@phdthesis{VuXuan2008, author = {Vu Xuan, Nghia}, title = {Generation of tools to investigate Chikungunya virus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-28993}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {CHIKV is the prototype of Alphaviruses and it causes an acute febrile illness with rash, severely painful arthralgias, and sometimes arthritis. While CHIKV has first been identified in the 1950s in Africa, recent outbreaks of CHIKV in the islands of the Indian Ocean and particular in Italia have re-drawn attention to CHIKV. In the past CHIKV disease was considered self-limiting and non-fatal. However, a number of deaths on Reunion (Anonym, 2006) during the outbreak, which was affected directly or indirectly by CHIKV, have changed this view. To defeat CHIKV outbreaks diagnostic tools and anti CHIKV therapies are urgently needed. In this thesis, we generated tools to investigate CHIKV at the molecular level by serological tests. CHIKV was isolated from a German woman who was infected during her holidays on the Mauritius Island. To characterize this viral isolate the complete viral genome was amplified by PCR and molecular cloned. In order to analyse antibody responses of infected individuals some of the structural and non-structural genes were subcloned in bacterial expression vectors. The NSP2, proteinase, capsid, E1 and E2 were subsequently expressed in E.coli using purified successfully. In this thesis, the structural proteins were used to develop a screening test for anti-CHIKV antibodies in patient derived serum samples. These tests were evaluated with pre-characterized anti-CHIKV sera (30 samples) obtained from the BNI Hamburg and 100 serum samples from German blood donors used as negative controls. Immunoblotting analysis revealed that up to 77\% of precharacterised positive sera could recognize the recombinant proteins and there were no detectable reactivity of CHIKV-negative German donor sera. The recombinant proteins were also recognized by 71.4\% of positive sera in the newly established ELISA. In order to go further in analyses of the results, an in house IFA was performed. Positive sera (21 samples) were used. The results showed that all of them reacted positive, but this assay was less sensitive than the IFA from BNI. In comparison with the IFA result from BNI Hamburg, the results were not congruent in all test performed. This could be due to various drawbacks of the tests. A cross reaction in Alphaviruses and the different strains are mentioned as well as the denatured forms of the structural proteins. Besides the main structural proteins (E1, E2 and C), other proteins such as non-structural proteins, uncleaved precursor proteins could participate in the different outcomes of serological assays. In order to go further in the CHIKV diagnoses, the CHIKV recombinant proteins were applied to screen the anti-CHIKV antibodies in the Vietnamese population, who are considered to live in the high risk regions. In serological tests, 158 sera of Vietnamese donors were incubated with the recombinant proteins or the fixed CHIKV infected cells. The results showed that 24\% of Vietnamese donor sera recognized the recombinant proteins in immunoblot assay, while 36\% scored positive in the ELISA assay. In IFA, the sera considered positive were 11.4\%. While some discrepancies in serological tests were found, these results showed that the ratio of CHIKV-positive sera seem to be equal to the other regions in the world, which are affected by CHIKV. It is suggested that CHIKV infection in Vietnam has been repeatedly misdiagnosed. This study cohort consisted only of samples originating from Hanoi area of Northern Vietnam, thus, future studies should expand to include samples from other Vietnam areas. To do this the various subtypes of the virus in the different regions should be isolated and the sequences of these viruses should be well characterized.}, subject = {Viren}, language = {en} } @phdthesis{Ye2023, author = {Ye, Liqing}, title = {RNA-RNA interactions in viral genome packaging}, doi = {10.25972/OPUS-29636}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296361}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {RNA is one of the most abundant macromolecules and plays essential roles in numerous biological processes. This doctoral thesis consists of two projects focusing on RNA structure and RNA-RNA interactions in viral genome packaging. In the first project I developed a method called Functional Analysis of RNA Structure (FARS-seq) to investigate structural features regulating genome dimerization within the HIV-1 5'UTR. Genome dimerization is a conserved feature of retroviral replication and is thought to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. It also plays a role in genome integrity and evolution through recombination, and is linked to a structural switch that may regulate genome packaging and translation within cells. Despite its importance for HIV-1 replication, the RNA signals regulating genome dimerization, and the molecular mechanism leading to the selection of the genome dimer over the monomer for packaging are incompletely understood. The FARS-seq method combines RNA structural information obtained by chemical probing with single nucleotide resolution profiles of RNA function obtained by mutational interference. In this way, we found nucleotides that were critical for dimerization, especially within the well-characterized dimerization motif within stem-loop 1 (SL1). We also found stretches of nucleotides that enhanced genome dimerization upon mutation, suggesting their role in negatively regulating dimerization. A structural analysis identified distinct structural signatures within monomeric and dimeric RNA. The dimeric conformation displayed the canonical transactivation response (TAR), PolyA, primer binding site (PBS), and SL1-SL3 stem-loops, and contained a long range U5-AUG interaction. Unexpectedly, in monomeric RNA, SL1 was reconfigured into long- and short-range base-pairings with PolyA and PBS, respectively. Intriguingly, these base pairings concealed the palindromic sequence needed for dimerization and disrupted the internal loop in SL1 previously shown to contain the major packaging motif for Pr55Gag. We therefore rationally introduced mutations into PolyA and PBS, and showed how these regions regulate genome dimerization, and the binding of Pr55Gag in vitro, as well as genome packaging into virions. These findings give insights into late stages of the HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging. In the second project, I developed a proximity ligation and high-throughput sequencing-based method, RNA-RNA seq, which can measure direct (RNA-RNA) and indirect (protein-mediated) interactions. In contrast to existing methods, RNA-RNA seq is not limited by specific protein or RNA baits, nor to a particular crosslinking reagent. The genome of influenza A virus contains eight segments, which assemble into a "7+1" supramolecular complex. However, the molecular details of genome assembly are poorly understood. Our goal is to use RNA-RNA seq to identify the sites of interaction between the eight genomic RNAs of influenza, and to use this information to define the quaternary RNA architecture of the genome. We showed that RNA-RNA seq worked on model substrates, like the HIV-1 Dimerization Initiation Site (DIS) RNA and purified ribosome, as well as influenza A virus infected cells.}, subject = {RNS-Viren}, language = {en} } @phdthesis{Kibe2024, author = {Kibe, Anuja}, title = {Translational landscape and regulation of recoding in virus-infected cells}, doi = {10.25972/OPUS-31099}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-310993}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {RNA viruses rely entirely on the host machinery for their protein synthesis and harbor non-canonical translation mechanisms, such as alternative initiation and programmed -1 ribosomal frameshifting (-1PRF), to suit their specific needs. On the other hand, host cells have developed a variety of defensive strategies to safeguard their translational apparatus and at times transiently shut down global translation. An infection can lead to substantial translational remodeling in cells and translational control is critical during antiviral response. Due to their sheer diversity, this control is likely unique to each RNA virus and the intricacies of post-transcriptional regulation are unclear in certain viral species. Here, we explored different aspects of translational regulation in virus-infected cells in detail. Using ribosome profiling, we extensively characterized the translational landscape in HIV-1 infected T cells, uncovering novel features of gene regulation in both host and virus. Additionally, we show that substantial pausing occurs prior to the frameshift site indicating complex regulatory mechanisms involving upstream viral RNA elements that can act as cis- regulators of frameshifting. We also characterized the mechanistic details of trans- modulation of frameshifting by host- and virus-encoded proteins. Host antiviral protein ZAP-S binds to the SARS-CoV-2 frameshift site and destabilizes the stimulatory structure, leading to frameshift inhibition. On the other hand, EMCV 2A protein stabilizes the viral frameshift site, thereby, activating EMCV frameshifting. While both proteins were shown to be antagonistic in their mechanism, they interact with the host translational machinery. Furthermore, we showed that frameshifting can be regulated not just by proteins, but also by small molecules. High-throughput screening of natural and synthetic compounds identified two potent frameshift inhibitors that also impeded viral replication, namely trichangion and compound 25. Together, this work largely enhances our understanding of gene regulation mechanisms in virus-infected cells and further validates the druggability of viral -1 PRF site.}, subject = {Zelle}, language = {en} }