Research project in the Preludium-Bis program of the National Science Centre on “The competition between RNA binding proteins ProQ, Hfq and FinO in Escherichia coli“ (No. 2020/39/O/NZ1/02448)
Small regulatory RNAs play important roles in gene expression regulation in bacteria [1]. These RNAs contribute to bacterial adaptation to changes in environmental conditions, participate in maintenance of intracellular homeostasis, and contribute to the control of bacterial virulence. In RNA-dependent gene expression regulation in Escherichia coli participate proteins ProQ and Hfq, which bind numerous RNA molecules, and plasmid-encoded FinO protein, which recognizes few RNA molecules. The Hfq protein forms a ring consisting of six identical subunits, which contains on its surface three RNA binding sites. On the other hand, ProQ and FinO belong to the family of FinO-domain proteins, which are widely distributed in β- and γ-proteobacteria. The ProQ protein consists of the FinO domain connected by a linker to the C-terminal Tudor domain, while the plasmid-encoded FinO protein contains the FinO domain connected to the N-terminal region enriched in positively charged amino acids.
Recent global profiling studies showed that ProQ and Hfq proteins bind distinct as well as overlapping RNA pools in E. coli and Salmonella enterica. Because Rho-independent transcription terminator structures are major binding motifs recognized by both proteins, it poses an interesting question of how these proteins recognize distinct pools of RNAs. An unexpected recent discovery in our lab has been the observation that A-rich sequence motifs, present in top RNAs bound by ProQ in E. coli, prevent the binding of these RNAs by the Hfq protein . This suggests that the ability of ProQ to recognize specific RNAs depends not only on the binding of ProQ to appropriate RNA structure motifs, but also on the competition for binding to these RNAs against the Hfq protein.
We expect that the studies planned in this project will allow explaining the role of the competition between RNA binding proteins ProQ, Hfq and FinO in the tuning of gene expression regulation in bacteria. Additionally, they will help to better understand the biological functions of proteins belonging to the widely distributed and evolutionarily conserved family of FinO-domain proteins.
References
- Olejniczak M, Storz G. ProQ/FinO-domain proteins: another ubiquitous family of RNA matchmakers? Mol Microbiol. (2017) 104(6):905-915 Pubmed