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Compared to other human pathogens, S. aureus outstands with a remarkably broad spectrum of deseases: from minor skin infections over endocarditis, pneumoniae, and osteomyelitis, to septic shock. The prerequisite is an arsenal of adaptation strategies, encoded in the core and variable genome. It includes the coordinated expression of adhesins and toxins, evasion of the immune system, response to stress and starvation, adaptation of the metabolism, formation of biofilms and capsules, antibiotic resistance, and persistence on the skin, in nasal epithelial cells, and even in the inner of macrophages after phagocytosis. All these adaptation strategies enable S. aureus to colonize a diversity of niches within the human host. The inevitable requirement is the ability to activate the appropriate adaptation strategy at the right time and at the right place. S. aureus overcomes this challenge with a sophisticated regulatory network. This PhD thesis covers a broad spectrum of transcriptional regulators, involved in S. aureus pathogenesis: (1) the quorum sensing system Agr (regulation of early- and late stage virulence factors), (2) the Sar family (regulation of early- and late stage virulence factors), (3) SaeRS (regulation of accessory exotoxins and adhesins), (4) CodY (response to amino acid starvation, including extracellular proteases), (5) Sigma B (general stress response, including virulence factors), (6) Rex (anaerobic energy metabolism), (7) CtsR and HrcA (protein quality control), (8) PerR and Fur (oxidative stress response), and (9) antibiotic resistance. Traditionally, Proteomics constitute the long-lasting reputation of the Institute. In fact, the majority of investigations presented in this PhD thesis was initialized by proteomic analyses as the ultimate starting point. From the first day, a major goal of this PhD thesis was to add regulator-promoter interaction studies to the methodical spectrum. In particular, to complement transcriptomic and proteomic results by answering the logical follow-up question: Which regulator is responsible for the observed changes in gene expression and protein synthesis after application of a specific stimulus?
The first chapter provides specific analyses for three major regulators: Rex, CodY, and SarA. Publications were achieved for Rex (Hecker et al., 2009; Pagels et al., 2010). Results were mainly achieved by establishing regulator-promoter interaction methods (in particular EMSA and “footprinting”). Additionally, this chapter describes method development of a novel easy-to-apply method, named REPA (restriction endonuclease protection assay).
The second chapter presents method development for the genome-wide identification of regulator-promoter interactions, named “global footprinting”. This approach combines two already well-established methods: (A) Purification of a recombinant Strep-tagged regulator via Strep-tag affinity chromatography. The modification in “global footprinting” is to incubate the regulator with fragmented genomic S. aureus DNA, resulting in co-purification and enrichment of DNA streches with specific regulator binding sites. (B) Identification and quantification of these DNA streches via “next generation sequencing” (NGS). Using this combined approach, this PhD thesis was able to localize the most affine promoter binding site for the regulator Rex precisely down to one single base pair across the whole S. aureus genome.
The third chapter describes the assembly of a data library, collecting the majority of DNA microarray data and regulator-promoter interaction studies from the worldwide literature. This data library summarizes more than 50,000 regulatory events and more than 2,000 regulator binding sites. As published in the perspectives in Fuchs et al. (2018), this data library can be incorporated into the free-accessible online data base “Aureowiki” (provided and maintained by the Department of Functional Genomics, University of Greifswald). The major effort is the consolidation of these “big data” via in silico cluster analysis, comparing 282 different experimental conditions at once. The major finding of this analysis is the identification of seven functional and regulatory gene clusters in S. aureus pathogenesis that are conserved across S. aureus strain diversity. These findings allowed the creation of a prediction tool, to provide novel experimental starting points for the worldwide S. aureus research community. This prediction tool was successfully applied on several topics, and partially published: functional and regulatory prediction for a set of 20 selected lipoproteins as potential virulence factors (Graf et al., 2018), and prediciton of protein complexes (Liang et al., 2016).
Alltogether, this PhD thesis provides new insights into the molecular mechanisms of three pathogenesis-relevant regulators: Rex, CodY, and SarA. It describes the development of three novel experimental methods for wet and dry lab applications that can be used on research topics beyond S. aureus: REPA, “global footprinting”, and cluster analysis. Finally, cluster analysis identifies seven conserved fuctional and regulatory gene clusters, involved in S. aureus pathogenesis. This cluster anaysis is used as a prediction tool to provide novel experimental starting points, and to predict the physiological mode of action of newly discovered anti-staphylococcal agents.
Streptococcus pneumoniae colonizes asymptomatically the upper respiratory tract as a commensal, but has also a high virulence potential and can leave this ecological niche, thereby spreading to the lungs and blood. During this process, pneumococci must adapt to changing external environmental conditions and parameters such as nutrient availability, temperature, or oxygen levels. The transmission of these signals into the bacterial cell interior occurs via the process of signal transduction, which ultimately results in controlled differential gene expression. The most commonly strategy for signal transduction is the use of two-component regulatory systems (TCS), consisting of a membrane-bound histidine kinase as a sensor and a cytoplasmic response regulator that binds to the promoter region of its target genes and interferes with gene expression.
In this study the regulatory impact and influence of the TCS08 and TCS09 on the phenotype and pathophysiology of S. pneumoniae were investigated using two different serotypes
(serotype 2: D39 and serotype 4: TIGR4). For all functional assays, single (Δrr08/Δrr09 or Δhk08/Δhk09) and double (Δtcs08 or Δtcs09) mutants that were constructed by insertion-deletion mutagenesis, were applied.
In the first study a comparative transcriptome analysis using RNA-sequencing was conducted with our tcs09-mutants and the parental wild-type D39. The data indicated upregulation of the aga operon, which is related to galactose metabolism, and downregulation of the regulator AgaR, particularly in the absence of HK09. Interestingly, encapsulated and nonencapsulated hk09-mutants in D39 showed significant growth defects when galactose was used as sole carbohydrate source. Electron microscopy revealed morphological changes such as an increased number of membrane vesicles and cell wall degradation for the nonencapsulated hk09- and tcs09-mutants of strain D39. An increased capsule production was indicated for the encapsulated hk09- and tcs09-mutants in D39. The latter two mutants as well as the encapsulated rr09-mutant also showed altered colony morphology. While D39Δhk09 formed only opaque colonies, the mutants D39Δrr09 and D39Δtcs09 showed increased numbers of transparent colonies. In a Triton X-100 induced autolysis assay and in the presence of oxidative stress, a negative effect of the morphological changes of D39ΔcpsΔhk09 and D39ΔcpsΔtcs09 on their survivability was demonstrated. In conclusion, we observed that TCS09 in S. pneumoniae D39 is important for its fitness through regulation of carbohydrate metabolism. This indirectly influences cell wall integrity and capsular polysaccharide amount via other regulatory mechanisms, which ultimately affects stress tolerance.
In a second study, we investigated the virulence potential of TCS09 in pneumococcal strain TIGR4. In vitro growth analyses in complex medium showed no effect after loss of function of TCS09 on pneumococcal fitness. In contrast, using the disaccharides lactose and sucrose in chemically defined medium, an extended lag phase of tcs09-mutants was monitored. To assess changes of virulence factor expression, immunoblots were applied to demonstrate the abundance of various essential virulence factors of S. pneumoniae. The results revealed a decreased amount for RrgB, which is the backbone pilus component of type 1 pili, in the hk09-mutant. Field emission scanning electron microscopy and transmission electron microscopy images were applied to study alterations of the bacterial cell shape. The illustrations by FESEM and TEM showed no effect of TCS09-deletion on pneumococcal cell morphology. Cell culture-based infection analyses revealed a similar adhesion capacity of the parental strain and isogenic mutants to lung epithelial cells. However, phagocytosis assays indicated a significantly increased killing rate of intracellular TIGR4ΔcpsΔtcs09, when compared to the isogenic parental strain. In experimental mouse infection models of acute pneumonia and systemic infection the tcs09-mutants were not attenuated. However, to decipher in more detail differences between the wild-type and tcs09-mutants, in vivo co-infection were performed, which highlighted a significantly lower bacterial load of TIGR4luxΔhk09 and TIGR4luxΔtcs09 especially in the lungs, blood, and brain after 48 h. In conclusion, the TCS09 in TIGR4 is necessary for maintaining metabolic fitness, which in turn contributes to dissemination in the host.
In the third study, the influence of TCS08 on gene expression and metabolic and pathophysiological processes of S. pneumoniae was analyzed. In particular, differential gene expression in the hk08-mutant of TIGR4 was detected using microarray and qPCR. The transcriptome analysis revealed a downregulation of cellobiose specific phosphotransferase systems as well as an upregulation of the fab operon, arc operon, and psa operon. These operons encode proteins involved in fatty acid biosynthesis, arginine catabolism, and manganese uptake, respectively. Furthermore, we measured a downregulation of pilus 1 genes in TIGR4ΔcpsΔtcs08 and an increased expression of pavB in TIGR4ΔcpsΔhk08. These data were confirmed by immunoblotting and surface localization studies. Using in silico analysis, a SaeR-like binding motif was identified in the promoter region of pavB. Furthermore, the impact of TCS08 on pneumococcal virulence was investigated in vivo using the acute pneumonia and sepsis models. These models showed a strain-dependent effect of the single TCS08 component deletions between D39 and TIGR4 pneumococci. Whereas loss of HK08 or TCS08 in D39 attenuated the mutants in the pneumonia model, loss of RR08 in TIGR4 was responsible for a similar effect. In contrast, loss of HK08 in TIGR4 promoted increased virulence in the pneumonia and sepsis model. Overall, these data indicate that TCS08 is involved as key player in bacterial fitness during host colonization.
Das MRP4(ABCC4)-Protein gehört zur ABC-Transporter-Familie und ist neben einem vielfältigen Expressionsmuster durch ein sehr breites Substratspektrum charakterisiert. Es wird in zahlreichen Geweben, beispielsweise in der Niere, im Gehirn, in Blutzellen und in vaskulären glatten Muskelzellen exprimiert. Das MRP4-Protein vermittelt den Efflux und damit auch Resistenz gegenüber einer großen Anzahl exogener Substanzen, wie z.B. Nukleosid-basierten Standardtherapeutika der antiviralen und zytostatischen Krebstherapie, aber auch den zellulären Export verschiedener endogener Signalmoleküle insbesondere von zyklischen Nukleotiden. Der Export zyklischer Nukleotide durch MRP4 gewann hinsichtlich der Beeinflussung intrazellulärer cAMP-Spiegel in jüngster Vergangenheit immer mehr an Beachtung. Während die Daten zur Expression und zum Substratspektrum von MRP4 schon recht umfangreich sind, ist bislang sehr wenig über die Regulationsmechanismen des Transporters bekannt. Im Hinblick darauf war es das zentrale Thema der vorliegenden Arbeit neue Erkenntnisse bezüglich der Regulation von MRP4 zu gewinnen. Dabei wurden insbesondere zwei Aspekte untersucht, die den Einfluss des zyklischen Nukleotids cAMP auf transkriptioneller und der Proteinkinase C (PKC) auf posttranslationaler Ebene in den Fokus stellen. Mithilfe von Reportergen-Analysen, quantitativer Real-Time PCR sowie proteinanalytischen Methoden konnte gezeigt werden, dass die MRP4-Expression durch eine langanhaltende Steigerung der intrazellulären cAMP-Konzentrationen signifikant erhöht wird. Untersuchungen zu den involvierten Signalwegen dieser Regulation deuten auf eine Beteiligung der direkt durch cAMP aktivierten EPAC-Proteine hin, die über die MEK/ERK Proteinkinasen-Kaskade zur Aktivierung der MRP4/ABCC4-Transkription führt. In der Folge resultiert ein erhöhter Efflux von cAMP und möglicherweise weiterer MRP4-Substrate. Bei dieser Art der Regulation könnte es sich um einen autoregulatorischen feedback-Mechanismus handeln. Pharmakologisch bedeutend könnte dies hinsichtlich einer Langzeittherapie mit cAMP-steigernden Arzneistoffen, beispielsweise Phosphodiesterase-Hemmstoffen oder β-Adrenozeptor-Agonisten, sein, da dieser Rückkopplungsmechanismus zu einer Toleranzentwicklung mit einer Abnahme der Wirkung beitragen kann. Ein weiterer Teil dieser Arbeit fokussierte sich auf den Einfluss der PKC auf die MRP4Expression und -Lokalisation. Anhand von Transportstudien und Immunfluoreszenzanalysen konnte eine PKC-vermittelte MRP4-Regulation gezeigt werden. Es wurde ein signifikant verringerter Substratexport mit einhergehender Abnahme des MRP4-Anteils in der Plasmamembran in verschiedenen Zellsystemen beobachtet. Dabei wurde nach Aktivierung der PKC eine vermehrte Lokalisation von MRP4 in intrazellulären Vesikeln beobachtet, deren Herkunft aufgrund von Versuchen mit einer Biotin-Markierung der Zelloberfläche der Plasmamembran zugeordnet werden konnte. Im Anschluss an die Internalisierung kam es zur Verschmelzung mit frühen Endosomen, über die durch Recycling-Prozesse der erneute Protein-Einbau in die Membran realisiert werden kann. Untersuchungen mit einer CFP-getaggten MRP4Deletionsvariante ohne die carboxy-terminale PDZ-Bindedomäne ließen auf eine Beteiligung des PDZ-Interaktionsmotivs im Rahmen der PKC-modulierten MRP4Regulation schließen. Möglicherweise kommt es über dieses Bindungsmotiv zu einer Interaktion zwischen MRP4 und möglichen Adapterproteinen, die für diesen regulatorischen Mechanismus notwendig sein könnten. Da keine Zelltyp-abhängigen Unterschiede festgestellt wurden, könnte es sich bei dieser posttranslationalen Art der MRP4-Regulation um einen ubiquitär verbreiteten Mechanismus handeln, der mittlerweile auch für bestimmte andere Transporter beobachtet wurde und in vivo auch die Aufnahme bzw. Elimination von Pharmaka beeinflussen könnte. Diese Arbeit lieferte neue Erkenntnisse zur Regulation von MRP4 auf transkriptioneller und posttranslationaler Ebene. Durch weitere Untersuchungen sollte die pharmakologische und physiologische Relevanz dieser Regulationsmechanismen noch intensiver charakterisiert werden.