Biology subjects

Scheller, D.

Publications and source records attributed to Scheller, D..

3 recordsLinked to original sources

bioRxiv2026

Structural similarities of molecules selectively binding the prfA thermosensor RNA

In light of the "silent" AMR pandemic, new avenues to combat pathogenic bacteria are needed. In this work, we screened a large molecule library (n=35 684 unique compounds) with the aim of identifying molecules being able to bind and block translation of the prfA-thermosensor transcript in the bacterial pathogen Listeria monocytogenes. Using a thiazole-orange displacement approach, 468 ([~]1.3% of all molecules) showed the ability to reduce fluorescence. After dose response testing, 32 compounds remained promising and eight of them showed sufficient purity and availability to be further validated. Interestingly, four compounds, being structurally very similar, showed specificity for prfA at a varying degree. All four compounds carried 3 aromatic rings with one connecting amine between two of the rings and an amide linking an aliphatic amine side chain. The most selective compounds, M5, showed a Kd of [~]0.8 {micro}M for the prfA RNA at 35{degrees}C. However, none of the eight most efficient compounds were able to inhibit prfA translation in vitro, suggesting that the molecules are able to bind but not affect the stability of the overall structure. Through this work, we have been able to identify a set of molecules, able to bind the prfA thermosensor RNA selectively, but without affecting translation. These molecules could constitute an important scaffold for further drug development.

microbiology↗

bioRxiv2026

Anthracyclines inhibit -1 programmed ribosomal frameshifting and restrict HCoV-OC43 infection

Human coronavirus OC43 (HCoV-OC43) constitutes one of the most common causes of the seasonal cold but can also cause severe disease among elderly and immuno-compromised. Currently, there are no approved antiviral drugs to combat HCoV-OC43 infection. Coronaviruses are positive-sense single-stranded RNA (+ssRNA) viruses and utilize -1 programmed ribosomal frameshifting (-1 PRF) to produce the correct stoichiometry of viral protein components. Due to its high conservation, the ribosomal frameshifting stimulation element (FSE) is a promising target for antiviral drug discovery. Aminoglycosides and anthracyclines interact with structured nucleic acids and some of these compounds affect -1 PRF in SARS-CoV-2. To get a comprehensive view of their putative efficacy, we examined all commercially available aminoglycosides and anthracyclines for their ability to affect -1 PRF in HCoV-OC43 and their potential to reduce HCoV-OC43 infection. Of 25 candidates tested, we identified 3 anthracyclines (Idarubicin, Nogalamycin and Daunorubicin) to reduce HCoV-OC43 -1 PRF using in vitro assays. We further demonstrate that the active anthracyclines, but not the inactive anthracycline, bind to the HCoV-OC43 FSE. The active anthracyclines did not significantly affect -1 PRF in SARS-CoV-2, suggesting differences in the interactions of the anthracyclines and FSEs, despite being relatively conserved in HCoV-OC43 and SARS-CoV-2 RNAs. Interestingly, these potent anthracyclines also significantly reduced HCoV-OC43 infection in human host cells. Although, the anthracyclines show some toxicity and introduce lesions in cellular DNA they could constitute an important scaffold for further antiviral development, with the aim to increase efficacy and reduce toxicity. Author summaryThe recent Covid-19 pandemic caused by SARS-CoV-2 showed the need for functional antivirals to immediately combat infections at the onset of future pandemics. In addition to SARS-CoV-2, four other human coronaviruses can cause mild to severe infection. Among those is HCoV-OC43, a coronavirus particularly troublesome for immunocompromised patients. Despite this clinical relevance, no approved antiviral therapies are currently available for the prevention or treatment of HCoV-OC43 infections. In this work, we have identified a subset of anthracyclines (Idarubicin, Nogalamycin and Daunorubicin) that selectively and significantly reduce HCoV-OC43 infection. In contrast to a non-active anthracycline, the same anthracyclines that reduce infection also reduce ribosomal frameshifting and interact with a structured RNA in the viral RNA-genome. Interestingly, Idarubicin, a clinically used anticancer drug, shows selectivity for HCoV-OC43, but not for SARS-CoV-2 RNA. Our work demonstrates that anthracyclines could be important for pandemic preparedness and serve as attractive scaffolds when developing new antivirals targeting coronaviruses.

microbiology↗

bioRxiv2023

The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis

Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5-untranslated region (5-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37{degrees}C. The trxA gene is transcribed into two mRNA isoforms, of which the short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25{degrees}C suggesting partially open structures available to the ribosome in the living cell. Upstream of katY we uncovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37{degrees}C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with temperature regulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37{degrees}C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature. Author summaryThe external conditions dramatically change when a bacterial pathogen enters a mammalian host. Sensing the new situation and rapidly responding to it is of critical importance for pathogens, like Yersinia pseudotuberculosis, since they often circulate between their environmental reservoirs and a warm-blooded host. Many virulence-related genes encode a temperature-sensitive mRNA element, a so-called RNA thermometer (RNAT), in the 5-end of their transcript. Melting of this structure at 37{degrees}C allows ribosome binding and translation initiation. The host immune system typically fights microbial pathogens by the production of reactive oxygen species (ROS). Here, we find that several ROS defense genes in Yersinia are upregulated at host body temperature to counteract the ROS attack. In particular, the massive RNAT-mediated upregulation of the catalase KatY confers protection against H2O2 at 37{degrees}C. Our study reveals a close regulatory link between temperature sensing and the oxidative stress response in a notorious food borne pathogen.

microbiology↗