Mechanisms of Hfq-mediated gene regulation by small regulatory RNAs in Clostridium difficile

• Applicant: Professorin Dr. Franziska Faber
• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology ; Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2020 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 441649355

Small non-coding RNAs (sRNAs) are important modulators of post-transcriptional gene regulation in a broad range of bacterial species which regulate both physiological and virulence pathways. The RNA-binding protein Hfq is an important regulator of this process because it facilitates the imperfect base-pairing of sRNAs to their target mRNAs affecting the translation and turnover rates of these regulated targets. While Hfq functions have been intensively studied in many gram-negative bacteria, its role in gram-positive bacteria, and especially in Clostridium difficile (C. difficile), remains elusive. Our preliminary work provides the first example of a Gram-positive Hfq homolog with global sRNA-binding function. Specifically, we show that Hfq binds a wide and dynamic repertoire of sRNAs in response to changing growth conditions and we identify potential sRNA-regulated mRNAs encoding for the central Stickland enzyme glycine reductase. Activity of this enzyme is not only important for growth of C. difficile but influences toxin production.Based on our data, we hypothesize that RNA-based regulation plays a central role in the adaptation and response to the intestinal environment in which infection occurs. Focusing on the identified Hfq-associated sRNAs, we will explore the molecular mechanisms of gene regulation and identify regulated targets with a focus on virulence-associated pathways. In parallel, we will apply a global approach to characterize the Hfq-associated sRNA target network in conditions associated with the infection process to reveal how these sRNAs are embedded in global networks of post-transcriptional gene regulation.We plan to apply the knowledge gained from this fundamental research towards our future goal of exploring antisense-RNA-based antibiotics against C. difficile as a sequence-specific treatment alternative to broad-spectrum antibiotics. Specifically, we intend to leverage the mechanistic knowledge of RNA-based gene regulation in C. difficile for the design of antisense-RNA-based antibiotics and for the identification of target sequences in C. difficile.

• DFG Programme: Research Grants