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RNA recognition by minimal ProQ from Neisseria meningitidis

Maciej Basczok¹, Mikołaj Olejniczak²

¹Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland.

RNA (New York, N.Y.)

|January 28, 2025

Abstract:

Neisseria meningitidis minimal ProQ is a global RNA-binding protein belonging to the family of FinO-domain proteins. The N. meningitidis ProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs, rpmG-3' and AniS, were subject to further mutational studies. The data showed that N. meningitidis ProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5' and 3' side of the terminator stem are required for tight binding. However, the specific lengths of 5' and 3' RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2'-OH and 3'-OH groups of the 3' terminal ribose contribute to RNA binding by N. meningitidis ProQ. In summary, the minimal ProQ protein from N. meningitidis has generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.

Insights

Neisseria meningitidis ProQ, a minimal FinO-domain protein, binds RNA terminators via specific single-stranded sequences and ribose hydroxyl groups. Binding requirements vary slightly between different RNA ligands.

Area of Science:

Microbiology
Molecular Biology
RNA Biology

Background:

* Neisseria meningitidis ProQ is a minimal RNA-binding protein featuring a FinO domain.
* Understanding its RNA recognition mechanism is crucial for bacterial gene regulation.

Purpose of the Study:

* To investigate the RNA binding specificity of the minimal N. meningitidis ProQ protein.
* To identify key RNA features and sequences essential for ProQ-RNA interactions.

Main Methods:

* Comparative binding analysis of ProQ with seven natural RNA ligands.
* Site-directed mutagenesis of two specific RNA ligands (rpmG-3' and AniS).
* Characterization of RNA structural elements and chemical groups involved in binding.

Main Results:

* N. meningitidis ProQ binds the lower stem of intrinsic transcription terminator hairpins.
* Single-stranded 5' and 3' sequences flanking the terminator stem are critical for tight binding.
* Optimal binding depends on specific lengths of these flanking sequences and the 2'-OH/3'-OH groups of the 3' terminal ribose.

Conclusions:

* Minimal ProQ exhibits RNA binding requirements similar to other FinO-domain proteins.
* Subtle differences in RNA features dictate specific RNA recognition by N. meningitidis ProQ.
* The study elucidates the molecular basis of RNA recognition by a minimal FinO-domain protein.

Read full analysis

Keywords:

Neisseria ProQ RNA-binding proteins in bacteria bacterial regulatory RNA the FinO domain

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