@phdthesis{Zachary2021,
  author    = {Zachary, Marie},
  title     = {Functional characterization of small non-coding RNAs of \(Neisseria\) \(gonorrhoeae\)},
  doi       = {10.25972/OPUS-24582},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-245826},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {During infection, bacteria need to adapt to a changing environment and have to endure various stress conditions. Small non-coding RNAs are considered as important regulators of bacterial gene expression and so allow quick adaptations by altering expression of specific target genes. Regulation of gene expression in the human-restricted pathogen Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoea, is only poorly understood. The present study aims a better understanding of gene regulation in N. gonorrhoeae by studying small non-coding RNAs. The discovery of antisense RNAs for all opa genes led to the hypothesis of asRNA-mediated degradation of out-of-frame opa transcripts. Analysis of asRNA expression revealed a very low abundance of the transcripts and inclusion of another phase-variable gene in the study indicates that the asRNAs are not involved in degradation of out-of-frame transcripts. This doctoral thesis focuses on the analysis of trans-acting sRNAs. The sibling sRNAs NgncR_162 and NgncR_163 were discovered as post-transcriptional regulators altering expression of genes involved in metabolic processes, amino acid uptake and transcriptional regulation. A more detailed analysis by in silico and transcriptomic approaches showed that the sRNAs regulate a broad variety of genes coding for proteins of central metabolism, amino acid biosynthesis and degradation and several transport processes. Expression levels of the sibling sRNAs depend on the growth phase of the bacteria and on the growth medium. This indicates that NgncR_162 and NgncR_163 are involved in the adaptation of the gonococcal metabolism to specific growth conditions. This work further initiates characterisation of the sRNA NgncR_237. An in silico analysis showed details on sequence conservation and a possible secondary structure. A combination of in silico target prediction and differential RNA sequencing resulted in the identification of several target genes involved in type IV pilus biogenesis and DNA recombination. However, it was not successful to find induction conditions for sRNA expression. Interestingly, a possible sibling sRNA could be identified that shares the target interaction sequence with NgncR_237 and could therefore target the same mRNAs. In conclusion, this thesis provides further insights in gene regulation by non-coding RNAs in N. gonorrhoeae by analysing two pairs of sibling sRNAs modulating bacterial metabolism or possibly type IV pilus biogenesis.},
  subject      = {Neisseria gonorrhoeae},
  language  = {en}
}
@phdthesis{WasgebHouben2023,
  author    = {Was [geb. Houben], Nina},
  title     = {Die Rolle der nicht-kodierenden RNAs miR-26 und \(Malat1\) bei der \(in\) \(vitro\) Differenzierung zu Neuronen},
  doi       = {10.25972/OPUS-30371},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303714},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {W{\"a}hrend der embryonalen Neurogenese spielt die Repression neuraler Gene in nicht neuralen Zellen, sowie in neuralen Vorl{\"a}uferzellen durch den REST (repressor element silencing transcription factor)-Komplex eine wichtige Rolle. Durch die schrittweise Inaktivierung diese Komplexes im Verlauf der Differenzierung werden neurale Genexpressionsprogramme gesteuert. Zus{\"a}tzlich kommt bei der Kontrolle der r{\"a}umlichen und zeitlichen Regulation der Genexpression w{\"a}hrend der Neurogenese verschiedenen miRNAs eine wichtige Rolle zu. So konnte in vorangegangenen Arbeiten im Zebrafischen gezeigt werden, dass miR-26b die Transkription eines wichtigen Effektorproteins des REST-Komplexes, CTDSP2 (C-terminal domain small phosphatases), w{\"a}hrend der Neurogenese negativ reguliert. Da dar{\"u}ber hinaus die miR-26 Repression zu einer stark verminderten neuronalen Differenzierung f{\"u}hrte, kommt diesem regulatorischen Schaltkreis eine zentrale Rolle bei der Neurogenese im Zebrafisch zu. Die zusammen mit ihren Ctdsp-Wirtsgenen koexprimierte miR-26 Familie liegt in Vertebraten evolution{\"a}r hoch konserviert vor. Analog zum Zebrafisch konnte im murinen in vitro ES-Zell Differenzierungssystem gezeigt werden, dass miR-26 die Expression von Ctdsp2 reprimiert. Weiterhin konnte in diesem System gezeigt werden, dass auch Rest ein miR-26 Zielgen ist und dass der Verlust der miR-26 zu einem Arrest der differenzierenden Zellen im neuronalen Vorl{\"a}uferstadium f{\"u}hrt. Zusammengenommen deuten diese vorangegangenen Arbeiten auf eine zentrale Rolle der miR-26 w{\"a}hrend der Neurogenese hin. Die hier vorgestellte Arbeit zielte zun{\"a}chst darauf ab die Regulation des REST-Komplexes durch die miR-26 auf molekularer Ebene besser zu verstehen. Der Verlust der miR-26 Bindestelle in der Ctdsp2 mRNA f{\"u}hrte zu einer erh{\"o}hten Ctdsp2 Expression, beeinflusste aber nicht die terminale Differenzierung zu Neuronen. Im Gegensatz hierzu f{\"u}hrte der Verlust der miR-26 Bindestelle in der Rest mRNA zu einem Arrest der Differenzierung im neuralen Vorl{\"a}uferzellstadium. Zellen in denen die miR-26 Bindestelle in Rest deletiert war, zeigten zudem, genau wie miR-26 knockout (KO) Zellen, eine erh{\"o}hte Expression von REST-Komplex Komponenten, sowie eine verringerte Expression von REST-regulierten miRNAs. Zusammengenommen weisen diese Daten daraufhin, dass w{\"a}hrend der Neurogenese im S{\"a}ugersystem die Inaktivierung von Rest durch miR-26 f{\"u}r die Maturierung von Neuronen eine zentrale Rolle spielt. Ein weiterer Fokus dieser Arbeit lag auf der Regulation der miR-26 Expression w{\"a}hrend der Neurogenese. Vorangegangene Arbeiten in nicht-neuronalen Zelltypen identifizierten die lnc (long-non-coding) RNA Malat1 als eine ce (competitive endogenous) RNA der miR-26. Um den Einfluss von Malat1 auf die miR-26 Expression w{\"a}hrend der Neurogenese zu untersuchen, wurde zun{\"a}chst mittels CRISPR/Cas9 der vollst{\"a}ndige Malat1-Lokus in ESCs deletiert. Der Verlust von Malat1 f{\"u}hrte zu einer erh{\"o}hten Expression der miR-26 Familienmitglieder sowie deren Ctdsp-Wirtsgene. Weiterhin war die Proliferation von Malat1 KO neuronalen Vorl{\"a}uferzellen stark vermindert, was mit einer Erh{\"o}hung der Frequenz seneszenter Zellen einherging. Durch die Inaktivierung von miR-26 in differenzierenden Malat1 KO ESCs konnte dieser proliferative Ph{\"a}notyp aufgehoben werden. Dar{\"u}ber hinaus konnte eine verst{\"a}rkte neuronale Differenzierung dieser Zellen beobachtet werden. Zusammenfassend zeigen diese Daten, dass neben der Regulation des REST-Komplexes durch miR-26 auch die Kontrolle des Zellzyklus {\"u}ber die Malat1-vermittelte Regulation der miR-26 in neuronalen Vorl{\"a}uferzellen einen kritischen Schritt bei der Differenzierung von neuronalen Vorl{\"a}uferzellen zu maturen Neuronen darstellt.},
  subject      = {Neurogenese},
  language  = {de}
}
@phdthesis{Horn2019,
  author    = {Horn, Jessica},
  title     = {Molecular and functional characterization of the long non-coding RNA SSR42 in \(Staphylococcus\) \(aureus\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-175778},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2019},
  abstract  = {Staphylococcus aureus asymptomatically colonizes the skin and anterior nares of 20-30\% of the healthy human population. As an opportunistic human pathogen it elicits a variety of infections ranging from skin and soft tissue infections to highly severe manifestations such as pneumonia, endocarditis and osteomyelitis. Due to the emergence of multi resistant strains, treatment of staphylococcal infections becomes more and more challenging and the WHO therefore classified S. aureus as a "superbug". The variety of diseases triggered by S. aureus is the result of a versatile expression of a large set of virulence factors. The most prominent virulence factor is the cytotoxic and haemolytic pore-forming α-toxin whose expression is mediated by a complex regulatory network involving two-component systems such as the agr quorum-sensing system, accessory transcriptional regulators and alternative sigma-factors. However, the intricate regulatory network is not yet understood in its entirety. Recently, a transposon mutation screen identified the AraC-family transcriptional regulator 'Repressor of surface proteins' (Rsp) to regulate haemolysis, cytotoxicity and the expression of various virulence associated factors. Deletion of rsp was accompanied by a complete loss of transcription of a 1232 nt long non-coding RNA, SSR42. This doctoral thesis focuses on the molecular and functional characterization of SSR42. By analysing the transcriptome and proteome of mutants in either SSR42 or both SSR42 and rsp, as well as by complementation of SSR42 in trans, the ncRNA was identified as the main effector of Rsp-mediated virulence. Mutants in SSR42 exhibited strong effects on transcriptional and translational level when compared to wild-type bacteria. These changes resulted in phenotypic alterations such as strongly reduced haemolytic activity and cytotoxicity towards epithelial cells as well as reduced virulence in a murine infection model. Deletion of SSR42 further promoted the formation of small colony variants (SCV) during long term infection of endothelial cells and demonstrated the importance of this molecule for intracellular bacteria. The impact of this ncRNA on staphylococcal haemolysis was revealed to be executed by modulation of sae mRNA stability and by applying mutational studies functional domains within SSR42 were identified. Moreover, various stressors modulated the transcription of SSR42 and antibiotic challenge resulted in SSR42-dependently increased haemolysis and cytotoxicity. Transcription of SSR42 itself was found under control of various important global regulators including AgrA, SaeS, CodY and σB, thereby illustrating a central position in S. aureus virulence gene regulation. The present study thus demonstrates SSR42 as a global virulence regulatory RNA which is important for haemolysis, disease progression and adaption of S. aureus to intracellular conditions via formation of SCVs.},
  subject      = {Staphylococcus aureus},
  language  = {en}
}