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Phylogeny of the Koi herpesvirus and development of a vaccine against the Koi herpesvirus disease
(2019)
The aim of this presented dissertation was a stable, live attenuated and protective KHV usable as vaccine. Moreover this vaccine should by cost effective and easy to apply. Differentiation of infected and vaccinated animals was preferred by genetic and / or serological means. After achieving an attenuated virus, whole genome sequencing should be done to examine the genetic of the vaccine as one feature of biosafety. Besides biosafety additional knowledge on the virulence of Alloherpesviruses, especially of KHV was anticipated. Additionally the diagnostics of KHV and KHVD should be improved to increase reliability and to gain more insights into the relationship of different KHVs and hopefully to detect the source of an outbreak.
Hepeviruses are small viruses with a RNA-genome of positive polarity that form the family Hepeviridae. The family includes two genera: members of the genus Piscihepevirus were detected in fish species and members of the genus Orthohepevirus were found in different mammal and bird species. The genus Orthohepevirus contains four different species, namely Orthohepevirus A, B, C and D. The species Orthohepevirus A contains five human pathogenic genotypes, with three of them being zoonotic. The species Orthohepevirus C contains mammal-associated pathogens, which were identified in rats and carnivores. The human pathogenic genotypes are responsible for a self-limiting acute hepatitis in humans, which could become chronically in immunocompromised individuals. The main route of transmission is the consumption of undercooked meat and direct contact with HEV-positive excreta or blood. In Germany, hepatitis E is a notifiable disease since 2001 with an increased number of cases per year. Rats are the reservoir of rat-associated HEV (ratHEV), but also the zoonotic HEV-3 genotype was detected in rats. The European rabbit (Oryctolagus cuniculus) was identified as a reservoir host of a subgenotype of human pathogenic HEV-3 (HEV-3ra).
For the development of small mammal animal models, the objective of this study was to evaluate different small mammal populations for novel hepeviruses and to study the presence of HEV and sequence divergence of ratHEV and rabbitHEV in rat and rabbit populations from Europe.
Approximately 3000 rodents from Germany and the Czech Republic were screened by broad spectrum HEV-RT-PCR. As a result, 13 common voles (Microtus arvalis) and one bank vole (Myodes glareolus) were detected to be HEV-RNA positive. Comparison of the obtained sequences, complete genome determination and phylogenetic analysis indicated the finding of a novel common vole-associated HEV (cvHEV), which shows a high sequence divergence towards other members of the species Orthohepevirus C, but shares a high sequence similarity to a HEV-genome derived from a kestrel (Falco tinnunculus). The finding of cvHEV-RNA in a bank vole might be caused by a spillover infection. The cvHEV genome shares the hepevirus-typical open reading frames, but also has unique cvHEV-specific attributes in its genome.
The investigation of 420 Norway rats (Rattus norvegicus) and 88 Black rats (Rattus rattus) identified HEV-RNA in Norway rats from eight of nine and Black rats from two of four European countries. In a single Norway rat from Belgium, a HEV-3-strain with high sequence similarities to rabbitHEV (HEV-3ra), was detected. The investigation of zoo animals revealed a ratHEV spillover infection in a Syrian brown bear (Ursus arctos syriacus). This infection was most likely caused by ratHEV-infected free-living, wild rats from the same zoo.
Investigation of wild rabbit populations trapped in and around Frankfurt am Main, Germany, showed anti-HEV antibodies (34.7%) and rabbitHEV-RNA (25%). A high sequence similarity of rabbitHEV in the animals trapped at the urban site was observed, whereas a high sequence divergence was seen for the animals trapped at the rural trapping sites.
In conclusion, hepeviruses are widespread among different small mammal populations in Europe. The broad geographical distribution of these hepeviruses should be taken into account in further public health risk assessments. Further investigations are needed to characterize the presence of cvHEV in more detail, especially by taking the population dynamics of common voles into account. The detected HEV-strains could be taken as basis for the establishment of novel HEV-animal models, which might replace the so far used swine and non-human primate models.
The advances in high-throughput sequencing technologies have revolutionized the possibilities for pathogen identification in cases of unknown disease origin. Diagnostic metagenomics allows the unbiased and simultaneous detection of almost all nucleic acids in a clinical sample, with the potential to provide pivotal insights into otherwise undeterminable causes of human or animal disease.
In this thesis, possibilities, pitfalls and the suitability of Ion Torrent and Illumina sequencing platforms for comprehensive use in diagnostic metagenomics were assessed and optimized procedures developed. Clinical field samples, undiagnosable by standard diagnostics, were taken as real-life examples for the investigations. The results show that cross-contamination due to index swapping and run-to-run-carryover constitute a major issue on Illumina platforms, severely compromising the correct interpretation of results for clinical specimens. In contrast, Ion Torrent platforms did not display any form of cross-contamination, however, the commercial library preparation method is less efficient. Combining the advantages of both platforms, customized Y adapters, facilitating highly efficient library preparation, were developed for Ion Torrent sequencing and applied in further experiments. The obstacles of strongly degraded RNA in formalin-fixed paraffin-embedded samples were identified and the workflow adapted to meet the requirements of smaller fragments. Additionally, it was shown that adequate sampling is a very important step, if not the most important step, in the workflow, as well as subsequent validation of the obtained results in terms of causation. The achievements in this study allow other researchers the application of a sensitive and optimized diagnostic metagenomics workflow.
Furthermore, the investigations on the clinical samples resulted in the discovery of a novel respirovirus with putative zoonotic potential, the first description of Borna disease virus 1 in human organ transplant recipients, and the discovery of a very distantly related novel ovine picornavirus. These discoveries build a basis for further research and expand the knowledge regarding new and emerging viruses.
Phenolics and its derivatives are aromatic compounds with a wide range of industrial applications. Gallic acid, protocatechuic acid, catechol or pyrogallol are only a few examples of industrially relevant aromatics. The production of bulk fine chemicals primarily for chemical and pharmaceutical industry has put a strong emphasis on optimizing manufacturing conditions. Commercial production of many chemicals is still based on organic chemical synthesis using petroleum derivatives as starting material. Since these processes are considered environmentally unfriendly and posing an irresponsible strain on limited fossil resources, much attention is paid to the development of new microbial factories for the bioproduction of industrially relevant chemicals using renewable sources or organic pollutants as starting material. Arxula adeninivoras is a non-conventional yeast possessing attractive properties for industrial application such as thermo- and osmotolerance. Another major advantage of this organism is its broad substrate spectrum with tannin at the forefront. The present project is dedicated to the study of the tannic acid degradation pathway in A. adeninivorans. Two genes encoding enzymes annotated as gallic acid decarboxylase (AGDC1) and catechol-1,2-dioxygenase (ACDO1) have been selected and investigated. Both enzymes were characterized and their function in tannin catabolism analyzed.
The proteasome is a major part of the ubiquitin-proteasome-system playing an important role in cell homeostasis due to its protein quality control function. Moreover, the proteasome is involved in cell cycle regulation and in the regulation of transcription factors. Upon induction of interferons, or treatment with lipopolysaccharides, an isoform of the standard-proteasome is composed, named immunoproteasome (i-proteasome). The i-proteasome is constitutively expressed in immune cells and deficiency of proteolytic subunits of this multiprotein complex has been associated with a poor outcome during infectious diseases. I-proteasome-deficiency has been shown to result in reduced MHC class I presentation. Using mice which are deficient for all three proteolytic active subunits LMP2, MECL-1 and LMP7, we could demonstrate that i-proteasome-deficiency lead to an altered recruitment of immune cells to the CNS when challenged with the intracellular parasite Toxoplasma gondii, resulting in increased frequencies of neutrophils and other cells of myeloid origin. The shift to reduced frequencies of CD45highCD11blow lymphocytes can be further explained by a decreased migratory capacity of i-proteasome-deficient CD8+ T cells. In contrast to previous studies using other pathogens, effector function of CD8+ as well as CD4+ T cells, measured by frequencies of IFNγ, TNF, IL-2 and granzyme B producing cells, were not impaired in these mice, whereas induction of CD4+ Tregs was strongly reduced. In addition, we found that parasite control was comparable to control mice and that i-proteasome deletion caused an overall pro-inflammatory cytokine milieu within the brain. Our results indicate that i-proteasome-deficiency lead to prolonged tissue inflammation during T. gondii infection which could be an explanation for the more severe course of disease observed in these mice.
The Src homology domain containing phosphatase 2 (SHP2) is a tyrosine phosphatase modulating several signaling pathways and therefore has an influence in cell cycle, differentiation, proliferation and cell activation. However, SHP2 is assumed to play a negative role during T-cell activation as the phosphatase has been shown to inhibit T-cell receptor-induced signaling cascades. Although, various gain-of-function mutations in the SH2 or PTP domain of this phosphatase, such as D61Y, have been associated with myeloproliferative diseases such as juvenile myelomonocytic leukemia (JMML), effects of such mutations on T cells have not been addressed in scientific literature so far. Therefore, in the second part of this thesis we could demonstrate that D61Y mutation in the SH2 domain of SHP2 did not cause JMML pathology when only introduced into T cells. Especially in aged mice, T cells of SHP2 mutant mice showed an increased expression of cell adhesion molecule CD44. In accordance with these findings, we observed increased influenza A virus-specific T cells in the bone marrow of SHP2 D61Y mutant mice, indicating a role of the phosphatase in memory formation or maintenance of CD8+ Tem. Although SHP2D61Y mice revealed a comparable viral clearance, IFNγ production of virus experienced CD4+ and CD8+ T cells was diminished compared to control mice, underlining a negative involvement of the phosphatase in the JAK/STAT1 signaling axis as suggested before by studies using mice with SHP2-/- T cells.
Type I interferonopathies cover a phenotypically heterogeneous group of rare genetic diseases including the recently described proteasome-associated autoinflammatory syndromes (PRAAS). By definition, PRAAS are caused by inherited and/or de novo loss-of-function mutations in genes encoding proteasome subunits such as PSMB8, PSMB9, PSMB7, PSMA3, or proteasome assembly factors including POMP and PSMG2, respectively. Disruption of any of these subunits results in perturbed intracellular protein homeostasis including accumulation of ubiquitinated proteins which is accompanied by a type I interferon (IFN) signature. The observation that, similarly to pathogens, proteasome dysfunctions are potent type I IFN inducers is quite unexpected and, up to now, the underlying molecular mechanisms of this process remain largely unknown. One promising candidate for triggering type I IFN under sterile conditions is the unfolded protein response (UPR) which is typically initiated in response to an accumulation of unfolded and/or misfolded proteins in the endoplasmic reticulum (ER) (also referred to as ER stress). The recent observation that the UPR is engaged in subjects carrying POMP mutations strongly suggests its possible implication in the cause-and-effect relationship between proteasome impairment and interferonopathy onset. The purpose of this present review is therefore to discuss the possible role of the UPR in the pathogenesis of PRAAS. We will particularly focus on pathways initiated by the four ER-membrane proteins ATF6, PERK, IRE1-α, and TCF11/Nrf1 which undergo activation under proteasome inhibition. An overview of the current understanding of the mechanisms and potential cross-talk between the UPR and inflammatory signaling casacades is provided to convey a more integrated picture of the pathophysiology of PRAAS and shed light on potential biomarkers and therapeutic targets.
The spatio-temporal reduction and oxidation of protein thiols is an essential mechanism in signal transduction inall kingdoms of life. Thioredoxin (Trx) family proteins efficiently catalyze thiol-disulfide exchange reactions andthe proteins are widely recognized for their importance in the operation of thiol switches. Trx family proteinshave a broad and at the same time very distinct substrate specificity–a prerequisite for redox switching. Despiteof multiple efforts, the true nature for this specificity is still under debate. Here, we comprehensively compare theclassification/clustering of various redoxins from all domains of life based on their similarity in amino acidsequence, tertiary structure, and their electrostatic properties. We correlate these similarities to the existence ofcommon interaction partners, identified in various previous studies and suggested by proteomic screenings. Theseanalyses confirm that primary and tertiary structure similarity, and thereby all common classification systems, donot correlate to the target specificity of the proteins as thiol-disulfide oxidoreductases. Instead, a number ofexamples clearly demonstrate the importance of electrostatic similarity for their target specificity, independent oftheir belonging to the Trx or glutaredoxin subfamilies
Reversible posttranslational modifications play an important role during the regulation of many central processes in bacterial cells. Protein phosphorylation, in particular, can influence signal transduction processes and thus enables a distinct reaction of the cell to different stress and environmental conditions. In the case of the human pathogen Staphylococcus aureus, protein phosphorylation is involved in the adaptation to changing conditions during colonisation of human hosts. For this reason, the investigation of phosphorylations in S. aureus allows a better understanding of pathophysiology and virulence of this organism. Apart from stable phosphorylations at the amino acids serine, threonine and tyrosine, insights into energy-rich phosphorylations, for instance at arginine residues, gain more and more scientific attention. For this reason, one purpose of this study was the investigation of incidence and physiological relevance of this protein modification at a global scale. Firstly, the analysis of this modification was methodically optimised resulting in the identification of eight arginine phosphorylations in wild type cells of S. aureus COL. Secondly, the deletion mutant ΔptpB missing the gene that codes for an arginine phosphatase, was analysed. The characterisation of PtpB in vitro proved its activity and specificity towards arginine phosphorylations. This enabled the global analysis of the phosphoproteome with a focus on arginine phosphorylations. In addition to the optimisation of the phosphopeptide enrichment as part of the sample preparation, the data analysis process was adapted to the special challenges of energy-rich phosphorylations. Here, classical database search was extended by spectral library based analyses. In addition, synthetic peptides allow the generation of high quality mass spectra and the verification of database based evaluation strategies to ensure the quality of the spectral library. Next, S. aureus COL was cultivated under various conditions and several subcellular fractions were analysed with the aim to cover a broad part of the proteome. The combination of the spectra of synthetic peptides, the spectra of non-phosphorylated peptides from extensive cultivation experiments and the spectra of enriched phosphopeptides rendered the construction of a spectral library possible. This contained 2,270 proteins out of which 392 were found to be phosphorylated. A comparison of the database based analysis with spectral library based analysis showed the advantages of the latter when comparing the reproducibility of biological replicates. Thereby a permanent issue in phosphoproteomics was investigated. Hence, spectral libraries were used for the analysis of the phosphoproteome of S. aureus under control and stress conditions. 215 arginine phosphosites were identified within the mutant under control conditions and 117 under oxidative stress conditions. Oxidative stress was chosen because phenotypic characterisation of the mutant revealed that the most distinct growth changes in comparison with the wild type occurred after oxidative stress. These phenotypic changes were quantitatively approached in the last part of this work. Total proteome quantification of the wild type and mutant under control and stress conditions revealed an influence of the ptpB deletion on amino acid metabolism, oxidative stress response and virulence. The quantification of phosphopeptides by means of a combination of spectral library with Census based analysis finally confirmed the observations made during total proteome quantification.