Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element.

Flagellin is one of the most abundant proteins in motile bacteria, yet its expression requires a low abundance sigma factor (sigma 28). We show that transcription from the Bacillus subtilis flagellin promoter is stimulated 20-fold by an upstream A+T-rich region [upstream promoter (UP) element] both in vivo and in vitro. This UP element is contacted by sigma 28 holoenzyme bound at the flagellin promoter and binds the isolated alpha 2 subassembly of RNA polymerase. The UP element increases the affinity of RNA polymerase for the flagellin promoter and stimulates transcription when initiation is limited by the rate of RNA polymerase binding. Comparison with other promoters in the flagellar regulon reveals a bipartite architecture: the -35 and -10 elements confer specificity for sigma 28, while promoter strength is determined largely by upstream DNA sequences.

Desempenho de bezerros leiteiros recebendo probiótico contendo Bacillus subtilis e Bacillus licheniformis

O objetivo deste estudo foi avaliar a suplementação de um probiótico composto por cepas de Bacillus subtilis e Bacillus licheniformis, fornecidos via sucedâneo lácteo, no que se refere ao escore e pH fecal, contagem de microrganismos intestinais, parâmetros sanguíneos e desempenho geral dos animais. Foram utilizados 24 animais da raça Holandês que receberam 4L/dia de sucedâneo comercial (15PB:15EE), além de livre acesso a água e concentrado inicial. O desaleitamento ocorreu na 8ª semana de vida. Os animais foram distribuídos em delineamento de blocos casualizados, em dois tratamentos: 1) Controle - sem a suplementação de probiótico; 2) Suplementação de 2g/d (1,6 x 109 UFC) de Bacillus subtilis e Bacillus licheniformis via sucedâneo lácteo. Semanalmente foram realizadas pesagens e aferições de medidas corporais (altura de cernelha, perímetro torácico e largura de garupa); e colheitas de sangue para determinação de glicose, proteína total, ureia e albumina, além de determinação de hematócrito. Foram colhidas amostras semanalmente para contagem de bactérias ácido láticas e enterobactérias e determinação de pH fecal. O monitoramento do consumo de concentrado e do escore fecal foi realizado diariamente. O peso corporal, o ganho de peso médio diário e as medidas corporais não foram alteradas (P>0,05) pela suplementação do probiótico contendo Bacillus subtilis e Bacillus licheniformis; muito embora tenham apresentado efeito significativo de idade dos animais (P<0,001). O escore fecal, pH fecal e consumo de concentrado diário também não foram afetados pela suplementação com probiótico. No entanto, o consumo de concentrado e o pH fecal sofreram influência da idade em resposta ao crescimento natural dos bezerros. A contagem de bactérias ácido láticas foi maior que número de enterobactérias durante todo o período (P<0,05). Apenas as enterobactérias sofreram efeito da idade (P<0,05), enquanto as bactérias ácido láticas permaneceram variando, porém dentro de um padrão constante. Os parâmetros sanguíneos também não foram afetados pela suplementação com probiótico (P>0,05) mas todos, com a exceção da albumina, tiveram influência da idade (P<0,001). A suplementação com o probiótico contendo Bacillus subtilis e Bacillus licheniformis via sucedâneo não apresentou benefícios no desempenho ou no metabolismo de bezerros leiteiros, bem como não reduziu a ocorrência de casos de diarreia.

Investigation of the roles of CheD in the Bacillus subtilis chemotactic signal transduction

Abstract The two-component based chemotaxis signal transduction system allows flagellated bacteria to sense their surrounding chemical environment and move towards more favorable conditions. The attractant signals can be sensed by transmembrane chemoreceptors, and then transmitted to the histidine kinase CheA. Once activated, CheA interacts with the response regulator CheY through phosphorelay, which causes a change in the rotation of the flagella. The direction of flagella rotation determines whether a cell swims straight or just tumbles. Cells also need adaptation to respond to a change in chemical concentrations, and return to their prestimulated level. Adaptation in the B. subtilis chemotaxis system is achieved by three coordinated systems: the methylation system, the CheC/CheD/CheY-p system and the CheV system. CheD, the previously identified receptor deamidase, was shown to be critical to the ability of B. subtilis to perform chemotaxis and is the main focus of this study. This study started from characterization of the enzymatic mechanism of CheD. Results showed that CheD deamidase uses a cysteine hydrolase mechanism. The catalytic triad consisting of Cys33-His50-Thr27, and Ser27 is essential for receptor recognition and binding. In addition, in this study CheC was found to inhibit CheD’s deamidase activity. Through mutant screening, Phe102 on CheD was found to be the essential site to interact with CheC. Furthermore, the CheD/CheC interaction is necessary for the robust chemotaxis in vivo as demonstrated by the cheD (F102E) mutant, which lacks the ability to swim on swarm plates. Despite its deamidase activity, we hypothesized that CheD’s main role is its involvement in the CheD-CheC-CheY-p negative feedback pathway during adaptation. In particular, CheD is likely to help stabilize the transient kinase-activating state through binding to receptors. When CheY-p level is increased, CheC-CheY-p complex may attract CheD away from receptors. In this study, CheC-CheD binding kinetics with CheY or CheYp presence was successfully obtained by a series of SPR experiments. The increased affinity of CheD for CheC in presence of CheYp but not CheY makes likely the hypothesis that CheC-CheD-CheY interact as part of a negative feedback pathway during adaptation. Last, the interaction between CheD and chemoreceptor McpC was studied in order to better understand the role of CheD in adaptation. Results showed that Q304 and Q305 on McpC are essential to recruit CheD. Additionally, the reduced levels of CheD in mcpC (Q304A) or (Q305A) mutants suggested that the dynamic interaction between CheD and receptors is vital to maintain the normal CheD level. These findings suggest more complicated roles of CheD than its previously identified function as a receptor deamidase, and will lead to a clearer picture of the coordination of the three adaptational systems in the B. subtilis chemotactic sensory transduction system.

Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis

The Bacillus subtilis DnaI, DnaB and DnaD proteins load the replicative ring helicase DnaC onto DNA during priming of DNA replication. Here we show that DnaI consists of a C-terminal domain (Cd) with ATPase and DNA-binding activities and an N-terminal domain (Nd) that interacts with the replicative ring helicase. A Zn2+-binding module mediates the interaction with the helicase and C67, C70 and H84 are involved in the coordination of the Zn2+. DnaI binds ATP and exhibits ATPase activity that is not stimulated by ssDNA, because the DNA-binding site on Cd is masked by Nd. The ATPase activity resides on the Cd domain and when detached from the Nd domain, it becomes sensitive to stimulation by ssDNA because its cryptic DNA-binding site is exposed. Therefore, Nd acts as a molecular 'switch' regulating access to the ssDNA binding site on Cd, in response to binding of the helicase. DnaI is sufficient to load the replicative helicase from a complex with six DnaI molecules, so there is no requirement for a dual helicase loader system.

The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA

The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.

Análise da viabilidade comercial de produtos à base de Bacillus subtilis e Bacillus pumilus para o controle de fitopatógenos no Brasil.

2009

Bacillus subtilis para el control del oidio de la calabaza.

2009

Caracterización funcional de las proteínas TasA y TapA en la formación de fibras de tipo amiloide en Bacillus subtilis

Las proteínas amiloides son un grupo heterogéneo de proteínas diferentes en secuencia aminoacídica, pero similares en su estructura cuaternaria: fibras enriquecidas en láminas beta, con gran estabilidad, resistencia y capacidad de unión de colorantes específicos, como el rojo congo o la thioflavina T. Estas proteínas han estado tradicionalmente asociadas a patologías neurodegenerativas en humanos como el Alzheimer o el Parkinson. Sin embargo, los miembros dentro de esta familia están ampliamente distribuidas en la naturaleza, desde bacterias hasta humanos, e intervienen en un amplio rango de funciones biológicas, motivo por el que se han denominado “amiloides funcionales”. En bacterias, los amiloides funcionales son responsables de participar en funciones muy diversas como la interacción célula-célula, con superficies abióticas, y formación de biofilms. En Bacillus subtilis, la proteína amiloide TasA es el componente proteico mayoritario de la matriz extracelular del biofilm de este microorganismo y el principal elemento que constituye las fibras amiloides, mientras que la proteína auxiliar TapA, presente en mucha menor proporción, actúa favoreciendo el ensamblaje de las mismas. Estas actúan como un andamiaje proteico donde se disponen el resto de componentes de la matriz extracelular, lo que confiere a esta estructura una mayor estabilidad y, por consiguiente, proporcionan una mayor robustez al biofilm. En este este trabajo se pretende llevar a cabo el análisis de regiones o dominios tanto de TasA como de TapA importantes para la amiloidogénesis, así como para la funcionalidad de ambas proteínas. Para ello, el estudio se ha enfocado desde un punto de vista multidisciplinar, combinando pruebas clásicas de caracterización de amiloides con técnicas de biología molecular y diversas pruebas biofísicas. Los resultados obtenidos hasta la fecha han demostrado la existencia de pequeñas secuencias, dentro de las proteínas TasA o TapA con capacidad para polimerizar en la forma de fibras, lo que muestra su importancia en el proceso de fibrilación y en la funcionalidad de ambas proteínas. En el caso de la proteína TapA, las regiones analizadas ponen de manifiesto la importancia de su extremo amino-terminal tanto en la funcionalidad de la proteína como en su interacción con TasA.

Respostas fisiológicas de pirarucu ao probiótico Bacillus subtilis (Cohn 1872).

O uso de probióticos na alimentação dos peixes pode estimular o sistema imunológico e agir na prevenção de enfermidades. O presente estudo avaliou a fisiologia de pirarucu Arapaima gigas após alimentação por 30 dias com dietas enriquecidas com probiótico Bacillus subtilis em 3 níveis de inclusão: 0 (Controle); 0,02 (BS0,02%) e 0,05% (BS0,05%) (triplicata), sendo realizada biometria e coleta de amostras de sangue. Os grupos foram comparados entre si (P<0,05). O peso, comprimento e o índice hepatossomático (IHS) dos pirarucus BS0,05% foram menores que os do Controle. As análises hematológicas e bioquímicas indicaram que BS0,02% promoveu aumento do hematócrito e da albumina, com relação aos demais grupos; e diminuição da concentração de hemoglobina corpuscular média (CHCM) e da glicose plasmática com relação ao Controle. A hemoglobina corpuscular média (HCM) e atividade respiratória dos leucócitos do BS0,05% diminuíram com relação ao Controle. BS0,02% apresentaram redução do número de leucócitos, com relação ao Controle, que refletiu na diminuição de monócitos, neutrófilos, LG-PAS e eosinófilos. Assim, os níveis de B. subtilis avaliados não promoveram crescimento ou alterações fisiológicas nos pirarucus, que indiquem melhoria do seu sistema imune.

Controle da ferrugem do cafeeiro com produtos à base de Bacillus subtilis.

1994

Cereulide producing B. cereus and amylosin producing B. subtilis and B. mojavensis : characterization of strains and toxigenicities

B. cereus is one of the most frequent occurring bacteria in foods . It produces several heat-labile enterotoxins and one stable non-protein toxin, cereulide (emetic), which may be pre-formed in food. Cereulide is a heat stable peptide whose structure and mechanism of action were in the past decade elucidated. Until this work, the detection of cereulide was done by biological assays. With my mentors, I developed the first quantitative chemical assay for cereulide. The assay is based on liquid chromatography (HPLC) combined with ion trap mass spectrometry and the calibration is done with valinomycin and purified cereulide. To detect and quantitate valinomycin and cereulide, their [NH4+] adducts, m/z 1128.9 and m/z 1171 respectively, were used. This was a breakthrough in the cereulide research and became a very powerful tool of investigation. This tool made it possible to prove for the first time that the toxin produced by B. cereus in heat-treated food caused human illness. Until this thesis work (Paper II), cereulide producing B. cereus strains were believed to represent a homogenous group of clonal strains. The cereulide producing strains investigated in those studies originated mostly from food poisoning incidents. We used strains of many origins and analyzed them using a polyphasic approach. We found that the cereulide producing B. cereus strains are genetically and biologically more diverse than assumed in earlier studies. The strains diverge in the adenylate kinase (adk) gene (two sequence types), in ribopatterns obtained with EcoRI and PvuII (three patterns), tyrosin decomposition, haemolysis and lecithine hydrolysis (two phenotypes). Our study was the first demonstration of diversity within the cereulide producing strains of B. cereus. To manage the risk for cereulide production in food, understanding is needed on factors that may upregulate cereulide production in a given food matrix and the environmental factors affecting it. As a contribution towards this direction, we adjusted the growth environment and measured the cereulide production by strains selected for diversity. The temperature range where cereulide is produced was narrower than that for growth for most of the producer strains. Most cereulide was by most strains produced at room temperature (20 - 23ºC). Exceptions to this were two faecal isolates which produced the same amount of cereulide from 23 ºC up until 39ºC. We also found that at 37º C the choice of growth media for cereulide production differed from that at the room temperature. The food composition and temperature may thus be a key for understanding cereulide production in foods as well as in the gut. We investigated the contents of [K+], [Na+] and amino acids of six growth media. Statistical evaluation indicated a significant positive correlation between the ratio [K+]:[Na+] and the production of cereulide, but only when the concentrations of glycine and [Na+] were constant. Of the amino acids only glycine correlated positively with high cereulide production. Glycine is used worldwide as food additive (E 640), flavor modifier, humectant, acidity regulator, and is permitted in the European Union countries, with no regulatory quantitative limitation, in most types of foods. B. subtilis group members are endospore-forming bacteria ubiquitous in the environment, similar to B. cereus in this respect. Bacillus species other than B. cereus have only sporadically been identified as causative agents of food-borne illnesses. We found (Paper IV) that food-borne isolates of B. subtilis and B. mojavensis produced amylosin. It is possible that amylosin was the agent responsible for the food-borne illness, since no other toxic substance was found in the strains. This is the first report on amylosin production by strains isolated from food. We found that the temperature requirement for amylosin production was higher for the B. subtilis strain F 2564/96, a mesophilic producer, than for B. mojavensis strains eela 2293 and B 31, psychrotolerant producers. We also found that an atmosphere with low oxygen did not prevent the production of amylosin. Ready-to-eat foods packaged in micro-aerophilic atmosphere and/or stored at temperatures above 10 °C, may thus pose a risk when toxigenic strains of B. subtilis or B. mojavensis are present.

Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these `transcriptional regulatory networks' (TRNs) in bacteria have an inherently hierarchical architecture, although the design principles and the specific advantages offered by this type of organization have not yet been fully elucidated. In this study, we focussed on the hierarchical structure of the TRN of the gram-positive bacterium Bacillus subtilis and performed a comparative analysis with the TRN of the gram-negative bacterium Escherichia coli. Using a graph-theoretic approach, we organized the transcription factors (TFs) and sigma-factors in the TRNs of B. subtilis and E. coli into three hierarchical levels (Top, Middle and Bottom) and studied several structural and functional properties across them. In addition to many similarities, we found also specific differences, explaining the majority of them with variations in the distribution of s-factors across the hierarchical levels in the two organisms. We then investigated the control of target metabolic genes by transcriptional regulators to characterize the differential regulation of three distinct metabolic subsystems (catabolism, anabolism and central energy metabolism). These results suggest that the hierarchical architecture that we observed in B. subtilis represents an effective organization of its TRN to achieve flexibility in response to a wide range of diverse stimuli.

Obtención de cepas autóctonas de Bacillus spp. y su evaluación probiótica in vitro

El presente trabajo se enfocó en la obtención de la cepa de Bacillus spp., las muestras evaluadas fueron sangre, leche, concentrado, heces y ciego de pollo; estas se procesaron mediante técnicas convencionales de laboratorio para lograr adquirir una cepa pura de este bacilo, para esto se realizaron pruebas macroscópicas, microscópicas y bioquímicas que determinaron la identificación microbiológica del Bacillus subtilis. Las pruebas de proteólisis de caseína con la cual se determinó las cepas que poseían actividad proteolítica y enzimática y las pruebas de resistencia de pH y sales biliares que se utilizaron para determinar la actividad probiótica de la cepa in vitro. Al finalizar el análisis, se obtuvieron un total de tres cepas con la actividad probiótica requerida “X5-9 (2)C, X5-9 (2)CD, X2-10 (2)”, pero se eligió aquella que obtuvo los parámetros óptimos en la prueba de halo de hidrólisis de caseína siendo la cepa identificada con el código X5-9 (2)C la cual pertenecía a las muestras tomadas de los ciegos derechos de los pollos. Cabe destacar que este estudio constituye un proyecto innovador en el que se implementó tecnología existente en el país, con la finalidad de desarrollar la producción de cepas autóctonas para su empleo en sustitución de antibióticos promotores del crecimiento por un probiótico nacional elaborado a nivel industrial.

杉木连栽致害真菌拮抗菌Bacillus subtilis3728的研究

杉木是我国重要的速生丰产树种，分布在北纬21°41′到33°41′，东经102°到122°的广大地区，杉木人工林面积约占我国人工林总面积的1/4，随着连栽代数的增加，土壤中毒和生产力下降程度日趋严重。 本论文以分离自与红树林、珍珠贝、海兔子、海绵、软珊瑚等与海洋动、植物共栖或共生存的106株海洋微生物(54株放线菌，52株细菌)为资源，以杉木连栽致害真菌尖孢镰刀菌萎蔫专化型(Fusarium oxysporum f.sp.vasinfectum)菌株SF2为靶菌，通过平板对峙试验和土壤原位定殖试验，筛选到一株分离自红树林木榄(Bruguiera gymnorrhizo)根际土壤的海洋细菌3728菌株；该菌对SF2具有很强抑菌活性，能够高密度在杉木根际土壤中定殖，对杉木幼苗的生长有一定的促进作用。采用传统的细菌学和分子生物学的鉴定方法对其进行了菌种鉴定，为枯草芽孢杆菌(Bacillus subtilis)。 通过对抗菌谱的研究，发现海洋细菌3728除了对杉木连栽主要致害真菌尖孢镰刀菌萎蔫专化型菌株SF2有很强的抑菌活性外，对大豆连作致害菌 (Penicillium purpurogenum)，棉花枯萎病菌(Fusarium oxysporum)，棉花立枯病菌(Rhizoctonia solani)，大豆根腐病菌(Fusarium solani)以及小麦赤霉病菌(Fusarium graminerum)等也有较强的抑制作用。室内模拟试验还表明，在土壤中接种海洋细菌3728后，能够明显增加土壤中氨化细菌和氨化真菌的数量，能够增加土壤中功能性微生物——纤维素分解细菌和纤维素分解真菌的数量和种类，增强了纤维素分解能力。再添加C/N比较低的白三叶草凋落物，土壤中氨化细菌、氨化真菌的数量继续增加，土壤纤维素分解能力更显著提高。这为进一步开展对杉木连栽障碍的生物调控试验，提供了一定的科学依据。