@phdthesis{ReuterWeissenberger2022,
  author    = {Reuter-Weissenberger, Philipp},
  title     = {The role of a fungal-specific transcription regulator on vacuolar biology and host interaction in \(Candida\) \(albicans\)},
  doi       = {10.25972/OPUS-25928},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259287},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Microorganisms that colonize the human body face large fluctuations in their surroundings. Therefore, those microbes developed sophisticated mechanisms that allow them to adapt their cell biology and maintain cellular homeostasis. One organelle vital to preserve cell physiology is the vacuole. The vacuole exhibits a wide range of functions and is able to adjust itself in response to both external and internal stimuli. Moreover, it plays an important role in host interaction and virulence in fungi such as Candida albicans. Despite this connection, only a few regulatory proteins have been described to modulate vacuolar biology in fungal pathogens. Furthermore, whether such regulation alters fungus-host interplay remains largely unknown. This thesis focuses on the characterization of ZCF8, a fungus-specific transcription regulator in the human-associated yeast C. albicans. To this end, I combined genome-wide protein-DNA interaction assays and gene expression analysis that identified genes regulated by Zcf8p. Fluorescence microscopy uncovered that several top targets of Zcf8p localize to the fungal vacuole. Moreover, deletion and overexpression of ZCF8 resulted in alterations in vacuolar morphology and in luminal pH and rendered the fungus resistant or susceptible to a vacuole-disturbing drug. Finally, in vitro adherence assays showed that Zcf8p modulates the attachment of C. albicans to human epithelial cells in a vacuole-dependent manner. Given those findings, I posit that the previously uncharacterized transcription regulator Zcf8p modulates fungal attachment to epithelial cells in a manner that depends on the status of the fungal vacuole. Furthermore, the results highlight that vacuolar physiology is a substantial factor influencing the physical interaction between Candida cells and mammalian mucosal surfaces.},
  subject      = {Vakuole},
  language  = {en}
}
@phdthesis{Popp2021,
  author    = {Popp, Christina},
  title     = {Evolution of antifungal drug resistance of the human-pathogenic fungus \(Candida\) \(albicans\)},
  doi       = {10.25972/OPUS-24351},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243515},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Infections with the opportunistic yeast Candida albicans are frequently treated with the first-line drug fluconazole, which inhibits ergosterol biosynthesis. An alarming problem in clinics is the development of resistances against this azole, especially during long-term treatment of patients. Well-known resistance mechanisms include mutations in the zinc cluster transcription factors (ZnTFs) Mrr1 and Tac1, which cause an overexpression of efflux pump genes, and Upc2, which results in an overexpression of the drug target. C. albicans strains with such gain-of-function mutations (GOF) have an increased drug resistance conferring a selective advantage in the presence of the drug. It was previously shown that this advantage comes with a fitness defect in the absence of the drug. This was observed in different conditions and is presumably caused by a deregulated gene expression. One aim of the present study was to examine whether C. albicans can overcome the costs of drug resistance by further evolution. Therefore, the relative fitness of clinical isolates with one or a combination of different resistance mutations in Mrr1, Tac1 and/or Upc2 was analyzed in competition with the matched fluconazole-susceptible partner. Most fluconazole-resistant isolates had a decreased fitness in competition with their susceptible partner in vitro in rich medium. In contrast, three fluconazole-resistant strains with Mrr1 resistance mutations did not show a fitness defect in competition with their susceptible partner. In addition, the fitness of four selected clinical isolate pairs was examined in vivo in mouse models of gastrointestinal colonization (GI) and disseminated infection (IV). In the GI model all four fluconazole-resistant strains were outcompeted by their respective susceptible partner. In contrast, in the IV model only one out of four fluconazole-resistant isolates did show a slight fitness defect in competition with its susceptible partner during infection of the kidneys. It can be stated, that in the present work the in vitro fitness did not reflect the in vivo fitness and that the overall fitness was dependent on the tested conditions. In conclusion, C. albicans cannot easily overcome the costs of drug resistance caused by a deregulated gene expression. In addition to GOFs in Mrr1, Tac1 and Upc2, resistance mutations in the drug target Erg11 are a further key fluconazole resistance mechanism of C. albicans. Clinical isolates often harbor several resistance mechanisms, as the fluconazole resistance level is further increased in strains with a combination of different resistance mutations. In this regard, the question arises of how strains with multiple resistance mechanisms evolve. One possibility is that strains acquire mutations successively. In the present study it was examined whether highly drug-resistant C. albicans strains with multiple resistance mechanisms can evolve by parasexual recombination as another possibility. In a clonal population, cells with individually acquired resistance mutations could combine these advantageous traits by mating. Thereupon selection could act on the mating progeny resulting in even better adapted derivatives. Therefore, strains heterozygous for a resistance mutation and the mating type locus (MTL) were grown in the presence of fluconazole. Derivatives were isolated, which had become homozygous for the resistance mutation and at the same time for the MTL. This loss of heterozygosity was accompanied by increased drug resistance. In general, strains which are homozygous for one of both MTL configurations (MTLa and MTLα) can switch to the opaque phenotype, which is the mating-competent form of the yeast, and mate with cells of the opposite MTL. In the following, MTLa and MTLα homozygous strains in the opaque phenotype were mated in all possible combinations. The resulting mating products with combined genetic material from both parents did not show an increased drug resistance. Selected products of each mating cross were passaged with stepwise increasing concentrations of fluconazole. The isolated progeny showed high levels of drug resistance and loss of wild-type alleles of resistance-associated genes. In conclusion, selective pressure caused by fluconazole exposure selects for resistance mutations and at the same time induces genomic rearrangements, resulting in mating competence. Therefore, in a clonal population, cells with individually acquired resistance mutations can mate with each other and generate mating products with combined genetic backgrounds. Selection can act on these mating products and highly drug-resistant und thus highly adapted derivatives can evolve as a result. In summary, the present study contributes to the current understanding of the evolution of antifungal drug resistance by elucidating the effect of resistance mutations on the fitness of the strains in the absence of the drug selection pressure and investigates how highly drug-resistant strains could evolve within a mammalian host.},
  subject      = {Evolution},
  language  = {en}
}
@phdthesis{Boehm2020,
  author    = {B{\"o}hm, Lena},
  title     = {Dissecting Mechanisms of Host Colonization by C. albicans},
  doi       = {10.25972/OPUS-19230},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192303},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {The human body is laden with trillions of microorganisms that belong to all three domains of life. Some species of this microbiota subsist as harmless commensals in healthy adults, but under certain circumstances, they can cause mucosal disease or even systemic, life-threatening infections. While the bacterial members of our microbiota are heavily studied today, much less attention is afforded to eukaryotic species that colonize different mucocutaneous surfaces of the human body. This dissertation focuses on identifying regulatory circuits that enable a prominent member of these eukaryotes, C. albicans, to, on the one hand, live on a specific mammalian mucosal surface as a harmless commensal and, on the other hand, proliferate as a pathogen. Since the ultimate source of many fatal Candida infections is the gastrointestinal (GI) tract of the infected individual, this organism is particularly suited to distinguishing traits essential for the gut colonization of commensal fungi and their ability to cause disease. Sequence-specific DNA-binding proteins that regulate transcription are important to most biological processes; I thus used these proteins as starting points to gain insights into 1) how a specific transcription regulator promotes virulence in C. albicans; 2) which traits C. albicans requires to inhabit the GI tract of a specific, well-defined mouse model as a harmless commensal; and 3) how three previously undescribed transcriptional regulators contribute to the commensal colonization of the digestive tract of this mouse model. Altogether, this work advances the knowledge concerning the biology of commensal fungi in the mammalian gut and genetic determinants of fungal commensalism, as well as pathogenicity.},
  subject      = {Candida albicans},
  language  = {en}
}
@phdthesis{Eckstein2020,
  author    = {Eckstein, Marie-Therese},
  title     = {Exploring the biology of the fungus Candida albicans in the gut of gnotobiotic mice},
  doi       = {10.25972/OPUS-21870},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218705},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {The human body is colonized by trillions of microbes from all three domains of life - eukaryotes, bacteria and archaea. The lower gastrointestinal tract is the most densely colonized part of the body, harbouring a diverse and dynamic community of microbes. While the importance of bacteria in this so-called microbiota is well acknowledged, the role of commensal fungi remains underexplored. The most prominent fungus of the human gastrointestinal microbiota is Candida albicans. This fungus occasionally causes life-threatening disseminated infections in individuals with debilitated immune defences. It is this "pathogenic" facet that has received the most attention from researchers in the past, leaving many aspects of its "commensal" lifestyle understudied. Using gnotobiotic mice as a model system to explore the biology of C. albicans in the mammalian gut, in this dissertation I establish the global response of the host to C. albicans monocolonization as well as the spatial distribution of the fungus in the intestine in the context of co-colonization with single gut bacterial species. The fungus elicited transcriptome changes in murine intestinal tissue, which included the activation of a reactive oxygen species-related defence mechanism and the induction of regulators of the circadian clock circuitry. Both responses have previously been described in the context of a complete bacterial microbiota. Imaging the intestine of animals monocolonized with the fungus or co-colonized with C. albicans and the gut bacteria Bacteroides thetaiotaomicron or Lactobacillus reuteri revealed that the fungus was embedded in a B. thetaiotaomicron-promoted outer mucus layer in the murine colon. The gel-like outer mucus constitutes a unique microhabitat, distinct in microbial composition from the adjacent intestinal lumen. This finding indicates that bacteria can shape the specific microhabitat occupied by the fungus in the intestine. Overall, the results described in this dissertation suggest that gnotobiotic mice constitute a valuable tool to dissect multiple aspects of the interactions among host, commensal fungi and cohabiting bacteria.},
  subject      = {Candida albicans},
  language  = {en}
}
@phdthesis{delOlmoToledo2019,
  author    = {del Olmo Toledo, Valentina},
  title     = {Evolution of DNA binding preferences in a family of eukaryotic transcription regulators},
  doi       = {10.25972/OPUS-18789},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187890},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2019},
  abstract  = {Regulation of gene expression by the control of transcription is essential for any cell to adapt to the environment and survive. Transcription regulators, i.e. sequence-specific DNA binding proteins that regulate gene expression, are central elements within the gene networks of most organisms. Transcription regulators are grouped into distinct families based on structural features that determine, to a large extent, the DNA sequence(s) that they can recognise and bind. Less is known, however, about how the DNA binding preferences can diversify within transcription regulator families during evolutionary timescales, and how such diversification can affect the biology of the organism. In this dissertation I study the SREBP (sterol regulatory element binding protein) family of transcriptional regulators in yeasts, and in Candida albicans in particular, as an experimental system to address these questions. The SREBPs are conserved from fungi to humans and represent a subgroup of basic helix-loop-helix DNA binding proteins. Early chromatin immunoprecipitation experiments with SREBPs from humans and yeasts showed that these proteins bound in vivo to the canonical DNA sequence, termed E-box, most basic helix-loop-helix proteins bind to. By contrast, most recent analysis carried out with less-studied fungal SREBPs revealed a non-canonical DNA motif to be the most overrepresented sequence in the bound regions. This study aims to establish the intrinsic DNA binding preferences of key branches of this family and to determine how the divergence in DNA binding affinities originated. To this end, I combined phylogenetic and ancestral reconstruction with extensive biochemical characterisation of key SREBP proteins. The results indicated that while the most-studied SREBPs (in mammals) indeed show preference for the E-box, a second branch of the family preferentially binds the non-E-box, and a third one is able to bind both sequences with similar affinity. The preference for one or the other DNA sequence is an intrinsic property of each protein because their purified DNA binding domain was sufficient to recapitulate their in vivo binding preference. The ancestor that gave rise to these two different types of SREBPs (the branch that binds E-box and the one that binds non-E-box DNA) appears to be a protein with a broader DNA binding capability that had a slight preference for the non-canonical motif. Thus, the results imply these two branches originated by either enhancing the original ancestral preference for non-E-box or tilting it towards the E-box DNA and flipping the preference for this sequence. The main function associated with members of the SREBP family in most eukaryotes is the control of lipid biosynthesis. I have further studied the function of these proteins in the lineage that encompasses the human associated yeast C. albicans. Strikingly, the three SREBPs present in the fungus' genome contribute to the colonisation of the mammalian gut by regulating cellular processes unrelated to lipid metabolism. Here I describe that two of the three C. albicans SREBPs form a regulatory cascade that regulates morphology and cell wall modifications under anaerobic conditions, whereas the third SREBP has been shown to be involved in the regulation of glycolysis genes. Therefore, I posit that the described diversification in DNA binding specificity in these proteins and the concomitant expansion of targets of regulation were key in enabling this fungal lineage to associate with animals.},
  subject      = {Candida albicans},
  language  = {en}
}
@phdthesis{Bergfeld2018,
  author    = {Bergfeld, Arne},
  title     = {Das pH-regulierte Protein 1 (Pra1) von \(Candida\) \(albicans\) moduliert CD4\(^+\) T-Zell-Antworten der Maus in vitro durch direkte Bindung an die T-Zell-Oberfl{\"a}che},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169716},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Infektionen durch C. albicans auf den Schleimh{\"a}uten sind eine h{\"a}ufige Erkrankung bei Patienten mit einer Schw{\"a}chung der T-Zellimmunit{\"a}t. Blutstrominfektionen mit der Hefe C. albicans (Candid{\"a}mie) stellen, vor allem bei Patienten auf Intensivstationen, eine nach wie vor bedrohliche Komplikation mit hoher Letalit{\"a}t dar. Das pH-regulierte Antigen 1 (Pra1) ist ein Protein, das von C. albicans produziert wird, auf der Oberfl{\"a}che des Pilzes gebunden vorkommt und auch vom Pilz in den {\"U}berstand sezerniert wird. Im humanen System bindet das Protein an T-Zellen an das Oberfl{\"a}chenprotein CD46. Es ist des Weiteren bekannt, dass das Pra1 an bestimmte Immunzellen der Maus (Monozyten und Phagozyten) binden kann. Eine Bindung an T-Zellen der Maus ist bisher nicht beschrieben. Eine genaue Charakterisierung der Interaktion von Pra1 mit Immunzellen der Maus ist interessant, da die Maus als biologischer Modellorganismus zur Erforschung der Infektion mit C. albicans dient. In dieser Arbeit konnte gezeigt werden, dass rekombinantes Pra1 (rPra1) auch an Maus-CD4+ T-Zellen binden kann. Es wurden Einflussfaktoren auf die gefundene Bindung von Pra1 an CD4+ T- Zellen gesucht. Als ein Einflussfaktor wurde Zink identifiziert. Pra1 kann an freies Zink binden und durch Zugabe von ZnCl2 w{\"a}hrend der Inkubation von Pra1 mit T-Zellen kann das Signal von gebundenem Pra1 an CD4+ T-Zellen erh{\"o}ht werden. Aspf2, ein Protein aus Aspergillus fumigatus mit großer Homologie zu Pra1, kann nicht an diese Zellen binden. Im in-vivo-Experiment mit Tieren, die mit C. albicans infiziert wurden, konnte kein wildtypisches sezerniertes Pra1 gebunden an T-Zellen nachgewiesen werden. Zellkultur{\"u}berst{\"a}nde von C. albicans zeigten nach Inkubation in vitro mit T-Zellen ein Signal f{\"u}r gebundenes Pra1 an CD4+ T-Zellen. Die Bindungskinetik von Pra1 an T-Zellen zeigte eine {\"u}ber die Zeit der Inkubation konstante Zunahme des Signals von zellgebundenem rPra1 an CD4+ T-Zellen. In der off-Kinetik fand sich eine Abnahme des Signals {\"u}ber die Zeit bis an die Grenze der Nachweisbarkeit. Der Bindungspartner von Pra1 auf T-Zellen konnte nicht identifiziert werden. Die strukturell und funktionell verwandten Oberfl{\"a}chenproteine Crry, CD59a und CD55 wurden auf Bindungsf{\"a}higkeit an T-Zellen in entsprechenden Knockout- M{\"a}usen getestet, konnten jedoch als Rezeptor f{\"u}r Pra1 ausgeschlossen werden. Durch die Bindung von sezerniertem Pra1 an neutrophile Granulozyten wird die F{\"a}higkeit dieser Zellen zur Phagozytose eingeschr{\"a}nkt. Die Bindung von Pra1 an CD4+ T-Zellen f{\"u}hrt zur Kostimulation der T-Zellen, also zur verst{\"a}rkten Zellaktivierung und Proliferation. Durch die Zugabe von 10 μM Zinkchlorid wird die kostimulatorische Aktivit{\"a}t von Pra1 verst{\"a}rkt. W{\"a}hrend der Zellaktivierung von Effektor-Memory-CD4+ T-Zellen reduziert rPra1 die Sekretion von IFN-γ. Diese Reduktion von IFN-γ-produzierenden Zellen entsteht nicht durch einen Einfluss von Pra1 w{\"a}hrend der Zellaktivierung von naiven CD4+ T-Zellen zu Th1-Zellen und auch nicht durch die Ausl{\"o}sung von Apoptose in IFN-γ-produzierenden Th1-Zellen. Die Bindung von Pra1 an CD4+- T-Zellen, die {\"u}ber den T-Zell-Rezeptor aktiviert werden, reduziert in vitro die Sekretion des Zytokins. Zus{\"a}tzlich werden weitere Zytokine in ihrer sezernierten Menge reduziert wie IL-2 und TNF-α.},
  subject      = {Candida albicans},
  language  = {de}
}
@phdthesis{Hampe2018,
  author    = {Hampe, Irene Aurelia Ida},
  title     = {Analysis of the mechanism and the regulation of histatin 5 resistance in \(Candida\) \(albicans\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159634},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {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.},
  subject      = {Histatin 5},
  language  = {en}
}
@phdthesis{Schaefer2014,
  author    = {Sch{\"a}fer, Christin Marliese},
  title     = {Approaching antimicrobial resistance - Structural and functional characterization of the fungal transcription factor Mrr1 from Candida albicans and the bacterial ß-ketoacyl-CoA thiolase FadA5 from Mycobacterium tuberculosis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-108400},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {The number of fungal infections is rising in Germany and worldwide. These infections are mainly caused by the opportunistic fungal pathogen C. albicans, which especially harms immunocompromised people. With increasing numbers of fungal infections, more frequent and longer lasting treatments are necessary and lead to an increase of drug resistances, for example against the clinically applied therapeutic fluconazole. Drug resistance in C. albicans can be mediated by the Multidrug resistance pump 1 (Mdr1), a membrane transporter belonging to the major facilitator family. However, Mdr1-mediated fluconazole drug resistance is caused by the pump's regulator, the transcription factor Mrr1 (Multidrug resistance regulator 1). It was shown that Mrr1 is hyperactive without stimulation or further activation in resistant strains which is due to so called gain of function mutations in the MRR1 gene. To understand the mechanism that lays behind this constitutive activity of Mrr1, the transcription factor should be structurally and functionally (in vitro) characterized which could provide a basis for successful drug development to target Mdr1-mediated drug resistance caused by Mrr1. Therefore, the entire 1108 amino acid protein was successfully expressed in Escherichia coli. However, further purification was compromised as the protein tended to form aggregates, unsuitable for crystallization trials or further characterization experiments. Expression trials in the eukaryote Pichia pastoris neither yielded full length nor truncated Mrr1 protein. In order to overcome the aggregation problem, a shortened variant, missing the N-terminal 249 amino acids named Mrr1 '250', was successfully expressed in E. coli and could be purified without aggregation. Similar to the wild type Mrr1 '250', selected gain of function variants were successfully cloned, expressed and purified with varying yields and with varying purity. The Mrr1 `250' construct contains most of the described regulatory domains of Mrr1. It was used for crystallization and an initial comparative analysis between the wild type protein and the variants. The proposed dimeric form of the transcription factor, necessary for DNA binding, could be verified for both, the wild type and the mutant proteins. Secondary structure analysis by circular dichroism measurements revealed no significant differences in the overall fold of the wild type and variant proteins. In vitro, the gain of function variants seem to be less stable compared to the wild type protein, as they were more prone to degradation. Whether this observation holds true for the full length protein's stability in vitro and in vivo remains to be determined. The crystallization experiments, performed with the Mrr1 '250' constructs, led to few small needle shaped or cubic crystals, which did not diffract very well and were hardly reproducible. Therefore no structural information of the transcription factor could be gained so far. Infections with M. tuberculosis, the causative agent of tuberculosis, are the leading cause of mortality among bacterial diseases. Especially long treatment times, an increasing number of resistant strains and the prevalence of for decades persisting bacteria create the necessity for new drugs against this disease. The cholesterol import and metabolism pathways were discovered as promising new targets and interestingly they seem to play an important role for the chronic stage of the tuberculosis infection and for persisting bacteria. In this thesis, the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis was characterized and the potential for specifically targeting this enzyme was investigated. FadA5 catalyzes the last step of the β-oxidation reaction in the side-chain degradation pathway of cholesterol. We solved the three dimensional structure of this enzyme by X-ray crystallography and obtained two different apo structures and three structures in complex with acetyl-CoA, CoA and a hydrolyzed steroid-CoA, which is the natural product of FadA5. Analysis of the FadA5 apo structures revealed a typical thiolase fold as it is common for biosynthetic and degradative enzymes of this class for one of the structures. The second apo structure showed deviations from the typical thiolase fold. All obtained structures show the enzyme as a dimer, which is consistent with the observed dimer formation in solution. Thus the dimer is likely to be the catalytically active form of the enzyme. Besides the characteristic structural fold, the catalytic triad, comprising two cysteines and one histidine, as well as the typical coenzyme A binding site of enzymes belonging to the thiolase class could be identified. The two obtained apo structures differed significantly from each other. One apo structure is in agreement with the characteristic thiolase fold and the well-known dimer interface could be identified in our structure. The same characteristics were observed in all complex structures. In contrast, the second apo structure followed the thiolase fold only partially. One subdomain, spanning 30 amino acids, was in a different orientation. This reorientation was caused by the formation of two disulfide bonds, including the active site cysteines, which rendered the enzyme inactive. The disulfide bonds together with the resulting domain swap still permitted dimer formation, yet with a significantly shifted dimer interface. The comparison of the apo structures together with the preliminary activity analysis performed by our collaborator suggest, that FadA5 can be inactivated by oxidation and reactivated by reduction. If this redox switch is of biological importance requires further evaluation, however, this would be the first reported example of a bacterial thiolase employing redox regulation. Our obtained complex structures represent different stages of the thiolase reaction cycle. In some complex structures, FadA5 was found to be acetylated at the catalytic cysteine and it was in complex with acetyl-CoA or CoA. These structures, together with the FadA5 structure in complex with a hydrolyzed steroid-CoA, revealed important insights into enzyme dynamics upon ligand binding and release. The steroid-bound structure is as yet a unique example of a thiolase enzyme interacting with a complex ligand. The characterized enzyme was used as platform for modeling studies and for comparison with human thiolases. These studies permitted initial conclusions regarding the specific targetability of FadA5 as a drug target against M. tuberculosis infection, taking the closely related human enzymes into account. Additional analyses led to the proposal of a specific lead compound based on the steroid and ligand interactions within the active site of FadA5.},
  subject      = {Multidrug-Resistenz},
  language  = {en}
}
@phdthesis{Schillig2013,
  author    = {Schillig, Rebecca},
  title     = {Funktionelle Analyse der Zink-Cluster-Transkriptionsfaktorfamilie von Candida albicans durch artifizielle Aktivierung},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-79608},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Der Hefepilz Candida albicans geh{\"o}rt zu den opportunistischen Infektionserregern. Er ist Teil der nat{\"u}rlichen Mikroflora der Schleimh{\"a}ute des Gastrointestinal- und Urogenitaltraktes des Menschen. Bei St{\"o}rungen des nat{\"u}rlichen Gleichgewichts dieser Flora kann es zu oberfl{\"a}chlichen Mykosen, z. B. der oropharyngealen Candidiasis (Mundsoor), kommen. Besonders immunsupprimierte Patienten, wie AIDS-Patienten, leiden h{\"a}ufig unter immer wiederkehrenden Infektionen, die mitunter auch zu schwerwiegenden Infektionsverl{\"a}ufen, bis hin zu lebensbedrohlichen systemischen Mykosen f{\"u}hren k{\"o}nnen. Zur Therapie solcher Erkrankungen werden oft Ergosterolbiosyntheseinhibitoren, wie Fluconazol, eingesetzt. Besonders bei wiederkehrenden Infektionen und wiederholender Therapie ist C. albicans in der Lage, gegen diese h{\"a}ufig verabreichten Antimykotika Resistenzen zu entwickeln. Hierbei spielen Zink-Cluster-Transkriptionsfaktoren eine zentrale Rolle. Zink-Cluster-Proteine geh{\"o}ren zu einer pilzspezifischen Familie von Transkriptionsfaktoren, die ein großes Spektrum an zellul{\"a}ren Prozessen regulieren. Die gut charakterisierten Regulatoren Upc2, Tac1 und Mrr1 geh{\"o}ren zu den Zink-Cluster-Transkriptionsfaktoren, die maßgeblich zur Resistenzentwicklung von C. albicans beitragen. Upc2 kontrolliert die Expression vieler Ergosterolbiosynthesegene, besonders die von ERG11, welches f{\"u}r die Zielstruktur des g{\"a}ngigen Antimykotikums Fluconazol kodiert. Tac1 und Mrr1 hingegen regulieren die Expression von Multidrug-Effluxpumpen, den ABC-Transportern CDR1 und CDR2 bzw. dem Major Facilitator MDR1. Gain-of-function-Mutationen in diesen Transkriptionsfaktoren resultieren in einer konstitutiven {\"U}berexpression ihrer Zielgene und sind verantwortlich f{\"u}r die Resistenz vieler klinischer Isolate. In dieser Arbeit wurde gezeigt, dass die Fusion von Mrr1 mit der Gal4-Aktivierungsdom{\"a}ne von Saccharomyces cerevisiae zu einem konstitutiv aktiven Hybridtranskriptionsfaktor f{\"u}hrte, der eine MDR1-{\"U}berexpression bewirkte und Fluconazolresistenz vermittelte. Dieses Hybridprotein vermittelte sogar eine h{\"o}here Resistenz als ein Mrr1 mit nat{\"u}rlich vorkommenden gain-of-function-Mutationen. Analoge Fusionen mit Tac1 und Upc2 resultierten ebenfalls in einer konstitutiven Aktivierung dieser Transkriptionsfaktoren, die einen starken Anstieg der Fluconazolresistenz zur Folge hatte. Daraus ergab sich die Schlussfolgerung, dass dies eine generelle Methode sein k{\"o}nnte, die Zink-Cluster-Transkriptionsfaktoren k{\"u}nstlich zu aktivieren und so ihre biologischen Funktionen zu offenbaren, ohne die genauen Bedingungen f{\"u}r ihre Aktivit{\"a}t zu kennen. Deshalb wurde auf der Basis dieser Strategie eine Bibliothek von C.-albicans-St{\"a}mmen konstruiert, in der alle 82 putativen Zink-Cluster-Transkriptionsfaktoren in dieser m{\"o}glicherweise hyperaktiven Form exprimiert werden. Untersuchungen dieser Bibliothek offenbarten neue Transkriptionsfaktoren, die Fluconazolresistenz vermittelten, aber auch noch unbekannte Regulatoren der Morphogenese und andere Ph{\"a}notypen konnten beobachtet werden. Um einen tieferen Einblick in die Funktionsweise zu bekommen, wurden die Transkriptionsprofile der vier Transkriptionsfaktoren ermittelt, die in ihrer hyperaktiven Form die h{\"o}chste Fluconazolresistenz bewirkten. Dabei stellte sich heraus, dass die zwei k{\"u}nstlich aktivierten (*) Regulatoren ZCF34* und ZNC1* die Expression der wichtigsten Multidrug-Effluxpumpe CDR1 stark hochregulierten. Der Transkriptionsfaktor mit dem vorl{\"a}ufigen Namen ZCF34 konnte im Verlauf dieser Arbeit als ein wichtiger Regulator f{\"u}r die CDR1-Expression identifiziert werden. Er ist sowohl an der Aktivierung der Expression von CDR1 beteiligt als auch f{\"u}r die basale CDR1-Promotoraktivit{\"a}t notwendig. Aus diesem Grund wurde er in MRR2 (multidrug resistance regulator 2) umbenannt. Mit der Entdeckung eines neuen Regulators der wichtigsten Multidrug-Effluxpumpe von C. albicans wurde ein wichtiger Beitrag zum Verst{\"a}ndnis der Regulation solcher Transporter geleistet. Die {\"U}berexpression dieser Pumpen ist einer der h{\"a}ufigsten Resistenzmechanismen in C. albicans. Auf diesem Wege kann Resistenz gegen strukturell v{\"o}llig unterschiedliche Antimykotika bewirkt werden. Somit stellen sowohl diese Effluxpumpen, als auch deren Regulatoren m{\"o}gliche Angriffsziele f{\"u}r die Entwicklung neuer oder Weiterentwicklung bereits vorhandener Antimykotika dar.},
  subject      = {Candida albicans},
  language  = {de}
}
@phdthesis{Dunkel2013,
  author    = {Dunkel, Nico},
  title     = {Regulation of virulence-associated traits of the human fungal pathogen Candida albicans by nitrogen availability},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-83076},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Nitrogen-regulated pathogenesis describes the expression of virulence attributes as direct response to the quantity and quality of an available nitrogen source. As consequence of nitrogen availability, the opportunistic human fungal pathogen Candida albicans changes its morphology and secretes aspartic proteases [SAPs], both well characterized virulence attributes. C. albicans, contrarily to its normally non-pathogenic relative Saccharomyces cerevisiae, is able to utilize proteins, which are considered as abundant and important nitrogen source within the human host. To assimilate complex proteinaceous matter, extracellular proteolysis is followed by uptake of the degradation products through dedicated peptide transporters (di-/tripeptide transporters [PTRs] and oligopeptide transporters [OPTs]). The expression of both traits is transcriptionally controlled by Stp1 - the global regulator of protein utilization - in C. albicans. The aim of the present study was to elucidate the regulation of virulence attributes of the pathogenic fungus C. albicans by nitrogen availability in more detail. Within a genome wide binding profile of Stp1, during growth with proteins, more than 600 Stp1 target genes were identified, thereby confirming its role in the usage of proteins, but also other nitrogenous compounds as nitrogen source. Moreover, the revealed targets suggest an involvement of Stp1 in the general adaption to nutrient availability as well as in the environmental stress response. With the focus on protein utilization and nitrogen-regulated pathogenesis, the regulation of the major secreted aspartic protease Sap2 - additionally one of the prime examples of allelic heterogeneity in C. albicans - was investigated in detail. Thereby, the heterogezygous SAP2 promoter helped to identify an unintended genomic alteration as the true cause of a growth defect of a C. albicans mutant. Additionally, the promoter region, which was responsible for the differential activation of the SAP2 alleles, was delimited. Furthermore, general Sap2 induction was demonstrated to be mediated by distinct cis-acting elements that are required for a high or a low activity of SAP2 expression. For the utilization of proteins as nitrogen source it is also crucial to take up the peptides that are produced by extracellular proteolysis. Therefore, the function and importance of specific peptide transporters was investigated in C. albicans mutants, unable to use peptides as nitrogen source (opt1Δ/Δ opt2Δ/Δ opt3Δ/Δ opt4Δ/Δ opt5Δ/Δ ptr2Δ/Δ ptr22Δ/Δ septuple null mutants). The overexpression of individual transporters in these mutants revealed differential substrate specificities and expanded the specificity of the OPTs to dipeptides, a completely new facet of these transporters. The peptide-uptake deficient mutants were further used to elucidate, whether indeed proteins and peptides are an important in vivo nitrogen source for C. albicans. It was found that during competitive colonization of the mouse intestine these mutants exhibited wild-type fitness, indicating that neither proteins nor peptides are primary nitrogen sources required to efficiently support growth of C. albicans in the mouse gut. Adequate availability of the preferred nitrogen source ammonium represses the utilization of proteins and other alternative nitrogen sources, but also the expression of virulence attributes, like Sap secretion and nitrogen-starvation induced filamentation. In order to discriminate, whether ammonium availability is externally sensed or determined inside the cell by C. albicans, the response to exterior ammonium concentrations of ammonium-uptake deficient mutants (mep1Δ/Δ mep2Δ/Δ null mutants) was investigated. This study showed that presence of an otherwise suppressing ammonium concentration did not inhibit Sap2 proteases secretion and arginine-induced filamentation in these mutants. Conclusively, ammonium availability is primarily determined inside the cell in order to control the expression of virulence traits. In sum, the present work contributes to the current understanding of how C. albicans regulates expression of virulence-associated traits in response to the presence of available nitrogen sources - especially proteins and peptides - in order to adapt its lifestyle within a human host.},
  subject      = {Candida albicans},
  language  = {en}
}