@phdthesis{Eltschkner2020,
  author    = {Eltschkner, Sandra},
  title     = {Targeting the Bacterial Fatty-Acid Synthesis Pathway: Towards the Development of Slow-Onset Inhibitors and the Characterisation of Protein-Protein Interactions},
  doi       = {10.25972/OPUS-15664},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156643},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {A continuous arms race between the development of novel antibiotics and the evolution of corresponding resistance mechanisms in bacteria has been observed, since antibiotic agents like arsphenamines (e.g. Salvarsan, developed by Paul Ehrlich [1]), sulphonamides (e.g. Prontosil, Gerhard Domagk [2]) and penicillin (Alexander Fleming [3]) were first applied to effectively cure bacterial infections in the early 20th century. The rapid emergence of resistances in contrast to the currently lagging discovery of antibiotics displays a severe threat to human health. Some serious infectious diseases, such as tuberculosis or melioidosis, which were either thought to be an issue only in Third-World countries in case of tuberculosis, or regionally restricted with respect to melioidosis, are now on the rise to expand to other areas. In contrast, methicillin-resistant Staphylococcus aureus (MRSA) is already present in clinical setups all over the world and causes severe infections in immunocompromised patients. Thus, there is an urgent need for new and effective antimicrobial agents, which impair vital functions of the pathogen's metabolism. One central metabolic pathway is represented by the bacterial fatty-acid synthesis pathway (FAS II), which is essential for the synthesis of long and branched-chain fatty acids, as well as mycolic acids. These substances play a major role as modulating components of the properties of the most important protective barrier - the cell envelope. The integrity of the bacterial cell wall and the associated membrane(s) is crucial for cell growth and for protection against physical strain, intrusion of antibiotic agents and regulation of uptake of ions and other small molecules. Thus, this central pathway represents a promising target for antibiotic action against pathogens to combat infectious diseases. The last and rate-limiting step is catalysed by the trans-2-enoyl-ACP reductase (ENR) FabI or InhA (in mycobacteria), which has been demonstrated to be a valuable target for drug design and can be addressed, amongst others, by diphenyl ether (DPE) compounds, derived from triclosan (TCL) - the first one of this class which was discovered to bind to ENR enzymes [4, 5]. Based on this scaffold, inhibitors containing different combinations of substituents at crucial positions, as well as a novel type of substituent at position five were investigated regarding their binding behaviour towards the Burkholderia pseudomallei and Mycobacterium tuberculosis ENR enzymes bpFabI and InhA, respectively, by structural, kinetic and in-vivo experiments. Generally, substitution patterns modulate the association and dissociation velocities of the different ENR inhibitors in the context of the two-step slow-onset binding mechanism, which is observed for both enzymes. These alterations in the rapidity of complex formation and decomposition have a crucial impact on the residence time of a compound and hence, on the pharmacokinetic properties of potential drug candidates. For example, the substituents at the 2'-position of the DPE scaffold influence the ground- and transition state stability during the binding process to bpFabI, whereas 4'-substituents primarily alter the transition state [6]. The novel triazole group attached to the 5-position of the scaffold, targeting the hydrophobic part of the substrate-binding pocket in InhA, significantly enhances the energy barrier of the transition state of inhibitor binding [7] and decelerates the association- as well as the dissociation processes. Combinations with different substituents at the 2'-position can enhance or diminish this effect, e.g. by ground-state stabilisation, which will result in an increased residence time of the respective inhibitor on InhA. Further structural investigations carried out in this work, confirm the proposed binding mode of a customised saFabI inhibitor [8], carrying a pyridone moiety on the DPE scaffold to expand interactions with the protein environment. Structural and preliminary kinetic data confirm the binding of the same inhibitor to InhA in a related fashion. Comparisons with structures of the ENR inhibitor AFN-1252 [9] bound to ENR enzymes from other organisms, addressing a similar region as the pyridone-moiety of the DPE inhibitor, suggest that also the DPE inhibitor bears the potential to display binding to homologues of saFabI and InhA and may be optimised accordingly. Both of the newly investigated substituents, the pyridone moiety at the 4'-position as well as the 5-triazole substituent, provide a good starting point to modify the DPE scaffold also towards improved kinetic properties against ENR enzymes other than the herein studied and combining both groups on the DPE scaffold may have beneficial effects. The understanding of the underlying binding mechanism is a crucial factor to promote the dedicated design of inhibitors with superior pharmacokinetic characteristics. A second target for a structure-based drug-design approach is the interaction surface between ENR enzymes and the acyl-carrier protein (ACP), which delivers the growing acyl chain to each distinct enzyme of the dissociated FAS-II system and presumably recognises its respective interaction partner via electrostatic contacts. The interface between saACP and saFabI was investigated using different approaches including crosslinking experiments and the design of fusion constructs connecting the ACP and the FabI subunits via a flexible linker region of varying lengths and compositions. The crosslinking studies confirmed a set of residues to be part of the contact interface of a previously proposed complex model [10] and displayed high crosslinking efficiency of saACP to saFabI when mutated to cysteine residues. However, crystals of the complex obtained from either the single components, or of the fusion constructs usually displayed weak diffraction, which supports the assumption that complex formation is highly transient. To obtain ordered crystals for structural characterisation of the complex it is necessary to trap the complex in a fixed state, e.g. by a high-affinity substrate attached to ACP [11], which abolishes rapid complex dissociation. For this purpose, acyl-coupled long-residence time inhibitors might be a valuable tool to elucidate the detailed architecture of the ACP-FabI interface. This may provide a novel basis for the development of inhibitors that specifically target the FAS-II biosynthesis pathway.},
  subject      = {Fetts{\"a}urestoffwechsel},
  language  = {en}
}
@phdthesis{Jung2016,
  author    = {Jung, Lisa Anna},
  title     = {Targeting MYC Function as a Strategy for Tumor Therapy},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146993},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {A large fraction of human tumors exhibits aberrant expression of the oncoprotein MYC. As a transcription factor regulating various cellular processes, MYC is also crucially involved in normal development. Direct targeting of MYC has been a major challenge for molecular cancer drug discovery. The proof of principle that its inhibition is nevertheless feasible came from in vivo studies using a dominant-negative allele of MYC termed OmoMYC. Systemic expression of OmoMYC triggered long-term tumor regression with mild and fully reversible side effects on normal tissues. In this study, OmoMYC's mode of action was investigated combining methods of structural biology and functional genomics to elucidate how it is able to preferentially affect oncogenic functions of MYC. The crystal structure of the OmoMYC homodimer, both in the free and the E-box-bound state, was determined, which revealed that OmoMYC forms a stable homodimer, and as such, recognizes DNA via the same base-specific DNA contacts as the MYC/MAX heterodimer. OmoMYC binds DNA with an equally high affinity as MYC/MAX complexes. RNA-sequencing showed that OmoMYC blunts both MYC-dependent transcriptional activation and repression. Genome-wide DNA-binding studies using chromatin immunoprecipitation followed by high-throughput sequencing revealed that OmoMYC competes with MYC/MAX complexes on chromatin, thereby reducing their occupancy at consensus DNA binding sites. The most prominent decrease in MYC binding was seen at low-affinity promoters, which were invaded by MYC at oncogenic levels. Strikingly, gene set enrichment analyses using OmoMYC-regulated genes enabled the identification of tumor subgroups with high MYC levels in multiple tumor entities. Together with a targeted shRNA screen, this identified novel targets for the eradication of MYC-driven tumors, such as ATAD3A, BOP1, and ADRM1. In summary, the findings suggest that OmoMYC specifically inhibits tumor cell growth by attenuating the expression of rate-limiting proteins in cellular processes that respond to elevated levels of MYC protein using a DNA-competitive mechanism. This opens up novel strategies to target oncogenic MYC functions for tumor therapy.},
  subject      = {Myc},
  language  = {en}
}
@phdthesis{Wencker2022,
  author    = {Wencker, Freya Dorothea Ruth},
  title     = {The methionine biosynthesis operon in \(Staphylococcus\) \(aureus\): Role of concerted RNA decay in transcript stability and T-box riboswitch turnover},
  doi       = {10.25972/OPUS-20712},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207124},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Methionine is the first amino acid of every newly synthesised protein. In combination with its role as precursor for the vital methyl-group donor S-adenosylmethionine, methionine is essential for every living cell. The opportunistic human pathogen Staphylococcus aureus is capable of synthesising methionine de novo, when it becomes scarce in the environment. All genes required for the de novo biosynthesis are encoded by the metICFE-mdh operon, except for metX. Expression is controlled by a hierarchical network with a methionyl-tRNA-specific T-box riboswitch (MET-TBRS) as centrepiece, that is also referred to as met leader (RNA). T-box riboswitches (TBRS) are regulatory RNA elements located in the 5'-untranslated region (5'-UTR) of genes. The effector molecule of T-box riboswitches is uncharged cognate tRNA. The prevailing mechanism of action is premature termination of transcription of the nascent RNA in the absence of the effector (i.e. uncharged cognate tRNA) due to formation of a hairpin structure, the Terminator stem. In presence of the effector, a transient stabilisation of the alternative structure, the Antiterminator, enables transcription of the downstream genes ('read-through'). Albeit, after the read-through the thermodynamically more stable Terminator eventually forms. The Terminator and the Antiterminator are two mutually exclusive structures. Previous work of the research group showed that in staphylococci the MET-TBRS ensures strictly methionine-dependent control of met operon expression. Uncharged methionyl-tRNA that activates the system is only present in sufficient amounts under methionine-deprived conditions. In contrast to other bacterial TBRS, the staphylococcal MET-TBRS has some characteristic features regarding its length and predicted secondary structure whose relevance for the function are yet unkown. Aim of the present thesis was to experimentally determine the structure of the met leader RNA and to investigate the stability of the met operon-specific transcripts in the context of methionine biosynthesis control. Furthermore, the yet unknown function of the mdh gene within the met operon was to be determined. In the context of this thesis, the secondary structure of the met leader was determined employing in-line probing. The structural analysis revealed the presence of almost all highly conserved T-box riboswitch structural characteristics. Furthermore, three additional stems, absent in all T-box riboswitches analysed to date, could be identified. Particularly remarkable is the above average length of the Terminator stem which renders it a potential target of the double-strand-specific endoribonuclease III (RNase III). The RNase III-dependent cleavage of the met leader could be experimentally verified by the use of suitable mutants. Moreover, the exact cleavage site within the Terminator was determined. The unusual immediate separation of the met leader from the met operon mRNA via the RNase III cleavage within the Terminator stem induces the rapid degradation of the met leader RNA and, most likely, that of the 5'-region of the met mRNA. The met mRNA is degraded from its 5'-end by the exoribonuclease RNase J. The stability of the met mRNA was found to vary over the length of the transcript with an instable 5'-end (metI and metC) and a longer half-life towards the 3'-end (metE and mdh). The varying transcript stability is reflected by differences in the available cellular protein levels. The obtained data suggest that programmed mRNA degradation is another level of regulation in the complex network of staphylococcal de novo methionine biosynthesis control. In addition, the MET-TBRS was studied with regard to a future use as a drug target for novel antimicrobial agents. To this end, effects of a dysregulated methionine biosynthesis on bacterial growth and survival were investigated in met leader mutants that either caused permanent transcription of the met operon ('ON') or prevented operon transcription ('OFF'), irrespective of the methionine status in the cell. Methionine deprivation turned out to be a strong selection pressure, as 'OFF' mutants acquired adaptive mutations within the met leader to restore met operon expression that subsequently re-enabled growth. The second part of the thesis was dedicated to the characterisation of the Mdh protein that is encoded by the last gene of the met operon and whose function is unknown yet. At first, co-transcription and -expression with the met operon could be demonstrated. Next, the Mdh protein was overexpressed and purified and the crystal structure of Mdh was solved to high resolution by the Kisker research group (Rudolf-Virchow-Zentrum W{\"u}rzburg). Analysis of the structure revealed the amino acid residues crucial for catalytic activity, and zinc was identified as a co-factor of Mdh. Also, Mdh was shown to exist as a dimer. However, identification of the Mdh substrate was, in the context of this thesis, (still) unsuccessful. Nevertheless, interactions of Mdh with enzymes of the met operon could be demonstrated by employing the bacterial two-hybrid system. This fact and the high conservation of mdh/Mdh on nucleotide and amino acid level among numerous staphylococcal species suggests an important role of Mdh within the methionine metabolism that should be a worthwhile subject of future research.},
  subject      = {Staphylococcus aureus},
  language  = {en}
}
@phdthesis{Klemm2020,
  author    = {Klemm, Theresa Antonia},
  title     = {Minor differences cause major effects: How differential oligomerization regulates the activities of USP25 and USP28},
  doi       = {10.25972/OPUS-19108},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191080},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Deubiquitinases are regulators of the ubiquitin proteasome system that counteract the ubiquitination cascade by removing ubiquitin from substrates and cleaving ubiquitin chains. Due to their involvment in various important pathways, they are associated with several diseases and may thus present promising drug targets. The two related ubiquitin specific proteases USP25 and USP28 share a highly conserved amino acid sequence but perform distinct biological functions. USP28 plays roles in cell cycle regulation and was also linked to several types of cancer. It adopts oncogenic functions by rescuing the oncoproteins MYC and JUN from proteasomal degradation, which is induced by the E3-ligase SCF (FBW7). Opposingly, USP28 also regulates the stability of the tumor suppressor FBW7 itself. USP25 contributes to a balanced innate immune system by stabilizing TRAF3 and TRAF6 and lately was found to promote Wnt-signaling by deubiquitinating TNKS. Due to the high level of identity of both proteases, a recent attempt to inhibit USP28 led to cross reactivity against USP25. In our study, we characterized both USP25 and USP28 structurally and functionally using x-ray crystallography, biochemical as well as biophysical approaches to determine similarities and differences that can be exploited for the development of specific inhibitors. The crystal structure of the USP28 catalytic domain revealed a cherry-couple like dimer that mediates self-association by an inserted helical subdomain, the USP25/28 catalytic domain inserted domain (UCID). In USP25, the UCID leads to formation of a tetramer composed of two interlinked USP28-like dimers. Structural and functional analysis revealed that the dimeric USP28 is active, whereas the tetrameric USP25 is auto inhibited. Disruption of the tetramer by a cancer-associated mutation or a deletion-variant activates USP25 through dimer formation in in vitro assays and leads to an increased stability of TNKS in cell studies. Furthermore, in vitro data showed that neither ubiquitin nor substrate binding led to the activation of the USP25 tetramer construct. With the structure of the C-terminal domain of USP25, we determined the last unknown region in the enzyme as a separately folded domain that mediates substrate interactions. Combined the structures of the USP25 and USP28 catalytic domains and the functional characterization of both enzymes provide novel insights into the regulation of USPs by oligomerization. Furthermore, we identified individual features of each protease that might be explored for the development of specific small molecule inhibitors.},
  subject      = {Oligomerisation},
  language  = {en}
}
@phdthesis{Schoenwetter2021,
  author    = {Sch{\"o}nwetter, Elisabeth Sofie},
  title     = {Towards an understanding of the intricate interaction network of TFIIH},
  doi       = {10.25972/OPUS-16892},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168926},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The integrity of its DNA is fundamental for every living cell. However, DNA is constantly threatened by exogenous and endogenous damaging agents that can cause a variety of different DNA lesions. The severe consequences of an accumulation of DNA lesions are reflected in cancerogenesis and aging. Several DNA repair mechanisms ensure the repair of DNA lesions and thus maintain DNA integrity. One of these DNA repair mechanisms is nucleotide excision repair (NER), which is famous for its ability to address a large variety of structurally unrelated DNA lesions. A key component of eukaryotic NER is the transcription factor II H (TFIIH) complex, which is not only essential for DNA repair but also for transcription. The TFIIH complex is composed of ten subunits. How these subunits work together during NER to unwind the DNA around the lesion is, however, not yet fully understood. High-resolution structural data and biochemical insights into the function of every subunit are thus indispensable to understand the functional networks within TFIIH. The importance of an intact TFIIH complex is reflected in the severe consequences of patient mutations in the TFIIH subunits XPB, XPD or p8 leading to the hallmark diseases xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Defects in the NER pathway are further associated with several types of cancer including skin cancer. The herein described work focused on five TFIIH subunits derived from the thermophilic fungus Chaetomium thermophilum, the p34/p44 pair and the ternary XPB/p52/p8 complex. The interaction between p34 and p44 was characterized based on a high-resolution structure of the p34_vWA/p44_RING minimal complex. Biochemical studies of the p34/p44 interaction led to the disclosure of an additional interaction between the p34 and p44 subunits, which had not been characterized so far. The p34/p44 interaction was shown to be central to TFIIH, which justifies the presence of several redundant interfaces to safeguard the interaction between the two proteins and might explain why so far, no patient mutations in these subunits have been identified. The p52 subunit of TFIIH was known to be crucial to stimulate the ATPase activity of XPB, which is required during NER. This work presents the first entire atomic resolution structural characterization of p52, which was derived of several crystal structures of p52 variants and a p52/p8 variant thereby demonstrating the interaction between p52 and p8. The precise structural model of p52 offered the possibility to investigate interactions with other TFIIH subunits in more detail. The middle domain 2 of p52 and the N-terminal domain of XPB were shown to mediate the main interaction between the two subunits. An analysis of the p52 crystal structures within recently published cryo-electron microscopy structures of TFIIH provides a model of how p52 and p8 stimulate the ATPase activity of XPB, which is essential for NER and transcription. The structural and biochemical findings of this work provide an additional building block towards the uncovering of the architecture and function of this essential transcription factor.},
  subject      = {DNS-Reparatur},
  language  = {en}
}
@phdthesis{Bathon2019,
  author    = {Bathon, Kerstin},
  title     = {Mutations in protein kinase A catalytic subunit as a cause of adrenal Cushing's syndrome: mechanisms and functional consequences},
  doi       = {10.25972/OPUS-16893},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168937},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2019},
  abstract  = {Protein kinase A (PKA) is the main effector of cyclic-adenosine monophosphate (cAMP) and plays an important role in steroidogenesis and proliferation of adrenal cells. In a previous study we found two mutations (L206R, 199_200insW) in the main catalytic subunit of protein kinase A (PKA C) to be responsible for cortisol-producing adrenocortical adenomas (CPAs). These mutations interfere with the formation of a stable holoenzyme, thus causing constitutive PKA activation. More recently, we identified additional mutations affecting PKA C in CPAs associated with overt Cushing syndrome: S213R+insIILR, 200_201insV, W197R, d244 248+E249Q, E32V. This study reports a functional characterization of those PKA Cmutations linked to CPAs of Cushing's patients. All analyzed mutations except for E32V showed a reduced interaction with at least one tested regulatory (R) subunit. Interestingly the results of the activity differed among the mutants and between the assays employed. For three mutants (L206R, 199_200insW, S213R+insIILR), the results showed enhanced translocation to the nucleus. This was also observed in CRISPR/Cas9 generated PRKACA L206R mutated HEK293T cells. The enhanced nuclear translocation of this mutants could be due to the lack of R subunit binding, but also other mechanisms could be at play. Additionally, I used an algorithm, which predicted an effect of the mutation on substrate specificity for four mutants (L206R, 199_200insW, 200_201insV, d244 248+E249Q). This was proven using phosphoproteomics for three mutants (L206R, 200_201insV, d244 248+E249Q). In PRKACA L206R mutated CPAs this change in substrate specificity also caused hyperphosphorylation of H1.4 on serine 36, which has been reported to be implicated in mitosis. Due to these observations, I hypothesized, that there are several mechanisms of action of PRKACA mutations leading to increased cortisol secretion and cell proliferation in adrenal cells: interference with the formation of a stable holoenzyme, altered subcellular localization and a change in substrate specificity. My data indicate that some PKA C mutants might act via just one, others by a combination of these mechanisms. Altogether, these findings indicate that several mechanisms contribute to the development of CPAs caused by PRKACA mutations. Moreover, these findings provide a highly illustrative example of how alterations in a protein kinase can cause a human disease.},
  subject      = {Proteinkinase A},
  language  = {en}
}
@phdthesis{Schmitt2017,
  author    = {Schmitt, Dominik},
  title     = {Structural Characterization of the TFIIH Subunits p34 and p44 from C. thermophilum},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-104851},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {Several important cellular processes, including transcription, nucleotide excision repair and cell cycle control are mediated by the multifaceted interplay of subunits within the general transcription factor II H (TFIIH). A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these pathways. This becomes especially important in the context of severe diseases like xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy, that arise from single point mutations in some of the TFIIH subunits. In an attempt to structurally characterize the TFIIH complex, we harnessed the qualities of the eukaryotic thermophile Chaetomium thermophilum, a remarkable fungus, which has only recently been recognized as a novel model organism. Homologues of TFIIH from C. thermophilum were expressed in E. coli, purified to homogeneity and subsequently utilized for crystallization trials and biochemical studies. The results of the present work include the first crystal structure of the p34 subunit of TFIIH, comprising the N-terminal domain of the protein. The structure revealed a von Willebrand Factor A (vWA) like fold, which is generally known to be involved in a multitude of protein-protein interactions. Structural comparison allowed to delineate similarities as well as differences to already known vWA domains, providing insight into the role of p34 within TFIIH. These results indicate that p34 assumes the role of a structural scaffold for other TFIIH subunits via its vWA domain, while likely serving additional functions, which are mediated through its C-terminal zinc binding domain and are so far unknown. Within TFIIH p34 interacts strongly with the p44 subunit, a positive regulator of the XPD helicase, which is required for regulation of RNA Polymerase II mediated transcription and essential for eukaryotic nucleotide excision repair. Based on the p34 vWA structure putative protein-protein interfaces were analyzed and binding sites for the p34 p44 interaction suggested. Continuous crystallization efforts then led to the first structure of a p34 p44 minimal complex, comprising the N-terminal vWA domain of p34 and the C-terminal C4C4 RING domain of p44. The structure of the p34 p44 minimal complex verified the previous hypothesis regarding the involved binding sites. In addition, careful analysis of the complex interface allowed to identify critical residues, which were subsequently mutated and analyzed with respect to their significance in mediating the p34 p44 interaction, by analytical size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The structure of the p34 p44 complex also revealed a binding mode of the p44 C4C4 RING domain, which differed from that of other known RING domains in several aspects, supporting the hypothesis that p44 contains a novel variation of this domain.},
  subject      = {DNA-Reparatur},
  language  = {en}
}
@phdthesis{Buechner2014,
  author    = {B{\"u}chner, Claudia Nadine},
  title     = {Single molecule studies of DNA lesion search and recognition strategies},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-111886},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {The integrity of our genome is continuously endangered by DNA damaging factors. Several cellular mechanisms have evolved to recognize and remove different types of DNA lesions. Despite the wealth of information on the three-dimensional structure and the catalytic mechanism of DNA repair enzymes, the essential process of target site search and identification remains more elusive. How can a small number of repair proteins find and detect the rare sites of damage rapidly and efficiently over an excess of millions of undamaged bases? To address this pivotal question in DNA repair, I focused on the central players from the two DNA damage excision repair pathways in my studies: nucleotide excision repair (NER) and base excision repair (BER). As examples for completely different approaches of damage search, recognition and verification, I compared the NER protein Xeroderma pigmentosum group D (XPD) with the BER proteins human thymine DNA glycosylase (hTDG) and human 8-oxoguanine glycosylase (hOgg1). In particular, the single molecule approach of atomic force microscopy (AFM) imaging and complementary biochemical and biophysical techniques were applied. I established a simple, optimized preparation approach, which yields homogeneous and pure samples of long (several hundreds to thousands of base pairs) DNA substrates suitable for the AFM studies with DNA repair proteins. Via this sample preparation, a single target site of interest can be introduced into DNA at a known position, which allows separate analysis of specific protein-DNA complexes bound to the lesion site and nonspecific complexes bound to non-damaged DNA. The first part of the thesis investigates the XPD protein involved in eukaryotic NER. In general, the NER mechanism removes helix-distorting lesions - carcinogenic UV light induced photoproducts, such as cyclobutane pyrimidine dimers (CPDs) as well as bulky DNA adducts. The 5'-3' helicase XPD has been proposed to be one of the key players in DNA damage verification in eukaryotic NER, which is still a matter of hot debate. In the studies, I focused on XPD from the archaeal species Thermoplasma acidophilum (taXPD), which shares a relatively high sequence homology with the sequence of the human protein and may serve as a good model for its eukaryotic counterpart. Based on AFM experiments and accompanying DNA binding affinity measurements with the biosensor technology Biolayer Interferometry (BLI), a clear role of XPD in damage verification was deciphered. Specifically, the data suggested that the ATP-dependent 5'-3' helicase activity of XPD was blocked by the presence of damage leading to stalled XPD-DNA damage verification complexes at the lesion sites. Successful damage verification led to ATP-dependent conformational changes visible by a significant transition in DNA bend angles from ~ 50° to ~ 65° at the site of the bound protein. Remarkably, this DNA bend angle shift was observed both in the presence of ATP and ATPγs (non-hydrolyzable ATP analog) indicating that ATP-binding instead of ATP hydrolysis was sufficient to induce repair competent conformational changes of XPD. Most importantly, detailed protein binding position and DNA bend angle analyses revealed for the first time that XPD preferably recognizes a bulky fluorescein lesion on the translocated strand, whereas a CPD lesion is preferentially detected on the opposite, non-translocated strand. Despite the different recognition strategies for both types of damages, they share a common verification complex conformation, which may serve as a signal for the recruitment of further NER factors. In the second part of the thesis, AFM imaging and a 2-Aminopurine fluorescence-based base-flipping assay were combined to investigate damage search and recognition by DNA glycosylases in BER. Exemplarily, I chose to study hTDG as a representative of the vast glycosylase family. hTDG excises thymine and uracil from mutagenic G:T and G:U mispairs contributing to cancer and genetic disease. The AFM data suggested that hTDG uses the intrinsic flexibility of G:T and G:U wobble pairs for initial damage sensing, while scanning DNA as a search complex (SC, slightly bent DNA). Remarkably, hTDG has been indicated to continuously switch between the search and interrogation conformation (IC, stronger bent DNA) during damage search. In the IC, target bases are interrogated by extrahelical base flipping, which is facilitated by protein-induced DNA bending and enhanced DNA flexibility at mismatches. AFM and fluorescence analyses revealed that the flipped base is stabilized via hTDG's arginine finger. Correct target bases are perfectly stabilized within the enzyme's catalytic pocket resulting in prolonged residence time and enhanced excision probability. To test for the generalizability of the proposed hTDG damage search model to BER glycosylases, identical studies were performed with a second glycosylase, hOgg1. The data on hOgg1, which removes structurally more stable 8-oxoguanine lesions, supported the hypothesis developed for lesion recognition by hTDG as a common strategy employed by BER glycosylases},
  subject      = {Rasterionenmikroskop},
  language  = {en}
}
@phdthesis{Selle2018,
  author    = {Selle, Martina},
  title     = {Interaktionen zwischen sekretierten Proteinen von Staphylococcus aureus und der Immunantwort des Wirtes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128031},
  school      = {Universit{\"a}t W{\"u}rzburg},
  pages     = {XVII, 216},
  year      = {2018},
  abstract  = {Staphylococcus aureus ist ein grampositives Bakterium, welches h{\"a}ufig als kommensaler Besiedler auf der Nasen- und Rachenschleimhaut von S{\"a}ugetieren vorkommt. Dar{\"u}ber hinaus besitzt dieser fakultativ pathogene Mikroorganismus die F{\"a}higkeit schwer zu behandelnde Krankenhausinfektionen auszul{\"o}sen. Aufgrund der weiten Verbreitung von Antibiotikaresistenzen und dem Mangel an effektiven Therapien, verursachen S. aureus Infektionen j{\"a}hrlich enorme Kosten f{\"u}r das Gesundheitssystem. S. aureus wird meist von der Nase zum prim{\"a}ren Infektionsort {\"u}bertragen, wodurch zun{\"a}chst sehr h{\"a}ufig Wund- und Weichteilinfektionen hervor gerufen werden. Von diesem prim{\"a}ren Infektionsort ausgehend, kann der Erreger tiefer liegende Gewebsschichten infizieren oder sich {\"u}ber den Blutstrom im gesamten Organismus ausbreiten. Das Spektrum an Krankheitsbildern reicht von leichten Abszessen der Haut bis zu schweren, lebensbedrohlichen Erkrankungen wie Pneumonien und akuter Sepsis. F{\"u}r die erfolgreiche Kolonisierung und Infektion des Wirtes exprimiert S. aureus eine Vielzahl unterschiedlicher Virulenzfaktoren. Die wohl gr{\"o}ßte Gruppe an Virulenzfaktoren umfasst die Proteine, die an der Immunevasion und der Umgehung von verschiedenen Abwehrstrategien des Immunsystems beteiligt sind. Das bisherige Wissen {\"u}ber die Interaktion von S. aureus mit dem Immunsystem des Wirtes und die zugrunde liegenden Pathogenit{\"a}tsmechanismen ist bisher limitiert. Um neue Erkenntnisse {\"u}ber die Interaktion von Wirt und Pathogen zu erlangen, wurden im Rahmen dieser Arbeit bislang unbekannte sekretierte und Oberfl{\"a}chen-assoziierte Proteine von S. aureus funktionell charakterisiert. Die Funktion der ausgew{\"a}hlten Proteine wurde in vitro hinsichtlich Einfluss auf Komponenten des Immunsystems, Adh{\"a}sion an Wirtsfaktoren und Invasion in eukaryotische Zellen untersucht. Mit Hilfe der vorangegangenen in-vitro-Charakterisierung der putativen Virulenzfaktoren, konnte f{\"u}r die cytoplasmatische Adenylosuccinat-Synthase PurA eine neuartige Funktion identifiziert werden. PurA ist bekannt als essentielles Enzym der de novo Purin-Synthese. In dieser Arbeit wurde nun gezeigt, dass PurA zudem an der Immunevasion beteiligt ist. Durch die Bindung des humanen Faktor H des Komplementsystems sch{\"u}tzt PurA S. aureus vor der lytischen Aktivit{\"a}t des Komplementsystems und verhindert die Opsonisierung des Pathogens. Basierend auf diesen Ergebnissen wurde PurA detailliert charakterisiert. In Bindungsstudien mit rekombinantem Faktor H und PurA wurde eine direkte Interaktion beider Proteine nachgewiesen, wobei Faktor H mit dem N-terminalen Bereich von PurA interagiert. Weiterhin konnte PurA durch Immunfluoreszenz und FACS-Analysen auf der Zelloberfl{\"a}che nachgewiesen werden, wo es wahrscheinlich mit der Zellwand assoziiert vorliegt. Dort rekrutiert es Faktor H an die bakterielle Oberfl{\"a}che und verhindert das Fortschreiten der Komplement-Kaskade und damit die Lyse des Pathogens. Aufgrund der Multifunktionalit{\"a}t z{\"a}hlt PurA somit zur Gruppe der Moonlighting Proteine. Des Weiteren wurde die Rolle von PurA im Infektionsgeschehen in zwei unabh{\"a}ngigen Tiermodellen untersucht. In beiden Modellen wurde ein signifikant reduziertes Virulenzpotential der ΔpurA-Mutante beobachtet. Zuk{\"u}nftig soll gekl{\"a}rt werden, ob die verminderte Virulenz in der fehlenden Komplementevasion oder im Defekt in der Purin-Synthese begr{\"u}ndet ist. Aufgrund der sehr starken Attenuation in allen untersuchten Infektionsmodellen sollte PurA als potentielles Target f{\"u}r eine Therapie von S. aureus Infektionen weiter charakterisiert werden. Im Ergebnis dieser Arbeit wurde demnach mit PurA ein neues Moonlighting Protein identifiziert, das als Inhibitor des Komplementsystems wesentlich zur Immunevasion von S. aureus beitr{\"a}gt. F{\"u}r das bessere Verst{\"a}ndnis der humoralen S. aureus-spezifischen Immunantwort, Unterschieden in der Antik{\"o}rperantwort und der gebildeten Antik{\"o}rperspezifit{\"a}ten wurde weiterhin das w{\"a}hrend der Kolonisierung und Infektion gebildete S. aureus-spezifische Antik{\"o}rperprofil untersucht. Dazu wurden Plasmen von humanen nasalen Tr{\"a}gern und Nicht-Tr{\"a}gern sowie murine Seren von infizierten Tieren untersucht. Insbesondere wurde das Pathogen-spezifische Antik{\"o}rperprofil in unterschiedlichen Infektionsmodellen mit Hilfe eines Proteinarrays analysiert, der im Rahmen dieser Arbeit in einer Kooperation mit der Firma Alere Technologies (Jena, Deutschland) und universit{\"a}ren Forschergruppen der Universit{\"a}ten Greifswald, M{\"u}nster und Jena mitentwickelt wurde. Die Antik{\"o}rperprofile von intramuskul{\"a}r und intraven{\"o}s infizierten Tieren resultierten in jeweils spezifischen Antik{\"o}rperprofilen. Diese Ergebnisse deuten auf einen Zusammenhang zwischen der Art der Infektion und der gebildeten Antik{\"o}rperspezifit{\"a}ten hin. Wahrscheinlich beruht dies auf einer gewebespezifischen Genexpression als Anpassung an die individuellen Bed{\"u}rfnisse im Wirtsorganismus. Das ausgebildete Antik{\"o}rperprofil gibt somit einen Einblick in das Expressionsmuster von Virulenzfaktoren von S. aureus unter in vivo Bedingungen und tr{\"a}gt damit zum Verst{\"a}ndnis der komplexen Interaktion von Pathogen und Wirt bei. Diese Untersuchungen erg{\"a}nzen zudem die bisherigen Kenntnisse {\"u}ber die Anpassung der humoralen Immunantwort an eine asymptomatische Kolonisierung im Gegensatz zu einer akuten Infektion durch S. aureus. Dar{\"u}ber hinaus k{\"o}nnen die gewonnenen Ergebnisse f{\"u}r diagnostische Zwecke und zur Identifikation von neuen Zielstrukturen f{\"u}r eine Vakzin-Entwicklung genutzt werden.},
  subject      = {Staphylococcus aureus},
  language  = {de}
}
@phdthesis{Rohleder2014,
  author    = {Rohleder, Florian},
  title     = {The Intricate Network of Replication-dependent Interstrand Crosslink DNA Repair},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-113121},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {The Fanconi anemia (FA) pathway is a replication-dependent DNA repair mechanism which is essential for the removal of interstrand crosslink (ICL) DNA damages in higher eukaryotes (Moldovan and D'Andrea, 2009). Malfunctions in this highly regulated repair network lead to genome instability (Deans and West, 2011). Pathological phenotypes of the disease FA which is caused by mutations in the eponymous pathway are very heterogeneous, involving congenital abnormalities, bone-marrow failure, cancer predisposition and infertility (Auerbach, 2009). The FA pathway comprises a complex interaction network and to date 16 FA complementation groups and associated factors have been identified (Kottemann and Smogorzewska, 2013). Additionally, components of nucleotide excision repair (NER), homologous recombination repair (HRR), and translesion synthesis (TLS) are involved and coordinated by the FA proteins (Niedzwiedz et al., 2004; Knipscheer et al., 2009). One of the FA proteins is the DEAH helicase FANCM. In complex with its binding partners FAAP24 and MHF1/2 it binds the stalled replication fork and activates the FA damage response (Wang et al., 2013). However, the exact steps towards removal of the ICL damage still remain elusive. To decipher the underlying process of FA initiation by FANCM, this thesis mainly focuses on the archaeal FANCM homolog helicase-associated endonuclease for fork-structured DNA (Hef). Hef from the archaeal organism Thermoplasma acidophilum (taHef) differs from other archaeal Hef proteins and exclusively comprises an N-terminal helicase entity with two RecA and a thumb-like domain while others additionally contain a nuclease portion at the C-terminus. I solved the crystal structure of full-length taHef at a resolution of 2.43 {\AA}. In contrast to the crystal structure of the helicase domain of Hef from Pyrococcus furiosus (pfHef), taHef exhibits an extremely open conformation (Nishino et al., 2005b) which implies that a domain movement of the RecA-like helicase motor domains of 61° is possible thus highlighting the flexibility of helicases which is required to translocate along the DNA. However, small-angle x-ray scattering (SAXS) measurements confirm an intermediate conformation of taHef in solution indicating that both crystal structures represent rather edge states. Most importantly, proliferating cell nuclear antigen (PCNA) was identified as an interaction partner of Hef. This interaction is mediated by a highly conserved canonical PCNA interacting peptide (PIP) motif. Intriguingly, the presence of PCNA does not alter the ATPase nor the helicase activity of taHef, thus suggesting that the interaction is entirely dedicated to recruit taHef to the replication fork to fulfill its function. Due to a high level of flexibility the taHef-taPCNA complex could not be crystallized and therefore SAXS was utilized to determine a low-resolution model of this quaternary structure. This newly discovered PCNA interaction could also be validated for the eukaryotic FANCM homolog Mph1 from the thermophilic fungus Chaetomium thermophilum (ctMph1). As the first step towards the characterization of this interaction I solved the crystal structure of PCNA from Chaetomium thermophilum (ctPCNA). Furthermore, it was possible to achieve preliminary results on the putative interaction between the human proteins FANCM and PCNA (hsFANCM, hsPCNA). In collaboration with Detlev Schindler (Human Genetics, W{\"u}rzburg) and Weidong Wang (National Institute on Aging, Baltimore, USA) co-immunoprecipitation (CoIP) experiments were performed using hsFANCM and hsPCNA expressed in HEK293 cells. Although an interaction was reproducibly observed in hydroxyurea stimulated cells further experiments and optimization procedures are required and ongoing.},
  subject      = {DNS-Reparatur},
  language  = {en}
}