Open Access

Clostridioides difficile infections have become a major challenge in medical facilities. The bacterium is capable of spore formation allowing the survival of antibiotic treatment. Therefore, research on the physiology of C. difficile is important for the development of alternative treatment strategies. In this study, we investigated eight putative flavodoxins of C. difficile 630. Flavodoxins are small electron transfer proteins of specifically low potential. The unusually high number of flavodoxins in C. difficile suggests that they are expressed under different conditions. We determined high transcription levels for several flavodoxins during the exponential growth phase, especially for floX. Since flavodoxins are capable of replacing ferredoxins under iron deficiency conditions in other bacteria, we also examined their expression in C. difficile under low iron and no iron levels. In particular, the amount of fldX increased with decreasing iron concentration and thus could possibly replace ferredoxins. Moreover, we demonstrated that fldX is increasingly expressed under different oxidative stress conditions and thus may play an important role in the oxidative stress response. While increased fldX expression was detectable at both RNA and protein level, CD2825 showed increased expression only at mRNA level under H2O2 stress with sufficient iron availability and may indicate hydroxyl radical-dependent transcription. Although the exact function of the individual flavodoxins in C. difficile needs to be further investigated, the present study shows that flavodoxins could play an important role in several physiological processes and under infection-relevant conditions.

The proteasome is one of the major cellular protein degradation systems. The respective substrates include cell cycle regulators, kinases, transcription factors, antigens and enzymes. As such the proteasome plays a major role in cell function, survival and proliferation. Another key target of the proteasome are damaged and misfolded proteins as well as those proteins that are no loner required. Therefore, the proteasome is key in maintaining proteostasis, which describes the balance between the synthesis of new proteins and the removal of damaged, old and misfolded ones. Several factors such as ageing, disease and certain medications can impair proteasome function and thus disturb cellular proteostasis. The current work focused on novel genetic mutations in the various subunits constituting the proteasome. The proteasomal mutations were found to cause two very distinct disease phenotypes, PRAAS (an autoinflammatory disorder) and NDD (neurodevelopmental delay). The novel mutations discussed in this work were found to impair proteasome function through a variety of mechanisms and lead to decreased proteolytic capacity in the cells of the patients, resulting in a disturbance of cellular proteostasis and disease manifestation.

Hepatitis E virus (HEV) is emerging worldwide as a zoonotic pathogen that has remained largely undetected for decades, if not centuries. Its enormous success can be attributed to the wide range of host species, which can transmit the virus to humans, depending on the viral genotype. As a result, HEV is likely to remain a challenge even when the remaining hepatitis viruses (HAV, HBV, HCV), which are transmitted exclusively between humans, are under control. Although millions of HEV infections occur each year, little is known about this puzzling pathogen. One major issue in HEV research is the lack of reliable model systems. Established animal models are inefficient, expensive, or simply not representative of human HEV. On the other hand, cell culture systems are limited by the slow growth of the virus and inefficient replication and infection. The aim of this work is to with deepen the understanding of zoonotic HEV in animal hosts in Germany. For this purpose, a molecular and phylogenetic characterization of HEV sequences from rabbits and swine was conducted. A novel subtype of the zoonotic genotype HEV-3 was identified in a rabbit sample, further emphasizing the role of rabbits as HEV host species and possible reservoir of zoonotic HEV infections in Germany. On the other hand, a molecular biological screening of pigs and wild boars in Mecklenburg-Western Pomerania indicates a wide range of HEV-3 subtypes circulating in swine in north-east Germany. Furthermore, an optimized replicon system was established in order to enable characterization of various HEV sequences by reverse genetics. As a proof of concept, two rabbit HEV derived replicons were compared with two established, cell culture adapted HEV strains. The influence of different regions of the nonstructural protein on HEV replication was determined and quantified. In particular, a system was established, to reproducibly compare different strains and genotypes. This refined replicon system will enable the characterization of further HEV sequences and thus expand the knowledge on the determinants of the viral life cycle.

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.

As the animal-to-human interface becomes increasingly narrow, transmission events of zoonotic pathogens between animals and humans become more and more probable. While SARS-CoV-2 already accomplished a spillover infection to humans and is responsible for the current pandemic, the bat H9N2 IAV with so far unknown zoonotic potential was only recently discovered. In order to identify I) the role and potential of a newly discovered, potentially pre-pandemic virus, such as the bat H9N2, or II) possible future prevailing virus mutant variants of an already known pandemic virus, such as SARS-CoV-2, it is important to characterize these emerging viruses in vivo as soon and as good as possible. The first objective in this dissertation (Publications I and II) therefore deals with the characterization of bat H9N2 and the estimation of its zoonotic or even pandemic potential. In Publication I, a general susceptibility of directly inoculated Egyptian fruit bats to bat H9N2 was confirmed by successful seroconversion, although exhibiting only moderate viral shedding. All three contact animals remained seronegative, though one contact bat showed slight lesions in the histopathological analysis. Publication II further addressed the question of the zoonotic potential of this virus. Inoculation of day-old turkey hatchlings demonstrated moderate susceptibility to bat H9N2 infection with a measurable seroconversion, while day-old chicken hatchlings were not susceptible to bat H9N2. Ferrets proved to be highly susceptible to bat H9N2 with high viral shedding, a transmission efficiency rate of 100% to direct contact animals at 2 days post contact, but with only minimal clinical signs. Importantly, the virus demonstrated the ability to evade the MxA-restriction factor and to replicate efficiently in human lung tissue explants. Furthermore, seasonal IAV- and standard IAV-vaccines showed no cross reactivity against the bat-N2 protein in humans. Therefore, further research on such viruses is urgently needed in order to prevent a renewed pandemic situation in the future as caused by SARS-CoV-2. The second objective in this dissertation dealt with the identification and characterization of emerging SARS-CoV-2 Variants of Concern (VOCs). Therefore, in Publication III, competitive infection experiments were performed using the Syrian golden hamster, the ferret, and transgenic mouse models (K18-hACE2 and hACE2-KI). These studies revealed replicative and transmissive predominance of Alpha VOC over Beta VOC, but not over SARS-CoV-2 WT in the hamster model, although Beta VOC substantially replicated in the lungs of donor animals. In contrast, the Alpha VOC had an unambiguous replication and transmission advantage over WT SARS-CoV-2 in the ferret and both mouse models. A recombinant SARS-CoV-2 WT-SAlpha virus helped to assign the fitness advantage of this variant particularly to the spike protein-associated mutations. In Publication IV, in vitro results inferred an early replicative fitness advantage of Omicron BA.1 over Delta VOC, although the opposite was observed in competitively inoculated hamsters, ferrets and naive hACE2-KI mice. In addition, Publication IV demonstrated a disadvantage in transmission for the VOC Omicron BA.1 over the Delta VOC and a lack of susceptibility of ferrets after a single infection with the VOC Omicron BA.1. An mRNA vaccination of K18-hACE2 mice caused a drastic reduction of infectious virus particles in organ material following an infection with a recombinant SARS-CoV-2 WT-SDelta, but not when challenged with the SARS-CoV-2 SOmicron BA.1 clone. This dissertation includes numerous, comprehensive experimental studies that are generally important for the characterization of emerging, potentially pre-pandemic viruses and may provide crucial information about the future dominance of certain virus variants in an ongoing pandemic. Here, the need for the use of a variety of animal models becomes apparent. By characterizing and classifying potentially zoonotic strains, these methods will help to better prepare for potentially upcoming pandemics and, in the case of a zoonotic or even pandemic event, to better detect and understand the circulating strains and their evolution.