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

• Final Report Year: 2025

Final Report Abstract

Small regulatory RNAs (sRNAs) are ubiquitous post-transcriptional regulators in bacteria. Their regulatory functions provide an integral non-coding component in transcriptional virulence and stress-associated regulons, influencing nearly all aspects of bacterial physiology. However, there are still few bacterial species in which gene regulation by sRNAs and associated RNA-binding proteins (RBPs) has been thoroughly and mechanistically characterized. Our work on Clostridioides difficile reveals the existence of a complex post-transcriptional network, coordinated by the global RBP Hfq, and highlights its significance in regulating infectionassociated pathways, particularly sporulation. In addition to our recently published sRNAs that regulate the initiation of sporulation, our global identification of RNA-RNA interactions, using RIL-seq, has identified several intriguing sRNAs and their target genes with implications for the infection process. Many of these sRNAs exhibit distinct expression profiles, with some being directly controlled by specialized sigma factors, such as the stress-response sigma factor σB. This suggests that these sRNAs are part of mixed regulatory feedback programs that involve both sRNAs and transcription factors. Looking forward, we will investigate these complex networks to understand how they shape virulence in response to changes in the intestinal environment.

Publications

• An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium. Proceedings of the National Academy of Sciences, 118(25).
  Fuchs, Manuela; Lamm-Schmidt, Vanessa; Sulzer, Johannes; Ponath, Falk; Jenniches, Laura; Kirk, Joseph A.; Fagan, Robert P.; Barquist, Lars; Vogel, Jörg & Faber, Franziska
  
• Grad-seq identifies KhpB as a global RNA-binding protein inClostridioides difficilethat regulates toxin production. microLife, 2.
  Lamm-Schmidt, Vanessa; Fuchs, Manuela; Sulzer, Johannes; Gerovac, Milan; Hör, Jens; Dersch, Petra; Vogel, Jörg & Faber, Franziska
  
• A network of small RNAs regulates sporulation initiation in Clostridioides difficile. The EMBO Journal, 42(12).
  Fuchs, Manuela; Lamm‐Schmidt, Vanessa; Lenče, Tina; Sulzer, Johannes; Bublitz, Arne; Wackenreuter, Janet; Gerovac, Milan; Strowig, Till & Faber, Franziska
  
• An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus. Nucleic Acids Research, 53(1).
  Velasco-Gomariz, Manuel; Sulzer, Johannes; Faber, Franziska & Fröhlich, Kathrin S.
  
• The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile. PLOS Biology, 22(12), e3002948.
  Lenče, Tina; Sulzer, Johannes; Andress, Kilian; Gribling-Burrer, Anne-Sophie; Lamm-Schmidt, Vanessa; Barquist, Lars; Smyth, Redmond P. & Faber, Franziska