Multidrug efflux pumps are membrane proteins that actively transport foreign objects out of cells. The active efflux of these pumps is a critical self-defense mechanism that enables the survival of bacteria under hostile environments. Efflux pump AcrB is a member of the Resistance-Nodulation-Division (RND) super family. In E. coli, it associates with periplasmic protein AcrA and outer membrane channel TolC to extrude a variety of noxious compounds out of cell from both the cytoplasm and the periplasm. My dissertation research focused on two aspects of this multidrug efflux pump: the oligomerization process during the biogenesis of AcrB and its degradation. Oligomerization is an important aspect of the structure and function for many proteins and has been the subject of many studies. However, most of such studies focused on soluble proteins. The oligomerization process of membrane proteins, including AcrB, is rarely explored. In chapter 2, the co-assembly of AcrB variants co-expressed in the same cell was used as a tool to investigate the assembly of AcrB trimers during its bio-production. By monitoring the portion of pure trimers containing only one type of subunit and hybrid trimers containing a mixture of the two kinds of subunits, it was found that the oligomerization of membrane proteins is not a random process as the formation of pure trimer is favored. In chapter 3, the GALLEX system was used to monitor AcrB oligomerization in cells under the native condition. Previously GALLEX has only been used to monitor the oligomerization of small transmembrane proteins. By constructing a series of fusion proteins with different linker length between LexA and AcrB, and optimizing inducer concentration, we finally developed a system that could be used to differentiate AcrB trimers of different oligomerization affinities. While chapters 2 and 3 focus on the trimerization of AcrB, a critical step of its biogenesis, chapters 4 and 5 focus on its life time and degradation. In chapter 4, the life time of AcrB was measured by incorporating non-natural amino acid azidohomoalanine (AHA) into protein translation. Using this method, it was determined that that the half-life of both AcrA and AcrB in E. coli were six days. The surprisingly long lifetime of these detoxification proteins might represent a strategy by the bacteria to conserve energy and maximize their competition niche for survival in a hostile environment. In chapter 5, the degradation process of ssra tagged AcrB was investigated. In-vivo degradation test showed that properly inserted AcrB can be digested after addition of ssra-tag to its C-terminus. It was found that cytoplasmic unfoldase-protease complex ClpXP and chaperone SspB are involved in the degradation. In vitro assay is still being optimized to quantitatively analyze the activity of ClpXP in the degradation of AcrB.

Multiple drug resistance (MDR) has been a severe issue in treatment and recovery from infection.Gram-negative bacteria intrinsically exhibit higher drug tolerance than Gram-positive microbes. In this thesis, two proteins involved in Gram-negative bacterial MDR were studied, AcrB and SurA. Resistance-nodulation-cell division pump AcrAB-TolC is the major MDR efflux system in Gram-negative bacteria and efficiently extrudes a broad range of substances from the cells. To study subtle conformational changes of AcrB in vivo, a reporter platform was designed. Cysteine pairs were introduced into different regions in the periplasmic domain of the protein, and the extents of disulfide bond formation were examined. Using this platform, an inactive mutant, AcrB∆loop, was created that existed as a well-folded monomer in vivo. Next, random mutageneses were performed on a functionally compromised mutant, AcrBP223G, to identify residues that restored the function loss. The mechanism of function restoration was examined. SurA is a periplasmic molecular chaperone for outer membrane biogenesis. Deletion of SurA decreased outer membrane density and bacterial drug resistance. The dependence of SurA function on structural flexibility and stability was examined. In addition, the effect of molecular crowding on SurA interaction with its outer membrane protein substrates was examined.

Acinetobacter baumannii is an opportunistic pathogen which has been implicated in a variety of nosocomial infections among immunocompromised patients worldwide. Recently, Multi-drug resistant (MDR) isolates of A. baumannii have been isolated from military personnel returning from service in Iraq and Afghanistan. Antibiotic resistance of A. baumannii has limited the number of active antibacterial, making very difficult to treat these types of infections. This work investigated the role of Resistance-Nodulation-cell Division (RND) efflux pumps in the antibiotic resistance mechanism of A. baumannii. Expression of six different RND pumps was analyzed in clinical isolates of A. baumannii. A novel RND family pump, AdeMNO, was found to be present in a majority of isolates. The adeMNO operon was cloned, sequenced, and characterized using the single copy gene expression system in an efflux sensitized surrogate Pseudomonas aeruginosa strain. Antibiotics, trimethoprim, chloramphenicol, and clindamicin were identified as the substrates of this pump. In order to understand the mechanisms of regulation of adeMNO operon, a putative regulator belonging to the lysR-family was identified, cloned, and sequenced from the upstream region of the operon. Promoter regions of the adeMNO operon were also sequenced from various clinical isolates and sequence polymorphisms identified that could be implicated in the regulation of adeMNO expression. / UOIT

Staphylococcus aureus é uma bactéria que pode ser encontrada colonizando diversas partes do corpo humano, entretanto os diversos fatores de virulência que a bactéria possui, ancorados a sua superfície ou excretados para o meio extracelular, tornam essa bactéria um potencial patógeno, causando infecções de pele e tecidos moles, osteomielite, infecções respiratórias, infecções relacionadas a cateteres e outros dispositivos e bacteremia. Um dos fatores de virulência da bactéria, é a habilidade em formar biofilmes. Biofilmes são comunidades bacterianas tridimensionais complexas, que vivem organizadas e aderidas a uma superfície biótica ou abiótica, embebidas em uma matriz exopolimérica. Cerca de 80% das bactérias vivem organizadas na forma de biofilme, pois nestas estruturas são menos sensíveis aos antibióticos e à resposta imune do hospedeiro. A habilidade de S. aureus em formar biofilme é importante pois o torna uma das principais bactérias que infecta dispositivos médicos e implantes, aumentando a morbidade e mortalidade dos pacientes que apresentam esse tipo de infecção. Os medicamentos da classe dos β-lactâmicos eram a principal escolha para o tratamento de S. aureus, entretanto nos últimos anos essa bactéria adquiriu resistência a esses antimicrobianos, através da aquisição do gene mecA, tornando escassa as opções terapêuticas. Como se não bastasse, os biofilmes bacterianos são particularmente mais resistentes a tratamentos com antibióticos, não só devido ao aumento da transmissão de mecanismos de resistência dentro da comunidade, mas também por causa das limitações de difusão da droga colocados pela matriz extracelular, inativação de antibióticos pela alta concentração de íons de metal e baixo pH, entre outros fatores. Combinados, esses atributos tornam o biofilme bacteriano em torno de 1000 vezes mais tolerante e/ou resistente aos antimicrobianos comparado às células planctônicas. A investigação de estudos epidemiológicos para prevenção dessas infecções, bom como de novas estratégias para prevenção e tratamento de infecções por biofilmes, especialmente em isolados clínicos sabidamente multirresistentes, é urgentemente necessária. Dentre estas estratégias estão a pesquisa de diferentes mecanismos ou substâncias capazes de provocar a inibição da formação ou a erradicação do biofilme formado. Neste contexto, 8 os sistemas de bombas de efluxo e inibidores de bombas de efluxo representam uma fonte promissora de erradicação do biofilme formado. O principal objetivo deste estudo é investigar características clínico-epidemiológicas em isolados clínicos que estejam associadas a formação de biofilme, bem como investigar o papel de bombas de efluxo, inibidores dessas bombas e novos genes envolvidos na habilidade de isolados clínicos de S. aureus em formar biofilme. O capítulo 1 associa características clínicas e epidemiológicas com a habilidade de formação de biofilme. O capítulo 2 mostra o papel da adição de antimicrobianos na inibição e erradicação de biofilmes, a associação com inibidores de bomba de efluxo para melhor entender os sistemas de bomba de efluxo na capacidade desses isolados em formar biofilme e por último, novos genes que participam desse processo, em isolados clínicos de MRSA. Este estudo permite planejar ações preventivas para essas infecções relacionadas a biofilmes. Além disso, demonstra que os sistemas de bombas de efluxo parecem ser alvos promissores para erradicar infecções associadas a biofilmes bacterianos. / Staphylococcus aureus can be found colonizing the human body, however its virulence factors anchored to its surface or secreted into the extracellular medium, makes this bacteria as a potential pathogenic, causing skin and soft tissue infections, osteomyelitis, respiratory infections, catheter-related and other devices infections and bacteremia. One of the virulence factors that bacteria produce is the ability to form biofilms. Biofilms are complex three-dimensional bacterial communities, living organized and attached on a biotic or abiotic surface, embedded in a matrix exopolimérica. About 80% of live bacteria are organized in the form of biofilms because in these structures are less sensitive to antibiotic and the host immune response. The ability of S. aureus to form biofilms is important because it makes it one of the main bacteria that infects medical devices and implants, increasing patient morbidity and mortality. The class of β-lactam drugs used to be main choice for the treatment of S. aureus infections, however in recent years the bacteria acquired resistance to these antibiotics by acquiring mecA gene, so therapeutic options becoming scarce. Besides that, bacterial biofilms are particularly resistant to antibiotic treatments, not only due to increased transmission resistance mechanisms within the community, but also because limitations in drug diffusion by extracellular matrix, inactivation of antibiotics due to high concentration of metal ions and low pH, and other factors. Combined, these attributes make the bacterial biofilm around 1000 times more tolerant and / or resistant to antimicrobial compared to planktonic cells. Investigation of epidemiological studies to prevent such infections, as well as new strategies for prevention and treatment of biofilm infections, especially in known multidrug-resistant clinical isolates, is urgently needed. Among these strategies we could list the different search engines or substances capable of causing or inhibiting the formation of biofilm eradication. In this context, system efflux pumps and efflux pump inhibitors represent a promising source of biofilm eradication. The aim of this study is to investigate the clinical and epidemiological characteristics in clinical isolates that are associated with biofilm formation and investigate the role of efflux pumps and inhibitors of these pumps in the ability of S. 10 aureus clinical isoltes to form biofilms. The chapter 1 associates clinical and epidemiological characteristics with biofilm formation ability. Chapter 2 shows the role of the addition of antimicrobials in inhibition and eradication of biofilms, the association with efflux pump inhibitors to better understand the efflux pump systems in the ability of these isolates to form biofilm and, finally, new genes important in MRSA clincal isolates biofilm formation. This study allows planning preventive actions for these biofilm-related infections. In addition, it demonstrates that efflux pump systems appear to be promising targets for eradicating infections associated with bacterial biofilms.

Staphylococcus aureus é uma bactéria que pode ser encontrada colonizando diversas partes do corpo humano, entretanto os diversos fatores de virulência que a bactéria possui, ancorados a sua superfície ou excretados para o meio extracelular, tornam essa bactéria um potencial patógeno, causando infecções de pele e tecidos moles, osteomielite, infecções respiratórias, infecções relacionadas a cateteres e outros dispositivos e bacteremia. Um dos fatores de virulência da bactéria, é a habilidade em formar biofilmes. Biofilmes são comunidades bacterianas tridimensionais complexas, que vivem organizadas e aderidas a uma superfície biótica ou abiótica, embebidas em uma matriz exopolimérica. Cerca de 80% das bactérias vivem organizadas na forma de biofilme, pois nestas estruturas são menos sensíveis aos antibióticos e à resposta imune do hospedeiro. A habilidade de S. aureus em formar biofilme é importante pois o torna uma das principais bactérias que infecta dispositivos médicos e implantes, aumentando a morbidade e mortalidade dos pacientes que apresentam esse tipo de infecção. Os medicamentos da classe dos β-lactâmicos eram a principal escolha para o tratamento de S. aureus, entretanto nos últimos anos essa bactéria adquiriu resistência a esses antimicrobianos, através da aquisição do gene mecA, tornando escassa as opções terapêuticas. Como se não bastasse, os biofilmes bacterianos são particularmente mais resistentes a tratamentos com antibióticos, não só devido ao aumento da transmissão de mecanismos de resistência dentro da comunidade, mas também por causa das limitações de difusão da droga colocados pela matriz extracelular, inativação de antibióticos pela alta concentração de íons de metal e baixo pH, entre outros fatores. Combinados, esses atributos tornam o biofilme bacteriano em torno de 1000 vezes mais tolerante e/ou resistente aos antimicrobianos comparado às células planctônicas. A investigação de estudos epidemiológicos para prevenção dessas infecções, bom como de novas estratégias para prevenção e tratamento de infecções por biofilmes, especialmente em isolados clínicos sabidamente multirresistentes, é urgentemente necessária. Dentre estas estratégias estão a pesquisa de diferentes mecanismos ou substâncias capazes de provocar a inibição da formação ou a erradicação do biofilme formado. Neste contexto, 8 os sistemas de bombas de efluxo e inibidores de bombas de efluxo representam uma fonte promissora de erradicação do biofilme formado. O principal objetivo deste estudo é investigar características clínico-epidemiológicas em isolados clínicos que estejam associadas a formação de biofilme, bem como investigar o papel de bombas de efluxo, inibidores dessas bombas e novos genes envolvidos na habilidade de isolados clínicos de S. aureus em formar biofilme. O capítulo 1 associa características clínicas e epidemiológicas com a habilidade de formação de biofilme. O capítulo 2 mostra o papel da adição de antimicrobianos na inibição e erradicação de biofilmes, a associação com inibidores de bomba de efluxo para melhor entender os sistemas de bomba de efluxo na capacidade desses isolados em formar biofilme e por último, novos genes que participam desse processo, em isolados clínicos de MRSA. Este estudo permite planejar ações preventivas para essas infecções relacionadas a biofilmes. Além disso, demonstra que os sistemas de bombas de efluxo parecem ser alvos promissores para erradicar infecções associadas a biofilmes bacterianos. / Staphylococcus aureus can be found colonizing the human body, however its virulence factors anchored to its surface or secreted into the extracellular medium, makes this bacteria as a potential pathogenic, causing skin and soft tissue infections, osteomyelitis, respiratory infections, catheter-related and other devices infections and bacteremia. One of the virulence factors that bacteria produce is the ability to form biofilms. Biofilms are complex three-dimensional bacterial communities, living organized and attached on a biotic or abiotic surface, embedded in a matrix exopolimérica. About 80% of live bacteria are organized in the form of biofilms because in these structures are less sensitive to antibiotic and the host immune response. The ability of S. aureus to form biofilms is important because it makes it one of the main bacteria that infects medical devices and implants, increasing patient morbidity and mortality. The class of β-lactam drugs used to be main choice for the treatment of S. aureus infections, however in recent years the bacteria acquired resistance to these antibiotics by acquiring mecA gene, so therapeutic options becoming scarce. Besides that, bacterial biofilms are particularly resistant to antibiotic treatments, not only due to increased transmission resistance mechanisms within the community, but also because limitations in drug diffusion by extracellular matrix, inactivation of antibiotics due to high concentration of metal ions and low pH, and other factors. Combined, these attributes make the bacterial biofilm around 1000 times more tolerant and / or resistant to antimicrobial compared to planktonic cells. Investigation of epidemiological studies to prevent such infections, as well as new strategies for prevention and treatment of biofilm infections, especially in known multidrug-resistant clinical isolates, is urgently needed. Among these strategies we could list the different search engines or substances capable of causing or inhibiting the formation of biofilm eradication. In this context, system efflux pumps and efflux pump inhibitors represent a promising source of biofilm eradication. The aim of this study is to investigate the clinical and epidemiological characteristics in clinical isolates that are associated with biofilm formation and investigate the role of efflux pumps and inhibitors of these pumps in the ability of S. 10 aureus clinical isoltes to form biofilms. The chapter 1 associates clinical and epidemiological characteristics with biofilm formation ability. Chapter 2 shows the role of the addition of antimicrobials in inhibition and eradication of biofilms, the association with efflux pump inhibitors to better understand the efflux pump systems in the ability of these isolates to form biofilm and, finally, new genes important in MRSA clincal isolates biofilm formation. This study allows planning preventive actions for these biofilm-related infections. In addition, it demonstrates that efflux pump systems appear to be promising targets for eradicating infections associated with bacterial biofilms.

Master of Science / Department of Plant Pathology / Revathi Govind / Clostridium difficile, a gram-positive, anaerobic bacterium, is a major cause of antibiotic-related diarrhea and pseudomembraneous colitis. In the last decades, C. difficile has emerged as a major threat because of its tendency to cause frequent and severe disease. Because of the severity of the infection and its high rate of recurrence, there is a significant financial burden on healthcare systems. Antibiotic treatments are a primary risk factor for the development of C. difficile infection because they disrupt the normal gut flora in the host, enabling the antibiotic resistant bacterium to colonize the colon. Most of the resistance mechanisms in C. difficile reported to date can be classified as either antibiotic-degrading enzymes or modification of target sites. Another mechanism that can contribute to antibiotic resistance in C. difficile is the extrusion of antimicrobial compounds by efflux pumps. The goal of this project was to provide initial insights into the roles and mechanisms of a putative efflux pump complex. To do this, a number of experiments were designed to provide information about the structures, localization, and functions of this protein complex. It was determined that acidic pH conditions and a small number of antimicrobials, including inorganic compounds, organic compounds, fungicides, and antibiotics, inhibit growth of a C. difficile mutant lacking this pump system. Interestingly, higher NaCl in the medium and alkaline pH seem to promote the growth of a C. difficile mutant lacking this pump or, surprisingly, only inhibit growth of the wild type strain. The experiments performed in this project suggest that this efflux pump might have an essential role in C. difficile physiology, possibly by serving as an efflux pump for toxic metabolites.

Staphylococcus aureus é uma bactéria que pode ser encontrada colonizando diversas partes do corpo humano, entretanto os diversos fatores de virulência que a bactéria possui, ancorados a sua superfície ou excretados para o meio extracelular, tornam essa bactéria um potencial patógeno, causando infecções de pele e tecidos moles, osteomielite, infecções respiratórias, infecções relacionadas a cateteres e outros dispositivos e bacteremia. Um dos fatores de virulência da bactéria, é a habilidade em formar biofilmes. Biofilmes são comunidades bacterianas tridimensionais complexas, que vivem organizadas e aderidas a uma superfície biótica ou abiótica, embebidas em uma matriz exopolimérica. Cerca de 80% das bactérias vivem organizadas na forma de biofilme, pois nestas estruturas são menos sensíveis aos antibióticos e à resposta imune do hospedeiro. A habilidade de S. aureus em formar biofilme é importante pois o torna uma das principais bactérias que infecta dispositivos médicos e implantes, aumentando a morbidade e mortalidade dos pacientes que apresentam esse tipo de infecção. Os medicamentos da classe dos β-lactâmicos eram a principal escolha para o tratamento de S. aureus, entretanto nos últimos anos essa bactéria adquiriu resistência a esses antimicrobianos, através da aquisição do gene mecA, tornando escassa as opções terapêuticas. Como se não bastasse, os biofilmes bacterianos são particularmente mais resistentes a tratamentos com antibióticos, não só devido ao aumento da transmissão de mecanismos de resistência dentro da comunidade, mas também por causa das limitações de difusão da droga colocados pela matriz extracelular, inativação de antibióticos pela alta concentração de íons de metal e baixo pH, entre outros fatores. Combinados, esses atributos tornam o biofilme bacteriano em torno de 1000 vezes mais tolerante e/ou resistente aos antimicrobianos comparado às células planctônicas. A investigação de estudos epidemiológicos para prevenção dessas infecções, bom como de novas estratégias para prevenção e tratamento de infecções por biofilmes, especialmente em isolados clínicos sabidamente multirresistentes, é urgentemente necessária. Dentre estas estratégias estão a pesquisa de diferentes mecanismos ou substâncias capazes de provocar a inibição da formação ou a erradicação do biofilme formado. Neste contexto, 8 os sistemas de bombas de efluxo e inibidores de bombas de efluxo representam uma fonte promissora de erradicação do biofilme formado. O principal objetivo deste estudo é investigar características clínico-epidemiológicas em isolados clínicos que estejam associadas a formação de biofilme, bem como investigar o papel de bombas de efluxo, inibidores dessas bombas e novos genes envolvidos na habilidade de isolados clínicos de S. aureus em formar biofilme. O capítulo 1 associa características clínicas e epidemiológicas com a habilidade de formação de biofilme. O capítulo 2 mostra o papel da adição de antimicrobianos na inibição e erradicação de biofilmes, a associação com inibidores de bomba de efluxo para melhor entender os sistemas de bomba de efluxo na capacidade desses isolados em formar biofilme e por último, novos genes que participam desse processo, em isolados clínicos de MRSA. Este estudo permite planejar ações preventivas para essas infecções relacionadas a biofilmes. Além disso, demonstra que os sistemas de bombas de efluxo parecem ser alvos promissores para erradicar infecções associadas a biofilmes bacterianos. / Staphylococcus aureus can be found colonizing the human body, however its virulence factors anchored to its surface or secreted into the extracellular medium, makes this bacteria as a potential pathogenic, causing skin and soft tissue infections, osteomyelitis, respiratory infections, catheter-related and other devices infections and bacteremia. One of the virulence factors that bacteria produce is the ability to form biofilms. Biofilms are complex three-dimensional bacterial communities, living organized and attached on a biotic or abiotic surface, embedded in a matrix exopolimérica. About 80% of live bacteria are organized in the form of biofilms because in these structures are less sensitive to antibiotic and the host immune response. The ability of S. aureus to form biofilms is important because it makes it one of the main bacteria that infects medical devices and implants, increasing patient morbidity and mortality. The class of β-lactam drugs used to be main choice for the treatment of S. aureus infections, however in recent years the bacteria acquired resistance to these antibiotics by acquiring mecA gene, so therapeutic options becoming scarce. Besides that, bacterial biofilms are particularly resistant to antibiotic treatments, not only due to increased transmission resistance mechanisms within the community, but also because limitations in drug diffusion by extracellular matrix, inactivation of antibiotics due to high concentration of metal ions and low pH, and other factors. Combined, these attributes make the bacterial biofilm around 1000 times more tolerant and / or resistant to antimicrobial compared to planktonic cells. Investigation of epidemiological studies to prevent such infections, as well as new strategies for prevention and treatment of biofilm infections, especially in known multidrug-resistant clinical isolates, is urgently needed. Among these strategies we could list the different search engines or substances capable of causing or inhibiting the formation of biofilm eradication. In this context, system efflux pumps and efflux pump inhibitors represent a promising source of biofilm eradication. The aim of this study is to investigate the clinical and epidemiological characteristics in clinical isolates that are associated with biofilm formation and investigate the role of efflux pumps and inhibitors of these pumps in the ability of S. 10 aureus clinical isoltes to form biofilms. The chapter 1 associates clinical and epidemiological characteristics with biofilm formation ability. Chapter 2 shows the role of the addition of antimicrobials in inhibition and eradication of biofilms, the association with efflux pump inhibitors to better understand the efflux pump systems in the ability of these isolates to form biofilm and, finally, new genes important in MRSA clincal isolates biofilm formation. This study allows planning preventive actions for these biofilm-related infections. In addition, it demonstrates that efflux pump systems appear to be promising targets for eradicating infections associated with bacterial biofilms.

Antimycotics such as fluconazole are frequently used to treat C. albicans infections of the oral mucosa. Prolonged treatment of the fungal infection with fluconazole pose a risk to resistance development. C. albicans can adapt to these stressful environmental changes by regulation of gene expression or by producing genetically altered variants that arise in the population. Adapted variants frequently carry activating mutations in zinc cluster transcription factors, which cause the upregulation of their target genes, including genes encoding efflux pumps that confer drug resistance. MDR1, regulated by the zinc cluster transcription factor Mrr1, as well as CDR1 and CDR2, regulated by the zinc cluster transcription factor Tac1, are well-known examples of genes encoding efflux pumps that extrude the antimycotic fluconazole from the fungal cell and thus contribute to the survival of the fungus. In this study, it was investigated if C. albicans can develop resistance to the antimicrobial peptide histatin 5, which serves as the first line of defence in the oral cavity of the human host. Recently, it was shown that C. albicans transports histatin 5 outside of the Candia cell via the efflux pump Flu1. As efflux pumps are often regulated by zinc cluster transcription factors, the Flu1 efflux pump could also be regulated by a zinc cluster transcription factor which could in a hyperactive form upregulate the expression of the efflux pump, resulting in increased export of histatin 5 and consequently in histatin 5 resistance. In order to find a zinc cluster transcription factor that upregulates FLU1 expression, a comprehensive library of C. albicans strains containing artificially activated forms of zinc cluster transcription factors was screened for suitable candidates. The screening was conducted on medium containing mycophenolic acid because mycophenolic acid is also a substrate of Flu1 and a strain expressing a hyperactive zinc cluster transcription factor that upregulates FLU1 expression should exhibit an easily recognisable mycophenolic acid-resistant phenotype. Further, FACS analysis, quantitative real-time RT-PCR analysis, broth microdilution assays as well as histatin 5 assays were conducted to analyse the mechanism and the regulation of histatin 5 resistance. Several zinc cluster transcription factors caused mycophenolic acid resistance and upregulated FLU1 expression. Of those, only hyperactive Mrr1 was able to confer increased histatin 5 resistance. Finding Mrr1 to confer histatin 5 resistance was highly interesting as fluconazole-resistant strains with naturally occurring Mrr1 gain of function mutations exist, which were isolated from HIV-infected patients with oral candidiasis. These Mrr1 gain of function mutations as well as artificially activated Mrr1 cause fluconazole resistance by upregulation of the efflux pump MDR1 and other target genes. In the course of the study, it was found that expression of different naturally occurring MRR1 gain-of-function mutations in the SC5314 wild type background caused increased FLU1 expression and increased histatin 5 resistance. The same was true for fluconazole-resistant clinical isolates with Mrr1 gain of function mutations, which also caused the overexpression of FLU1. Those cells were less efficiently killed by histatin 5 dependent on Mrr1. Surprisingly, FLU1 contributed only little to histatin 5 resistance, rather, overexpression of MDR1 mainly contributed to the Mrr1-mediated histatin 5 resistance, but also additional Mrr1-target genes were involved. These target genes are yet to be uncovered. Moreover, if a link between the yet unknown Mrr1-target genes contributing to fluconazole resistance and increased histatin 5 resistance can be drawn remains to be discovered upon finding of the responsible target genes. Collectively, this study contributes to the understanding of the impact of prolonged antifungal exposure on the interaction between host and fungus. Drug therapy can give rise to resistance evolution resulting in strains that have not only developed resistance to fluconazole but also to an innate host mechanism, which allows adaption to the host niche even in the absence of the drug. / Antimykotika wie Fluconazol werden häufig zur Behandlung von C. albicans Infektionen der Mundschleimhaut verwendet. Dabei stellt eine langzeitige Behandlung der Pilzinfektion mit Fluconazol ein Risiko zur Resistenzentwicklung dar. C. albicans kann sich an solche Umweltveränderungen anpassen, indem es die Genexpression reguliert oder genetisch veränderte Varianten produziert, welche in der Population entstehen. Adaptierte Varianten tragen häufig aktivierende Mutationen in Zink-Cluster-Transkriptionsfaktoren, welche die Hochregulierung der Expression von Genen verursachen, darunter solche, die für Multidrug-Effluxpumpen kodieren und dadurch Antimykotikaresistenz verleihen können. MDR1, reguliert durch den Zink-Cluster-Transkriptionsfaktor Mrr1, sowie CDR1 und CDR2, reguliert durch den Zink-Cluster-Transkriptionsfaktor Tac1, sind bekannte Beispiele für Effluxpumpen, die das Antimykotikum Fluconazol aus der Pilzzelle extrudieren und somit zum Überleben der Pilzzelle beitragen. In dieser Arbeit wurde untersucht, ob C. albicans eine Resistenz gegen das antimikrobielle Peptid Histatin 5 entwickeln kann, das in der Mundhöhle des menschlichen Wirtes als erste Verteidigungsbarriere gegen den Pilz dient. Kürzlich wurde gezeigt, dass C. albicans Histatin 5 über die Effluxpumpe Flu1 aus der Candia-Zelle heraustransportiert (Li et al., 2013). Da Effluxpumpen häufig durch Zink-Cluster-Transkriptionsfaktoren reguliert werden, könnte auch die Flu1-Effluxpumpe durch solch einen Transkriptionsfaktor reguliert werden, der in einer hyperaktiven Form die Expression der Effluxpumpe hochregulieren könnte, was wiederrum zu einem erhöhten Export von Histatin 5 und folglich zur Histatin 5 Resistenz führen könnte. Um einen Zink-Cluster-Transkriptionsfaktor zu finden, der die FLU1-Expression hochreguliert, wurde mit Hilfe einer Bibliothek von C. albicans-Stämmen, die künstlich aktivierte Formen von Zink-Cluster-Transkriptionsfaktoren enthält, nach geeigneten Kandidaten gesucht. Das Screening wurde auf Mycophenolsäure-haltigem Medium durchgeführt, da Mycophenolsäure ebenfalls ein Substrat von Flu1 ist. Folglich sollte ein Stamm mit hyperaktivem Zink-Cluster-Transkriptionsfaktor, welcher die FLU1-Expression hochreguliert, einen leicht erkennbaren Mycophenolsäure-resistenten Phänotyp aufweisen. Weiterhin wurden FACS-Analysen, quantitative real-time RT-PCR-Analysen, Broth microdilution-Assays sowie Histatin 5-Assays durchgeführt, um den Mechanismus und die Regulierung der Histatin-5-Resistenz zu analysieren. Mehrere Zink-Cluster-Transkriptionsfaktoren verursachten Mycophenolsäure-Resistenz und erhöhten die FLU1-Expression. Von diesen war nur hyperaktives Mrr1 in der Lage, eine erhöhte Histatin-5-Resistenz zu verleihen. Das Auffinden von Mrr1 als Regulator der Histatin 5-Resistenz war hochinteressant, da fluconazolresistente Stämme mit natürlich vorkommenden MRR1 gain-of-function Mutationen existieren, die aus HIV-infizierten Patienten mit oropharyngealer Candidiasis isoliert wurden. Diese gain-of-function Mutationen sowie künstlich aktivierendes Mrr1 verursachen Fluconazol-Resistenz durch Hochregulation der Effluxpumpe MDR1 und anderer Zielgene. Im Verlauf der Studie wurde herausgefunden, dass verschiedene natürlich vorkommende MRR1 gain-of-function Mutationen im SC5314 Wildtyp Hintergrund eine erhöhte FLU1-Expression und eine erhöhte Histatin-5-Resistenz verursachten. Das Gleiche galt für Fluconazol-resistente klinische Isolate mit Mrr1 gain-of-function Mutationen, welche die Überexpression von FLU1 verursachten. Zellen dieser Isolate wurden, abhängig von Mrr1, weniger wirksam durch Histatin 5 abgetötet. Überraschenderweise trug FLU1 nur wenig zur Histatin-5-Resistenz bei, vielmehr trug die Überexpression von MDR1 hauptsächlich zur Mrr1-vermittelten Histatin-5-Resistenz bei, aber auch weitere Mrr1-Zielgene waren daran beteiligt. Diese Mrr1-Zielgene gilt es nun noch zu entdecken. Ob ein Zusammenhang zwischen diesen noch unbekannten Mrr1-Zielgenen hergestellt werden kann, die zur Fluconazolresistenz sowie zu einer erhöhten Histatin-5-Resistenz beitragen, wird erst nach dem Auffinden der verantwortlichen Zielgene geprüft werden können. Zusammenfassend trägt diese Studie zum Verständnis der Auswirkungen einer anhaltenden antimykotischen Exposition auf die Interaktion zwischen Wirt und Pilz bei. Eine medikamentöse Therapie kann zu einer Resistenzentwicklung führen, aus der Stämme hervorgehen, welche nicht nur eine Resistenz gegen Fluconazol entwickelt haben, sondern gleichzeitig eine Resistenz gegen einen angeborenen Wirtsabwehrmechanismus, der eine Adaption an die Wirtsnische auch in Abwesenheit des Antimykotikums ermöglicht.

Bacterial antibiotic resistance is a globally recognized problem that has prompted extensive research into novel antimicrobial compounds. This dissertation describes research focusing on two types of potential antimicrobial molecules, organometallic compounds (OMC) and peptide nucleic acids (PNA). Organometallic compounds show promise as antimicrobial drugs because of their structural difference from conventional antibiotics and antimicrobials, and because of the ability to "tune" their chemical and biological properties by varying ligand attachments. Peptide nucleic acids, when linked to a cell-penetrating peptide (CPP), can suppress bacterial gene expression by an antisense mechanism and are attractive candidates for antimicrobial drugs because they bind strongly to target nucleic acids and are resistant to nucleases. Chapters 1 and 2 of the dissertation provide an introduction and broad literature review to frame the experimental questions addressed. Chapter 3 describes work to test the cytotoxicity and cellular penetration capabilities of novel OMCs by evaluating their effects on J774A.1 murine macrophage-like cells that were either uninfected or were infected with Mycobacterium bovis BCG. Results indicate that OMCs with an iridium (Ir) metal center and an amino acid ligand show minimal cytotoxicity against eukaryotic cells but likely do not penetrate the intracellular compartment in significant amounts. Chapter 4 presents research into in vitro effects of CPP-PNAs targeting the tetA and tetR antibiotic resistance genes (CPP-anti-tetA PNA and CPP-anti-tetR PNA, respectively) in tetracycline-resistant Salmonella enterica ssp. enterica serovar Typhimurium DT104 (DT104). Through the use of modified minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays it was shown that both the CPP-anti-tetA PNA and CPP-anti-tetR PNA increase tetracycline susceptibility in DT104. Chapter 5 explores the molecular mechanism of the CPP-anti-tetA PNA and CPP-anti-tetR PNA through the use of reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Results indicate good specificity of the CPP-anti-tetA PNA for its nucleic acid target as evidenced by suppression of tetA mRNA expression in DT104 cultures treated with a combination of tetracycline and the PNA. Chapter 6 describes the development of a mouse model of DT104 infection using BALB/c mice, followed by implementation of that model to test in vivo antimicrobial effects of the CPP-anti-tetA PNA and the CPP-Sal-tsf PNA, which targets expression of the essential tsf gene. An optimal dose of DT104 was identified that causes clinical illness within 2-4 days. At the doses tested, concurrent treatment of infected mice with tetracycline and the CPP-anti-tetA PNA or with the CPP-Sal-tsf PNA alone did not have a protective effect. Final conclusions are 1) that further research with the OMCs should focus on compounds with an Ir center and an amino acid ligand, and should explore ways to enhance intracellular penetration, 2) that the in vitro results of the PNA studies suggest that PNAs targeting expression of antibiotic resistance genes could allow for repurposing of antibiotics to which bacteria are resistant, and 3) additional study of the behavior of PNAs in vivo is advised. / Doctor of Philosophy / Antibiotic-resistant bacteria are increasingly recognized as a threat to global health, and new antibacterial drugs are urgently needed. Before a chemical compound can advance far in the journey to becoming a new drug it must be tested for toxicity against mammalian cells. A portion of this dissertation research involved testing the toxicity of several organometallic compounds (OMCs) previously shown to have antibacterial potential. Mouse-derived mammalian cells were treated with several of the OMCs, and initial results indicated that one of the OMCs is non-toxic and is likely a safe option for additional analysis. This OMC was further tested to see if it could inhibit mycobacterial growth inside of the mammalian cells. It did not effectively clear bacteria from inside of the mammalian cells, likely because of poor penetration of the cell membrane. Further research with this compound should focus on ways to effectively transport the OMC inside infected mammalian cells so that it can reach the bacteria it is meant to target. A second portion of this research involved using a peptide nucleic acid (PNA) to try and reverse tetracycline antibiotic resistance in the bacterial strain Salmonella enterica ssp. enterica serovar Typhimurium DT104 (DT104). Peptide nucleic acids are short linear molecules that can bind strongly to complementary DNA and RNA sequences and thus be used to interfere with expression of specific genes. A PNA was designed to inhibit expression of the bacterial tetA gene that codes for a protein called the TetA tetracycline efflux pump, which imparts resistances to tetracycline. Treating the bacteria with the PNA resulted in a lower dose of tetracycline needed to inhibit bacterial growth, indicating a successful increase in tetracycline susceptibility. By using a molecular analysis technique called reversetranscriptase quantitative polymerase chain reaction (RT-qPCR), it was possible to measure the amount of tetA messenger RNA (mRNA) in cultures of DT104 treated only with tetracycline or with a combination of tetracycline and the PNA. As expected, bacteria treated with both the antibiotic and the PNA had less tetA mRNA than the cultures treated only with tetracycline, supporting the hypothesis that the PNA prevents the bacteria from effectively expressing the tetA gene. The PNA was next used in conjunction with tetracycline as an experimental treatment for mice infected with DT104. The PNA did not provide the expected protective effect under these circumstances. The overall conclusion for this part of the research is that PNAs offer an exciting potential avenue for counteracting antibiotic resistance, but additional experimentation is needed. Future research should focus on investigating more effective ways to get the PNAs inside the bacteria and on understanding more about how the PNAs behave in live animals. Several other PNAs targeting different genes involved in antibiotic resistance or essential bacterial functions were also tested against DT104 with variable success.

La surexpression des pompes d’efflux (PE) appartenant à la famille Resistance-Nodulation-Division (RND) est l’un des contributeurs majeurs de la multirésistance (MDR) et la pathogénicité des bactéries Gram-négatives. Ces transporteurs sont capables d'expulser à l’extérieur de la cellule bactérienne différentes classes d'antibiotiques, ce qui contribue de manière significative à l'échec thérapeutique du traitement des maladies infectieuses. Dans ce contexte, les PEs sont des cibles intéressantes pour la découverte de nouveaux antimicrobiens. Afin de combattre ce mécanisme de résistance, des inhibiteurs des pompes d’efflux (EPIs) sont développés comme adjuvants d'antibiotiques dans le but de restaurer ou d'améliorer leur activité. L'archétype AcrAB-TolC est particulièrement répandu chez les espèces d’Enterobacter pertinentes en clinique (pathogènes « ESKAPE »). Cette étude décrit une stratégie basée sur des analogues des fluoroquinolones pour le drug design des EPIs, contre la pompe AcrB chez E. aerogenes. Ainsi, la synthèse et l'évaluation microbiologique des dérivés de quinazoline-4(3H)-one ont été effectuées. Les propriétés structurales et moléculaires des composés testés (i.e. rigidité et flexibilité) ont également été étudiées. Pour cela, de nouveaux scaffolds ont été évaluées. Plusieurs molécules ont montré une augmentation de la sensibilité des bactéries à la norfloxacine et au chloramphénicol. Les résultats obtenus, appuyés par la modélisation moléculaire, suggèrent que la flexibilité moléculaire et la nature des fonctions chimiques des EPIs jouent un rôle essentiel dans l'amélioration de l'activité et la sélectivité vis-à-vis des fluoroquinolones. / Overexpression of Resistance-Nodulation-Division (RND) efflux pumps (EP) is a major contributor in multidrug resistance (MDR) and pathogenicity in Gram-negative bacteria. These transporters are able to expel out of the bacterial cell clinically important antibiotic classes, contributing in a significant manner to the treatment failure of infectious diseases. With the worrying levels of bacterial resistance reported worldwide and the continuous spreading of MDR pathogens, EPs are interesting targets for the discovery of new antimicrobial drugs. Therefore, to overcome this mechanism, efflux pump inhibitors (EPIs) are being developed as adjuvants in order to restore or improve the activity of usual antibiotics. The AcrAB-TolC archetype is particularly widespread in Enterobacter spp. presenting clinical relevance (ESKAPE pathogens). In this study, we described the drug design strategy based on fluoroquinolone antibiotic analogs, against the AcrB pump of E. aerogenes. Thus, synthesis and microbiological evaluation of quinazolin-4(3H)-one derivatives were performed. The structural and molecular properties of the tested compounds (i. e. rigidity and flexibility) were also investigated. In this purpose, a scaffold hopping of the quinazolinone core to homologous benzoquinazolinones and precursors benzamides were carried out. Several molecules increased the bacterial susceptibility towards norfloxacin and chloramphenicol. The obtained results, supported by molecular modeling, suggest that molecular flexibility and the nature of chemical functions play a critical role to improve activity and selectivity on fluoroquinolone potentiation targeting AcrB efflux pump.