Post-transcriptional regulation of the SOS response in the major human pathogen Klebsiella pneumoniae

• Applicant: Dr. Kathrin Fröhlich
• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology ; Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 553150513

Klebsiella pneumoniae is a Gram-negative, capsulated and non-motile bacterium within the family of Enterobacteriaceae. The continuous evolution of K. pneumoniae has resulted in the emergence and spread of strains with resistances against multiple antibiotics, drastically limiting treatment options. Cellular stress responses can actively promote mutation frequency by stimulating the SOS pathway which cumulates in the activation of an error-prone replication machinery. The SOS response in bacteria is an evolutionarily conserved pathway that allows cells to adapt and survive after a genomic insult. Under standard conditions, this pathway is kept inactive by the master regulator, LexA, which binds to operator sequences within the promoters of SOS response genes and prevents their transcription. Repression of the LexA regulon is suspended when the cellular DNA is compromised, for example by physical or chemical stressors. While the SOS response is a major control element of genome integrity and cell survival, the LexA regulon, its spatiotemporal control and the contribution of post-transcriptional regulation to the process remain unstudied in K. pneumoniae. To address this paucity, our proposal is designed to define the species-specific response to DNA damage in a multi-drug-resistant K. pneumoniae isolate. We will establish a comprehensive transcriptomic map of the response to DNA damage to understand the contribution of individual stress pathways under this condition. Chromatin immunoprecipitation coupled to sequencing (ChIP-seq) will enable us to define the direct LexA regulon in K. pneumoniae, and an in-depth analysis of the individual binding sites will help us understand the hierarchy of individual promoters within the SOS pathway. Our investigation of the transcriptional control mechanisms governing the response to DNA damage will be complemented by a comprehensive analysis of the post-transcriptional control layer. To define the reorganization of the RNA-RNA interactome in K. pneumoniae during the SOS response, we will employ RIL-seq (RNA interaction by ligation and sequencing) of the two major RNA-binding proteins, Hfq and ProQ. For selected RNA-RNA interactions recovered from the RIL-seq datasets, we will confirm base-pairing predictions and assess the biological relevance of the post-transcriptional regulation for the SOS program. In combination, the results of our different experimental approaches will merge to form a global view of the regulatory layers employed by K. pneumoniae to coordinate the SOS response to DNA damage.

• DFG Programme: Research Grants