NMR resonance assignments of the FinO-domain of the RNA chaperone RocC
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ARTICLE
NMR resonance assignments of the FinO‑domain of the RNA chaperone RocC Reiner Eidelpes1 · Hyeong Jin Kim2 · J. N. Mark Glover2 · Martin Tollinger1 Received: 30 August 2020 / Accepted: 31 October 2020 © The Author(s) 2020
Abstract In prokaryotic species, gene expression is commonly regulated by small, non-coding RNAs (sRNAs). In the gram-negative bacterium Legionella pneumophila, the regulatory, trans-acting sRNA molecule RocR base pairs with a complementary sequence in the 5’-untranslated region of mRNAs encoding for proteins in the bacterial DNA uptake system, thereby controlling natural competence. Sense-antisense duplexing of RocR with targeted mRNAs is mediated by the recently described RNA chaperone RocC. RocC contains a 12 kDa FinO-domain, which acts as sRNA binding platform, along with an extended C-terminal segment that is predicted to be mostly disordered but appears to be required for repression of bacterial competence. In this work we assigned backbone and side chain 1H, 13C, and 15N chemical shifts of RocC’s FinO-domain by solution NMR spectroscopy. The chemical shift data for this protein indicate a mixed α/β fold that is reminiscent of FinO from Escherichia coli. Our NMR resonance assignments provide the basis for a comprehensive analysis of RocC’s chaperoning mechanism on a structural level. Keywords NMR resonance assignment · Protein · Ribonucleic acid · Chaperone · Base-pairing
Biological context The formation of molecular interactions in RNA-based regulatory processes often requires chaperoning by proteins (Woodson et al. 2018). In prokaryotic species, RNA chaperones play a particularly critical role in the regulation of gene expression. The protein RocC (repressor of competence chaperone) from the bacterium Legionella pneumophila, which is involved in post-transcriptional gene regulation, is such an RNA chaperone (Attaiech et al. 2016). RocC specifically binds to a non-coding 66-nucleotide RNA molecule, RocR, which in turn recognizes and binds to the 5’-untranslated region of mRNAs that encode for a variety of proteins in the bacterial DNA uptake system, such as * J. N. Mark Glover [email protected] * Martin Tollinger [email protected] 1
Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
Department of Biochemistry, University of Alberta, T6G 2H7 Edmonton, AB, Canada
2
ComEA, ComEC and ComF, controlling their expression (Attaiech et al. 2016). Within this scheme, RocC acts as an RNA chaperone by promoting strand exchange and intermolecular base pairing between the regulatory sRNA molecule RocR and its target mRNAs. Intriguingly, RocC binds to a polyU overhang at the 3’-tail of RocR, while sense-antisense base pairing occurs in a stem loop at the 5’-end of RocR, which contains a 6-nucleotide antisense sequence that binds to the complementary “RocR-box” in mRNAs. In addition, RocC binding appears to protect RocR from degradation and maintain its steady-state level.
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