PD Dr. Sabine Brantl (PI)

Identification of novel peptide encoding and dual-function sRNAs in Bacillus subtilis and related Bacillus species

Friedrich-Schiller-University Jena (Germany), Bacterial Genetics

B. subtilis is the most important non-pathogenic Gram-positive model organism that can secrete proteins in large quantities into the growth medium and is, therefore, used for the industrial production of a number of enzymes such as amylases and proteases. 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, since 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.

The major aims of this project are to identify novel peptide encoding and dual-function sRNAs in B. subtilis and to further characterize them in terms of their expression, targets and biological role. We expect to discover novel functions for small peptides encoded by either short mRNAs or new dual function sRNAs.

The experimental work will be divided into the following three parts:

(1) Analysis of expression profiles and expression control of four peptide encoding sRNAs under different growth and stress conditions. Identification of potential transcriptional regulators.

(2) Search for peptide targets using co-elution and co-immunoprecipitation assays with C- and N-terminally tagged peptides and transcriptomics and peptidomics with wild-type, knockout- and overexpression strains. Elucidation of the biological role of these peptides.

(3) Investigation of additional base-pairing functions of these spRNAs using transcriptomics and a combination of in vitro and in vivo techniques

  1. Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S.,  A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol. 2010 May;76(4):990-1009.
  2. Gimpel M, Brantl S., Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biol. 2016 Sep;13(9):916-26.
  3. Gimpel M, Brantl S., Dual-function small regulatory RNAs in bacteria. Mol Microbiol. 2017 Feb;103(3):387-397.
  4. Gimpel M, Maiwald C, Wiedemann C, Görlach M, Brantl S., Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis. Microbiology. 2017 Aug;163(8):1248-1259.