Projects and grants

Current projects:

Novel regulatory RNAs interacting with the transcription machinery in bacteria

Goal: Regulatory 6S RNA molecules that interact with RNA polymerase (RNAP) in complex with the primary sigma factor are widespread among bacteria. In Mycobacterium smegmatis, we discovered a new type of small RNA which binds to RNAP core, named it Ms1 and showed that Ms1 regulates the amount of RNAP. We found Ms1 homologs in other actinobacteria, e.g. scr3559 sRNA binds RNAP core in Streptomyces coelicolor. We plan to perform RIP-seq (RNA immunoprecipitation and next-generation sequencing) to identify a complete set of RNAs interacting with the transcription machinery in M. tuberculosis, Bifidobacterium bifidum and Corynebacterium glutamicum, where no 6S/Ms1 have been reported. Our preliminary data show that in addition to 6S/Ms1, other RNAs associate with bacterial RNAP. These novel RNAP-binding RNAs suggest the existence of so far unknown mechanisms of bacterial transcription regulation and we will focus on their function(s). We propose that 6S RNA and Ms1 were the first RNAs identified due to their high abundance; but other; less abundant regulatory RNAs are waiting to be discovered.

Principal investigator: J. Hnilicová

Grantor: Czech Science Foundation 

Duration: 2023-01 to 2025-12

Grant number: 23-05622S

CrsL – a novel transcriptional regulator in mycobacteria

Goal: The regulation of mycobacterial transcription is not yet fully understood, unlike in the extensively studied bacterial model organism, E. coli. Therefore, thorough molecular and structural studies are necessary. In our laboratory, we have discovered a novel transcription factor, CrsL. The overarching aim of this project is to gain a deep understanding of CrsL’s function in mycobacteria.

Principal investigator: Mahmoud Shoman

Grantor: Charles University Grant Agency (GA UK)

Duration: 2023-01 to 2024-12

Grant number: 275823