production suggested that the adh gene was expressed in transformants of C. acetobutylicum ATCC 824 and C. beijerinckii NRRL B592. Northern analysis indicated that the expression of the adh gene was regulated at the transcriptional level in the transformants of C. beijerinckii. The transcriptional start site for the adh gene was identified by the primer extension method. A promoter-probing vector was constructed and tested with the promoter from the ferredoxin(fer) gene. The expression of the adh gene under the control of the fer promoter was at a low and similar level during acidogenesis and solventogenesis. The expression pattern of the adh gene under the control of the promoter of the adh gene differed from that under the control of the promoter of the fer gene. / Ph. D.

Clostridium beijerinckii is a spore-forming, obligate anaerobe that is capable of producing butanol, acetone and isopropanol. These industrial chemicals are traditionally known as solvents. The regulation of solventogenic fermentation is linked to the onset of sporulation, so that by the time the organism begins to produce solvents, it is also entering into spore formation and metabolic slowdown. The goal of this research project was to study the effect of placing the solvent-production genes from C. beijerinckii under the control of constitutive promoters from other genes, in an attempt to allow an earlier start of butanol production during the growth phase than is the case with the wild-type cells. The aldehyde dehydrogenase from C. beijerinckii NRRL B593 (ald) and alcohol dehydrogenase from C. beijerinckii NRRL B592 (adhA) were placed under the control of the promoter from the acid-producing operon (the BCS operon) in one vector, and under the control of the promoter from the ferredoxin gene in another. In both cases, aldehyde dehydrogenase activity was produced earlier in the growth phase in transformed cells, but alcohol dehydrogenase activity was not. The adhA gene from C. beijerinckii NRRL B592 was paired with the adhB gene from the same organism in a third vector, both under the control of the promoter from the BCS operon. In cells transformed with this vector, alcohol dehydrogenase activity was observed earlier in the growth phase than it was in wild-type NRRL B592 cells. / Ph. D.

A digestão anaeróbia termofílica é uma opção vantajosa para efluentes descartados a altas temperaturas, além de estimular rotas mais eficientes de produção de H2. No entanto, os resultados da literatura divergem bastante, os rendimentos de H2 são inferiores ao valor teórico possível e poucos estudos avaliaram diferentes configurações para indicar a mais eficiente. Assim, este estudo avaliou a produção de H2 a partir da sacarose em três tipos de reator: reator anaeróbio de fluxo ascendente e manta de lodo (UASB), reator tubular de fluxo ascendente com leito empacotado (TCS) e sem material suporte (TSS), operados a 55°C. Os tempos de detenção hidráulica (TDH) aplicados ao reator UASB foram 12, 6 e 2 h e aos reatores TCS e TSS foram 2 e 0,5 h. Pré-tratamento térmico (100°C por 15 min) foi aplicado ao inóculo metanogênico do UASB e TCS e TSS foram auto inoculados. O efeito de nutrientes e a concentração nutricional ótima para a produção de H2 foram investigados através de ensaios em batelada. Com TDH de 2 h, o material suporte afetou a transferência de massa, resultando em menor teor de H2 no biogás quando presente, porém, maior conversão de sacarose e produção de H2. O pré-tratamento térmico não inibiu a metanogênese, sendo as condições operacionais mais importantes para a seleção dos microrganismos. TCS e TSS com TDH de 0,5 h apresentaram produção de H2 similar e o material suporte afetou apenas as rotas metabólicas. Entre todas as operações, TCS e UASB com TDH de 2 h alcançaram os maiores valores de rendimento de H2 (YH2), respectivamente, 1,99 ± 0,36 e 2,56 ± 0,84 molH2.mol-sac-1, através da via metabólica do etanol. TCS2 também demonstrou estabilidade e, apesar de o U2 ter gerado maiores porcentagens de H2 no biogás, pode ser apontado como o mais eficiente para a produção de H2. A relação C:N:P, Fe+2 e Ni+2 tiveram efeito significativo sobre a produção de H2, e YH2 ótimo foi estimado para concentrações de 4,53 mgFe+2.L-1 e 0,045 mgNi+2.L-1. / The thermophilic anaerobic digestion is a suitable option for wastewater discharged at high temperatures; in addition, it is suitable for more efficient pathways for H2 production. However, the results found in literature have divergences; the H2 yields are lower than the theoretical possible value and only few studies evaluated different types of reactors and defined the more advantageous one. Therefore, this study evaluated H2 production from sucrose in three types of reactor: upflow anaerobic sludge blanket (UASB), upflow tubular reactor with packed-bed (TCS) and without support materials (TSS), operated at 55°C. The hydraulic retention time (HRT) applied to UASB reactor was 12, 6 and 2h and to TCS and TSS was 2 and 0.5h.Thermal pretreatment (at 100°C, for 15 min) was applied to the methanogenic inoculum of UASB and TCS and TSS was inoculated through natural fermentation process. The effect of nutrients and the optimal concentration of t nutrients for H2 production were evaluated through batch assays. At HRT of 2h, the support material affected the mass transferring, leading to lower content of H2 in the biogas when it is used; however, in this condition it was found higher sucrose conversion and H2 production. The operational conditions showed to be more efficient for methanogenesis than pretreatment. TCS and TSS at HRT of 0.5h presented similar H2 production and the support material affected only the metabolic pathways. Among all the conditions assessed, TCS and UASB at HRT of 2h reached the highest values of H2 yield highest YH2, respectively, 1.99 ± 0.36 and 2.56 ± 0.84 molH2.mol-sac-1, through ethanol pathway. TCS2 demonstrated stability production also and, despite the U2 have achieved higher percentage of H2 in biogas, it can be pointed out as more efficient for H2 production. The ratio C:N:P, Fe+2 and Ni+2 showed significant effect on H2 production, and the optimal YH2 was estimated for 4.53 mgFe+2.L-1 e 0.045 mgNi+2.L-1.

A digestão anaeróbia termofílica é uma opção vantajosa para efluentes descartados a altas temperaturas, além de estimular rotas mais eficientes de produção de H2. No entanto, os resultados da literatura divergem bastante, os rendimentos de H2 são inferiores ao valor teórico possível e poucos estudos avaliaram diferentes configurações para indicar a mais eficiente. Assim, este estudo avaliou a produção de H2 a partir da sacarose em três tipos de reator: reator anaeróbio de fluxo ascendente e manta de lodo (UASB), reator tubular de fluxo ascendente com leito empacotado (TCS) e sem material suporte (TSS), operados a 55°C. Os tempos de detenção hidráulica (TDH) aplicados ao reator UASB foram 12, 6 e 2 h e aos reatores TCS e TSS foram 2 e 0,5 h. Pré-tratamento térmico (100°C por 15 min) foi aplicado ao inóculo metanogênico do UASB e TCS e TSS foram auto inoculados. O efeito de nutrientes e a concentração nutricional ótima para a produção de H2 foram investigados através de ensaios em batelada. Com TDH de 2 h, o material suporte afetou a transferência de massa, resultando em menor teor de H2 no biogás quando presente, porém, maior conversão de sacarose e produção de H2. O pré-tratamento térmico não inibiu a metanogênese, sendo as condições operacionais mais importantes para a seleção dos microrganismos. TCS e TSS com TDH de 0,5 h apresentaram produção de H2 similar e o material suporte afetou apenas as rotas metabólicas. Entre todas as operações, TCS e UASB com TDH de 2 h alcançaram os maiores valores de rendimento de H2 (YH2), respectivamente, 1,99 ± 0,36 e 2,56 ± 0,84 molH2.mol-sac-1, através da via metabólica do etanol. TCS2 também demonstrou estabilidade e, apesar de o U2 ter gerado maiores porcentagens de H2 no biogás, pode ser apontado como o mais eficiente para a produção de H2. A relação C:N:P, Fe+2 e Ni+2 tiveram efeito significativo sobre a produção de H2, e YH2 ótimo foi estimado para concentrações de 4,53 mgFe+2.L-1 e 0,045 mgNi+2.L-1. / The thermophilic anaerobic digestion is a suitable option for wastewater discharged at high temperatures; in addition, it is suitable for more efficient pathways for H2 production. However, the results found in literature have divergences; the H2 yields are lower than the theoretical possible value and only few studies evaluated different types of reactors and defined the more advantageous one. Therefore, this study evaluated H2 production from sucrose in three types of reactor: upflow anaerobic sludge blanket (UASB), upflow tubular reactor with packed-bed (TCS) and without support materials (TSS), operated at 55°C. The hydraulic retention time (HRT) applied to UASB reactor was 12, 6 and 2h and to TCS and TSS was 2 and 0.5h.Thermal pretreatment (at 100°C, for 15 min) was applied to the methanogenic inoculum of UASB and TCS and TSS was inoculated through natural fermentation process. The effect of nutrients and the optimal concentration of t nutrients for H2 production were evaluated through batch assays. At HRT of 2h, the support material affected the mass transferring, leading to lower content of H2 in the biogas when it is used; however, in this condition it was found higher sucrose conversion and H2 production. The operational conditions showed to be more efficient for methanogenesis than pretreatment. TCS and TSS at HRT of 0.5h presented similar H2 production and the support material affected only the metabolic pathways. Among all the conditions assessed, TCS and UASB at HRT of 2h reached the highest values of H2 yield highest YH2, respectively, 1.99 ± 0.36 and 2.56 ± 0.84 molH2.mol-sac-1, through ethanol pathway. TCS2 demonstrated stability production also and, despite the U2 have achieved higher percentage of H2 in biogas, it can be pointed out as more efficient for H2 production. The ratio C:N:P, Fe+2 and Ni+2 showed significant effect on H2 production, and the optimal YH2 was estimated for 4.53 mgFe+2.L-1 e 0.045 mgNi+2.L-1.

Genome-scale modeling and new strategies for constraining these models were applied in this research to find new insights into cellular metabolism and identify potential metabolic engineering strategies. A newly updated genome-scale model for Clostridium acetobutylicum, iMM864, was constructed, largely based on the previously published iRS552 model. The new model was built using a newly developed genome-scale model database, and updates were derived from new insights into clostridial metabolism. Novel methods of proton-balancing and setting flux (defined as reaction rate (mmol/g biomass/hr)) ratio constraints were applied to create simulations made with the iMM864 model approximate observed experimental results. It was determined that the following constraints must be applied to properly model C. acetobutylicum metabolism: (1) proton-balancing, (2) constraining the specific proton flux (SPF), and (3) installing proper flux ratio constraints. Simulations indicate that the metabolic shift into solventogenesis is not due to optimizing growth at different pH conditions. However, they provide evidence that C. acetobutylicum has developed strictly genetically regulated solventogenic metabolic pathways for the purpose of increasing its surrounding pH to decrease the toxic effects of high proton concentrations. Applying a ratio constraint for the P/O ratio (a measure of aerobic respiratory efficiency) to the iAF1260 genome-scale model of E. coli K12 MG1655 was explored. Relationships were found between: (1) the P/O ratio, (2) the SPF, (3) the growth rate, and (4) the production of acetate. As was expected, higher acetate production correlates with lower P/O ratios, while higher growth correlates with higher P/O ratios. For the first time, a genome-scale model was able to quantify this relationship and targeting both the P/O ratio and the SFP is required to produce an E. coli K12 strain with either (i) maximized growth rate (and minimized acetate production) or (ii) maximized acetate production (at the expense of cell growth). A gene knockout mutant, Î ndh, was created with E. coli BL-21 to study the effects of forcibly higher P/O ratios on growth. The results suggest that a metabolic bottleneck lies with the NADH-1 complex, the NADH dehydrogenase that contributes to the generation of a proton motive force. / Master of Science

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