A pesquisa que ora se apresenta visou estabelecer as condições nutricionais adequadas para o uso do sedimento do estuário de Santos - São Vicente do Estado de São Paulo, como inóculo no reator anaeróbio horizontal de leito fixo (RAHLF) no processo de degradação anaeróbia do pentaclorofenol (PCP) em busca da aplicação da tecnologia em escala real, assim como identificar grupos microbianos envolvidos no processo. Para tanto, sedimento do estuário de Santos-São Vicente, com características metanogênicas foi utilizado. Os microrganismos provenientes do sedimento estuarino foram enriquecidos sob condições metanogênicas e halofílicas, visando a utilização do sedimento como inoculo nos ensaios nutricionais e na operação dos reatores do tipo RAHLF. O meio de cultivo salino Biota, suplementado com glicose e formiato, foi utilizado para o desenvolvimento da comunidade microbiana metanogênica halofílica. Testes de degradação do PCP foram realizados previamente sob diferentes concentrações de nitrogênio e fósforo, com vistas a uma melhor compreensão da relação N:P adequada para o processo anaeróbio. Os resultados provenientes do acompanhamento da diversidade microbiana do domínio Bacteria nas diferentes relações testadas indicaram a seleção de distintas comunidades microbianas, resultando em diferentes velocidades de degradação do PCP. A relação N:P de 10:1 foi a que apresentou melhores resultados, pois além da rápida degradação do PCP quando comparada com as outras relações, apresentou a maior diversidade de microrganismos. Posteriormente, o sistema RAHLF foi operado com vazão média afluente de aproximadamente 44 mL/hora, com meio mineral salino Biota (DQO:N:P de 1000:130:45) para R1 e com a alteração para relação DQO:N:P de 1000:10:1 para R2. Duas diferentes estratégias foram adotadas para partida dos reatores. Para R1, optou-se por acrescentar PCP na concentração inicial de 10,0 mg/L, durante 110 dias causando desestabilização da metanogênese e acúmulo de PCP, requerendo intervenção para recuperação do reator pelo período de 90 dias. Na partida do RAHLF 2, optou-se pelo aumento gradual de concentração do PCP de 0,5 mg/L a 12,0 mg/L durante 52 dias. Após estabelecimento da metanogêsenese, R1 foi alimentado durante 270 dias com 5,0 mg PCP/L, durante 41 dias com 8,0 mg/L e 59 dias com 12 mg/L. O balanço de massa no reator RAHLF 1 demonstrou que 0,52% do PCP adicionado saiu no efluente e que não ocorreu adsorção no sistema. 22,34 mg de 2,4,6 TCP, intermediário da degradação do PCP, ficaram adsorvidos na biopartícula. Os resultados das análises de diversidade microbiana apontaram para mudança da comunidade microbiana do domínio Bacteria ao longo do período operacional e morfologias de bacilos fluorescentes semelhantes a Methanobacterium sp estiveram presentes no reator. No RAHLF 2, a degradação do PCP foi de 100%, até a concentração de 10,0 mg/L. No final da fase com 12,0 mg PCP/L, a concentração no efluente foi de 1,4 mg PCP/L, com eficiência média de remoção de 93,2 \'+ ou -\' 5,5%. 2,4,6 TCP foi o intermediário principal no efluente do reator. 4,06% do PCP adicionado ao sistema foram encontradas no efluente e 15,94% ficaram adsorvidas nas biopartículas do reator. Portanto, considera-se que 80% do PCP adicionado sofreu degradação anaeróbia microbiana. A presença dos microrganismos Methanocalcullus e Methanosaeta na fase final de operação do RAHLF 2 e determinadas no sedimento coletado foi considerada fundamental para manter estabilidade do reator. Essa descoberta contribui com informações sobre a real diversidade microbiana de ecossistemas tropicais, sobretudo em habitats anaeróbios, bem como sobre as condições nutricionais e os procedimentos necessários para confiná-la em reatores e usá-la em processos de biorremediação. / The research presented here aimed to determine the optimal nutritional conditions for the use of sediment from the Santos-São Vicente estuary in the state of São Paulo, Brazil, as an inoculum for a horizontal-flow anaerobic immobilized biomass reactor (HAIB) applied to the anaerobic degradation of pentachlorophenol (PCP), seeking to apply the technology on the real scale and to identify the microbial groups involved in the process. To this end, sediment with methanogenic characteristics from the Santos-São Vicente estuary was used. The microorganisms from the estuarine sediment were enriched under methanogenic and halophilic conditions, aiming to use the sediment as an inoculum in nutritional assays and in the operation of HAIB reactors. Biota saline culture medium supplemented with glucose and formiate was used to develop the halophilic methanogenic microbial community. PCP degradation tests were carried out previously under different concentrations of nitrogen and phosphorus in order to gain a better understanding of the optimal N:P ratio for the anaerobic process. The findings on the microbial diversity of the domain Bacteria at the various ratios tested here indicated the selection of distinct microbial communities, resulting in different PCP degradation velocities. The N:P ratio utilized was 10:1 since it presented the best results not only in terms of faster PCP degradation than the other ratios but also highest diversity of microorganisms. The HAIB reactor was then operated with a mean inflow of approximately 44 mL/hour, using the biota saline mineral medium with a COD:N:P ratio of 1000:130:45 in R1 (reactor 1) and a COD:N:P ratio of 1000:10:1 in R2. Two distinct strategies were adopted to start up the reactors. In R1 PCP was added at an initial concentration of 10.0 mg/L for 100 days, causing destabilization of the methanogenesis and accumulation of PCP, requiring a 90-day intervention for the reactor\'s recovery. To start up R2, the PCP concentration was increased gradually from 0.5 mg/L to 12.0 mg/L for 52 days. After methanogenesis was established, R1 was fed for 270 days with 5.0 mg of PCP/L, followed by 41 days with 8.0 mg/L and 59 days with 12 mg/L. The mass balance in R1 indicated that 0.52% of the added PCP exited through the reactor\'s outflow and that adsorption of the system did not occur. 22.34 mg of 2,4,6 TCP, an intermediary of PCP degradation, was adsorbed in the bioparticles. The results of the analysis of microbial diversity indicated a change in the microbial community of the domain Bacteria along the operational period, with fluorescent bacilli morphologies resembling Methanobacterium sp present in the reactor. PCP degradation in R2 was 100% up to a concentration of 10.0 mg/L. At the end of the phase with 12.0 mg PCP/L, the effluent concentration was 1.4 mg PCP/L, with a mean removal efficiency of 93.2 \'+ or -\' 5,5%. 2,4,6 TCP was the main intermediary in the reactor\'s effluent. 4.06% of the PCP added to the system was found in the effluent and 15.94% was absorbed in the bioparticles of the reactor. Therefore, it was concluded that 80% of the added PCP underwent microbial anaerobic degradation. The presence of Methanocalcullus and Methanosaeta microorganisms in the final operating phase of R2, which was determined in the collected sediment, was considered fundamental for maintaining the reactor\'s stability. This discovery contributes to the body of information about the real microbial diversity of tropical ecosystems, above all in anaerobic habitats, and about the nutritional conditions and procedures involved in confining these microorganisms in reactors and using them in bioremediation processes.

La pseudouridylation, l'isomérisation du résidu urine (U) en pseudouridine ([PSI]) est la modification post-transcriptionnelle la plus fréquemment retrouvée dans les ARN. Elle est catalysée par une enzyme ARN:PSI-synthase. Chez les archées et les eucaryotes, cette activité est également portée par des particules ribonucléoprotéiques à boîtes H/ACA (RNP H/ACA). Chez les archées, le complexe comprend quatre protéines invariables dont l'ARN:PSI-synthase aCBF5 et trois protéines partenaires L7Ae, aNOP10 et aGAR1, ainsi qu'un ARN guide qui cible par appariement de bases la position de l'uridine à modifier de l'ARN substrat. Le rôle des partenaires a pu être identifié par des analyses structure-fonction basées sur des approches biochimiques, biophysiques et radiocristallographiques. Au cours de ce travail, nous avons démontré l'existence de disparités fonctionnelles entre les ARN guides d'un même organisme, et l'importance de l'interaction entre L7Ae et aNOP10 pour le positionnement correct de l'ARN substrat. Nous avons testé in vitro l'assemblage et l'activité de particules reconstituées en présence d'ARN guides non conventionnels. L'étude sur la dynamique de l'ARN substrat lors de la pseudouridylation a également été abordée et a permis de déterminer que aGAR1 n'était pas nécessaire pour le mécanisme de turnover de la particule, que la température jouait un rôle crucial pour cette activité, et que la nature du nucléotide cible ainsi que la longueur de l'ARN substrat étaient des éléments importants pour la sélection de cet ARN. Nous avons également mis au point une nouvelle technique basée sur le phénomène de FRET permettant de suivre l'association de l'ARN substrat à la RNP H/ACA / Pseudouridylation reaction that consists in the isomerization of uridines (U) into pseudouridines (PSI) is the most frequent post-transcriptional modification found in RNAs. It is catalyzed by enzymes with RNA:PSI-synthase activity. In Archaea and Eukarya, ribonucleoprotein particles, the so-called box H/ACA RNPs, possess such activity. In Archaea, the box H/ACA complex comprises four invariable proteins namely the RNA:PSI-synthase aCBF5 and three protein partners L7Ae, aNOP10 and aGAR1, and specific to each RNP, an RNA acting as a guide to secure by base pairing the RNA substrate and define the position to be modify. During these last years, several crystal structures of components of archaeal H/ACA RNP and fully assembled RNP have been resolved. Complementary biochemical and biophysical studies allowed detailed structure-function analyses to identify the role of the different components. During this work we identified functional differences between two RNA guides expressed in the same archaea, and demonstrated that the interaction between L7Ae and aNOP10 is important for a correct positioning of substrate RNA. We also tested in vitro the assembly and activity of RNP reconstituted on H/ACA-like guide RNAs. We investigated dynamics of substrate RNA during the pseudouridylation. We found that aGAR1 was not necessary for the turnover of the particle, that the temperature was crucial for such activity, and that the chemical structure of the targeted residue and length of the substrate RNA were important determinants for substrate selectivity. Finally, we have also developed a new technic based on FRET adapted to monitor binding of the susbtrate RNA to the box H/ACA RNP enzyme

科学研究費補助金 研究種目:基盤研究(C)(2) 課題番号:14560051 研究代表者:浅川 晋 研究期間:2002-2003年度

A pesquisa que ora se apresenta visou estabelecer as condições nutricionais adequadas para o uso do sedimento do estuário de Santos - São Vicente do Estado de São Paulo, como inóculo no reator anaeróbio horizontal de leito fixo (RAHLF) no processo de degradação anaeróbia do pentaclorofenol (PCP) em busca da aplicação da tecnologia em escala real, assim como identificar grupos microbianos envolvidos no processo. Para tanto, sedimento do estuário de Santos-São Vicente, com características metanogênicas foi utilizado. Os microrganismos provenientes do sedimento estuarino foram enriquecidos sob condições metanogênicas e halofílicas, visando a utilização do sedimento como inoculo nos ensaios nutricionais e na operação dos reatores do tipo RAHLF. O meio de cultivo salino Biota, suplementado com glicose e formiato, foi utilizado para o desenvolvimento da comunidade microbiana metanogênica halofílica. Testes de degradação do PCP foram realizados previamente sob diferentes concentrações de nitrogênio e fósforo, com vistas a uma melhor compreensão da relação N:P adequada para o processo anaeróbio. Os resultados provenientes do acompanhamento da diversidade microbiana do domínio Bacteria nas diferentes relações testadas indicaram a seleção de distintas comunidades microbianas, resultando em diferentes velocidades de degradação do PCP. A relação N:P de 10:1 foi a que apresentou melhores resultados, pois além da rápida degradação do PCP quando comparada com as outras relações, apresentou a maior diversidade de microrganismos. Posteriormente, o sistema RAHLF foi operado com vazão média afluente de aproximadamente 44 mL/hora, com meio mineral salino Biota (DQO:N:P de 1000:130:45) para R1 e com a alteração para relação DQO:N:P de 1000:10:1 para R2. Duas diferentes estratégias foram adotadas para partida dos reatores. Para R1, optou-se por acrescentar PCP na concentração inicial de 10,0 mg/L, durante 110 dias causando desestabilização da metanogênese e acúmulo de PCP, requerendo intervenção para recuperação do reator pelo período de 90 dias. Na partida do RAHLF 2, optou-se pelo aumento gradual de concentração do PCP de 0,5 mg/L a 12,0 mg/L durante 52 dias. Após estabelecimento da metanogêsenese, R1 foi alimentado durante 270 dias com 5,0 mg PCP/L, durante 41 dias com 8,0 mg/L e 59 dias com 12 mg/L. O balanço de massa no reator RAHLF 1 demonstrou que 0,52% do PCP adicionado saiu no efluente e que não ocorreu adsorção no sistema. 22,34 mg de 2,4,6 TCP, intermediário da degradação do PCP, ficaram adsorvidos na biopartícula. Os resultados das análises de diversidade microbiana apontaram para mudança da comunidade microbiana do domínio Bacteria ao longo do período operacional e morfologias de bacilos fluorescentes semelhantes a Methanobacterium sp estiveram presentes no reator. No RAHLF 2, a degradação do PCP foi de 100%, até a concentração de 10,0 mg/L. No final da fase com 12,0 mg PCP/L, a concentração no efluente foi de 1,4 mg PCP/L, com eficiência média de remoção de 93,2 \'+ ou -\' 5,5%. 2,4,6 TCP foi o intermediário principal no efluente do reator. 4,06% do PCP adicionado ao sistema foram encontradas no efluente e 15,94% ficaram adsorvidas nas biopartículas do reator. Portanto, considera-se que 80% do PCP adicionado sofreu degradação anaeróbia microbiana. A presença dos microrganismos Methanocalcullus e Methanosaeta na fase final de operação do RAHLF 2 e determinadas no sedimento coletado foi considerada fundamental para manter estabilidade do reator. Essa descoberta contribui com informações sobre a real diversidade microbiana de ecossistemas tropicais, sobretudo em habitats anaeróbios, bem como sobre as condições nutricionais e os procedimentos necessários para confiná-la em reatores e usá-la em processos de biorremediação. / The research presented here aimed to determine the optimal nutritional conditions for the use of sediment from the Santos-São Vicente estuary in the state of São Paulo, Brazil, as an inoculum for a horizontal-flow anaerobic immobilized biomass reactor (HAIB) applied to the anaerobic degradation of pentachlorophenol (PCP), seeking to apply the technology on the real scale and to identify the microbial groups involved in the process. To this end, sediment with methanogenic characteristics from the Santos-São Vicente estuary was used. The microorganisms from the estuarine sediment were enriched under methanogenic and halophilic conditions, aiming to use the sediment as an inoculum in nutritional assays and in the operation of HAIB reactors. Biota saline culture medium supplemented with glucose and formiate was used to develop the halophilic methanogenic microbial community. PCP degradation tests were carried out previously under different concentrations of nitrogen and phosphorus in order to gain a better understanding of the optimal N:P ratio for the anaerobic process. The findings on the microbial diversity of the domain Bacteria at the various ratios tested here indicated the selection of distinct microbial communities, resulting in different PCP degradation velocities. The N:P ratio utilized was 10:1 since it presented the best results not only in terms of faster PCP degradation than the other ratios but also highest diversity of microorganisms. The HAIB reactor was then operated with a mean inflow of approximately 44 mL/hour, using the biota saline mineral medium with a COD:N:P ratio of 1000:130:45 in R1 (reactor 1) and a COD:N:P ratio of 1000:10:1 in R2. Two distinct strategies were adopted to start up the reactors. In R1 PCP was added at an initial concentration of 10.0 mg/L for 100 days, causing destabilization of the methanogenesis and accumulation of PCP, requiring a 90-day intervention for the reactor\'s recovery. To start up R2, the PCP concentration was increased gradually from 0.5 mg/L to 12.0 mg/L for 52 days. After methanogenesis was established, R1 was fed for 270 days with 5.0 mg of PCP/L, followed by 41 days with 8.0 mg/L and 59 days with 12 mg/L. The mass balance in R1 indicated that 0.52% of the added PCP exited through the reactor\'s outflow and that adsorption of the system did not occur. 22.34 mg of 2,4,6 TCP, an intermediary of PCP degradation, was adsorbed in the bioparticles. The results of the analysis of microbial diversity indicated a change in the microbial community of the domain Bacteria along the operational period, with fluorescent bacilli morphologies resembling Methanobacterium sp present in the reactor. PCP degradation in R2 was 100% up to a concentration of 10.0 mg/L. At the end of the phase with 12.0 mg PCP/L, the effluent concentration was 1.4 mg PCP/L, with a mean removal efficiency of 93.2 \'+ or -\' 5,5%. 2,4,6 TCP was the main intermediary in the reactor\'s effluent. 4.06% of the PCP added to the system was found in the effluent and 15.94% was absorbed in the bioparticles of the reactor. Therefore, it was concluded that 80% of the added PCP underwent microbial anaerobic degradation. The presence of Methanocalcullus and Methanosaeta microorganisms in the final operating phase of R2, which was determined in the collected sediment, was considered fundamental for maintaining the reactor\'s stability. This discovery contributes to the body of information about the real microbial diversity of tropical ecosystems, above all in anaerobic habitats, and about the nutritional conditions and procedures involved in confining these microorganisms in reactors and using them in bioremediation processes.

The high affinity, ATP-dependent K+ uptake system KdpFABC of Halobacterium salinarum, is highly induced under K+ limitation. In contrast to the well-characterized Kdp system in Escherichia coli, in which the kdpFABC genes are transcriptionally regulated by the sensor kinase/response regulator system KdpD/KdpE, transcriptional regulation of the kdp genes in H. salinarum was unknown due to the absence of halobacterial homologues of KdpD/KdpE. Furthermore, the physiological relevance of the KdpFABC K+ uptake system of H. salinarum was puzzling, since hypersaline habitats usually comprise K+ concentrations which do not induce kdp expression. In order to analyze the regulation of kdp gene expression, it was essential to gain information about the transcriptional unit(s) involved. Northern blotting, primer extension analysis and real-time RT-PCR revealed the presence of a polycistronic leaderless kdpFABCQ transcript with a putative kdp terminator or at least a potential mRNA processing site downstream of kdpQ. Furthermore, promoter truncation studies verified the so far only predicted basal transcription elements together with an upstream-located operator sequence. Since deletions of this putative operator sequence did not lead to a constitutive expression, a further component has to be involved in the regulation of the kdpFABCQ genes. However, truncation and scanning mutagenesis analyses of the kdp promoter as well as translational fusions of a halophilic beta-galactosidase to the kdp promoter excluded an additional regulatory element up- or downstream of the basal transcription elements and in the kdp-coding region. These results lead to speculations of multiple basal transcription factors to be involved. Furthermore, an inducible expression vector (shuttle vector) was constructed based on the promoter of the kdpFABCQ operon due to its, K+-sensitive features. Inducible expression systems are yet not available for H. salinarum. The resulting, replicating vector pKIX is functional and enables a K+-dependent expression from the kdp promoter with rather high induction ratios of 50-fold. Expression levels could further be improved by plasmid- and additional chromosomally encoded kdpQ and mutations generated in the kdp promoter. Since transcript levels from pKIX were found to be independent of differential target genes, the general application of pKIX as an inducible expression system is strongly supported and pKIX could, thus, be made accessible to the scientific community. To decipher the physiological relevance of the halobacterial Kdp system, H. salinarum was encountered to desiccation stress and salt crystal (halite) entombment. Halite crystals grown under non-inducing K+ concentrations with entombed strains of H. salinarum and H. salinarum deleted in the kdpFABCQ genes revealed a significantly reduced survival rate of the deletion strain upon recultivation. Additionally, a kdpFABCQ-inducing desiccation stress could already be determined on agar plates under non-limiting K+ concentrations. Furthermore, the cell morphology of H. salinarum entrapped in halite crystals resembled that of H. salinarum grown under K+-limiting conditions. Therefore, the Kdp system promotes survival of H. salinarum under desiccation stress. Furthermore, the Kdp system could be identified as at least one of the systems important for long-term survival of H. salinarum in halite.