Identification and characterization of new sRNA/mRNA targets of CsrA in Bacillus subtilis

• Applicant: Privatdozentin Dr. Sabine Brantl
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 435337256

B. subtilis is the most important non-pathogenic Gram-positive model species that can secrete proteins in large quantities into the growth medium and is, therefore, used for the industrial production of a number of enzymes. In contrast to the Gram-negative model organism E. coli, B. subtilis is naturally competent and can sporulate in response to nutritional stress to survive extreme conditions. Moreover, as it is related to pathogenic Bacilli as e.g. B. anthracis or B. cereus, it can be used as a model organism for the regulation of metabolic responses or stress of such pathogenic bacteria as well. Whereas the RNA chaperone Hfq plays an important role for sRNA stability and sRNA/target mRNA interactions in Gram-negative bacteria, no such role has been found in B. subtilis and the majority of other Gram-positive bacteria. Until recently no RNA chaperones were known that were demonstrated experimentally to impact base-pairing between trans-encoded sRNAs and their target RNAs in Bacillus subtilis.In 2019, we have discovered and investigated in detail a new function for the widespread RNA chaperone CsrA in this respect, namely the promotion of complex formation between the trans-encoded sRNA SR1 and its target, ahrC mRNA, in Bacillus subtilis. We assume that this function is not confined to the SR1/ahrC mRNA regulatory system. The two major aims of this project are 1) to identify new CsrA-dependent mRNA targets of SR1 in B. subtilis and to further characterize the role of CsrA in these systems and 2) to employ a global approach to identify all CsrA-bound RNAs in B. subtilis.The experimental work will be divided into the following three parts which might be performed in parallel1) Identification of new mRNA targets of SR1 that depend on CsrA, elucidation of the mechanism of action of CsrA on these mRNAs and characterization of the role of CsrA in these systems2) Investigation of a possible role of CsrA for the mRNA function of SR13) Identification of all RNA binding partners of B. subtilis CsrA by CLIP Seq and verification of CsrA binding of selected RNAs by EMSA and DRaCALA

• DFG Programme: Research Grants