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The synthesis of valuable chemicals via traditional chemical methods can be often outperformed by the use of enzymes because of their excellent chemo-, regio- and stereoselectivity in aqueous solvents at ambient temperatures. On the other hand, enzymes often suffer from several limitations that hamper their industrial application. Protein engineering is commonly applied to overcome these limitations although the generation and the validation of mutants is often a laborious process that may not lead to the desired results within reasonable time frames. This thesis focuses on engineering the enantioselectivity and the substrate scope of industrially relevant enzymes, such as esterases and transaminases. Semi-rational protein engineering was employed to identify improved variants for the synthesis of valuable chemicals ensuring a reduced screening effort. Compared to previous works, 3DM’s applicability was extended to the study of correlated mutations and proved effective in the acceleration of the comprehension and in the mutation of these enzymatic scaffolds. Semi-rational approaches require an extensive amount of information such as protein structures, reaction mechanisms, previous mutational experiments reported in literature and a considerable amount of amino acid sequences from similar proteins to analyze amino acid distributions and correlated mutations. Here, we have exploited 3DM as a tool that can combine all this wealth of information: 3DM is a convenient solution to retrieve and integrate information simplifying decision making in the planning of a semi-rational mutant library since in 3DM’s multiple sequence alignments (MSA) is summarized Nature’s screening process for alternative variants. Furthermore, naturally evolving enzymes often require mutations at more than one position for the acquisition of a new property. Such mutations generate patterns that are recognized by the 3DM algorithm, which creates networks that can be investigated to design strategies that aim to improve the property of interest. Finally, these correlated mutations are connected to the mutations described in publications covered in the PubMed database, thus helping to investigate the role certain positions might play in the network. Article I shows that it is possible to improve the enantioselectivity of an esterase towards a highly symmetrical substrate while drastically reducing the screening effort. This was achieved through the creation of libraries that limit the variants to those identified in the 3DM alignment. Article II shows that networks of correlated mutations are composed of positions that may cluster around a function. These functions can be investigated because 3DM connects the positions in the network to their related publications. In this article, a mutant of the esterase PFE-I from Pseudomonas fluorescens was generated having increased enantioselectivity in the hydrolysis of important target compounds. Article III suggests that the in silico modelling software YASARA, combined with the use of the 3DM database, can further reduce the screening effort: it was possible to identify a hot-spot because both the 3DM database and YASARA docking studies, indicated its importance. This led to a further improved enantioselectivity of the enzyme variant identified in Article II. Article IV shows how MSA may be used to get structural insights into the catalytic properties of enzymes with documented activity. The study of the patterns observed in a large subfamily alignment allowed the definition of the structural determinants important for the substrate recognition in amine transaminases. Article V and VI apply the knowledge acquired for the improvement of the substrate scope in the amine transaminase from Vibrio fluvialis.
Interactions between bacteria and the human body are manifold and happen constantly. Most parts of the skin and gastrointestinal tract, the saliva, the oral mucosa, the conjunctiva and the vaginal mucosa are colonized with a multitude of bacterial species forming the human microbiota. Strikingly, the estimated amount of bacterial cells outnumbers the human body by 10 to 1. However, most of these bacteria colonize the human body without positive or negative effects and are regarded as commensals. Staphylococcus aureus a Gram positive bacterium is such a commensal bacterium of 25 % to 30 % of the world population. It is also an opportunistic pathogen and is able to cause infections in the lung, skin and heart and to induce sepsis. Its pathogenicity is mainly facilitated by the secretion of a broad spectrum of virulence factors which interact with the host. Some are distracting the immune system, others are targeting the host cell membrane or degrade macromolecular structures of the host in order to provide nutrients. Furthermore S. aureus is able to invade the host cell and to survive and replicate in the host cell cytosol or other compartments. The Gram negative proteobacterium Burkholderia pseudomallei is an environmental bacterium but still has the ability to enter the human body via body orifices or skin wounds. In a very efficient way it penetrates the host cell, replicates intracellular and the uses host structures to spread from cell to cell thereby causing the disease melioidosis often with fatal outcomes. Since the natural habitats of B. pseudomallei are wet soils, the change to the environment in the human body is drastic and requires a high degree of flexibility of the bacterium. Environmental stress conditions such as temperature, pH, nutrient limitation or presence of antibiotics induce a switch of colony morphology which is a special characteristic of this bacterium. Since it is assumed, that changes in colony morphology are connected to adaptive processes to the environmental changes, these morphology switches might also be important during infection. The host organism and the host cell on the other side try to kill and remove the bacterial threat by activating the immune system and cellular defence mechanisms. This includes generation of reactive oxygen and nitrogen species, production of antimicrobial peptides and cellular processes such as phagocytosis, autophagy, apoptosis and activation of the immune response. The actions and reactions on both, the pathogen side and the host side, are summarized as host-pathogen interactions. In the field of functional genomics, methods were developed to understand various levels of host-pathogen interactions. The holistic analysis of the mRNA (the transcriptome) or translated proteins (the proteome) were already very useful tools to describe important cellular processes on the host and the pathogen site. The level of metabolites with regard to host-pathogen interactions however, has been neglected so far. In this dissertation the metabolic composition in the intracellular and extracellular space of the host and the pathogen was analyzed. For this matter biochemical analytical tools were used such as 1H-nuclear magnetic resonance spectroscopy and chromatographic methods (GC and HPLC) coupled to mass spectrometry. The combination of these methods allows a broad coverage of physicochemical diverse metabolites. In accordance to the above mentioned biological levels like mRNA and proteins, the sum of all metabolites is referred as the metabolome. Consequently to transcriptomics and proteomics the analysis of the metabolome is referred as metabolomics. To gain insights into the infection relevant metabolome of the host-pathogen relationship between S. aureus and human lung cells several approaches were developed. First the distribution of the recently identified bacillithiol in different S. aureus strains was investigated with regard to its role during the infection. For that matter a HPLC-methodology was used with fluorescence based detection of labelled low molecular weight thiols (article I: Distribution and infection-related functions of bacillithiol in Staphylococcus aureus). After that the next aim was to reveal the effect of S. aureus on the host cell metabolism. To reduce the complexity of effects on the host cells an artificial model was chosen in a first approach. The lung cells were treated with the staphylococcal virulence factor alpha-hemolysin, a pore forming toxin and a holistic metabolomics approach was performed (article II: Staphylococcus aureus Alpha-Toxin Mediates General and Cell Type-Specific Changes in Metabolite Concentrations of Immortalized Human Airway Epithelial Cells). Using this approach, a protocol for cell culture metabolomics was established and first changes in the host cell metabolome that could be caused by S. aureus were described. However, this only describes specific changes caused by one single virulence factor and does not necessarily describes the reality during a S. aureus infection. Therefore in a next approach, an infection model using a human lung epithelial cell line and the S. aureus strain USA300 was established and used for metabolome analysis. Furthermore a combination of inhibitor treatment and metabolic labelling was used to clarify the metabolic activity in the host cell after exposure to S. aureus (article III: Metabolic features of a human airway epithelial cell line infected with Staphylococcus aureus revealed by a metabolomics approach). Finally this thesis deals with the host-pathogen interaction of B. pseudomallei and its host with a focus on the role of the switch in colony morphology in basic metabolism. Various morphotypes of two strains were generated by nutrient limitation and their uptake of nutrients was monitored. Furthermore the morphotypes were used in in vitro and in vivo infections and subsequently isolated out of the cell line and mice respectively. After isolation, the colony morphology was determined and again the nutrient uptake profile was monitored (article IV: Burkholderia pseudomallei morphotypes show a synchronized metabolic pattern after acute infection). The information provided by this thesis adds a new complexity to the knowledge about the host-pathogen interactions of S. aureus and B. pseudomallei and their hosts. It furthermore lays the groundwork for future studies, which will deal with these and other bacterial host-pathogen interactions in order to understand the interdependencies of infection and metabolism.
An interesting subclass of the SLs are Cers, the simplest SLs. Cers are assigned a special role within SLs because of their involvement in many cellular and biophysical processes.In literature Cers are describe to modulate many events in signaling including apoptosis. Besides its role as second messenger and therefore the involvement in many signal cascades, Cers are also known to be essential in physical modifications and structural alternations of membranes. Such regulatory functions on membrane formation are e.g. domain formation with other lipids (i.g. SM and Chol), phase separation with sterols (Chol), vesicular trafficking, fusion, membrane curvature fluidity and thickness and the induction of membrane leakiness. In contrast to phospholipids, Cers can move from one side of the membrane leaflet to the other, due to their strong hydrophobicity. This movement is called flip-flop or as transbilayer movement and is controversially discussed. Consequently, no exact value has been reported about the flip-flop property of Cers, which probably plays an important role during the transmission of an extra cellular signal through the membrane.In order to probe the biophysical properties of ceramides, a synthetic access to 1-thioceramides (1-SHCer) analogues with different N-acyl chain length has been developed in this study. With 1SHCer the flip-flop was investigated on pre-formed liposomes and the data indicated a very rapid flip-flop of Cers with a half time t1/2 <10s in raft- and non-raft like membrane models. Furthermore, the acyl chain length exhibited no measurable impact on the speed of the flip-flop. Utilizing the same probes the importance of hydrogen bond donor and acceptor properties of Cers upon interaction with sphingomyelin in the presence or absence of cholesterol (Chol) has been probed. Performed fluorescent quenching experiments (P.Slotte) proposed the following relative preference in interaction with pSM:pSM:DAGs > pSM:Cer > pSM:Chol > pSM: 1-pCerSH.Most strikingly, the importance of the 1-OH H-bond acceptor functionality to replace Chol around and above the melting temperature of pSM has been demonstrated. Recently, an unusual subclass of SLs, named 1-deoxysphingoids have come to the foreground, as biomarker for metabolic disorders. 1-doxSA is physiologically generated (10-40nM) due to substrate promiscuity of SPT and shown to be elevated in patients with metabolic disorders. In this study an organic synthetic access to fluorescent DSB derivatives was established, featuring a fluorescent moiety at the lipid tail, such as FITC 26. Comprehensive fluorescent studies of 26 revealed an unusual subcellular distribution. Exogenous 1-doxSA analogues, such as FB1 and 1-doxSA-FITC, enter via specific entry points. During the next few hours these lipids accumulate within the cytosol prior to N-acylation by CerS. Upon N-acylation, the newly formed 1-doxdhCer and its analogues insert into the ER membrane.The fluorescent probe and most likely FB1 analogues accumulate within the late endosomal and lysosomal system, probably via a direct connection with the ER. Analysis of the lipid metabolism of unlabeled 1-doxSA and FB1 revealed a strikingly similar behavior, pointing towards a common pharmacological effect. Complete consumption of TG within 24h in epithelia cells combined with GO analysis of 1-doxSA interacting lipids indicates significant modulation of fatty acid degradation, pointing towards regulation of the energy metabolism. This is in good agreement with the observed induction of autophagy. Together, this rapid and similar metabolic change of both 1-doxSA and FB1, points toward direct 1-doxSA head-group related lipid-protein interaction and less toward the influence of FB1 on CerS activity. This work suggests the biological significance of 1-doxSA as a primary nutrient sensor to maintain nutrient homeostasis and its role in the pathophysiology of metabolic diseases.
This thesis is about the establishment and the application of novel methods and tools that are re-lated to the most widely used enzyme class: hydrolases. It covers all fields from the identification to the application of these valuable enzymes with particular focus on lactonases, acylases and proteases. The activity assay introduced in Article I substantially extends the method toolbox for studies on lactonases and acylases that interfere with the bacterial cell-cell communication system. Article II describes a fully automatized robotic platform that represents the next-level tool for the high-throughput enzyme screening in the microtiter plate format. It was used, for instance, for the screening for improved porcine aminoacylase I variants. Diverse aspects of the protease-mediated hydrolysis of non-resistant proteins for the purification of resistant target proteins are highlighted in Article III.
Enzymatic evolution and the corresponding relationship to substrate scope and catalytic promiscuity were targeted in this thesis. As enzyme examples, pig liver esterase (PLE), oleate hydratases and linoleate isomerases, as well as epoxide hydrolases (EH) and haloalkane dehalogenases (HLD) were used. The substrate scope and the enantiopreference of PLE was analyzed by molecular modeling and substrate docking, since different enantiomeric excesses were detected for the conversion of malonate diethyl esters, depending on the PLE isoenzyme. Additionally, fatty acid converting enzymes with high identity were found and analyzed to comprehend the switch of both activities. Furthermore, the evolutionary connection between EH and HLD was investigated by interconversion studies to implement an HLD acitivity in an EH. By directed evolution and rational design, both possibilities of protein engineering were realized. Finally, a new methodology for targeted, continuous in vivo evolution was established by a temperature-dependent mutagenesis frequency.
Cascade reactions are not only of interest to chemists and biotechnologists, but also to life in general, because every metabolic reaction resembles a cascade reaction. This principle of substrate/intermediate channeling was only adapted by scientists. That way especially one-pot reactions became very attractive as for this no isolation of intermediates is necessary. Furthermore, unstable or toxic intermediates are only produced in low amounts and directly transformed in situ. In this PhD thesis two previously established cascade reactions were subject of further optimization. In the first part, a cascade reaction established in a DFG-funded project (Bo1862/6-1)in cooperation with the Vienna Technical University (Austria) for the production of chiral lactones was further optimized and extended. Therefore, on the one hand the genes encoding the needed enzymes were cloned for co-expression into a single plasmid in different arrangements to be expressed in pseudo-operon mode, with the aim to lower the metabolic burden of the cascade host cell. One out of the welve created constructs showed a reasonable activity of 15.3 ± 1.2 U · gCDW-1. On the other hand, this cascade reaction was aimed to be extended by the use of a hydroxylating enzyme to enable the use of limonene as renewable and chiral precursor for the proposed production of chiral polymers. Therefore, the feasibility of cytochrome P450-monooxygenases was studied. These turned out to be not applicable due to their bad regioselectivity for the hydroxylation of limonene or due to the difficulties of activity reconstitution. As alternative system for an initial hydroxylation step the use of a Rhodococcus equi strain, which was isolated from Cellulosimicrobium cellulans EB-8-4 and which is capable of very regioselective limonene-hydroxylation, was investigated. Therefore, the dioxygenase cluster responsible for the desired reaction was identified and especially the recombinant expression in a suitable host (Pseudomonas putida S12) was further studied. The results from these experiments revealed that the recombinant expression needs to be further optimized to enable the use of the recombinant dioxygenase in combination with the other enzymes for cascade reactions. The third part of this PhD thesis dealt with the immobilization of an established cascade reaction for the synthesis of poly-[caprolactone] precursors. Therefore, the use of a rotating bed reactor (RBR) was investigated. Preliminary studies using single enzymes involved in the desired cascade reaction demonstrated the general feasibility of this reactor concept. Especially the reusability of the catalysts was highly improved, because the catalytic particles were protected very effectively from mechanical forces within the voids of the reactor. For further work-flow optimization the immobilization was transformed into an in situ process by the application of a gas-shear device, which leads to decreased capsule size and thereby to increased mass transfer inside the particles. The developed methods were applied for encapsulation of the cells containing the enzymes needed for the reaction. After additional improvement of the reaction parameters a conversion of 93% (based on substrate depletion) was reached using catalysts produced by the established encapsulation procedure. In summary, the described cascade reactions were successfully optimized by either co-expression, extension applying a dioxygenase or immobilization. Furthermore, the general feasibility of an RBR was demonstrated.
Induction of Central Host Signaling Kinases during Pneumococcal Infection of Human THP-1 Cells
(2016)
Streptococcus pneumoniae is a widespread colonizer of the mucosal epithelia of the upper respiratory tract of human. However, pneumococci are also responsible for numerous local as well as severe systemic infections, especially in children under the age of five and the elderly. Under certain conditions, pneumococci are able to conquer the epithelial barrier, which can lead to a dissemination of the bacteria into underlying tissues and the bloodstream. Here, specialized macrophages represent an essential part of the innate immune system against bacterial intruders. Recognition of the bacteria through different receptors on the surface of macrophages leads thereby to an uptake and elimination of bacteria. Accompanied cytokine release triggers the migration of leukocytes from peripheral blood to the site of infection, where monocytes differentiate into mature macrophages. The rearrangement of the actin cytoskeleton during phagocytosis, resulting in the engulfment of bacteria, is thereby tightly regulated by receptor-mediated phosphorylation cascades of different protein kinases. The molecular cellular processes including the modulation of central protein kinases are only partially solved. In this study, the human monocytic THP-1 cell line was used as a model system to examine the activation of Fcγ and complement receptor-independent signal cascades during infection with S. pneumoniae. Pneumococci cultured either in chemically defined or complex medium showed no significant differences in pneumococcal phagocytosis by phorbol 12-myristate 13-acetate (PMA) differentiated THP-1 cells. Double immuno-fluorescence microscopy and antibiotic protection assays demonstrated a time-dependent uptake and killing of S. pneumoniae 35A inside of macrophages. Infections of THP-1 cells in the presence of specific pharmacological inhibitors revealed a crucial role of actin polymerization and importance of the phosphoinositide 3-kinase (PI3K) and Protein kinase B (Akt) as well during bacterial uptake. The participation of essential host cell signaling kinases in pneumococcal phagocytosis was deciphered for the kinase Akt, ERK1/2, and p38 and phosphoimmunoblots showed an increased phosphorylation and thus activation upon infection with pneumococci. Taken together, this study deciphers host cell kinases in innate immune cells that are induced upon infection with pneumococci and interfere with bacterial clearance after phagocytosis.
Complement resistance is an important virulence trait of Yersinia enterocolitica (Ye). The predominant virulence factor expressed by Ye is Yersinia adhesin A (YadA), which enables bacterial attachment to host cells and extracellular matrix and additionally allows the acquisition of soluble serum factors. The serum glycoprotein vitronectin (Vn) acts as an inhibitory regulator of the terminal complement complex by inhibiting the lytic pore formation. Here, we show YadA-mediated direct interaction of Ye with Vn and investigated the role of this Vn binding during mouse infection in vivo. Using different Yersinia strains, we identified a short stretch in the YadA head domain of Ye O:9 E40, similar to the ‘uptake region' of Y. pseudotuberculosis YPIII YadA, as crucial for efficient Vn binding. Using recombinant fragments of Vn, we found the C-terminal part of Vn, including heparin-binding domain 3, to be responsible for binding to YadA. Moreover, we found that Vn bound to the bacterial surface is still functionally active and thus inhibits C5b-9 formation. In a mouse infection model, we demonstrate that Vn reduces complement-mediated killing of Ye O:9 E40 and, thus, improved bacterial survival. Taken together, these findings show that YadA-mediated Vn binding influences Ye pathogenesis.
Psychiatric disorders are highly heritable. But the underlying molecular mechanisms are largely unknown or not understood. For many disorders, candidate genes have been proposed which are biologically driven or based on large GWAS studies. In this work different approaches were shown to investigate the impact of genetic risk factors for major psychiatric disorders in the general population. These genetic risk variants include single nucleotide polymorphisms associated with schizophrenia or major depression and were analyzed using the whole-genome information in polygenic scores or candidate marker analysis in GxE studies. Genetic data from SHIP-0 and SHIP-TREND have been used to calculate a polygenic risk score for schizophrenia. Here, the association between this genetic score and brain alterations is shown in three independent samples (SHIP-2, SHIP-TREND and BIG) which revealed no hint of a common genetic basis for schizophrenia and brain structure. These results are in line with other studies that also failed to find a genetic overlap. The same polygenic scores had been used in a PHEWAS analysis in SHIP-0 where an inverse association to migraine was found. This association could be attributed to the NMDA receptor activation via D-serine at the glutamatergic synapse. To assess the impact of environmental factors on the path from genes to phenotype, gene-environment interactions were applied. A significant interaction could be observed between rs7305115 (TPH2) and rs25531 (5-HTTLPR) and childhood abuse on current depression score in SHIP-LEGEND and SHIP-TREND. In summary, genetic variants associated with major psychiatric disorders can exhibit pleiotropic effects on common phenotypes in the general population.
Dilated cardiomyopathy (DCM) is a myocardial disorder characterised by ventricular dilation with reduced left ventricular ejection fraction (LVEF). Immunoadsorption (IA) followed by immunoglobulin (IgG) substitution (IA/IgG) has been shown to be a promising therapeutic intervention to recover myocardial functions in DCM patients. The beneficial effects of IA/IgG therapy are associated with increased LVEF, decreased left ventricular inner diameter at diastole (LVIDd) and reduced myocardial inflammation. Despite knowing the cardiac benefits of IA/IgG, the precise molecular mechanism induced by therapy is still elusive. Additionally, only ≈60 % DCM patients treated with IA/IgG demonstrated improved heart function. Moreover, the reasons for this differential outcome among DCM patients after treatment have not been clearly understood. In this study, efforts were made to uncover the therapy induced proteomic changes in the heart of responders (relative change in LVEF ≤ 20%, LVEF < 5% absolute value) and non-responders using a global proteomic approach. Apart from it, proteomic profiling of endomyocardial biopsies and plasma was performed to find protein biomarker candidates which might be useful to distinguish responder and non-responder DCM patients before immunoadsorption therapy and support a selective and individualized treatment. To reveal therapy induced myocardial proteomic changes, endomyocardial biopsies of DCM patients before and after therapy were compared. LVEF increased (32 ± 8 to 45±7, p<0.002) and LVIDd decreased (66 ± 6 to 60±6, p<0.040) after therapy in responders, whereas non-responders did not show any significant changes in these clinical parameters. To address the changes in the myocardial proteome induced by therapy, a label-free proteomic approach was applied. The most prominent proteomic differences between both subgroups were observed in cytoskeletal, fibrosis, and extracellular matrix proteins. Therapy linked benefit in responders seems to be highly associated with the lower abundance of fibrotic and extracellular matrix proteins which seems to reflect a lower activity of transforming growth factor-β signaling. To elucidate proteomic differences between responders and non-responders at baseline, endomyocardial biopsies and plasma proteome profiling were performed. Responder and non-responder DCM patients did not show any significant differences in the clinical parameters (LVEF, LVIDd, age, inflammation, etc.) before IA/IgG therapy except for disease duration that was in tendency higher among non-responders. Proteomics profiling of endomyocardial biopsies revealed 54 differentially abundant proteins between responders and non-responders. Among those proteins, Protein S100-A8 and kininogen-1 was found higher whereas perilipin-4 was found lower abundant in responders. Plasma profiling of these subgroups revealed five proteins (S100-A8, S100-A9, C-Reactive protein, lipopolysaccharide-binding protein, and cysteine-rich secretory protein) displaying strong discriminative power between responders and non-responders. Higher abundance of Protein S100-A8 was observed in myocardium as well as in plasma among responders. Protein S100-A8 might be a potential candidate to distinguish responders and non-responders at baseline, and its potential utility at clinical levels must be evaluated. The last objective of the thesis was to establish a workflow for the relative quantitation of phosphopeptides for samples generally obtained in small amounts like myocardial biopsies. To address this question, optimization was performed with HL-1 cardiomyocytes using a PolyMAC phosphopeptide enrichment kit and the effect of TGF-β1 on the phosphoproteome was evaluated as a proof-of-principle study. Using only 200µg protein of each sample up to 2000 phosphopeptides with an efficiency of >90 percent could be covered. In total, upon TGF-β1 incubation alterations of 214, 92, and 53 phosphopeptides were observed after 1, 6 and 24 hours, respectively. Differentially altered phosphopeptides belonged to many signaling pathways including the ubiquitin-proteasome pathway, cytoskeletal regulation by Rho GTPase, calcium signaling, and TGF-β signaling. Thus, in this study a workflow for relative quantitation of phosphopeptides was established that may be later applied to precious biopsy samples. Along with this, TGF- β1 induced phosphoproteome was analysed in HL-1 cardiomyocytes.