The goal of this project is to decipher the quorum sensing (cell-to-cell signaling) abilities of Shewanella oneidensis MR-1, a Gram-negative bacterium well known for its ability to use geologic substrates, such as Fe and Mn oxides, for respiratory purposes. Overall our results show that S. oneidensis cannot utilize either an acyl-homoserine lactone (AHL) or AI-2 quorum sensing signal, despite previous work that indicated that it produced an AHL that would enhance it ability to growth in certain anaerobic environments. Using a variety of quorum sensing signal sensors, no evidence could be found that S. oneidensis has a typical AHL signal. An in silco analysis of the genome also produced little evidence that S. oneidensis has the genes to accept or relay an AHL signal. S. oneidensis can produce a luminescence response in the AI-2 reporter strain, Vibrio harveyi MM32. This luminescence response is abolished upon deletion of luxS, the gene responsible for catalyzing AI-2. Deletion of luxS also affected biofilm formation. Within 16 hours of growth in a biofilm flow-through reactor, the luxS mutant had an inhibited ability to initiate biofilm formation. After 48 hours of growth, the mutant's biofilm had developed similarly to wild-type. The addition of synthetic AI-2 did not restore the mutant's ability to initiation biofilm formation, which led to the conclusion that AI-2 is not likely used as a quorum sensing signal in S. oneidensis for this phenotype. Because of the involvement of LuxS in the activated methyl cycle (AMC) in other organisms, growth on various sulfur sources was examined. A mutation in luxS produced a reduced ability to growth with methionine as the sole sulfur source. Methionine is a key metabolite used in the AMC to produce a methyl source in the cell and homocysteine. This data suggests that LuxS is important in metabolizing methionine and the AMC in S. oneidensis. / Ph. D.

Properly representing the principle physical interactions of complex biological systems is paramount for building powerful, yet simple models. As an in depth look into different biological systems at different scales, multiple models are presented. At the molecular scale, an analytical solution to the (linearized) Poisson-Boltzmann equation for the electrostatic potential of any size biomolecule is derived using spherical geometry. The solution is tested both on an ideal sphere relative to an exact solution and on a multitude of biomolecules relative to a numerical solution. In all cases, the bulk of the error is within thermal noise. The computational power of the solution is demonstrated by finding the electrostatic potential at the surface of a viral capsid that is nearly half a million atoms in size. Next, a model of the nucleosome using simplified geometry is presented. This system is a complex of protein and DNA and acts as the first level of DNA compaction inside the nucleus of eukaryotes. The analytical model reveals a mechanism for controlling the stability of the nucleosome via changes to the total charge of the protein globular core. The analytical model is verified by a computational study on the stability change when the charge of individual residues is altered. Finally, a multiple model approach is taken to study bacteria that are capable of different responses depending on the size of their surrounding colony. The first model is capable of determining how the system propagates the information about the colony size to those specific genes that control the concentration of a master regulatory protein. A second model is used to analyze the direct RNA interference mechanism the cell employs to tune the available gene transcripts of the master regulatory protein, i.e. small RNA - messenger RNA regulation. This model provides a possible explanation for puzzling experimentally measured phenotypic responses. / Ph. D.

Pantoea stewartii subsp. stewarti is the causative agent of Stewart's wilt disease in maize. Disease symptoms develop after the bacteria grow to high cell densities in the plant xylem and secrete an abundance of exopolysaccharide (EPS). EPS production is regulated by quorum sensing. Two regulatory proteins are key to the process of quorum sensing, the LuxI and LuxR homologues EsaI and EsaR. Most LuxR homologues function as activators of transcription in the presence of their cognate acylated homoserine lactone signal (AHL). EsaR utilizes an AHL-response opposite of the majority of the LuxR homologues. EsaR represses EPS production at low cell densities. However, at high cell densities when high concentrations of AHL are present, EsaR is inactivated and derepression of EPS production occurs. The mechanism that enables EsaR to respond to AHL in a manner opposite to that of most LuxR homologues remains elusive. A comparative study of EsaR and the well characterized quorum-sensing regulators LuxR from Vibrio fischeri and TraR from Agrobacterium tumefaciens was initiated. Previous studies demonstrated that in the absence of AHL, EsaR retains the ability to function as a weak activator of the lux operon in recombinant Escherichia coli. This thesis research further characterized the role of EsaR as an activator. Variant forms of EsaR with deletions or single residue substitutions were generated and their ability to regulate transcription was examined in vivo. Furthermore, a native EsaR-activated promoter has been identified, which controls expression of a putative regulatory sRNA in P. stewartii. It is apparent that EsaR functions as a transcription factor at low concentrations of AHL as demonstrated by its ability to inhibit EPS production. At high concentrations, the AHL appears to bind and cause a conformational shift in the protein leading to its inactivation. The second goal of this study was to further elucidate the mechanism by which AHL regulates EsaR. Pulse-chase experiments demonstrated that EsaR is resistant to proteases with or without AHL in vivo. Limited proteolytic digestions in vitro suggest that the protein does undergo conformational changes in response to AHL. Gel filtration chromatography, sucrose gradient ultracentrifugation, and cross-linking experiments proved that this conformational change does not impact the multimeric state of EsaR. To better understand the mechanism of regulation by AHL, the final goal of this project was to examine the interactions which result in EsaR-responsiveness to AHL. Several individual amino acid substitutions were identified that cause EsaR to function in an AHL-independent manner, by which variants retain the ability to bind and block gene expression in the presence of AHL. These residues have been mapped onto a homology model of EsaR and their role has been examined in vitro. The ability of these EsaR* variants to bind AHL and an analysis of the effects individual mutations have on the overall conformation of the protein was performed. Overall this study has revealed several unique aspects of the quorum-sensing system in P. stewartii whereby gene expression is regulated at both low and high cell density. Studies were also initiated to examine the mechanism of AHL-responsiveness of EsaR. The mechanism by which AHL modulates most LuxR homologues remains elusive. The ability to purify EsaR +/- its cognate AHL may prove critical in elucidating this mechanism. / Ph. D.

Pantoea stewartii subsp. stewartii is the causative agent of Stewart's wilt disease in maize plants. The bacteria are injected into the plant by corn flea beetles during feeding. They colonize the xylem and overproduce a capsular exopolysaccharide (EPS) at high cell densities. The production of EPS is regulated by an EsaI/EsaR quorum sensing mechanism, homologous to the LuxI/R system. Although activation of the EPS encoding genes by EsaR occurs after it complexes to the AHL (3-oxo-C6-HSL), unlike the LuxI/R system, this activation occurs by a different mechanism. At low cell densities, dimerized EsaR acts as a repressor. At a high cell population, derepression of the EPS genes occurs via an unknown mechanism once the AHL complexes to EsaR. Hence, a random mutagenesis genetic approach to isolate EsaR* variants that are immune to the effects of AHL has been utilized. Error-prone PCR and site-directed mutagenesis were used to generate desired mutants, which were subsequently screened for their ability to repress transcription in the presence of AHL. Several individual amino acids playing a critical role in the AHL-insensitive phenotype have been identified and mapped onto a homology model of EsaR. A separate study attempted to localize the dimerization region and analyze the stability of the N-terminal domain of EsaR. Truncations of EsaR at amino acids 169 and 178, without and with the extended linker region respectively, were generated using PCR. Dimerization assays similar to those by Choi and Greenberg in 1991 were performed but proved to be unsuccessful. However, the N-terminal domain is stable as determined by western blotting, which may facilitate its future structural analysis. Together, these efforts have contributed to the molecular understanding of AHL-dependent derepression of EsaR. / Master of Science

Orientador: Danielle Biscaro Pedrolli / Resumo: Os métodos de indução da expressão gênica disponíveis para linhagens bacterianas envolvem a adição de compostos indutores ao meio de cultura (por exemplo, isopropil β-D-1-tiogalactopiranosideo, xilose e arabinose), o que é indesejável para linhagens industriais, pois encarece o processo produtivo. Já a utilização da expressão constitutiva, alternativa à indução, pode ocasionar stress metabólico durante a fase lag de crescimento quando são utilizados promotores fortes. O objetivo do trabalho foi construir e padronizar um novo modelo de indução da expressão gênica para linhagens bacterianas industriais. O novo modelo de autoindução baseado no sistema de quorum-sensing bacteriano, permitindo que a célula se automonitore e induza a expressão gênica durante a fase exponencial de crescimento, eliminando assim não só a necessidade de adição de composto indutor como a necessidade de monitoramento da densidade celular pré-indução. Realizou-se amplificação e clonagem dos genes luxR e luxI, com e sem caudas de histidina, e suas respectivas sequências regulatórias de Aliivibrio fischeri, em plasmídeo contendo os genes responsáveis pela bioluminescência ou fluorescência com códons otimizados para Bacillus subtilis. Em seguida, foi realizada transformação e a integração do plasmídeo no cromossomo de B. subtilis. A funcionalidade do sistema foi avaliada em diferentes etapas de crescimento microbiano com o auxílio de um leitor de microplacas durante intervalos regulares. O sistema de autoind... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Current methods available for the autoinduction of gene expression in genetically engineered bacterial strains require addition of inducing compounds to the culture medium (e.g. Isopropyl β-D-1-thiogalactopyranoside, xylose, and arabinose), which is undesirable for industrial strains due to additional costs to the production process. Alternatively, constitutive gene expression is employed. However, the later can possibly cause metabolic stress during the lag growth phase if strong promoters are employed. The objective of this work was to construct and to standardize a new model for induction of gene expression in industrial bacterial strains. The new model is based on an autoinduction process triggered by the bacterial quorum-sensing system. It allows the cell to monitor itself and induce its own gene expression during the exponential growth phase, thereby eliminating both the need for an external inducing compound and the need for monitoring pre-inducing cell density. Bacterial cultures were grown in rich media, supplemented or not with antibiotics. Amplification and cloning of luxR and luxI genes, with and without histidine tags, and their respective regulatory sequences of Aliivibrio fischeri, were performed on a plasmid containing the genes responsible for bioluminescence or fluorescence with codons optimized for Bacillus subtilis. Next, transformation and integration of the plasmid into the B. subtilis chromosome were performed. The functionality of the system was evalua... (Complete abstract click electronic access below) / Doutor

Listeria monocytogenes é um micro-organismo Gram-positivo que está comumente associado a doenças de origem alimentar. Possui a capacidade de sobreviver a condições adversas e de formar biofilme em diferentes superfícies abióticas, tornando-se um problema constante para a indústria de alimentos, pois pode comprometer a sanitização e aumentar o risco de contaminação pós-processamento. A formação de biofilme pode ser regulada por um mecanismo denominado quorum sensing, no qual ocorre intensa comunicação célula-célula, mediada por moléculas químicas, chamadas de autoindutoras. Pouco se sabe sobre a ocorrência de interação entre bactérias Gram- positivas e negativas na formação de biofilmes, sendo mais frequentes estudos entre bactérias do mesmo grupo. A fim de avaliar a ocorrência de interação entre Escherichia coli e L. monocytogenes (Lm), desenvolveu-se esta pesquisa com os seguintes objetivos: i) verificar a capacidade de Lm sorotipo 1/2a selvagem e sua mutante isogênica (ΔprfA ΔsigB) formar biofilme em presença de Escherichia coli, avaliando-se a importância dos reguladores de virulência, prfA e sigB, no processo; e ii) verificar a produção e interferência de moléculas autoindutoras de E. coli E2348/69 na formação de biofilme por Lm. Os ensaios de formação de biofilme foram realizados utilizando-se lâminas de aço-inoxidável AISI 304 #4 imersas em caldo infusão de cérebro e coração (BHI) e em meio pré-condicionado (MPC) por E. coli, com incubação a 25 ºC. Foram testadas duas concentrações iniciais de Lm (102 e 106 UFC.mL-1) e amostragens em diferentes tempos de incubação. Utilizou-se um método de quantificação indireto com coloração do biofilme por cristal violeta e posterior leitura da absorbância. Observou-se que Lm 1/2a selvagem e sua mutante isogênica (ΔprfA ΔsigB) são capaz de formar biofilme na presença de Escherichia coli e que uma maior quantidade de biofilme foi formada por Lm selvagem quando comparada à sua mutante, em meio não pré-condicionado (controle), indicando que prfA e sigB estão envolvidos no processo de formação de biofilme. Quando em MPC, o biofilme formado pela cepa selvagem foi menor que no meio controle (BHI), indicando que E. coli E2348/69, utilizada no pré-condicionamento do meio, produz moléculas capazes de interferir no processo de formação e na quantidade de biofilme formado por Lm; e para o biofilme formado pela cepa mutante, houve uma maior quantificação em MPC em comparação ao meio controle, o que sugere que os genes deletados possam estar envolvidos no reconhecimento das moléculas autoindutoras. Assim, os dados obtidos permitem concluir que há interação e interferência por parte de E. coli na formação de biofilme por Lm mediante produção de moléculas autoindutoras. / Listeria monocytogenes (Lm) is a Gram-positive microorganism commonly associated with foodborne diseases. Due to its ability to survive under adverse environmental conditions and to form biofilm in different abiotic surfaces, this bacterium is a concern for the food industry, since it can compromise sanitation procedures and increase the risk of post-processing contamination. Biofilm formation can be regulated by a quorum sensing mechanism, in which there is intense cell-cell communication mediated by chemical molecules, called autoinducers. Little is known about the occurrence of interaction between Gram-positive and Gram-negative bacteria on biofilm formation. Thus, in order to evaluate the occurrence of interaction between Escherichia coli and Lm, this study was developed including the following objectives: i) to evaluate the ability of Lm 1/2a and its isogenic mutant strain (ΔprfAΔsigB) to form biofilm on the presence of Escherichia coli, assessing the importance of virulence regulators, prfA and sigB, in this process; and ii) to verify the production and interference autoinducers of E. coli E2348/69 on biofilm formation by Lm. Biofilm formation assays were conducted using stainless steel AISI 304 #4 immersed into broth brain heart infusion (BHI) and into preconditioned medium (MPC) by E. coli, following incubation at 25 °C. Lm at two initial concentrations (102 and 106 CFU.mL-1) and under different incubation time was tested. An indirect method for quantification of cells was applied, using crystal violet to color the biofilm, followed by optical density measurement. It was observed that Lm 1/2a and its isogenic mutant (ΔprfA ΔsigB) are able to form biofilm in the presence of Escherichia coli and a larger amount of biofilm was formed by wild strain Lm compared to its mutant, in a non-preconditioned medium (control), indicating that prfA and sigB are involved in biofilm formation. For MPC, the biofilm formation by the wild strain was lower than in the control (BHI), indicating that E. coli E2348/69, used in the preconditioned medium, produces molecules that can affect the formation process and the amount of biofilm formed by Lm; and in the biofilm formed by the mutant strain, there was a higher quantification of MPC compared to the control, suggesting that the deleted genes may be involved in recognition the of autoinducers. These results suggest that there is an interaction and interference of E. coli on biofilm formation by Lm due the production of autoinducers.

Nos últimos 30 anos, Acinetobacter tornou-se um dos patógenos de maior preocupação clínica pela falta de terapias eficazes em virtude do fenótipo de multirresistência frequentemente apresentado. Dentre as espécies do gênero Acinetobacter, A. baumannii, A. genoespécie 3 e A. genoespécie 13TU são as mais comumente encontradas a partir de amostras biológicas. Estas espécies ao lado de A. calcoaceticus constituem o complexo A. calcoaceticus-A. baumannii (ACB). Este estudo propõe um esquema composto de duas PCRs para a identificação das espécies de interesse médico que fazem parte do complexo ACB. O método é simples, rápido e, além de identificar as espécies, permite pesquisar a presença de genes de resistência. Foram identificadas 515 amostras do complexo ACB, isoladas de pacientes no período de janeiro de 2005 a dezembro de 2010. A identificação das espécies do complexo ACB foi realizada por esquema composto de duas reações de PCR. Foram avaliados os perfis de sensibilidade por disco difusão e a pesquisa da presença dos genes blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, blaOXA-58-like, blaIMP, blaVIM, blaSIM, blaSPM e blaGIM foi realizada por PCR utilizando-se iniciadores específicos. No grupo de amostras estudas, 82,5% são A. baumannii (425), 11,5% A. genoespécie 13TU (59) e 6,0% A. genoespécie 3 (30), sendo A. baumannii mais isolado em pacientes internados em UTIs (p=0,0407) e A. genoespécie 13TU mais isolado em pacientes de outros ambientes hospitalares (p=0,0204). A. baumannii apresentou menor sensibilidade a todos os antimicrobianos quando comparado com A. genoespécie 13TU e A. genoespécie. 3 (p<0,05). Foi possível observar ao longo do período estudado o aumento significativo da resistência aos carbapenêmicos e da sensibilidade a gentamicina por A. baumannii entre os isolados de pacientes de UTIs (p<0.05). Nenhum dos genes codificadores para metalo-lactamases foi detectado nas amostras estudadas Dentre os cepas resistentes aos carbapenêmicos (176) o gene blaOXA-23 foi detectado em 81,25% e uma amostra de A. baumannii apresentou o gene codificador para OXA-72. A tipagem molecular foi realizada por RAPD e para os isolados resistentes aos carbapenêmicos também por PFGE. Resultados obtidos por RAPD revelaram menor diversidade entre os isolados de pacientes internados em UTIs. O dendrograma obtido utilizando-se PFGE separou dois clones cujos componentes eram resistentes aos carbapenêmicos, no entanto não apresentavam o gene blaOXA-23-like. A produção de acil-homoserina lactona, autoindutor-2 e autoindutor-3 de três amostras de cada espécie clínica do complexo ACB foi pesquisada utilizando-se bioensaios. Apenas Autoindutor 3 foi detectado por bioensaio e em menor quantidade no meio précondicionados obtido a partir de A. genoespécie 3 quando comparado com A. genoespécie 13TU e A. baumannii (p<0.05). Três cepas de cada espécie clínica do complexo ACB foi avaliada quanto a capacidade de adesão em monocamada de células Hep-2, MRC-5 e NCI-H292, sendo essa última a que revelou diferenças entre as espécies clínicas do complexo ACB. A. baumannii apresentou adesão difusa, A. genoespécie 13 TU adesão com formação de agrupamentos e A. genoespécie 3 não aderiu. Esse mesmo ensaio foi realizado na presença de propanolol e notou-se a diminuição de células aderidas por campo observado. Dez cepas de cada espécie clínica do complexo ACB foram pesquisadas quanto a produção de biofilme por ensaio colorimétrico utilizando cristal violeta e foi possível notar a produção significativa de biofilme por A. baumannii, quando comparado com A. genoespécie 3 (p<0.05). Esse mesmo ensaio na presença de de fentolamina, mostrou a diminuição significativa na produção do biofilme por A. baumannii. A interferência no ensaio de adesão bacteriana e biofilme, na presença de fentolamina ou propanolol, sugerem o envolvimento do autoindutor-3 na regulação desses mecanismos de virulência. / The genus Acinetobacter has emerged as one of the most troublesome pathogens for health care institutions globally. Its clinical significance, especially over the last 15 years, has been driven by its remarkable ability to up regulate or acquire resistance determinants, making it one of the organisms threatening the current antibiotic era. A. baumannii, A. 3 and A. 13TU are the most commonly species found from biological samples. These species beside A. calcoaceticus are very closely related and difficult to distinguish from each other by phenotypic properties. Therefore, it has been proposed to refer to these species as the A.calcoaceticus-A. baumannii complex(ACB). In the period from 2005 to 2009, the most frequent bacterial isolates among the nosocomial infection at the HU-USP was ACB (18%). Due to the frequency with which species are involved in ACB outbreaks of infection in the HU-USP and the emergency clinic because of expression of the phenotype of resistance to several classes of antibiotics, this study aimed to identify and characterize the species of complex ACB by molecular methods, to study their mechanisms of resistance and to characterize the different clones from patients admitted to different hospital areas. Furthermore, the ability to characterize biofilm formation, adhesion to different cell lines as well as the mechanisms of cell-cell communication were analyzed. From the ACB complex, 515 samples were identified, isolated from patients from January 2005 to December 2010. The identification of clinical species of the ACB was performed by molecular methods that were developed and validated for identification of Acinetobacter sp. include two reactions of PCR. The profiles of sensibility were evaluated by disc diffusion and the detection of the presence of genes blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, blaOXA-58-like, blaIMP, blaVIM, blaSIM, blaGIM, and blaSPM were performed using specific primers. Molecular typing was performed by RAPD and isolates resistant to carbapenems also by PFGE. The production of autoinducers of three clinical species complex was sought using bioassays with sensor strains. The ability adhesion was evaluated in monolayer of Hep-2 cells, MRC-5 and NCI-H292E. Ten clinical strains of each species of ACB complex were screened for the production of biofilms by colorimetric assay using crystal violet. Among all the strains studied, 82.5% were A. baumannii (425), 11.5% A.13TU (59) and 6.0% A. 3 (30). A. baumannii strains were more isolated from intensive care unit (ICU) patients (p = 0.0407) and A. 13TU from other patients in different hospital settings (p = 0.0204). A. baumannii showed less sensitivity to all drugs when compared with A. 13TU and A.3 (p <0.05). It was possible to observe during the study period a significant increase in carbapenem resistance and sensitivity to gentamicin by A. baumannii isolates from patients in ICUs (p <0.05). No genes coding for metallo-lactamase was detected in the samples studied. blaOXA-23 gene was detected in 81.25% among the 176 strains resistant to carbapenems. Results obtained by RAPD revealed less diversity among isolates from ICU patients compared to isolates from patients from other hospitals. The dendrogram obtained by PFGE showed less diversity than RAPD It was unable to detect homoserine lactone and autoinducer-2 by bioassay. The survey was positive of autoinducer-3 observed differences in yield among clinical species, smaller amount produced by strains of A. 3 when compared with A. 13TU and A. baumannii (p <0.05). Among the cells studied in adhesion testing, line NCI-H292 showed the greatest power discrimination between adhesion pattern observed and species of the ACB. A. baumannii showed diffuse adherence, A. 13 TU strains showed adhesion clustering and A. 3 did not adhere. This experiment was repeated in the presence of 100 &#181;M of propranolol and it was noted a decrease in cell A. 13TU and A. baumannii adhered per field observed. The biofilm assay showed significantly higher production of biofilms by A.baumannii compared with A. 3 (p <0.05). When the test was conducted in the presence of phentolamine at 100&#181;M, it was observed a significant decrease in the biofilm productions by A. baumannii, which revealing the involvement of the autoinducer-3 in biofilm production. The data obtained suggest that the proposed method of identification is a method for identification of species of medical interest belonging to the ACB complex which could be used in a routine laboratory. The method is simple, fast and beside the identification species, provides data about the resistance genes. Moreover, it revealed that the isolates of A. baumannii are more resistant and OXAbla genes, that was restricted to the ACB complex studied in this work. A. baumannii has also increased capacity for adhesion and biofilm formation, which regulates the expression of the phenotype may be linked to the production of autoinducers-3.

O gene MAS1/GAS2, conhecido como \"Magnaporthe Apressoria Specific\", foi identificado como altamente expresso durante a formação do apressório do fungo filamentoso fito patogênico Magnaporthe grisea. Em Aspergillus fumigatus, fungo patogênico oportunista, o gene masA, ortólogo a MAS1/GAS2 foi identificado como upregulated em uma análise transcriptômica exposto a voriconazole e anidulafungina, antifúngicos que afetam a síntese do ergosterol e a parede celular, respectivamente. Em ambos os ortólogos apresentam uma estrutura na região N-terminal da proteína denominada peptídeo sinal o qual neste trabalho foi determinado em uma análise in silico a presença de peptídeo sinal na região N-terminal da proteína. Na caracterização fenotípica de uma linhagem masA - deletada de A. fumigatus não foi identificado alteração estrutural do conidióforo e no seu aspecto macromorfológico. A linhagem masA-deletada é resistente a voriconazol e farnesol, drogas que inibem a síntese de ergosterol e a uma molécula quorum sensing, respectivamente. Ao avaliar o nível de expressão gênica do masA frente a diferentes classes de drogas, foi observado que o gene esta super expresso quando ocorre dano na parede celular, membrana citoplasmática, DNA, inibições na síntese de lipídeos e ácidos graxos e no estresse oxidativo. Na presença de dano na parede celular fúngica causados por anidulafungina, a proteína MasA está localizado na parede celular próximo a ponta da hifa. Adicionalmente, foi capaz de transferir para o meio extra-celular a proteína fusionada a ele, a GFP. Assim, possivelmente MasA participa da via secretória do fungo principalmente em momentos de estresse como o desarranjo da parede celular. A capacidade de secreção natural dos fungos filamentosos tem sido explorada no contexto industrial há décadas. Indicando para este fim, uma possível aplicabilidade para este peptídeo sinal. / The MAS1/GAS2 gene, known as \"Magnaporthe Apressoria Specific\", was identified as highly expressed during the formation of the appressorium phyto pathogenic filamentous fungus Magnaporthe grisea. In Aspergillus fumigatus, opportunistic saprophytic fungus, masA gene orthologous to MAS1/GAS2 was identified as upregulated in a transcriptomic analysis exposed to voriconazole and anidulafungin, antifungals that affect the synthesis of ergosterol and the cell wall, respectively. In both orthologs have a structure at the N-terminus of the protein called signal peptide. During the phenotypic and functional characterization of masA gene in A. fumigatus, was determined on an in silico analysis the presence of signal peptide at the N-terminal region of the protein. In the phenotypic characterization of a strain masA - deleted, no structural change of conidiophores and its macromorfologic aspect was not identified. The characterization masA-deleted strain is resistant to voriconazol and farnesol drugs which inhibit ergosterol synthesis and a quorum sensing molecule, respectively. When evaluating the level of gene expression masA against different class of drugs was observed the super gene is expressed when damage occurs in the cell wall and membrane DNA, the synthesis of lipids and fatty acids, and oxidative stress. In the presence of damage in the fungal cell wall caused by anidulafungin, MasA protein is located near the cell wall and the tip of the hypha and additionally, was able to transfer the protein to the extracellular the protein fused to GFP. Thus, possibly MasA participates in the secretory pathway of the fungus especially in stress of the cell wall. The natural secretion capability of filamentous fungi has been exploited in the industrial context for decades. Indicating for this purpose, a possible applicability for this signal peptide.

O fitopatógeno Xanthomonas axonopodis pv citri (XAC) é o agente causal do cancro em citros. O desenvolvimento da infecção depende do sucesso de XAC na colonização do hospedeiro. Para isso, além do sistema de secreção tipo III, que injeta efetores de virulência dentro da célula do hospedeiro, Xanthomonas também conta com o processo de quorum-sensing. O aumento da densidade celular em XCC (Xanthomonas campestris pv campestris) promove o acúmulo da molécula sinalizadora difusível (DSF) produzida por RpfF, que ativa o sistema de dois componentes formado pelas proteínas RpfC e RpfG, as quais transduzem o sinal de ativação para o fator de transcrição Clp (CAP Like Protein - homóloga da proteína CAP de E. coli). A proteína RpfG contém um domínio de fosfodiesterase conservado (HD-GYP) que regula a concentração de diGMP cíclico (c-diGMP), um segundo mensageiro bacteriano. Dessa forma o domínio HD-GYP atua contrapondo-se à atividade dos domínios diguanilato ciclases (GGDEF). No caso de XCC, foi demonstrado que a ativação do domínio HD-GYP de RpfG reduz a concentração de c-diGMP na célula e promove a ligação e ação positiva de Clp no promotor do gene de engXCA. Com intuito de estudar a via Rpf em XAC, produzimos mutantes não-polares de rpfF, rpfC, rpfG, dos genes que codificam os domínios GGDEF que interagiram com RpfG (Andrade et al. 2006), clp, fliC, pilT, gumD e também geramos mutantes dos operons xcs e xps, que codificam sistemas de secreção do tipo 2 em XAC. Análise por HPLC-MS/MS mostrou que a deleção de rpfG, mas não clp, promoveu um aumento de aproximadamente 4 vezes dos níveis celulares de c-diGMP. Também foi demonstrado por EMSA que c-diGMP inibe a ligação de Clp ao promotor do operon xcs. Os mutantes &#916;rpfF-C-G e &#916;clp mostraram um comprometimento da mobilidade, redução da biossíntese de exopolissacarídeos e na produção de fatores de virulência. Em adição, observamos uma diminuição significativa no crescimento dos mutantes &#916;rpfG e &#916;clp dentro do hospedeiro. Além disso, identificamos também novos fatores envolvidos no metabolismo do c-diGMP e (p)ppGpp em XAC. Além do c-diGMP, outro segundo mensageiro o (p)ppGpp, cuja concentração na célula é regulada pelas proteínas SpoT e RelA, pode afetar a expressão de maneira dependente da subunidade &#969; da RNA polimerase em XAC. Finalmente, propusemos um modelo onde a concentração de c-diGMP sob controle da via do quorum-sensing e a sinalização por (p)ppGpp podem convergir para alguns efetores que regulam a mobilidade e a patogenicidade em XAC. / In Xanthomonas, the cell-cell signaling mediated by diffusible molecules is known to play an important role in regulating physiological process, including the formation and dispersal of biofilms and virulence. It has been shown that the ability of Xanthomonas species to incite disease depends on several factors, including adhesins, synthesis of extracellular enzymes, type III secretion system (T3SS) effectors and the exopolysaccharide (EPS) xanthan. The rpf genes act to positively regulate the synthesis of extracellular enzymes, EPS and pathogenicity. The rpfF, rpfC and rpfG genes are implicated in a regulatory system involving a diffusible signal factor (DSF) whose synthesis of DSF depends on RpfF. DSF perception and signal transduction are mediated by the two-component system comprising RpfC and RpfG. High cell densities are thought to lead to the phosphorylation of RpfG by RpfC which in turn activates the RpfG HD-GYP phosphodiestarase domain whose substrate has been shown to be the important second messenger cyclic diGMP (c-diGMP) (Ryan et al., 2006). This work was prompted to by the observation that the HD-GYP domain of RpfG interacts with a subset of diguanylate cyclase (GGDEF) proteins (Andrade et al., 2006), responsible for c-diGMP synthesis in Xanthomonas axonopodis pv citri (XAC). In order to study rpf signaling in XAC, we produced non-polar knockouts of rpfF, rpfC, rpfG, all genes coding the GGDEF domains shown to interact with RpfG, CAP-like protein (clp), fliC, pilT, gumD and polar insertions in the operons of both type 2 secretion systems coded by the XAC genome. HPLC-MS/MS analysis showed that the deletion of rpfG, but not clp, promoted an approximate 4-fold increase in cellular c-diGMP levels. We Also demonstrated that c-diGMP inhibits the binding of Clp to the promoter of the XAC0694 gene, the first gene in the operon coding the type 2 secretion system. The rpf genes and clp knockouts have impaired motility, reduction in exopolissacarides and extracellular enzyme production. Furthermore, we observe a significant decrease in the growth of rpfG and clp mutants in host tissues. Our results demonstrate that RpfF-RpfC-RpfG-Clp signaling in XAC is associated with cellular c-diGMP levels and is important for XAC virulence, motility, and EPS production. In addition, we have identified new factors involved to metabolism of c-diGMP and (p)ppGpp in XAC. The (p)ppGpp synthesis and degradation is under control of the proteins SpoT and RelA; However the effect of (p)ppGpp on gene expression seems to depend of the &#969; subunit of RNA polimerase in XAC. Finally, we propose the model where c-diGMP levels controlled by quorum-sensing and the (p)ppGpp signalization may converge to regulate the motility and pathogenicity of XAC.

L’identification, chez divers organismes, d’enzymes de dégradation des N-acyl homosérineslactones (NAHLs) impliquées dans la signalisation QS pose la question de leurs rôles dans lesinteractions bactéries-eucaryotes. Dans une première partie, une synthèse bibliographique analyse lesconnaissances acquises sur ces enzymes dégradant les NAHLs. Dans une seconde partie, la croissancedes bactéries dégradant les signaux NAHLs a été stimulée par l’application de g-caprolactone (GCL)dans la rhizosphère de plants de pommes de terre à des fins de phytoprotection. L’effet de cetraitement sur la diversité des communautés bactériennes rhizosphériques a été évalué en combinantdifférentes approches d’écologie microbienne moléculaire comme la DGGE, le pyroséquençaged’amplicons rrs, et la métagénomique fonctionnelle. Cette dernière approche appliquée à une banquede 30 000 clones environ a conduit à l’identification d’un gène qsdB codant la dégradation des signauxNAHL. Ce travail révèle ainsi l’existence d’une nouvelle classe d’enzymes de dégradation des NAHLsappartenant à la famille des enzymes possédant une signature amidase (AS) dont des membres sontpar ailleurs impliqués dans la dégradation de composés xénobiotiques. Dans une troisième partie, unsystème expérimental a été développé afin de mesurer le transfert conjugatif du plasmide de virulenceTi (tumor inducing) chez des dérivés du pathogène Agrobacterium tumefaciens, appelés «tricheurs»,incapables de produire des signaux NAHLs mais utilisateurs de ceux produits par les autres bactéries.Ce modèle a permis de montrer l’effet modérateur de lactonases dégradant les NAHLs exprimées chezdes agrobactéries produisant les NAHLs, chez des bactéries réceptrices du plasmide Ti, ou des planteshôtes des agrobactéries sur le transfert conjugatif initié par les tricheurs. L’ensemble de ce travailrévèle à la fois une nouvelle famille d’enzymes impliquées dans la dégradation des NAHLs, ainsiqu’un nouveau rôle de ces enzymes dans la modulation des flux de gènes entre bactériesphytopathogènes en interaction avec une plante hôte. / Identification of bacterial and eukaryotic enzymes that degrade N-acyl homoserine lactones(NAHLs) involved in QS signaling raises the question of their roles in bacteria-eucaryotesinteractions. In a first part of this study, a bibliographic report analyzes the current data on thoseNAHL-degrading enzymes. In a second part, the growth of NAHL-degrading bacteria was stimulatedby g-caprolactone (GCL) amendment in potato rhizosphere to protect this plant against the soft-rotpathogen Pectobacterium. The effect of the GCL treatment on rhizospheric bacterial communities wasevaluated by a combination of different molecular microbial ecology techniques such as DGGE,pyrosequencing and functional metagenomic. This last approach was applied to generate ametagenomic library of ca. 30,000 clones and lead to the identification of the qsdB gene that encodesNAHL degradation, This work revealed the occurrence of a novel class of NAHL-degrading enzymesthat belong to the amidase signature (AS) family, some members of which being involved inxenobiotic compound degradation. In a third part, an experimental system was developed to measurethe conjugative transfer of Ti plasmid in various strains of the pathogen Agrobacterium tumefaciens,including “cheaters”, i.e. bacteria unable to produce NAHL signals but capable to use signals producedby other bacteria. Using this model; variations of the plasmid transfer of cheaters were measured whenNAHL-degrading lactonases were expressed in agrobacteria that produce NAHL signals, in recipientbacteria of Ti plasmid, or in agrobacterial host plant. Taken together, thesis experiments revealed anovel class of enzymes involved in NAHL-degradation and a new role for thoses enzymes in themodulation of gene transfer between pathogenic bacteria interacting with host plants.