@article{ZukherNovikovaTikhonovetal.2014,
  author    = {Zukher, Inna and Novikova, Maria and Tikhonov, Anton and Nesterchuk, Mikhail V. and Osterman, Ilya A. and Djordjevic, Marko and Sergiev, Petr V. and Sharma, Cynthia M. and Severinov, Konstantin},
  title     = {Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C},
  series = {Nucleic Acids Research},
  volume    = {42},
  journal   = {Nucleic Acids Research},
  number    = {19},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gku880},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114839},
  pages     = {11891-11902},
  year      = {2014},
  abstract  = {Microcin C (McC) is a peptide-nucleotide antibiotic produced by Escherichia coli cells harboring a plasmid-borne operon mccABCDE. The heptapeptide MccA is converted into McC by adenylation catalyzed by the MccB enzyme. Since MccA is a substrate for MccB, a mechanism that regulates the MccA/MccB ratio likely exists. Here, we show that transcription from a promoter located upstream of mccA directs the synthesis of two transcripts: a short highly abundant transcript containing the mccA ORF and a longer minor transcript containing mccA and downstream ORFs. The short transcript is generated when RNA polymerase terminates transcription at an intrinsic terminator located in the intergenic region between the mccA and mccB genes. The function of this terminator is strongly attenuated by upstream mcc sequences. Attenuation is relieved and transcription termination is induced when ribosome binds to the mccA ORF. Ribosome binding also makes the mccA RNA exceptionally stable. Together, these two effects-ribosome induced transcription termination and stabilization of the message-account for very high abundance of the mccA transcript that is essential for McC production. The general scheme appears to be evolutionary conserved as ribosome-induced transcription termination also occurs in a homologous operon from Helicobacter pylori.},
  language  = {en}
}
@article{WhisnantJuergesHennigetal.2020,
  author    = {Whisnant, Adam W. and J{\"u}rges, Christopher S. and Hennig, Thomas and Wyler, Emanuel and Prusty, Bhupesh and Rutkowski, Andrzej J. and L'hernault, Anne and Djakovic, Lara and G{\"o}bel, Margarete and D{\"o}ring, Kristina and Menegatti, Jennifer and Antrobus, Robin and Matheson, Nicholas J. and K{\"u}nzig, Florian W. H. and Mastrobuoni, Guido and Bielow, Chris and Kempa, Stefan and Liang, Chunguang and Dandekar, Thomas and Zimmer, Ralf and Landthaler, Markus and Gr{\"a}sser, Friedrich and Lehner, Paul J. and Friedel, Caroline C. and Erhard, Florian and D{\"o}lken, Lars},
  title     = {Integrative functional genomics decodes herpes simplex virus 1},
  series = {Nature Communications},
  volume    = {11},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-020-15992-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229884},
  year      = {2020},
  abstract  = {The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.},
  language  = {en}
}
@article{WenckerMarincolaSchoenfelderetal.2021,
  author    = {Wencker, Freya D. R and Marincola, Gabriella and Schoenfelder, Sonja M. K. and Maaß, Sandra and Becher, D{\"o}rte and Ziebuhr, Wilma},
  title     = {Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay},
  series = {Nucleic Acids Research},
  volume    = {49},
  journal   = {Nucleic Acids Research},
  number    = {4},
  doi       = {10.1093/nar/gkaa1277},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259029},
  pages     = {2192-2212},
  year      = {2021},
  abstract  = {In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5′ untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5′-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3′-end. The obtained data suggest that coordinated RNA decay represents another checkpoint in a complex regulatory network that adjusts costly methionine biosynthesis to current metabolic requirements.},
  language  = {en}
}
@phdthesis{Surrey2020,
  author    = {Surrey, Verena},
  title     = {Identification of affected cellular targets, mechanisms and signaling pathways in a mouse model for spinal muscular atrophy with respiratory distress type 1 (SMARD1)},
  doi       = {10.25972/OPUS-17638},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176386},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a fatal monogenic motoneuron disease in children with unknown etiology caused by mutations in the immunoglobulin μ-binding protein 2 (IGHMBP2) gene coding for DNA/RNA ATPase/helicase. Despite detailed knowledge of the underlying genetic changes, the cellular mechanisms leading to this disease are not well understood. In the Nmd2J ("neuromuscular disorder") mouse, the mouse model for the juvenile form of SMARD1 patients, in which similar pathological features as diaphragmatic paralysis and skeletal muscle atrophy are observed. Ex vivo studies in Nmd2J mice showed that loss of the motor axon precedes atrophy of the gastrocnemius muscle and does not correlate with neurotransmission defects in the motor endplate. The already described independent myogenic anomalies in the diaphragm and heart of the Nmd2J mouse raised the question whether spinal motoneuron degeneration develops cell autonomously. Ighmbp2 is predominantly localized in the cytoplasm and seems to bind to ribosomes and polysomes, suggesting a role in mRNA metabolism. In this Ph.D. thesis, morphological and functional analyses of isolated Ighmbp2-deficient (Ighmbp2-def.) motoneurons were performed to answer the question whether the SMARD1 phenotype results from dysregulation of protein biosynthesis. Ighmbp2-deficient motoneurons show only negligible morphological alterations with respect to a slight increase in axonal branches. This observation is consistent with only minor changes of transcriptome based on RNA sequencing data from Ighmbp2-deficient motoneurons. Only the mRNA of fibroblast growth factor receptor 1 (Fgfr1) showed significant up-regulation in Ighmbp2-deficient motoneurons. Furthermore, no global aberrations at the translational level could be detected using pulsed SILAC (Stable Isotope Labeling by Amino acids in cell culture), AHA (L-azidohomoalanine) labeling and SUnSET (SUrface SEnsing of Translation) methods. However, a reduced β-actin protein level was observed at the growth cones of Ighmbp2-deficient motoneurons, which was accompanied with a reduced level of Imp1 protein, a known β-actin mRNA interactor. Live-cell imaging studies using fluorescence recovery after photobleaching (FRAP) showed translational down-regulation of eGFPmyr-β-actin 3'UTR mRNA in the growth cones and the cell bodies, although the amount of β-actin mRNA and the total protein amount in Ighmbp2-deficient motoneurons showed no aberrations. This compartment-specific reduction of β-actin protein occurred independently of a non-existent direct IGHMBPF2 binding to β-actin mRNA. Fgfr1, which was upregulated on the RNA level, did not show an increased protein amount in Ighmbp2-deficient motoneurons, whereas a reduced amount could be detected. Interestingly, a correlation could be found between the reduced amount of the Imp1 protein and the increased Fgfr1 mRNA, since the IMP1 protein binds the FGFR1 mRNA and thus could influence the transport and translation of FGFR1 mRNA. In summary, all data suggest that Ighmbp2 deficiency leads to a local but modest disturbance of protein biosynthesis, which might contribute to the motoneuron defects of SMARD1.},
  subject      = {Spinale Muskelatrophie},
  language  = {en}
}
@phdthesis{Schaeffler2011,
  author    = {Sch{\"a}ffler, Katrin M.},
  title     = {Regulation der eukaryotischen Translation durch RNA-bindende Faktoren: Strukturelle und funktionelle Charakterisierung des La-verwandten Proteins 4B (LARP4B)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69809},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {In Zellen liegen RNAs in Form von Ribonukleoprotein-Komplexen (RNP) vor, wobei das Zusammenwirken von RNA und Proteinen die Funktionen der einzelnen RNPs definiert. RNA-bindenden Proteinen kommt demnach eine zentrale Bedeutung beim Verst{\"a}ndnis des RNA-Metabolismus zu. Zu dieser Proteingruppe z{\"a}hlen auch die La-verwandten Proteine (engl. La-related proteins, LARPs), welche eine evolution{\"a}r konservierte Familie von Faktoren bilden und durch eine putative RNA-bindende Dom{\"a}ne, dem La Modul, charakterisiert sind. Bereits f{\"u}r zwei Vertreter dieser Proteinklasse (LARP3 und LARP7) konnte eine {\"u}ber das La Modul vermittelte spezifische Interaktion mit uridylreichen RNA-Sequenzen gezeigt werden. Ziel dieser Arbeit war es, einen Vertreter der LARP-Familie, das sogenannte LARP4B, sowohl biochemisch als auch strukturell zu untersuchen und es somit einem zellul{\"a}ren Prozess zuzuordnen. Zellbiologische Studien zeigten zun{\"a}chst, dass LARP4B unter normalen Wachstumsbedingungen eine homogene zytoplasmatische Verteilung aufweist. Unter Stressbedingungen akkumuliert LARP4B hingegen in diskreten subzellul{\"a}ren Dom{\"a}nen, den sogenannten Stress Granules (SGs). Obwohl SGs bislang noch wenig funktionell untersucht sind, wird davon ausgegangen, dass sie der reversiblen Speicherung von mRNA-gebundenen Translationsfaktoren dienen. Durch affinit{\"a}tschromatographische Strategien ließen sich spezifische Interaktionspartner von LARP4B identifizieren. Als direkte Bindungspartner wurden das zytoplasmatische Poly (A) bindende Protein 1 (PABPC1) und der Rezeptor f{\"u}r aktivierte C Kinase 1 (RACK1) gefunden. Dar{\"u}ber hinaus zeigten Sedimentationsanalysen, dass LARP4B nahezu quantitativ mit Ribosomen und Polyribosomen assoziiert vorliegt. Diese Studie identifizierte daher LARP4B als ein Protein, das mit Schl{\"u}sselfaktoren der eukaryotischen Translation wechselwirkt. In {\"U}bereinstimmung mit diesen Befunden reduziert ein RNAi-induzierter Mangel des Proteins die Translationsrate drastisch, w{\"a}hrend die {\"U}berexpression von LARP4B in vivo zu einer Stimulation der Proteinbiosynthese f{\"u}hrt. Da dieser stimulatorische Einfluss bei einer Vielzahl unterschiedlicher mRNA-Spezies detektiert werden konnte, kann LARP4B als genereller, positiver Translationsfaktor angesehen werden. Interessanterweise wurden in Studien, die zeitgleich f{\"u}r das verwandte LARP1 durchgef{\"u}hrt wurden, vergleichbare zellul{\"a}re Interaktionen wie f{\"u}r LARP4B beschrieben. Um zu kl{\"a}ren, ob beide LARPs Orthologe darstellen und funktionelle Redundanz zeigen, wurde in der vorgelegten Arbeit ein Vergleich von LARP4B mit LARP1 durchgef{\"u}hrt. Unabh{\"a}ngige in vivo Studien und Sedimentationsanalysen zeigten deutlich, dass beide Proteine im mRNA-Metabolismus agieren, jedoch in diesem unterschiedliche Phasen der eukaryotischen Proteinbiosynthese beeinflussen.},
  subject      = {Translation <Genetik>},
  language  = {de}
}
@article{PreisingSchneiderBucheretal.2015,
  author    = {Preising, Christina and Schneider, Reinhard and Bucher, Michael and Gekle, Michael and Sauvant, Christoph},
  title     = {Regulation of expression of renal organic anion transporters OAT1 and OAT3 in a model of ischemia/reperfusion injury},
  series = {Cellular Physiology and Biochemistry},
  volume    = {37},
  journal   = {Cellular Physiology and Biochemistry},
  number    = {1},
  doi       = {10.1159/000430328},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144504},
  year      = {2015},
  abstract  = {Background: Recently, we gained evidence that impairment of rOat1 and rOat3 expression induced by ischemic acute kidney injury (AKI) is mediated by COX metabolites and this suppression might be critically involved in renal damage. Methods: (i) Basolateral organic anion uptake into proximal tubular cells after model ischemia and reperfusion (I/R) was investigated by fluorescein uptake. The putative promoter sequences from hOAT1 (SLC22A6) and hOAT3 (SCL22A8) were cloned into a reporter plasmid, transfected into HEK cells and (ii) transcriptional activity was determined after model ischemia and reperfusion as a SEAP reporter gen assay. Inhibitors or antagonists were applied with the beginning of reperfusion. Results: By using inhibitors of PKA (H89) and PLC (U73122), antagonists of E prostanoid receptor type 2 (AH6809) and type 4 (L161,982), we gained evidence that I/R induced down regulation of organic anion transport is mediated by COX1 metabolites via E prostanoid receptor type 4. The latter signaling was confirmed by application of butaprost (EP2 agonist) or TCS2510 (EP4 agonist) to control cells. In brief, the latter signaling was verified for the transcriptional activity in the reporter gen assay established. Therein, selective inhibitors for COX1 (SC58125) and COX2 (SC560) were also applied. Conclusion: Our data show (a) that COX1 metabolites are involved in the regulation of renal organic anion transport(ers) after I/R via the EP4 receptor and (b) that this is due to transcriptional regulation of the respective transporters. As the promoter sequences cloned were of human origin and expressed in a human renal epithelial cell line we (c) hypothesize that the regulatory mechanisms described after I/R is meaningful for humans as well.},
  language  = {en}
}
@phdthesis{Pekarek2024,
  author    = {Pek{\´a}rek, Luk{\´a}š},
  title     = {Single-Molecule Approaches To Study Frameshifting Mechanisms},
  doi       = {10.25972/OPUS-34611},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346112},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The RNAs of many viruses contain a frameshift stimulatory element (FSE) that grants access to an alternate reading frame via -1 programmed ribosomal frameshifting (PRF). This -1PRF is essential for effective viral replication. The -1PRF efficiency relies on the presence of conserved RNA elements within the FSE, such as a slippery sequence, spacer, and a downstream secondary structure - often a hairpin or a pseudoknot. The PRF efficiency is also affected by trans-acting factors such as proteins, miRNAs and metabolites. The interactions of these factors with the RNA and the translation machinery have not yet been completely understood. Traditional ensemble methods used previously to study these events focus on the whole population of molecular species. This results in innate averaging of the molecular behavior and a loss of heterogeneity information. Here, we first established the experimental workflow to study the RNA structures and the effect of potential trans-acting factors using single-molecule force spectroscopy technique, optical tweezers. Additionally, to streamline the data analysis, we developed an algorithm for automatized data processing. Next, we harnessed this knowledge to study viral RNA elements responsible for stimulation of PRF and how the presence of trans-acting factors affects the RNA behavior. We further complemented these single-molecule structural data with ensemble functional assays to gain a complex view on the dynamics behind the programmed ribosomal frameshifting. Specifically, two different viral RNA elements have been studied in the presented work. First, the dynamics of SARS-CoV-2 FSE and the role of extended sequences have been explored. Then, the mode of action of the host-encoded trans-acting factor ZAP-S inhibition of SARS-CoV-2 PRF has been examined. Finally, the mechanism of the trans-acting viral factor induced PRF in Encephalomyocarditis virus (EMCV) has been uncovered.},
  language  = {en}
}
@article{MinnerupSutherlandBuchanetal.2012,
  author    = {Minnerup, Jens and Sutherland, Brad A. and Buchan, Alastair M. and Kleinschnitz, Christoph},
  title     = {Neuroprotection for Stroke: Current Status and Future Perspectives},
  series = {International Journal of Molecular Science},
  volume    = {13},
  journal   = {International Journal of Molecular Science},
  number    = {9},
  doi       = {10.3390/ijms130911753},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134730},
  pages     = {11753-11772},
  year      = {2012},
  abstract  = {Neuroprotection aims to prevent salvageable neurons from dying. Despite showing efficacy in experimental stroke studies, the concept of neuroprotection has failed in clinical trials. Reasons for the translational difficulties include a lack of methodological agreement between preclinical and clinical studies and the heterogeneity of stroke in humans compared to homogeneous strokes in animal models. Even when the international recommendations for preclinical stroke research, the Stroke Academic Industry Roundtable (STAIR) criteria, were followed, we have still seen limited success in the clinic, examples being NXY-059 and haematopoietic growth factors which fulfilled nearly all the STAIR criteria. However, there are a number of neuroprotective treatments under investigation in clinical trials such as hypothermia and ebselen. Moreover, promising neuroprotective treatments based on a deeper understanding of the complex pathophysiology of ischemic stroke such as inhibitors of NADPH oxidases and PSD-95 are currently evaluated in preclinical studies. Further concepts to improve translation include the investigation of neuroprotectants in multicenter preclinical Phase III-type studies, improved animal models, and close alignment between clinical trial and preclinical methodologies. Future successful translation will require both new concepts for preclinical testing and innovative approaches based on mechanistic insights into the ischemic cascade.},
  language  = {en}
}
@article{LibreSeisslerGuerreroetal.2021,
  author    = {Libre, Camille and Seissler, Tanja and Guerrero, Santiago and Batisse, Julien and Verriez, C{\´e}dric and Stupfler, Benjamin and Gilmer, Orian and Cabrera-Rodriguez, Romina and Weber, Melanie M. and Valenzuela-Fernandez, Agustin and Cimarelli, Andrea and Etienne, Lucie and Marquet, Roland and Paillart, Jean-Christophe},
  title     = {A conserved uORF regulates APOBEC3G translation and is targeted by HIV-1 Vif protein to repress the antiviral factor},
  series = {Biomedicines},
  volume    = {10},
  journal   = {Biomedicines},
  number    = {1},
  issn      = {2227-9059},
  doi       = {10.3390/biomedicines10010013},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-252147},
  year      = {2021},
  abstract  = {The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation, and protein degradation) that altogether reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5′ untranslated region (5′-UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation.},
  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}
}