Inspired by the RNA world hypothesis, the Schroeder team specifically looked for natural RNAs that interact with the RNA polymerase machinery (RNAP) and thereby can potentially modulate the transcriptional output. Renée Schroeder says: “Life is a self-organized process. If RNA is to play the role of the molecule that enabled life to emerge, it should be able to control its own synthesis”.

Together with experts from the leading institutes in Austria and the US, researchers developed a powerful approach to explore this “hidden” landscape of regulatory signals on the RNA level. Combining genomic SELEX (Systematic evolution of ligands by exponential enrichment) with the latest deep sequencing methods, the researchers identified numerous RNAs binding to RNA polymerases (RAPs) encoded throughout the E. coli genome. 

Through various in vivo and in vitro approaches, a subset of RAPs, called iRAPs, which downregulate transcription was further characterized in more details. RAPs were found to be highly abundant in E. coli, which points towards a high impact on the bacterial transcriptome. „Diversity makes it so interesting! We are looking forward to elucidating other types of RAPs activities. It is incredible, how much there is still to learn from bacteria! In general, the discovered RAPs could be used to improve the existing systems for recombinant RNA/protein production.,” says Nadezda Sedlyarova, the first author of the story.

Publication in Molecular Cell:

Nadezda Sedlyarova, Philipp Rescheneder, Andrés Magán, Niko Popitsch, Natascha Rziha, Ivana Bilusic, Vitaly Epshtein, Bob Zimmermann, Meghan Lybecker, Vitaly Sedlyarov, Renée Schroeder, and Evgeny Nudler: Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. In: Molecular Cell (June 2017). DOI: dx.doi.org/10.1016/j.molcel.2017.05.025