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Microbial infections can be either caused by a single species or complex multi-species consortia. One of the most prominent opportunistic human pathogens leading to mono- or mixed-species infections is the Gram-negative bacterium Pseudomonas aeruginosa. Understanding the molecular basis of its adaptation to infection-related stresses is an essential prerequisite for the prevention and treatment of P. aeruginosa infections. We therefore employed state-of-the-art proteomics approaches to elucidate the molecular adaptation mechanisms of P. aeruginosa to infection-related conditions. Moreover, structure, function and interaction of complex microbial consortia containing P. aeruginosa and causing catheter-associated urinary tract infections were investigated by metaproteomics analyses. Our investigations revealed that the adaptation of P. aeruginosa during infection is either based on gene expression changes caused by environmental signal integration or by gene mutations leading to a selective advantage in a particular host environment. In study I, investigating the proteome response of P. aeruginosa biofilms to the clinical relevant antibiotic ciprofloxacin, global changes in the protein profile were observed. Ciprofloxacin induced the expression of proteins involved in the Lex-induced SOS-response, drug efflux pumps and gene products of the ciprofloxacin-responsive prophage cluster and repressed the expression of porins and DNA-binding proteins. In study II the transcriptome and proteome of two clonal P. aeruginosa lineages during long-term colonization of cystic fibrosis (CF) patient’s lungs were analyzed. Point mutations in global regulator genes, i.e. retS, gacS, and gacA, were identified by genomic sequencing. Inactivation of RetS, found two years after the initial colonization, induced the expression of genes involved in chronic infections and coding for the type 6-secretion system (T6SS). Additional mutations in the GacS/GacA two-component regulatory system (TCS) were found to repress the expression of T6SS proteins and to induce the expression of proteins belonging to the type 3-secretion system (T3SS). In study III we elucidated the niche-specific adaptation of P. aeruginosa isolates from different infection sites by investigating their protein expression patterns and glucose metabolic fluxes. We could show that isolates from the urinary tract express a higher amount of proteins involved in the acquisition of micronutrients (i.e. iron) and carbohydrates compared to isolates from the CF lung. In study IV 16S rDNA sequencing and metaproteomics were employed to demonstrate that the investigated CAUTI-related biofilms consisted of two to five different species with one or two species dominating the mixed community. Following this line of research, we investigated in study V structure and function of a biofilm of a long-term catheterized patient, which was predominantly composed of P. aeruginosa and Morganella morganii, but also contained a minor proportion of the obligate anaerobe Bacteroides sp.. The comparison of in vivo and in vitro protein expression profiles of P. aeruginosa and M. morganii indicated that iron and carbohydrates are the major growth-limiting factors in the bladder. These results indicate different nutritional strategies of the two pathogens in the bladder environment. A comparison of urinary protein profiles of healthy persons and catheterized patients suggested that the human innate immune system is induced by CAUTIs. Moreover, numerous proteins involved in nutritional immunity, e.g. iron-, calcium- and magnesium-binding proteins, were found to be more abundant in the urine of catheterized patients. A follow-up (meta)proteomics study (study VI) aiming at the elucidation of interspecies interactions during multi-species infections indicated that the urease-positive uropathogen Proteus mirabilis induces the precipitation of metal ions by urine alkalization and thereby limits the availability of these important micronutrients for other co-infecting bacteria. This limitation seems to be sensed by the P. aeruginosa PhoP-PhoQ two-component system (TCS) leading to an increased resistance to antimicrobial peptides and biofilm-forming capacity of the pathogen. Also during co-cultivation of P. aeruginosa with Staphylococcus aureus a slight increase in the expression of the PhoP-PhoQ TCS and the alkaline protease could be observed (study VII). In study VIII a combined metagenomics and metaproteomics approach was employed to investigate structure and function of the lichen Lobaria pulmonaria, a complex consortium consisting of a fungus, an algal partner, cyanobacteria, and a highly diverse bacterial microbiome. The results presented in this work contribute to a better understanding of the manifold and complex bacterial adaptation mechanisms to infection-related and environmental stress and thereby foster the development of novel treatment and prevention strategies.
The toluene-degrading and solvent-tolerant strain Pseudomonas putida DOT-T1E was investigated with respect to its suitability and economic efficiency as biocatalyst in aqueous-organic two-phase systems with aliphatic solvents as organic phase (Rojas et al. 2004, chapter 4 and 5) and to its adaptive responses to the solvent decanol. The adaptive changes on the level of cell morphology (chapter 2), membrane fatty acids and permeability (chapter 3), as well as energetics and surface properties (chapter 5) of P. putida DOT-T1E have been investigated in order to ascertain information about the strain's suitability for two-phase biotransformation systems (chapter 4). The morphological adaptation to the presence of solvents was observable in changes of the cell size of P. putida DOT-T1E. Those changes were dependent on the cellular activity and occurred only after addition of non-lethal solvent concentrations. The cells reacted to the presence of organic solvents by decreasing the ratio between surface and volume of the cells and therefore reducing their relative surfaces (chapter 2). The cell surface and especially the cytoplasmic membrane are the major targets for toxic effects of membrane-active compounds like solvents. The mechanism of the cis-trans isomerisation of unsaturated fatty acids counteracts the fluidizing effect of solvents by increase the ordering of the membrane and therefore its rigidity. By comparing the responses of the cells to a series of stress factors (like solvents), a direct correlation between the activation of this mechanism and the well investigated K+-uptake pumps was observed (chapter 3). Huertas et al. (1998) reported that this strain tolerated concentrations of heptane, propylbenzene, octanol, and toluene of at least 10 % (vol/vol). 1-decanol is, in comparison to toluene, less hazardous and volatile, and it possesses good extraction properties for the desired fine chemical products. In further investigations of possible biotechnological processes, it was discovered that decanol is also a more suitable solvent as organic phase (chapter 4). Although the cells of P. putida DOT-T1E needed additional energy for their adaptation to the presence of the solvent decanol, they were able to maintain or activate their electron transport phosphorylation allowing homeostasis of ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities converging with more negative cell surface charges were observed in cells grown in the presence of 1-decanol (chapter 5). It is however important to note that all the cell’s properties observed are closely linked to each other since they are all part of the adaptive response of the cells. It can be concluded that the easy adaptability and good growth properties of Pseudomonas putida DOT-T1E in the presence of the organic solvent 1-decanol make this system an excellent candidate for two-phase fermentation processes. Moreover, the absence of differences in the energetics of the bacteria during exposure to 1-decanol as compared to bacteria that grew in the absence of 1-decanol, support that this organism can be used for the industrial production of fine chemicals in an economically sound manner.
Technological advances in light microscopy have always gone hand in hand with unprecedented biological insight. For microbiology, light microscopy even played a founding role in the conception of the entire discipline. The ability to observe pathogens that would otherwise evade human observation makes it a critical necessity and an indispensable tool to infectious disease research. Thus, the aim of this thesis was to optimize, extend, and functionally apply advanced light microscopy techniques to elucidate spatio-temporal and spatio-morphological components of bacterial and viral infection in vitro and in vivo.
Pathogens are in a constant arms race with the host’s immune system. By finding ways to circumvent host-mediated immune responses, they try to evade elimination and facilitate their own propagation. The first study (publication I) demonstrated that the obligate intracellular pathogen Coxiella burnetii is not just able to infect natural killer (NK) cells, but is actually capable of surviving the harsh degradative conditions in the cytotoxic lymphocyte’s granules. Using live-cell imaging of reporter-expressing Coxiella burnetii, the transient NK cell passage was closely monitored to provide detailed spatio-temporal information on this dynamic process in support of a range of static analyses. Bacterial release from NK cells was pinpointed to a time frame between 24 to 48 hours post-infection and the duration of release to about 15 minutes.
The second approach (publications II-V) aimed at shedding light on the greater spatio-morphological context of virus infection. Thus far, most studies investigating the distribution or tropism of viruses in vivo have used conventional immunohistochemistry in thin sections. Omitting the native spatial context of the infection site in vivo inherently bears the risk of incomplete description. While the microscopic tools and sample preparation protocols needed for volumetric 3D immunofluorescence imaging have recently been made available, they had not gained a foothold in virus research yet. An integral part of this thesis was concerned with the assessment and optimization of available tissue optical clearing protocols to develop an immunofluorescence-compatible 3D imaging pipeline for the investigation of virus infection inside its intact spatio-morphological environment (publication II). This formed the basis for all subsequent volumetric analyses of virus infection in vivo presented here. Consequently, this thesis provided a valuable proof of concept and blueprints for future virus research on the mesoscopic scale of host-pathogen interactions in vivo (publications II-V), using rabies virus (RABV; publications II-IV) and the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; publication V) as infection models for the nervous system and the respiratory tract, respectively.
Applying and further improving this volumetric 3D imaging workflow enabled unprecedented insights into the comprehensive in vivo cell tropism of RABV in the central (CNS) (publication III) and peripheral nervous system (PNS) (publication IV). Accordingly, differential infection of CNS-resident astrocytes by pathogenic and lab-attenuated RABV was demonstrated (publication III). While either virus variant showed equal capacity to infect neurons, as demonstrated by quantitative image analysis, only pathogenic field RABVs were able to establish non-abortive infection of astrocytes via the natural intramuscular inoculation route. A combined 3D LSFM-CLSM workflow further identified peripheral Schwann cells as a relevant target cell population of pathogenic RABV in the PNS (publication IV). This suggested that non-abortive infection of central and peripheral neuroglia by pathogenic RABV impairs their immunomodulatory function and thus represents a key step in RABV pathogenesis, which may contribute significantly to the establishment of lethal rabies disease.
Finally, utilizing the full volumetric acquisition power of LSFM, a further refined version of the established 3D imaging pipeline facilitated a detailed mesoscopic investigation of the distribution of SARS-CoV-2 in the respiratory tract of the ferret animal model (publication V). Particularly for this newly-emerged pathogen of global concern, in-depth knowledge of host-pathogen interactions is critical. By preserving the complete spatio-morphological context of virus infection in the ferret respiratory tract, this thesis provided the first specific 3D reconstruction of SARS-CoV-2 infection and the first report of 3D visualization of respiratory virus infection in nasal turbinates altogether. 3D object segmentation of SARS-CoV-2 infection in large tissue volumes identified and emphasized a distinct oligofocal infection pattern in the upper respiratory tract (URT) of ferrets. Furthermore, it corroborated a preferential replication of SARS-CoV-2 in the ferret URT, as only debris-associated virus antigen was detected in the lower respiratory tract of ferrets, thus providing crucial information on the spatial distribution of SARS-CoV-2.
African swine fever virus (ASFV) is one of the most threatening animal viruses which has dramatically expanded its distribution range within the last years. ASFV was first described and is endemic in sub-Saharan Africa where it is transmitted in a sylvatic cycle between indigenous suids and Ornithodoros soft ticks. Therefore, ASFV is the only known DNA-arbovirus and, in addition to that, the only member of the genus Asfivirus within the family Asfarviridae. Being highly infectious to domestic pigs and wild boar, the virus was introduced into Georgia in 2007 and has subsequently spread throughout eastern Europe reaching the European Union in 2014. Despite almost 100 years of intensive research and the occurrence of African swine fever (ASF) on four continents including Europe, many aspects of its epidemiology, vector dynamics and virus evolution are unknown. In our study, first evidence is presented on endogenous ASFV-like (EASFL)- elements which are integrated into the genome of ASFV natural vectors, O. moubata soft ticks. Through a series of experiments including next-generation sequencing, infection experiments, phylogenetic and BEAST analyses as well as PCR-screening, evidence is provided that these elements belong to an ancestral ASFV strain that might have existed 50,000 to 30,000 years BCE. Further results suggest that the EASFL-elements are involved in protecting ticks against ASFV infection and might belong to a generalised tick defence mechanism. In order to evaluate factors influencing ASFV epidemiology in eastern Europe, experiments were conducted on possible indigenous vector species and circulating virus isolates. In the absence of the natural tick vector, blow fly larvae were considered as possible mechanical vectors involved in ASFV transmission and persistence. Results are presented that even after feeding on highly infectious wild boar tissue, fly larvae and pupae showed no contamination with infectious virus. On the contrary, the maggots appeared to have inactivated the virus in the organ tissue through their salivary secretions. Further experiments conducted on an ASFV-strain isolated from northeastern Estonia resulted in the first report of an ASFV-strain with attenuated phenotype isolated in Eastern Europe. Results from NGS-analyses provided evidence for a major genome reorganisation in that strain that included a large deletion and a duplication of multiple ASFV genes.
Taken together, this study provides novel insights into the epidemiology of ASF and evolution of ASFV one of the major threats to animal health worldwide and therefore does not only contribute significantly to basic research but possibly also to specific knowledge necessary for future disease management.
Ebolaviruses are dependent on host cell proteins for almost all steps in their viral life cycle. While some cellular factors with crucial roles in the ebolavirus life cycle have been identified, many of them remain to be identified or fully characterised. This thesis focuses on the characterisation and identification of host cell interactions of the highly pathogenic Ebola virus (EBOV), probing host-virus interaction at various stages of the viral life cycle. Beginning with viral budding, the function of a recently proposed late domain motif within the EBOV matrix protein VP40 was examined using an EBOV transcription and replication-competent virus-like particle (trVLP) system. Although this motif has been suggested to interact with the endosomal sorting complex required for transport (ESCRT), we could show that this late domain motif does not contribute to EBOV budding.
While many host cell proteins have been identified so far that are important for viral budding, only a few proteins are known that are necessary for EBOV RNA synthesis. Thus, to identify host proteins that are involved in viral replication and transcription, we performed a genome-wide siRNA screen in the context of an EBOV minigenome assay. Using this approach, we identified several proteins that appear to be important for viral RNA synthesis or protein expression. Two of the most prominent hits in our screen were CAD (Carbamoyl-phosphate synthetase 2, aspartate transcarbamylase and dihydroorotase) and NXF1 (nuclear RNA export factor 1). CAD catalyses the first three steps in the de novo pyrimidine biosynthesis, while NXF1 is the main nuclear export protein for cellular mRNAs. In subsequent characterisation studies, using a range of life cycle modelling systems as well as molecular analyses, we could demonstrate that the canonical function of CAD during the pyrimidine biosynthesis is necessary for EBOV replication and transcription. In contrast to this, for NXF1 we discovered a so-far unknown function: Again, by applying different life cycle modelling alongside with molecular assays, we provided evidence that the EBOV nucleoprotein recruits NXF1 into inclusion bodies, the site of EBOV RNA synthesis, where it binds viral mRNAs to export them from these structures. Importantly, for both CAD and NXF1 we were able to recapitulate key data in the context of live EBOV infection, confirming their roles in the viral life cycle.
Both of these identified host factors are promising targets for antiviral therapies and indeed de novo pyrimidine synthesis is emerging as a possible antiviral target for a number of viruses. Similarly, as we could show NXF1 to be important in the life cycle of the highly pathogenic Junín virus, this raises the possibility that disruption of this interaction may result in broad-spectrum antiviral activity. Moreover, for an increasing number of negative-sense RNA viruses inclusion bodies as site of viral RNA synthesis are described to have a liquid organelle character. Therefore, our findings on NXF1 also provide an intriguing model to explain how negative-sense RNA viruses in general overcome this obstacle and export viral mRNAs from inclusion bodies.
Staphylococcus aureus is a pathogenic bacterium infecting the human host. It’s multifaced adaptation to various environmental conditions is mediated by a tight regulation of the virulence factors influencing the host’s immune system. In this thesis two regulators of gene expression were analysed: (i) the global influence of the two-component system SaePQRS and (ii) the regulation of superantigen gene expression by the alternative sigma factor σB. At the outset of this thesis, single target genes induced by SaeRS were known (hla, hlb, cap5, fnbA, coa). In order to get a general idea of the Sae-regulon, the influence of SaePQRS on gene-expression was analysed in two strain backgrounds by proteomics and transcriptomics aproaches. Recapitulatory, expression of at least 18 secreted and two covalently cell-wall bound proteins was decreased following inactivation of the Sae-system. Sae-dependently expressed were, amongst others, well decribed virulence factors like the y-hemolysins HlgA, HlgB, HlgC, LukM and LukF, the innate immune system modulating proteins Efb, CHIPS and SCIN-B as well as the enterotoxin SEB. SaeR acts as an activator of its target genes. Some proteins were detected in increased amounts in the extracellular proteome of the Sae-deficient strain. However, these changes did not occur at the transcriptional level. The expression of virulence factors is determined by other global regulators. No influence of SaePQRS on the transcription of five substancial regulators, namely the Agr-system and its effector molecule RNAIII, the alternative sigma factor σB, the two-component system ArlRS and the DNA-binding protein SarA, could be shown. In the second part of this thesis the issue was broached to the regulation of gene-expression of a subgroup of virulence factors, the superantigens (SAgs) of S. aureus by SaePQRS and σB. In contrast to their well described molecule structure and function, the regulation of their gene expression was largely unknown. Six different S. aureus strains (two laboratory strains and four clinical isolates) encoding one to seven SAg-genes each, were used for analysis of a total of twelve SAgs regarding their transcription and mitogenic activity. The transcriptional units were characterized using Northern-Blotting. The expression of SAgs could be correlated to the respective growth phase. While egc-SAgs were expressed mainly at low optical densities, seb was induced during late growth phase. In contrast, the transcription of sea, seh, sek, tst and sep remained constant and growth-phase independent. The transcriptional dataset was verified using T-cell proliferation assays. The expression of seh, tst and the egc-operon was dependent on σB. A potential σB-dependent promotor could be identified preceeding seo, the first gene of the egc-operon. In contrast, the expression of seb was increased in sigB-deficient background. This might be due to indirect effects. Expression of seb required SaePQRS. Transcriptional datasets were verified by Immuno-Blotting and T-cell-proliferation assays. In conclusion, the same mutation in sigB but in different strain backgrounds could result in opposite phenotypes with respect to their mitogenic activity. Besides well characterized virulence factors, some secreted proteins with so far unknown function belong to the Sae-regulon. Given that the influence of SaePQRS was restricted to virulence factors and induced especially modulators of the innate immune system, it can be assumed, that these proteins potentially play a role in virulence of S. aureus. In the third part of this thesis, one of these potential new virulence factors, namely SACOL0908, was analysed in detail. In cooperation with the group of Prof. Stehle, Tübingen, the crystal structure was solved. The protein folding of SACOL0908 is new with only minor similarities to described protein structures. Recombinantly expressed SACOL0908 binds to granulocytes. These cells belong to the innate immune system, incorporate bacteria by phagocytosis and kill them. The receptor for SACOL0908 on the surface of granulocytes could not be identified using immunoprecipitation, antibody-blocking assays and functional assays in cooperation with the group of Prof. Peschel, Tübingen. The gene encoding SACOL0908 was deleted in two S. aureus strain backgrounds (COL and Newman). These mutants are currently in use to characterize their phenotype in mouse-infection studies.
The here presented dissertation investigated the molecular mechanisms, by which the food industry model bacteria Pseudomonas fluorescens and Listeria monocytogenes, grown either as planktonic cultures, were inhibited by plasma treated water (PTW) produced by a microwave-induced plasma source (MidiPLexc). As a starting point, optimal operating parameters were determined with 5 standard liters per minutes(slm)compressed air during the treatment of 10 ml deionized water within a treatment time of up to 15 min (pre-treatment time). Treatment times of 1, 3 and 5 min were selected (post-treatment time). In addition to physical parameters, i.e. temperature measurements at different spots at the plasma source during the production of the PTW, the chemical composition of PTW was determined by pH measurements, chronoamperometry (determination of the H2O2 concentration), ion chromatography (determination of the NO2-, NO3- and ONOO- concentrations) and mass spectrometry (qualitative determination of the molecules). In addition, concentration changes of reactive species over a period of 3 h indicated a decrease of the NO2- concentration as well as an increase of the NO3- and ONOO- concentration in the PTW. Microbiological assays, i.e. quantification of colony-forming units (CFU), fluorescence and XTT assays, revealed a significant reduction of the proliferation ability of the cells, membrane damages and metabolic activity have been demonstrated for planktonic cultures as well as mono- and multispecies biofilms. PTW effects on biofilm structures were investigated using microscopic methods such as fluorescence microscopy, confocal laser scanning microscopy (CLSM), atomic force microscopy (AFM), and scanning electron microscopy (SEM), as well as physical methods such as contact angle measurements. Significant changes in the biofilm structure have been shown, which indicate an ablation of the biofilm mass from top to bottom by approximately 2/3 of the biofilm mass and a destruction of the extracellular matrix (ECM) by the reactive species within the PTW. Subsequently, fresh-cut lettuce has been treated with PTW produced by up-scaled plasma sources. Apart from qualitative parameters of the lettuce after PTW treatment such as texture and color, the concentration of PTW reactive species have been determined. These experiments showed that the composition of the reactive species were slightly different from that of the laboratory-scaled plasma source MidiPLexc. Notably, the PTW treatment did not cause significant changes in texture and color of the fresh-cut lettuce. Finally, a synergistic effect of PTW treatment followed by plasma-processed air (PPA) drying was demonstrated application-specific.
The respiratory epithelium acts as both, a barrier of the respiratory tract to Nipah virus (NiV) entry and at the same time as a significant determinant of virus shedding. Both, for humans and pigs, replication in the respiratory tract epithelia is considered a major factor in transmission to other hosts. To understand why the virus constitutes a high-risk pathogen for livestock and humans, knowledge about
viral replication and host responses in relevant cells and tissues is crucial. Most in vitro studies, however, have been performed in conventional cell lines or non-differentiated lung cells. Only a few examples exist where Henipavirus infections have been investigated in fully-differentiated lung
epithelial cell models.
Thus, one aim of this thesis was to investigate infection, replication, spread and host protein dynamics of NiV in primary bronchial epithelial cells (BEC) cultivated at the air-liquid-interphase (ALI). By
immunofluorescence imaging, the NiV infection dynamics in BEC-ALI cultures were monitored over a 12 day time course, in order to provide detailed information about the infection process in the
respiratory epithelium of pigs and ferrets. Compared to undifferentiated primary BEC, the specific infectivity of NiV in BEC-ALI cultures was low. Infections remained focal and complete infection of the
cultures was not observed, even at 12 dpi. Analysis of viral titers and viral mRNA indicated a limited
virion release from the infected ALI-cultures while most of the newly synthesized NiV-RNA remained
cell associated. Immunofluorescence analysis of cross sections from infected ALI-cultures revealed
large infected areas that exhibited a strong cytopathic effect (CPE). Disruption of the epithelium
resulted in apical release of virus antigen-positive cell detritus while ciliated areas and basal cells were
less affected. From these data it was concluded, that NiV transmission could be supported by
exhalation of cell debris associated NiV and thus may contribute to rapid spread of infection in swine
populations.
A second aim was to explore the dynamics of host responses to NiV infection in differentiated BEC-ALI
culture and to assess whether this differs to conventional cell line data available from literature. Even
though strong CPE appeared in later phases of NiV infection, at least the porcine PBEC-ALI cultures
remained robust enough to allow protein sampling over 12 days infection course. Subsequent MS-based proteomics enabled unprecedent insight in complex cell culture response upon NiV infection.
Previous reports indicated a lack of efficient interferon type I induction in non-differentiated pig or
human BEC which were considered a prerequisite for efficient replication in the respiratory epithelium
and virusspread. In contrast to non-differentiated pig BEC (PBEC), in PBEC-ALI cultures multiple factors
involved in interferon responses were upregulated upon NiV infection. Thereby it was demonstrated
that NiV infection induced a robust innate immune response upon infection with elevated components of antigen processing and presentation resulting in the conversion from the constitutive proteasome to the immunoproteasome. In contrast to previous reports about NiV-infected non-differentiated
PBEC or endothelial cells, incomplete immunoproteasome formation and limitations in interferon
response could be excluded. Thus, a model is proposed in which NiV infection and spread in differentiated PBECs is slowed by potent innate immune responses to the virus infection. Overall, the
findings highlight the important role of the respiratory epithelium not only as a physical barrier to virus
infections but also indicate itsrole as a primary site of adaptive immune induction through NiV induced
antigen processing and MHC I presentation.
Finally, to allow functional studies of Henipaviruses at the BSL-2 biosafety level a recombinant CedPV
was generated and rescued. An imaging based screening and quantitative analysis pipeline was established to investigate the role of cellular factors and to screen for potential virus and host gene
directed inhibitory factors. Accordingly, different host and viral genes were targeted with a siRNA-pool
either targeting virus or selected cellular mRNAs followed by the infection with the CedPV and the
quantification of infected cells. With proof of concept of the siRNA screening pipeline, the recombinant
CedPV clone was used as a backbone to insert variousfluorescence reporter genesin order to optimize
the analysis workflow by allowing direct virus quantification in live, unstained samples. Consequently,
this thesis provides a valuable proof for future approaches related to the function of virus proteins,
influence of host-factors and virusreplication and Henipavirus-inhibitorscreens at low biosafety levels.
Orthohantaviruses are rodent-borne pathogens distributed all over the world, which do not cause visible disease in their reservoir host. Puumala orthohantavirus (PUUV) causes most human hantavirus disease cases in Europe and is transmitted by the bank vole (Clethrionomys glareolus). Hantaviruses have a tri-segmented genome consisting of the large (L) segment, coding for the RNA-dependent RNA polymerase (RdRP), the medium (M) segment, encoding the glycoproteins, and the small (S) segment. The S-segment contains two major overlapping open reading frames (ORF) coding for the nucleocapsid (N) protein and a non-structural (NSs) protein, a putative type I interferon (IFN-I) antagonist. To date, pathogenesis and reservoir host adaptation of hantaviruses are poorly understood due to missing adequate cell culture and animal models.
In contrast to previous studies, in this work, data from spring and summer 2019 indicated a high vole abundance, a high PUUV prevalence in voles and high human incidence for some endemic regions in Germany, but elsewhere values were low to moderate. Regional and local human health institutions need to be aware about the heterogeneous distribution of human PUUV infection risk.
For a better understanding of virus-host associations, two novel cell lines from bank voles and common voles each were generated and their susceptibility and replication capacities for a variety of zoonotic and non-zoonotic viruses were analyzed. The PUUV strain Vranica/Hällnäs showed efficient replication in a new bank vole kidney cell line, but not in four other cell lines of bank and common voles. Vice versa, Tula orthohantavirus (TULV) replicated in the kidney cell line of common voles, but was hampered in its replication in other cell lines. Several viruses, such as Cowpox virus, Vaccinia virus, Rift Valley fever virus, and Encephalomyocarditis virus 1 replicated in all four cell lines. West Nile virus, Usutu virus, Sindbis virus and Tick-borne encephalitis virus replicated only in a part of the cell lines. These results indicate a tissue or species specific tropism for many of the tested viruses and the potential value of vole cell lines to address such questions in detail.
Using one of these new cell lines, the first German PUUV strains were isolated from bank voles caught in the highly endemic region around Osnabrück. Complete genomes were determined by target-enrichment-mediated high-throughput sequencing from original lung tissue, after isolation and after additional passaging in VeroE6 cells and a bank vole-derived kidney cell line. Different single amino acid substitutions were observed in the RdRP of the two stable PUUV isolates. The PUUV strain isolated on VeroE6 cells showed a lower titer when propagated on bank vole cells compared to VeroE6 cells. Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV strain from the same region allowed the generation of monoclonal antibodies that reacted with the isolated PUUV strains.
To investigate the role of PUUV and other vole-borne hantavirus NSs proteins, the evolution of the NSs and N encoding sequences was investigated by a field study in bank voles and the NSs sequences were characterized in vitro for their inhibitory effect on the human interferon-β promoter. Analysis of blood and lung samples of 851 bank voles trapped during 2010-2014 in Baden-Wuerttemberg and North Rhine-Westphalia resulted in detection of 27.8% PUUV-specific antibody positive bank voles, whereas in 22.3% PUUV-specific RNA was detected. In the hantavirus outbreak years 2010 and 2012 PUUV prevalence in bank voles was higher compared to 2011, 2013 and 2014. Sequences of the S segment of all positive bank voles showed amino acid and nucleotide sequence types of the NSs-ORF with temporal and/or local variation, whereas the N-ORF was highly conserved. One sequence type persisted over the whole observation period in both regions. The NSs coding sequence was highly divergent among regional bank vole populations in the outbreak year 2012.
Transfection experiments resulted in the detection of different products of the NSs-ORF of PUUV, TULV, Prospect Hill and Khabarovsk orthohantaviruses, due to translation initiation at different methionine codons along the coding sequence. Using luciferase reporter assays, the NSs proteins of PUUV, TULV, Prospect Hill and Khabarovsk orthohantaviruses showed inhibition of IFN-I induction of up to 70%, whereas Sin Nombre and Andes orthohantavirus NSs proteins showed a reduced effect compared to the other NSs proteins. The first 20 amino acids of the N-terminal region of PUUV NSs were found to be crucial for IFN-I promoter inhibition.
In conclusion, the newly established cell lines, antibodies, reporter assays and PUUV isolates are highly valuable tools for future hantavirus research. The activity of PUUV NSs protein in human cells contributes to our understanding of virus-host interactions and highlights the importance of corresponding future reservoir host studies. Hantavirus surveillance studies showed the necessity for timely information of the potential human PUUV infection risk to public health institutions in endemic areas to initiate appropriate actions.
In recent years, negative impact of pharmaceutical products on natural environment became an issue of high public interest. Pharmaceutical residues are detected in various ecosystems worldwide. Due to increasing production and consumption of medicines this problem is intensified. Therefore, an efficient way to restrain release into the world’s water system is required.
This work presents an enzymatic approach for the degradation of pharmaceuticals in wastewater treatment plants, using laccase and cytochrome P450 — two enzymes of high biotechnological and industrial potential. Laccase genes from fungi Trametes versicolor and Pycnoporus cinnabarinus were isolated and overexpressed in the non-conventional yeast Arxula adeninivorans. This organism served also as cytochrome P450 gene donor.
Recombinant laccase Tvlcc5 was purified by immobilized-metal ion affinity chromatography and biochemically characterized using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as substrate for enzyme activity assays. The optimal temperature and pH were found to be 50 °C and 4.5–5.5, respectively. The half-life of Tvlcc5 at 60 °C was around 20 min. It was demonstrated that the presence of copper ions is essential for the synthesis of active protein. Moreover, negative impact of chloride anions on laccase activity was shown.
Cultivation conditions for the Tvlcc5 producing strain A. adeninivorans G1212/YRC102-TEF1-TVLCC5-6H were optimized. It was found that maintaining the pH at a constant level between pH 6.0 and 7.0 is essential for the production of active enzyme. Optimal cell growth and laccase accumulation were reached at 20 °C and in medium supplemented with 0.5 mM CuSO4. Performed fed-batch cultivation resulted in a laccase activity of 4986.3 U L-1.
Factors influencing the synthesis of Tvlcc5 leading to increased production of this protein were investigated. It was found that using three non-native signal peptides (cutinase 2 from A. adeninivorans (ACut2), α-mating factor from S. cerevisiae (MFα), and acid phosphatase from P. pastoris (PHO1) signal peptides) enhances the secretion of active enzyme by 20–80%. Besides that, additional overexpression of copper transporters positively affects laccase production.
Finally, it was proven that recombinant Tvlcc5 is a promising agent for the degradation of certain pharmaceuticals. After 24 h of incubation, the concentration of diclofenac and sulfamethoxazole decreased to 46.8% and 51.1%, respectively. Furthermore, it was shown that the addition of the redox mediator ABTS significantly shortens the degradation time of these substances.
The aim of this work was to characterize the distribution of TULV in European common vole populations, to clarify the host association of TULV and to investigate correlations between host population dynamics and changes in TULV prevalence. Furthermore, the potential of common voles as reservoir for other rodent-borne pathogens was examined in comparison to other rodent species.
Molecular and serological analysis of rodents captured at 87 locations in Germany, France, Luxembourg, and Austria revealed TULV infections at 53.6 % of all trapping locations. The seroprevalence in common voles was low with a mean of 8.5 % (range: 0 – 19 %). TULV RNA was more often detected (mean: 15.3 %, range 0 - 37.5 %). Field voles (Microtus agrestis) and water voles (Arvicola amphibius) were less often tested positive for TULV: mean seroprevalence was 7 % for field voles and 6.7 % for water voles. RNA could be detected in 5.4 % of all tested field voles and 3.2 % of water voles and with exception of a single field vole only when TULV-RNA-positive common voles were trapped at the same location. Those results indicate that TULV infections of field and water voles are spillover infections from sympatric TULV-infected common voles. Phylogenetic analysis revealed distinct genetic differences between TULV sequences of regions of greater geographical distance which were associated with different evolutionary common vole lineages. Furthermore, we could detect genetic differences between TULV strains from trapping sites close to each other (ca. 10 km).
In a capture-mark-recapture study 1042 common voles captured in live traps in Germany were sampled as well as 225 captured in snap traps. When analyzing the seroprevalence of fluctuating common vole populations over several years and seasons we found a negative correlation between prevalence and population density in the current season but a delayed density-dependent positive correlation between the current population density and seroprevalence in the next season. However, this trend varied geographically between the four trapping locations. Usually, population density as well as seroprevalence peaked at the end of the reproductive period in autumn with the exception of Weissach (2010-2012), Jeeser (2010) and Gotha (2012) where population peaks in summer were observed.
In a pilot study in Austria common voles were captured as well as three other rodent species. They were investigated not only for presence of different viruses (TULV, Dobrava- Belgrade orthohantavirus (DOBV), Puumala orthohantavirus (PUUV), Lymphocytic choriomeningitis mammarenavirus (LCMV), Cowpox virus (CPXV)) but also pathogenic bacteria and endoparasites (Leptospira spp., Toxoplasma gondii, Borrelia afzelii, Coxiella burnetii, Rickettsia spp. und Bartonella spp.). Of all four captured species, common voles were most often infected with at least one pathogen (66.7 %), followed by wood mice (Apodemus sylvaticus) (57.7 %), bank voles (Myodes glareolus) (35 %) and yellow-necked field mice (Apodemus flavicollis) (34.5 %). Common voles were also exceptionally susceptible to multiple infections: 66.7 % of them were infected with two or three different pathogens, compared to 6.9 % of yellow-necked field mice and 2.5 % of bank voles. No multiple infections could be detected in wood mice.
The broad geographic distribution of TULV in its reservoir host is in contrast to the rare reports of human infection but might be explained with a low pathogenicity for humans or with the low prevalence in host populations. In addition, the rare detection of human TULV infections could be a result of the used diagnostic methods. Since the reservoir population is known for its dramatic changes in population density and recurring superabundances which facilitates frequent contact to humans, TULV should more often be considered as cause for human disease in future analysis. In
addition, several other zoonotic pathogens could be detected in common voles which could influence TULV infections in the reservoir host but also TULV transmission to humans and therefore deserve more attention in future research.
This thesis will discuss the different fields of application of the two soft ionization techniques ESI and MALDI in microbial proteomics and their importance for a better understanding of bacteria physiology. The general development in the past 25 years coming from 2D-gel analysis and protein identification by peptide mass fingerprint analysis via MALDI-TOF to genome wide quantitative LC-ESI-MS experiments with fast and sensitive ESI instruments is exemplary shown for the Gram-positive bacterium Bacillus subtilis in article I. Even though 2D-PAGE in conjunction with MALDI-MS is still an important tool in proteomic research, the more recently established global quantitative LC-ESI-MS workflows gain more and more relevance as they overcome 2D-PAGE based protein restrictions and enable the acquisition of higher accurate protein quantities. In article II such a workflow was used to analyze the physiological adaptation of Staphylococcus aureus to vancomycin treatment on a global-scale. Also post-translational modifications of proteins, that are important for regulation of their activity and allow rapid adaption to changed environmental conditions, could be analyzed by LC-ESI-MS workflows using special enrichment strategies (article III and IV). Despite the mentioned discrimination and less accurate quantification of proteins, 2D-PAGE analyses are still advantageous when analyzing large-scale time series experiments. To gain highly time resolved data but also very accurate relative quantities on a global-scale, 2D-PAGE-MALDI-MS and LC-ESI-MS techniques have been combined to investigate dynamic proteome adaptations of B. subtilis during nutrition shift as part of a global systems biology approach (article V). Also absolute quantities of proteins are of high interest for systems biology, but are still challenging to obtain on large-scale as well as with sufficient accuracy. In article VI a method that again combined 2D-PAGE-MALDI-MS and LC-ESI-MS was introduced to gain absolute protein quantities on global-scale. Utilizing the complementarity of 2D-PAGE and LC-ESI-MS this new workflow enabled fast and cost efficient data acquisition on absolute scale. In article VII we described for the first time a global quantitative LC-MALDI-MS workflow. Cross validation with an LTQ Orbitrap proofed that LC-MALDI-MS is able to process complex samples and obtain highly reliable quantities. The comparative analysis of data gained with both instrument types revealed biases for certain biochemical properties of MALDI as well as ESI instruments, resulting in a general complementarity of both ionization techniques. Article I Becher, D., Büttner, K., Moche, M., Hessling, B., Hecker, M., 2011. From the genome sequence to the protein inventory of Bacillus subtilis. Proteomics 11, 2971–2980. Article II Hessling,B., Bonn,F., Herbst,F.-A., Rappen,G.-M., Bernhardt,J., Hecker,M. and Becher,D. Global proteome analysis of vancomycin stress in Staphylococcus aureus. Submitted to Mol. Cell Proteomics. Article III Elsholz, A.K.W., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mäder, U., Bernhardt, J., Becher, D., Hecker, M., Gerth, U., 2012. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 109, 7451–7456. Article IV Chi, B.K., Gronau, K., Mäder, U., Hessling, B., Becher, D., Antelmann, H., 2011. S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol. Cell Proteomics 10, M111.009506. Article V Buescher,J.M., Liebermeister,W., Jules,M., Uhr,M., Muntel,J., Botella,E., Hessling,B., Kleijn,R.J., Le Chat,L., Lecointe,F., et al. (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science, 335, 1099–1103. Article VI Maass, S., Sievers, S., Zühlke, D., Kuzinski, J., Sappa, P.K., Muntel, J., Hessling, B., Bernhardt, J., Sietmann, R., Völker, U., Hecker, M., Becher, D., 2011. Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal. Chem. 83, 2677–2684. Article VII Hessling,B., Büttner,K., Hecker,M. and Becher,D. Global relative quantification with LC-MALDI – cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences. Submitted to Mol. Cell Proteomics.
The thyroid gland is of crucial importance in human metabolism. Its main secretion products, L-thyroxine (T4) and 3,3’,5-triiodo-L-thyronine (T3), are essential for proper development of multiple tissues and organs as well as for their functioning in the adult organism. The secretion of thyroid hormones (TH) is stimulated by thyrotropin (TSH) released from the pituitary gland. This tight connection between both hormones is of crucial importance for the clinical diagnosis of thyroid dysfunction. During the last two decades the concept of TH action developed to increased complexity. However, most of the recent advances in the field of TH research are based either on cell culture, tissue or animal models or stem from studies investigating specific hypotheses in humans. Thus, experimental approaches for the comprehensive, hypothesis-free characterization of metabolic effects of classical and non-classical TH in human are urgently needed. This holds true in particular for the TH derivative 3,5-diiodothyronine (3,5-T2). It was described to alleviate the typical detrimental metabolic consequences of a high-fat diet and even reversed hepatic steatosis. To replicate these experimental findings from rodents in humans, comprehensive data from the population-based Study of Health in Pomerania (SHIP) was analyzed in the present work. Based on a euthyroid, diabetes-free SHIP-subsample (N=761), non-linear associations between the serum concentrations of 3,5-T2 and glucose as well as TSH were detected. In contrast, no significant 3,5-T2 associations with several anthropometric markers or blood lipid parameters were observed, partially questioning the transferability of the beneficial metabolic 3,5-T2 effects reported for pharmacological intervention studies on rodents to humans. Recent advances in technological development now allow for the use of high-throughput spectrometric platforms to characterize the small molecule content (metabolome) of blood and urine samples. The detected metabolome constituents can be associated with any relevant parameters of interest, thereby extending the scope of classical association studies. Therefore, in the second part of the present thesis, the metabolic fingerprints of FT4, TSH as well as the ratio log(TSH)/FT4 as markers of thyroid function were profiled. Strong differences between the metabolic fingerprints of FT4 and TSH were observed, partially alleviated by the log(TSH)/FT4 ratio. These findings not only emphasize the high diagnostic value of the combined evaluation of TSH and FT4 in the assessment of thyroid function but additionally argue for a holistic approach in the diagnosis of thyroid function. More moderate endogenous effects of 3,5-T2 were evaluated by comparing its urinary metabolic fingerprint with that of the classical TH. A number of associations became apparent, indicating a function of endogenous 3,5-T2 in intermediary metabolism. Besides partially confirming associations with respect to the presented findings in animal studies, the strongest 3,5-T2-association was observed with trigonelline, a metabolite described earlier to exhibit similar beneficial effects as 3,5-T2 on glucose metabolism when used as a pharmacological agent in animal studies. An association towards hippurate indicated a partial overlap with the metabolic profile of TSH and hence consolidated results from the first two projects in the sense of a thyromimetic role of 3,5-T2 in the feedback regulation of TH. The diagnosis of thyroid disorders based on the classical markers TSH and FT4 suffers from restricted sensitivity in the subclinical range as both parameters have broad reference ranges in the general population. Therefore, in an approach to detect novel peripheral biomarkers of thyroid function, sixteen healthy young men were challenged with 250 µg of levothyroxine (L-T4) over a period of eight weeks in the fourth project presented here as part of this thesis. Monitoring of the volunteers over a period of sixteen weeks allowed delineation of the metabolic shifts first towards thyrotoxicosis and later in the context of the restoration of euthyroidism. The use of mass spectrometry for the comprehensive characterization of the metabolite as well as the protein content of samples taken at the different time points revealed profound molecular alterations, despite the lack of any clinical symptoms in the volunteers. Molecular signatures of thyrotoxicosis indicated increased energy expenditure, pronounced defense against systemic oxidative stress, a general drop in apolipoproteins, as well as increased abundances of proteins related to the coagulation cascade and the complement system. Good and robust classification of the thyroid state independent of TSH and FT4 was achieved using random forest analysis with a subset of fifteen metabolites and proteins, indicating new options in the individualized diagnosis of thyroid disorders.
Coding constraints imposed by the very small genome sizes of negative-strand RNA viruses (NSVs) have led to the development of numerous strategies that increase viral protein diversity, enabling the virus to both establish a productive viral replication cycle and effectively control the host antiviral response. Arenaviruses are no exception to this, and previous findings have demonstrated that the nucleoprotein (NP) of the highly pathogenic Junín virus (JUNV) exists as three additional N-terminally truncated isoforms of 53 kD (NP53kD), 47 kD (NP47kD), and 40 kD (NP40kD). The two smaller isoforms (i.e. NP47kD and NP40kD) have been characterized as products of caspase cleavage, which appears to serve a decoy function to inhibit apoptosis induction. However, whether they have additional functions in the viral replication cycle remains unknown. Further, the origin and function of NP53kD has not yet been described.
In order to first identify the mechanism responsible for production of the NP53kD variant, a possible role of additional caspase cleavage sites was first excluded using a site mutagenesis approach. Subsequently, alanine mutagenesis was then used to identify a region responsible for NP53kD production. As a result, three methionine residues were identified within the characterized sequence segment of NP, linking the production of NP53kD to an alternative in-frame translation initiation. Further site-directed mutagenesis of the previously identified putative in-frame methionine codons (i.e. M78, M80 and M100) finally led to the identification of translation initiation at M80 as being predominantly responsible for the production of NP53kD. Once the identity of all three NP isoforms was known, it was then of further interest to more deeply characterize their functional roles. Consistent with the N-terminal domain containing RNA binding and homotrimerization motifs that are relevant for the viral RNA synthesis process, it could be demonstrated that all three truncated NP isoforms lost the ability to support viral RNA synthesis in a minigenome assay. However, they also did not interfere with viral RNA synthesis by full-length NP, nor did they affect the ability of the matrix protein Z to inhibit viral RNA synthesis. Moreover, it was observed that loss of the oligomerization motifs in the N-terminus also affected the subcellular localization of all three NP isoforms, which were no longer localized in discrete perinuclear inclusion bodies, but rather showed a diffuse distribution throughout the cytoplasm, with the smallest isoform NP40kD also being able to enter the nucleus. Surprisingly, the 3'-5' exonuclease function of NP, which is associated with the C-terminal domain and plays a role in inhibiting interferon induction by digestion of double-stranded RNAs, was found to be retained only by the NP40kD isoform, despite that all three isoforms retained the associated domain. Finally, previous studies using transfected NP and chemical induction of apoptosis have suggested that cleavage of NP at the caspase motifs responsible for generating NP47kD and NP40kD plays a role in controlling activation of the apoptosis pathway. Therefore, to further characterize the connection between the generation of NP isoforms and the regulation of apoptosis in a viral context, recombinant JUNVs deficient in the respective isoforms were generated. Unlike infections with wild-type JUNV, mutations of the caspase cleavage sites resulted in the induction of caspases activation. Surprisingly, however, this was also the case for mutation of the alternate start codon responsible for NP53kD generation.
Taken together, the data from this study suggest a model whereby JUNV generates a pool of smaller NP isoforms with a predominantly cytoplasmic distribution. As a result of this altered localization, NP53kD appears to be able to serve as the substrate for further generation of NP47kD and NP40kD by caspase cleavage. Not only does this cleavage inhibit apoptosis induction during JUNV infection, it also results in a cytoplasmic isoform of NP that retains strong 3'-5' exonuclease activity (i.e. NP40kD) and thus may play an important role in preventing viral double-stranded RNA accumulation in the cytoplasm, where it can lead to activation of IFN signaling. Overall, such results emphasize the relevance of alternative protein isoforms in virus biology, and particularly in regulation of the host response to infection.
Degradation of branched chain aliphatic and aromatic petroleum hydrocarbons by microorganisms
(2008)
The overall aim of the work was to investigate the ability of several Gram-positive bacteria including Mycocbacterium neoaurum SBUG 109, Nocardia cyriacigeorgica SBUG 1472 and Rhodococcus ruber SBUG 82 and the yeast Trichosporon mucoides SBUG-Y 801 to degrade and transform branched chain hydrocarbons which occur in petroleum and its fraction products such as gasoline or gas oil and which are known as important and recalcitrant environmental pollutants. Pristane, iso-pentylbenzene and sec-octylbenzene were used in this work as model compounds. These compounds represent significant groups of petroleum constituents (branched chain alkanes and aromatic hydrocarbons). Three bacteria and the yeast T. mucoides SBUG-Y 801 were selected in a screen of 16 hydrocarbon-utilizing strains in the SBUG collection and from 21 isolated hydrocarbon-utilizing strains from oil-contaminated habitats of Saudi Arabian Desert and of Vietnam. The bacteria were identified in cooperation with DSZM (Deutsche Sammlung von Mikroorganismen und Zellkulturen) as M. neoaurum SBUG 109, N. cyriacigeorgica SBUG 1472, R. ruber SBUG 82. These bacterial and yeast strains were shown to possess high potential for degrading and transforming pristane, iso-pentylbenzene and sec-octylbenzene. The intermediates produced by these bacteria during incubation with pristane were analyzed by GC and GC/MS. The products 4-methyl pentanoic acid; methyl butanedioic acid; 2-methyl pentadioic acid; methyl propanedioic acid; 4-methyl heptanedioic acid and 2,6,10,14–tetramethyl-pentadecan–3–one were detected in M. neoaurum cultures. In R. ruber, methyl butanedioic acid; 2-methyl pentadioic acid; 4,8-dimethylnonanoic acid, 4-methyl heptanedioic acid; 2,6,10–trimethylundecanoic acid; 3,7-dimethyl decanedioic acid and 2,6,10,14–tetramethyl–pentadecan–3-one were identified. In N. cyriacigeorgica, 2-methylpentanedioic acid; 4,8-dimethylnonanedioic acid; 2,6-dimethylheptanedioic acid and pristanic acid were found. The detection of 11 intermediates during pristane degradation by the three Gram-positive bacteria provided sufficient information to elucidate in detail three degradative pathways of pristane involving mono-, di- and sub-terminal oxidations. The sub-terminal oxidation by M. neoaurum and R. ruber was demonstrated for the first time. This occurence of a sub-terminal oxidation in these strains was strengthened by further results of aromatic compounds transformation (see below). During this pathway, ketone mono-oxygenation reactions seem to be involved. Because of this it will be of interest to look more closely at the catalytic processes involved and their possible extension to the bio-degradation of other branched chain hydrocarbons. Since in the present study 59 %, 51 % and 84 % of pristane were degraded in 3 weeks by M. neoaurum, R. ruber and N. cyriacigeorgica, this illustrated that the degradation rates of this isoprenoid alkane were high. The bacteria we studied were not only effective degraders of multiple branched chain alkane but also useful transformers of aromatic hydrocarbons. The intermediates produced were analyzed by comparing the retention times and UV/Vis spectra of the HPLC elution profile as well as the retention times and mass spectra of the GC/MS with those of available standards. Using iso-pentylbenzene as a substrate, 8 metabolites were generated by M. neoaurum transformation including product A (phenylacetic acid), B (acetophenone), D (iso-valerophenone), E (succinic acid), F (benzoic acid), G [(2-hydroxy-phenyl)-acetic acid] and H (2-methyl-4-phenyl-butyric acid). We additionally identified an alkyl hydroxylated iso-pentylbenzene derivative as 2-methyl-4-phenyl-butan-2-ol or 2-methyl-4-phenyl-butan-1-ol. Two metabolites (C and D) were detected by N. cyriacigeorgica transformation and three metabolites (A, D and F) were identified by R. ruber transformation which led to the complete biotransformation of this substance. iso-Pentylbenzene transformation by M. neoaurum was initiated by attack on the alkyl side chain followed by ring cleavage. The appearance of iso-valeorophenone confirmed the occurrence of a sub-terminal oxidation mechanism in M. neoaurum and R. ruber. In addition to products A, C, D and G, the identification X-(3–methyl–butyl)-phenol (X means that position of the hydroxy group on the aromatic ring system, such as 2, 3 or 4 remained unclear) in T. mucoides cultivation demonstrated for the first time the capacity of alkyl side chain attack by this organism which was hitherto known only for its ability of ring cleavage. The detection of 15 degradation products of sec-octylbenzene (including 2-phenylpropionic acid, 3-phenylbutyric acid, ß-methylcinnamic acid, 5-phenylhexanoic acid, acetophenone, 2-hydroxy-acetophenone, 2,3-dihydroxy-benzoic acid, succinic acid, 7-phenyloctan-2-one, benzoic acid, phenylacetic acid, 7-phenyl-octan-2-ol, hydroxy-phenylacetic acid and 2-hydroxybenzoic acid), in the studied bacteria pointed to an effective sec-octylbenzene degradation pathway in which dehydrogenation of 3-phenylbutyric acid to form ß-methylcinnamic acid is a newly described option. The identification of 2-phenylpropionic acid and 3-phenylbutyric acid in sec-octylbenzene transformation experiments by T. mucoides confirmed the possibility of alkyl side chain attack by this yeast. Summarizing the results, we describe for the first time in detail the biotransformation of sec-octylbenzene by M. neoaurum, N. cyriacigeorgica, R. ruber and T. mucoides. Our results suggest that these microorganisms may be useful as potential strains for hydrocarbon degradation and it may be of interest to investigate their suitability to solve specific environmental pollutant problems associated with branched chain aliphatic and alkyl-branched compounds which contribute to the persistence of hydrocarbon fractions in the environment.
The following work is describing the development of two innovative biosensors for the detection of biologically relevant molecules in the field of ecology and medical diagnostics. Biosensors have the particularity to possess a biological partner which recognizes the target molecule and a physical detection method responsible for the transformation of this biological interaction into measurable information. In the present case, both biosensors are designed following the same strategy and use a recombinant produced human receptor as biological partner and the surface plasmon resonance (SPR) technique to transform the biological interaction in quantitative information. The progesterone biosensor is aimed to detect and quantify substances with affinity to the human progesterone receptor. The recent discoveries that some chemicals present in low quantities in the ecosystem called endocrine disrupting chemicals (EDCs) have a negative impact on the aquatic life fitness raised concerns about the effects of these same molecules to the human health. In order to assess the effects of these EDCs, the use of classical analytical detection methods like high performance liquid chromatography (HPLC) or gas chromatography (GC) is not sufficient as these techniques only quantify a defined molecule without giving information about its biological activity. By integrating a recombinant human progesterone receptor, the progesterone biosensor can determine the biological activity of an unknown molecule or of a mixture of molecules in a real sample. In this work, two different yeasts – one methylotrophic (Hansenula polymorpha) and one non-methylotrophic (Arxula adeninivorans) - were selected as host for the recombinant protein production and their performances were compared. Different purification strategies were assayed and the binding activity of the purified progesterone receptor was then confirmed by enzyme like receptor assay (ELRA) and SPR. This led to the design of a first version of the biosensor with the immobilization of a progesterone-BSA ligand to the surface of a SPR chip and the use of a progesterone receptor mixed with the target molecule as sample. This competitive assay format was successfully utilized with a commercial progesterone-BSA ligand as target molecule and the next step will be the adaptation of this biosensor for real samples measurements. The HER-2 biosensor was developed as an answer for one of the most critical issue in the field of breast cancer diagnostics. In approximately 30 % of cancer cases, the transmembrane protein HER-2 can be found in large amount at the surface of the carcinoma cells and these cases are known to be particularly aggressive. Based on the amount of HER-2 protein at the surface of the cells, the pathologists established a scale with four levels to adapt the treatment to each patient. Although effective therapies have been developed to treat the HER-2 positive breast cancer, one of the major challenges remains the classification of breast sample in this scale as the only accepted determination methods are immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) which are only qualitative. In this work, a biosensor has been designed to quantify the amount of the HER-2 protein in a crude cell extract from a breast cancer tissue sample. To achieve this, the strategy is to utilize an antibody specifically targeted against the HER-2 protein and bound to a SPR chip. As the development of this biosensor necessitated the use of large amount of purified HER-2 protein, it was decided to produce recombinant full-length HER-2 in two different yeasts and to purify it by chromatography. This recombinant protein production required particular attention due to the membrane localization of HER-2. The structural integrity of the recombinant protein was confirmed by Western Blot and ELISA and different antibodies were bound to SPR chips in order to detect the HER-2 protein. After finding the conditions giving an optimal SPR signal, a protocol was developed to extract native HER-2 from breast tissue sample and the biosensor was assayed with this crude cell extract.
The genus Capripoxvirus of the family Poxviridae consists of the species lumpy skin disease virus, sheeppox virus and goatpox virus that affect cattle, sheep and goats, respectively. Whereas lumpy skin disease virus (LSDV) is transmitted mainly mechanically via blood-feeding insects and possibly hard ticks, the major transmission routes of sheeppox virus (SPPV) and goatpox virus (GTPV) are via direct contact and aerosols. Affected animals develop fever and display clinical signs such as ocular and nasal discharge, lymphadenopathy and characteristic lesions of the skin. Severe clinical course, especially in combination with respiratory signs, can result in the death of the affected animals. In endemic regions, mortality of capripox virus-induced diseases is low (1-10%). However, mortalities of up to 75% have been reported for LSDV and up to 100% for SPPV and GTPV in exotic breeds and high-producing dairy or beef animals. The loss of quality of the leather, reduced weight gain and milk yield as well as complete loss of affected animals have severe impact on national and global economies. Therefore, capripox virus-induced diseases have significant impact on both the affected individual animal as well as on the existence of small-scale farmers and large agricultural enterprises. However, until now, only live attenuated vaccines are commercially available. These attenuated vaccines are not authorized in the European Union and their administration would comprise the disease-free status of the respective country. Thus, reliable diagnostic tools for the detection and characterization of capripox viruses as well as safe and efficient control measures are of high importance.
The objectives of the present thesis were the development, validation and comparison of diagnostic tools, the establishment of challenge infection models and the performance of pathogenesis studies for all three capripox virus species, and the development and testing of different inactivated prototype vaccine candidates against LSDV.
First, new real-time quantitative polymerase chain reaction (qPCR) assays for robust detection and differentiation of LSDV field strains, LSDV vaccine strains, SPPV and GTPV were developed and extensively validated. In the following, two single assays were combined to duplex assays, one for the differentiation between LSDV field strains and LSDV vaccine strains, and the second for discrimination of SPPV and GTPV. Finally, a diagnostic workflow based on these new duplex assays in combination with already published methods was established. This workflow enables time-saving, robust and reliable detection, species-specific identification and genetic and phylogenetic characterization of all three capripox virus species. In addition, already existing serological examination methods (serum neutralization assay and commercial enzyme-linked immunosorbent assay) were compared regarding their sensitivity and specificity. Furthermore, pathogenesis studies with different capripox virus isolates were performed in the respective target species, and the suitability of selected virus isolates as challenge viruses for future vaccine studies was analyzed. Pathogenesis studies with isolates GTPV-“V/103” and LSDV-“Macedonia2016” revealed that both are proper candidates for challenge models. Finally, three different SPPV isolates (SPPV-“V/104”, SPPV-“India/2013/Surankote” and SPPV-“Egypt/2018”) were tested in sheep regarding their virulence to find a suitable challenge model for SPPV, and SPPV-“India/2013/Surankote” was chosen for future vaccine studies.
Once appropriate challenge models were established, different inactivated prototype vaccines against LSDV were developed, and vaccine safety as well as vaccine efficacy were tested in cattle. Eventually, a Polygen-adjuvanted inactivated LSDV-vaccine candidate was selected that is able to fully prevent cattle from any LSDV-related clinical signs after severe challenge infection. Furthermore, molecular and serological data indicate that this inactivated prototype vaccine is even able to induce a kind of “sterile immunity” against LSDV in those cattle. It has to be mentioned that a commercially available vaccine similar to this prototype vaccine would be a great advance for the control of LSDV.
In the future, additional studies addressing diagnostics and optimized control of capripox viruses should be performed. Firstly, probe-based real-time qPCR assays for the differentiation of SPPV and GTPV vaccine strains from their respective virulent field strains should be developed and included into the diagnostic workflow. Secondly, further tests of the inactivated prototype vaccine, e.g. determination of the minimum protective dose and the possibility of cross-protection in sheep and goats against SPPV and GTPV, respectively, should be performed.
The present study deals with the spread and population genetics of the invasive Asian bush
mosquito Ae. japonicus in Europe and Germany. Since the first detection of Ae. japonicus
in Europe in 2000, the species spread rapidly through Europe, either actively by flying or
passively by human activities. In 2017, four confirmed populations of Ae. japonicus existed
in Europe. The largest population covered western Germany, parts of France, Switzerland,
Liechtenstein, Austria and Italy. The most northern population around Hanover, Germany,
did not spread since 2013. A very small population existed in Belgium and the second largest
population covered parts of Austria, Italy, Slovenia, Croatia and Hungary. By 2019, Ae.
japonicus had established in 15 European countries.
Most of the monitoring programmes in Europe dealing with the distribution and spread of
Ae. japoncus investigate cemeteries for juvenile stages. However, activities are not
harmonised, e.g. regarding numbers of investigated collection sites and declaration of
negative sites, making data comparison between different studies difficult. Therefore,
suggestions for a standardised Ae. japonicus monitoring method have been developed and
provided.
In the present study, 445 individuals of Ae. japonicus originating from five different
European countries were investigated for population genetic analyses by sequencing parts
of the nad4 gene and genotyping seven polymorphic microsatellite loci. In total, 16 different
nad4 haplotypes were identified with haplotype H1 being the most common and widespread
one through all populations.
Within Germany, Ae. japonicus has been spreading immensely over the last decade. Even
though the present results (2017) demonstrate incipient genetic admixture of populations as
compared to previous studies (2012-2015), no complete genetic mixture has taken place yet.
The populations of Ae. japonicus still fall into two genetic clusters, but the genetic diversity
on individual level had increased considerably (from three nad4 haplotypes in 2012 to 12
according to the present thesis). Both additional introductions and mutation are possible
reasons, but determining the origin of the German populations is not possible anymore.
In the years following the invasion of Germany, Ae. japonicus spread to southeastern
Europe. In 2013, it established in Croatia, in 2017 in Bosnia and Herzegovina and in 2018
in Serbia. In the current study, immature stages of Ae. japonicus were found at 19 sites in
Croatia, two sites in Bosnia and Herzegovina and one site in Serbia. The population genetic
analyses indicate at least two independent introductions in that area. Aedes japonicus collected west of Orahovica (Croatia) seemed to be genetically similar to samples previously
investigated from Southeast Germany/Austria and Austria/Slovenia. By contrast, samples
from east of Orahovica, together with those from Serbia and Bosnia and Herzegovina, were
characterised by another genetic make-up, but their origin could not be determined.
In 2021, individuals of Ae. japonicus were detected at two collection sites in the Czech
Republic for the first time: Prachatice close to the Czech-German border and Mikulov on
the Czech-Austrian border. Population genetics and comparison of genetic data showed a
close relationship of the Prachatice samples to a German population, while for Ae. japonicus
from Mikulov close relatives could not be identified.
In the future, the global spread and establishment of invasive mosquitoes through
international trade and travel will increase. Potential vectors, like the Asian bush mosquito
Ae. japonicus, can become a problem in Europe and Germany, especially in the course of
global warming which supports pathogen transmission. Monitoring the known populations
and identifying introduction and migration routes are therefore essential for vector
managing.
Encephalitides induced by lyssa-, borna- and astroviruses: molecular detection and characterization
(2017)
Encephalitis is a severe inflammatory disease of the brain which often has a fatal outcome or can lead to subsequent damages. In around two-thirds of all human encephalitis cases, the causative agent is, despite improved diagnostics, unknown today. Aim of this work was the development, improvement and validation of diagnostic methods, improvement of sampling strategies and the development of optimized systems for characterization of three viruses causing viral encephalitis. The main burden of RABV lies in developing countries, were standard diagnostic tools are often not realizable. Therefore, simple and rapid diagnostic tests for the use under resource limited settings, so called point-of-care tests (POCT), are favorable. Commercially available lateral flow device (LFD) based immunodiagnostic tests were analyzed and failed in terms of sensitivity compared to the standard FAT and RT-qPCR (Paper I). Therefore, molecular RABV alternative targeting genome tests were developed and combined with rapid nucleic acid extraction methods. The new HighSpeed RT-qPCR and RPA assays together with magnetic bead based automated or manual extraction methods delivered a specificity between 100% and 97.2% and a limit of detection of 10 or 1,000 genome copies per reaction, respectively and seem suitable as novel POCT (Paper II). Recently, a novel zoonotic VSBV-1, responsible for fatal encephalitis of three squirrel breeders, was detected. For further investigations of this new virus, methods for an in-vivo sampling approach of squirrels were established. They were useful to identify animals harboring this dangerous virus, and new sequence data could be obtained from the VSBV-1 positive animals. Until now, 3.5% of all investigated squirrels were VSBV-1 RNA positive and two subfamilies (Sciurinae and Callosciurinae) are affected. The pathogen occurs not only in Germany, but also squirrel holdings and zoological gardens in the Netherlands and Croatia were tested positive, indicating a serious human health threat of this virus (Paper III and IV). With the help of a metagenomic approach, astroviruses were detected to be associated to encephalitis in cattle and sheep. These viruses were detected in a cow in Germany (Paper V), and in brain samples from two sheep in the United Kingdom (Paper VI). In both cases, the sequences generated by high-throughput-sequencing (HTS) were confirmed by specific RT-qPCRs, which could be used for subsequent screening approaches. Together, methods for the detection of three different encephalitis viruses were developed, validated and applied for different sample material.
The introduction of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) enabled the separation and visualization of a substantial fraction of an organism’s entire proteome, and when mass spectrometry entered protein science, these proteins became even amenable to identification on a grand scale. Nevertheless, important classes of proteins elude a separation on classical 2 D gels, as the ones showing extremes in isoelectric point or molecular weight, and foremost very hydrophobic proteins naturally embedded in lipid membranes. This thesis aimed at the establishment and adaptation of alternatives to 2-D PAGE. New techniques allowing for an identification and quantification of critical protein classes were designed and adopted to physiological questions in the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. In a comprehensive study on cytoplasmic proteins of S. aureus COL the number of proteins identified by a 2-D gel based approach could be extended by 650 proteins employing gel free technologies. Application of these complementary methods resulted in the establishment of a comprehensive reference map of the cytosolic proteome in growing and non-growing S. aureus cells which can serve as basis for further physiological investigations. Gel free separation of complex protein digests was likewise used in a quantitative study on heat stress in B. subtilis. By implementation of the iTRAQ® technology four different physiological states could be relatively quantified in one experiment. A parallel generation of 2-D gel based data enabled the depiction of strengths and weaknesses of protein quantitation by both, spot intensities on 2-D gels and iTRAQ® signal intensities in MS/MS spectra. Furthermore, new insights into heat sensitivity of pivotal enzymes involved in amino acid biosynthesis could be delivered. The institution of gel free approaches and advancements in 2-D PAGE provide the tools to penetrate into yet unamenable scopes of proteomes. A review on proteome coverage in B. subtilis gives an overview on the strategies which have been explored for most comprehensive protein identification in various sub-proteomes. Although more than one third of B. subtilis’ open reading frames could be demonstrated on protein level, one has to be aware of the fact that it still is a long way to achieve complete coverage of its proteome. Integral membrane proteins make up about one quarter of the entirety of proteins in a cell. Despite their large portion they are clearly understudied due to the intricacy of identification. Their low abundance and non-accessibility of membrane-spanning domains represent major experimental difficulties. The establishment of a protocol efficiently depleting cytosolic proteins by membrane shaving and targeting trans-membrane peptides by novel digestion strategies essentially facilitated identification of highly hydrophobic integral membrane proteins. This protocol was not only successfully applied to the membrane proteome of growing S. aureus cells, but was shown to be applicable in B. subtilis as well. Both studies displayed the novel membrane shaving approach to be highly complementary to a previously established separation of membrane proteins via 1 D PAGE. A combination of the two techniques resulted in identification of about half of the theoretical membrane proteome in both bacteria, and hence layed the foundation for advanced and quantitative analyses. In this regard, 14N/15N metabolically labeled membrane samples of growing and non-growing cells of S. aureus COL were relatively quantified revealing a significant difference in amount for more than one third of the proteins. A corresponding experimental setup was used to compare the membrane proteomes of S. aureus SA113 and its mutant deficient in the lysylphosphatidylglycerol synthetase MprF. Interesting quantitative differences were obtained for proteins most likely involved in the regulation of cellular surface net charge as well as for virulence-associated proteins.