Candida albicans is one of the most commonly identified nosocomially acquired pathogens. This organism has a number of virulence traits including production of degrading enzymes, the ability to undergo phenotypic switching, and can rapidly undergo morphogenic switch from a blastospore (yeast) phase to that of a hyphal state. Interest in C. albicans morphogenic regulation has been the focus of a large number of studies, which have characterised transcriptional modulators of these morphologies. Recently, C. albicans has been shown to regulate its morphogenic shift through changes in cell density. It was observed that C. albicans inoculated at cell densities below 106 cells ml -1 under conditions which favour hyphal morphogenesis (pH 7.5, 37°C), will germinate to form hyphae. However, if cells densities are greater than 106 cells ml-1, little germination will occur and cells will maintain yeast morphology. The basis for this cell-density-dependent control of morphogenesis is similar to that which is seen with bacterial cells regulating their activities via quorum sensing (QS). A number of molecules have been identified which affect the ability of C. albicans to undergo the yeast-to-hyphal shift, and three compounds have been demonstrated to be quorum-sensing molecules. The scope of this review is to bring to light what is now understood about QS in C. albicans and address the roles of these molecules in relation to virulence in the host and potential roles in cross-kingdom interactions.

Biofouling and biocorrosion are due to unwanted deposition of microorganisms on surfaces that are exposed to different types of water. This dissertation focuses on the application of innovative strategies to inhibit biofouling and biocorrosion. Specifically, the strategies examined in this dissertation, namely the use of bacteriophages and quorum quenchers, aim to minimize reliance on the conventional chemical cleaning agents and to reduce chemical-induced hazards on health, safety and environment. First, we analyzed the use of bacteriophages to remove biofoulants on ultrafiltration membrane used in seawater reverse osmosis pretreatment. Our findings revealed that bacteriophages were able to remain active against membrane-associated Pseudomonas aeruginosa at a broad range of temperature, pH and salinity. Bacteriophages were also shown to inhibit biofilm and to reduce transmembrane pressure increment, when applied alone or in combination with chemical agents. Second, this dissertation explores the use of quorum quenchers to inhibit biocorrosion in seawater environment. To do so, we first examined for the presence of quorum sensing system in sulfate reducing bacteria (SRB). Through transcriptomic analysis, we further demonstrate a strong correlation between quorum sensing, biofilm formation and biocorrosion. Therefore, the use of quorum sensing inhibitors was suggested to prevent biofilm formation and biocorrosion caused by SRB in seawater. Through findings from Chapter 2 and 3, we introduced the use of alternative biocidal agents to tackle biofouling and biocorrosion. Compared to quorum quenchers, bacteriophages showed better antibiofilm potential and easier applicability at larger scale. However, bacteriophages alone were insufficient to reduce biofilm formation as phage resistance was observed over long-term experiments. Hence in the last chapter, we further explored the use of bacteriophages to alleviate biofouling that occurred during wastewater treatment process, by combining their infection with UV irradiation. UV was used both for its biocidal effect and to trigger phage infection against bacteria. Our findings indicate that the combined treatment was able to remove mature biofoulants from the membrane. Overall, this dissertation demonstrates the use of bacteriophages and quorum quenchers against biofilm. These two approaches can serve to reduce the amount of chemicals used during cleaning, thus providing a more sustainable way of minimizing biofilm-associated problems.

Yes / Pantoea stewartii is known to be the causative agent of Stewart's wilt, which usually affects sweet corn (Zea mays) with the corn flea beetle as the transmission vector. In this work, we present the whole-genome sequence of Pantoea stewartii strain M009, isolated from a Malaysian tropical rainforest waterfall. / University of Malaya via High Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01 no. A-000001- 50001 and UM C/625/1/HIR/MOHE/CHAN/14/1 no. H-50001-A000027)

Yes / Bacterial quorum sensing has been implicated in a number of pathogenic bacterial processes, such as biofilm formation, making it a crucial target for developing materials with a novel antibiotic mode of action. This paper describes poly(N-isopropyl acrylamide) that has been covalently linked, at multiple chain ends, to homoserine lactone to give a highly branched polymer functionalized with a key messenger molecule implicated in QS. This novel functional material has shown promising anti-QS activity in a Chromobacterium violaceum assay.

The quorum-sensing response of Vibrio fischeri involves a complex network of genes (encoding regulatory proteins as well as sRNAs), that govern host-association and production of bioluminescence. A key regulator of this system is LuxR, which is the transcriptional activator of the lux operon as well as several other genes in. LuxR also autoregulates its own transcription, which we have shown causes bistability and hysteresis in the quorum-sensing response. This behavior allows the system to maintain a stable and robust response in the face of environmental fluctuation or decreases in external autoinducer concentration caused by other sources. There are many factors that are known to regulate luxR expression, including the ArcA redox-responsive regulator, the cAMP-CRP secondary metabolism regulator, and components of the quorum-sensing pathway like LitR. Because of this, LuxR levels are critical in both the timing of quorum-sensing induction, as well as the maintenance of the response over time. This makes it a potential target for multiple levels of regulation in response to factors such as environmental and metabolic conditions, as well as other components of the quorum-sensing network. Another important global regulatory protein in V. fischeri (and most other species of Gram-negative proteobacteria) is the post-transcriptional regulator CsrA. CsrA controls processes involved in carbon storage and utilization, as well as the transition from exponential to stationary phase growth. We have demonstrated that CsrA is regulated by two sRNAs (CsrB1 and CsrB2) in V. fischeri. Because CsrA regulates changes in cell behavior and is an important metabolic regulator, there is a good possibility that it has some interactions with the quorum-sensing regulon, whose endproduct, bioluminescence, creates a large metabolic demand from the cell. In an effort to determine at which point in the quorum-sensing regulatory network CsrA regulation is important, epistasis experiments were designed using factorial design, which is a subset of statistical analysis of variance (ANOVA). This method was used to generate a high degree of confidence in the data, so that even minor interactions in the regulatory networks could be established. By altering the levels of CsrA expression in various mutant strains of V. fischeri, we have demonstrated that CsrA acts by an unknown mechanism to increase the transcription of luxR when the quorum-sensing regulator LitR is absent. Our results also demonstrated that CsrA mediates this effect through repression of ArcA activity, which is known to act directly on the luxR and luxI intergenic region as a repressor. This indicates that CsrA may bypass the upstream parts of the quorum-sensing regulatory cascade that lead to litR activation, so that LitR and LuxR may be regulated differently in response to certain conditions. This work has shown that the interactions between global regulons can coordinately control the amount of quorum-sensing induction by affecting the level of LuxR in the cell. The balance of these regulatory networks allows the cell to tightly regulate the quorum-sensing response. Thus, LuxR serves as a critical regulatory hub in the cell, at which multiple signals can be integrated in order to generate the appropriate cellular response. / Ph. D.

Influência dos sistemas de Quorum Sensing AI-1/AI-2/AI-3 nos fatores de virulência de EPEC atípica de origem animal. A secreção de moléculas sinalizadoras de baixo peso molecular que se acumulam no meio extracelular até atingir um limite crítico de concentração para sua detecção, acarretando em sinalizações intracelulares e respostas efetoras, define o sistema de comunicação bacteriano chamado Quorum Sensing. Este sistema, que regula comportamentos coletivos mostrou-se um mecanismo disseminado em diversas espécies bacterianas. Diversos estudos descreveram a existência de pelo menos 3 sistemas relacionados ao Quorum Sensing em bactérias Gram-negativas, LuxIR/AI-1, LuxS/AI-2 e QseBC/AI-3/Epinefrina/Norepinefrina. Fatores de virulência como formação de biofilme, motilidade e adesão ao epitélio do hospedeiro devem ser controlados de maneira adequada para tirar o melhor proveito da situação em que a bactéria se encontra. Este trabalho teve como objetivo analisar a influência e a correlação dos genes luxS, qseC e sdiA, relacionados ao sistema de comunicação bacteriana Quorum Sensing, nos principais fatores de virulência de uma amostra de EPEC atípica de origem animal. Foram construídos mutantes pela metodologia baseada na recombinação homóloga mediada pelo sistema Lambda Red, que foram submetidos a ensaios fenotípicos. A sinalização por AI-2 e luxS desempenham papéis na motilidade, formação de biofilme e adesão a células epiteliais. QseC influencia a produção de biofilme pela regulação de componentes da matriz extracelular, e participa de processos de motilidade e adesão. O hormônio epinefrina contribui na alteração de processos de motilidade, formação de biofilme e desenvolvimento da lesão A/E. O gene sdiA também tem um papel importante na regulação de fatores de virulência, mesmo na ausência de AHL. Uma interação antagônica parece existir entre os genes qseC e luxS. A ausência de sistemas de Quorum Sensing promove a produção de um biofilme robusto na amostra AP155. / The secretion of low molecular weight signaling molecules that accumulate in the extracellular medium until reaching a critical concentration limit for its detection, leading to intracellular signaling and effector responses, defines the bacterial communication system called Quorum Sensing. This system regulates collective behaviors and has been proven to be a widespread mechanism in several bacterial species. Several studies have described the existence of at least 3 Quorum Sensing-related systems in Gram-negative bacteria, LuxIR/AI-1, LuxS/AI-2 and QseBC/AI-3/Epinephrine/Norepinephrine. Virulence factors such as biofilm formation, motility and adhesion to the host epithelium should be adequately regulated to make the most of the situation in which the bacterium is found. The aim of this work was to analyze the influence and correlation of luxS, qseC and sdiA genes, related to the bacterial communication system Quorum Sensing, on the main virulence factors of an atypical EPEC strain isolated from an animal. Mutants were obtained through homologous recombination mediated by the Lambda Red system, and then were submitted to phenotypic assays. AI-2 signaling and luxS play roles in motility, biofilm formation, and adhesion to epithelial cells. QseC influences the production of biofilm by the regulation of components of the extracellular matrix, and participates in the processes of motility and adhesion as well. The epinephrine hormone alters the processes of motility, biofilm formation and development of the A/E lesion. The sdiA gene also plays an important role in the regulation of virulence factors, even in the absence of AHL. An antagonistic interaction seems to exist between the qseC and luxS genes. The absence of Quorum Sensing systems promotes the production of a robust biofilm in the AP155 strain.

Parte da produção de fatores de virulência em bactérias do gênero Xanthomonas esta sob controle de um grupo de genes localizados no locus rpf (regulation of pathogenicity factors), que respondem ao aumento da densidade celular num processo chamado quorum sensing. Os genes que codificam as proteínas do sistema Rpf de Xanthomonas axonopodis pv citri (Xac) foram clonados no vetor pOBD por Alegria (2004), e usados como iscas em ensaios de dois híbridos, contra uma biblioteca de Xac clonada no vetor pOAD. Neste ensaio, foram observadas interações entre RpfC-RpfG, RpfC-RpfF, RpfF-RpfF e RpfC-CMF. O gene cmf tem um ortólogo, cuja função esta relacionada com o processo de quorum sensing em Dictyostelium. Para confirmar essas interações, RpfC e seus domínios, RpfG, RpfF e CMF foram expressas e purificadas, produzidos anticorpos, e foram efetuados ensaios de ligação in vitro. Em adição, o domínio HD-GYP de RpfG, que apresenta atividade de fosfodiesterase, também foi usado como isca no ensaio de dois híbridos. Interessantemente, a maioria de suas presas foi derivada de domínios GGDEF (diguanilato ciclase) de um grupo de proteínas de Xac. Em bactérias, muitos fenótipos, como a ativação da virulência, a formação de biofilme e a mobilidade, são controlados pelo processo de quorum sensing e por diGMP cíclico. Neste trabalho demonstramos uma ligação direta entre quorum sensing e diGMP cíclico, representada pela interação entre HD-GYP/GGDEF. Finalmente, estudos com um mutante para o gene cmf interrompido, envolvendo formação de biofilme, produção de goma xantana e patogenicidade, evidenciam que CMF tem uma função relevante no processo de quorum sensing em Xanthomonas. / In Xanthomonas a group of genes named regulators of the pathogenicity factors (rpf) control the synthesis of virulence factors as a function of cellular density in a process termed quorum sensing. Alegria (2002) cloned the rpf genes from Xanthomonas axonopodis pv citri (Xac) in the pOBD vector and used them as baits in two hybrid assays against a Xac prey library cloned in the pOAD vector and showed that RpfC interacts with RpfG, RpfF and CMF. Homologous of the cmf gene are found only in amoebas such as Dictyostelium, where plays a central function in the quorum sensing process. In this work, we expressed and purified RpfC and its domains, RpfG, RpfF and CMF and raised antibodies against these polypeptides. In vitro assays demonstrated the following interactions: RpfC-RpfF, RpfC-RpfG and RpfC-CMF. We show that RpfG and CMF interact with the response regulator domain of RpfC, and interactions RpfG and CMF also interact with the histidine phosphotransfer domain of RpfC. In addition, the recently characterized HD-GYP phosphodiesterase domain of RpfG was used as bait in the two hybrid assays. Interestingly, the majority of its preys were derived from a set of Xac proteins that possess GGDEF domains (diguanilate cyclase). In bacteria, many complex processes such virulence, motility and biofilm production are controlled by quorum sensing process and by levels of the second messenger cyclic diGMP. Our results demonstrate a direct link between quorum sensing and diGMP cyclic signaling pathways in the form of a direct physical interaction between the RpfG HD-GYP domain and GGDEF domains. Finally, studies with a Xac cmf-mutant show that CMF plays an important role in the quorum sensing process in Xanthomonas, including biofilm production, synthesis of xanthan gum and pathogenicity.

Les opines sont des molécules produites dans les cellules végétales transformées par l’ADN-T d’A. tumefaciens. Ces opines peuvent être utilisées comme nutriments par le phytopathogène et certaines d’entre elles agissent comme signaux moléculaires contrôlant la dissémination du plasmide de virulence Ti via la signalisation quorum-sensing. Le présent travail vise à une compréhension élargie du rôle des opines au cours des interactions A. tumefaciens-plantes hôtes. En se basant d’abord sur des analyses transcriptomiques, le régulon AccR d’A. tumefaciens C58, contrôlé par les opines agrocinopines, a été défini : celui-ci inclut des fonctions associées (i) à l’assimilation des agrocinopines, (ii) à l’assimilation de la nopaline, (iii) à la signalisation quorum-sensing et la conjugaison du plasmide Ti, (iv) à la conjugaison du plasmide At. La corrélation entre la co-régulation des conjugaisons des plasmides Ti et At et le co-transfert des deux réplicons a en outre été mise en évidence. Dans un second temps, associant des approches de génétique fonctionnelle à des travaux collaboratifs en biologie structurale, l’avantage sélectif conféré par les opines nopaline et octopine à A. tumefaciens au sein des tumeurs végétales a été quantifié. Les bases moléculaires sous-jacentes à cet avantage sélectif, notamment celles associées à la perception et l’importation des deux opines dans le cytoplasme bactérien, ont été décrites. Enfin, en combinant des approches de métabolomique et de génétique inverse avec des tests de conjugaison in planta, les effets opposés de la signalisation GABA d’une part et des signalisations opine et quorum-sensing d’autre part sur la dissémination du plasmide Ti ont été démontrés. En conclusion, nos résultats révèlent l’intrication des signalisations opine, quorum-sensing et GABA au cours de l’interaction A. tumefaciens-plantes hôtes. Ils soulignent en particulier les impacts de cette intrication sur la colonisation de l’hôte ainsi que sur la dissémination des gènes de virulence et d’adaptation à l’environnement tumeur portés par les plasmides Ti et At. / Opines are produced in plant cells transformed with the A. tumefaciens T-DNA. These opines can be used as nutrients by the phytopathogen and some of them act as signaling molecules controlling Ti plasmid dissemination through quorum-sensing. The present study aims at an enlarged understanding of the roles of opines during A. tumefaciens/plant host interactions. First, based on transcriptomic investigations, the agrocinopine-controled AccR regulon from A. tumefaciens C58 was thoroughly characterized. This one includes functions associated with (i) agrocinopines assimilation, (ii) nopaline assimilation, (iii) quorum-sensing and Ti plasmid conjugation, (iv) At plasmid conjugation. Moreover our analysis showed that co-regulation of Ti and At plasmid conjugations correlated with the co-transfer of the two replicons. In a second step using functional genetic and structural biology we quantified the selective advantage conferred to colonizing A. tumefaciens populations by the assimilation of the opines nopaline and octopine. The molecular basis which underlies this selective advantage, especially regarding the sensing and import of the two opines within the bacterial cytoplasm, were also described. Finally combining metabolomics and reverse genetic with in planta conjugation assays we demonstrated the opposite effects of GABA and opine/quorum-sensing signaling on the dissemination of Ti plasmids. In conclusion our results reveal the interlink between opine, quorum-sensing and GABA signaling during A. tumefaciens/plant host interactions. They noticeably highlight the impact of this interlink on host colonization and the dissemination of Ti and At plasmid genes which are critical for the virulence and the adaption of the bacteria to the tumor lifestyle.

O ácido cis-11-metil-2-dodecenóico (DSF), substância utilizada como autoindutor nos sistemas de Quorum Sensing da bactéria Xanthomonas axonopodis pv. citri, foi utilizado como um modelo de estudos para a análise de moléculas secretadas por populações celulares utilizando técnicas eletroanalíticas. Cultivos celulares provenientes de três linhagens diferentes da bactéria Xanthomonas axonopodis pv. citri foram utilizados para os estudos. Uma linhagem selvagem (WT), que produzia DSF em quantidades naturalmente observadas, e duas linhagens geneticamente modificadas. Em uma linhagem (ΔC) a modificação genética resultava em elevada produção de DSF, para a segunda (ΔF) o resultado era a anulação da produção do autoindutor. As principais técnicas analíticas utilizadas foram: voltametria cíclica, eletroforese capilar e cromatografia líquida (com detecção UV-Vis e acoplada a espectrometria de massas), sendo a última para efeitos de comparação. Procedimentos de extração líquido-líquido com solventes orgânicos foram realizados como etapas de pré-tratamento de amostras, visando diminuir a quantidade de interferentes e realizar uma pré-concentração do analito. Três metodologias principais foram adotadas. Uma primeira voltada para a diferenciação dos cultivos celulares, analisando-se ou os sobrenadantes provenientes dos cultivos ou os extratos resultantes dos pré-tratamentos desses sobrenadantes, tendo como principal foco a identificação de um sinal diferencial entre os cultivos que correspondesse às quantidades de DSF, ou seja, inexistente para a linhagem ΔF, de alta intensidade para linhagem ΔC e de intensidade intermediária para a linhagem WT. A segunda metodologia foi baseada no uso de uma molécula modelo para realizar experimentos e obter dados como parâmetros físico-químicos, o ácido láurico (ácido dodecanóico) foi escolhido por sua semelhança estrutural e facilidade de obtenção, curvas de calibração e experimentos de separação de moléculas com estrutura semelhante foram realizados com a técnica de eletroforese capilar. Uma terceira metodologia foi desenvolvida utilizando o padrão do ácido cis-11-metil-2-dodecenóico (DSF), curvas de calibração foram obtidas com o padrão isolado apresentando ótimas linearidades, tanto com a técnica de eletroforese capilar quanto com cromatografia líquida com detecção UV-Vis, experimentos de adição de padrão às amostras também foram executados. Os experimentos realizados com as amostras não apresentaram os resultados esperados, os problemas foram associados principalmente à quantidade de interferentes na amostra e a baixa concentração do analito nos cultivos, sendo que os métodos de extração realizados não foram suficientes para solucioná-los. O insucesso da técnica de voltametria cíclica foi associado ao envenenamento do eletrodo, devido à alta quantidade de compostos orgânicos presentes na amostra, e dúvidas relacionadas à eletroatividade do DSF. As dificuldades encontradas com a técnica de eletroforese capilar foram associadas à alta força iônica da amostra, presença de interferentes e baixa concentração do analito nos cultivos. Mesmo os experimentos realizados com cromatografia líquida acoplada a detecção com espectrometria de massas não atenderam às expectativas, dificultando a elucidação dos problemas encontrados até então e impossibilitando o desenvolvimento de uma metodologia que atendesse aos objetivos propostos. / Cis-11-methyl-2-dodecenoic acid, also known as DSF (autoinducer of the Quorum Sensing system used by the bacteria Xanthomonas axonopodis pv. citri) was explored as a study model for the cell secreted molecules analysis by electroanalytical techniques. Cell cultures from three different cell lines of the bacteria Xanthomonas axonopodis pv. citri were used for this study. A wild type (WT), which produced DSF in naturally observed quantities and two genetically modified ones. One of the lines (ΔC) had a genetic modification that resulted in an elevated production of DSF, and the other (ΔF) had a modification that stopped DSF production. Main analytical techniques used were: cyclic voltammetry, capillary electrophoresis and liquid chromatography (with UV-Vis detection and coupled with mass spectrometry), this last one was used with comparison purposes. Liquid-liquid extractions with organic solvents were realized as sample pre-treatment steps aiming the reduction of interfering species and analyte pre-concentration. Three main methodologies were adopted. One based in the differentiation of cell cultures analyzing or the cell culture supernatants or the resulting extracts from the pre-treatment steps. The main focus was the identification of a differential signal between the cultures that corresponded to the DSF quantities, in other words, null for the ΔF line, high intensity for the ΔC line and a an intermediary intensity for the WT line. The second methodology was based in experiments with a model molecule to obtain some data such as physical-chemistry parameters. Lauric acid (dodecanoic acid) was chosen for its structural similarity and easily acquisition. Calibration curves and similar structure molecules separation experiments were realized using capillary electrophoresis. Third and last methodology was developed using standard cis-11-methyl-2-dodecenoic acid (DSF). Calibration curves were obtained with the isolated standard showing great linearities using both capillary electrophoresis and liquid chromatography with UV-Vis detection. Experiments of standard addiction to the samples were also realized. Experiments using the samples did not show the expected results. Problems found were mainly associated with high amount of interfering species and low analyte concentration at the cultures, extraction methods used were not enough to solve this. The failures with the cyclic voltammetric techniques were associated to electrode poisoning, due to the high amount of organic compounds present at the sample, and DSF lack of electroactivity. Difficulties found with capillary electrophoresis were associated with the samples high ionic strength, presence of interfering species and low analyte concentration. Even liquid chromatography coupled with mass spectrometry experiments didn\'t attended the expectations. Making it difficult to elucidate the problems and not allowing the development of a methodology that could achieve the proposed objectives.

Pseudomonas aeruginosa is an opportunistic human pathogen that infects immunocompromised individuals such as those suffering from burns or the genetic disorder cystic fibrosis. This organism utilizes a cell-cell communication mechanism known as quorum sensing (QS) to coordinate virulence gene expression and biofilm formation. It has three interconnected QS systems, namely las, rhl and pqs. Each system is comprised of autoinducer synthesis genes, lasI, rhlI, and pqsABCDH, and the cognate regulatory genes, lasR, rhlR, and pqsR, respectively. Here, we primarily focused on understanding the regulatory mechanisms of QS, which we investigated at two levels. First, we sought to identify additional activators that regulate QS at the level of the las and rhl systems, and second, we investigated the regulation of downstream genes, particularly biofilm exopolysaccharide genes, by QS. For the first approach, we employed a mutagenesis screen to identify global QS activators. We screened a non-redundant transposon library for mutants deficient in QS-dependent phenotypes. We identified a novel regulator, GidA, a glucose-inhibited cell division protein, that selectively controls QS gene expression posttranscriptionally via RhlR-dependent and –independent pathways. For the second part, we established a regulatory link between QS and Pel exopolysaccharide. We showed that the las system represses Pel and modulates colony biofilm structure through the pqs pathway. LasR mediated colony rugosity via 4-hydroxy-2-alkylquinolines in a PqsR-independent manner, ascribing a novel function to this class of signaling molecules in P. aeruginosa. Taken together, our study highlights the complexity of QS, which involves integration of various regulatory pathways to control downstream processes in response to different environmental conditions. / Graduation date: 2012