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. 2025 May 1;85(9):1824-1837.e7.
doi: 10.1016/j.molcel.2025.03.014. Epub 2025 Apr 7.

Modulation of protein activity by small RNA base pairing internal to coding sequences

Narumon Thongdee  1 , Miranda M Alaniz  1 , Ekaterina Samatova  2 , Aoshu Zhong  1 , Caroline Esnault  3 , Hongen Zhang  3 , Ryan K Dale  3 , Marina V Rodnina  2 , Gisela Storz  4
Affiliations

Modulation of protein activity by small RNA base pairing internal to coding sequences

Narumon Thongdee et al. Mol Cell. .

Abstract

Most characterized interactions between bacterial small RNAs (sRNAs) and their target mRNAs occur near ribosome binding sites, resulting in changes in translation initiation or target mRNA decay. To understand the consequences of sRNA pairing internal to coding sequences detected by global RNA-RNA interactome approaches, we examined the impact of sRNA overexpression on seven target proteins. Overexpression of the sRNA led to decreased target protein levels for two pairs, but there were no differences for the others. By further examining ArcZ-ligA and ArcZ-hemK, we discovered that ArcZ pairing with the mRNAs leads to translation pausing and increased protein activity. A ligA point mutation that eliminates sRNA pairing resulted in increased sensitivity to DNA damage, revealing the physiological consequences of the regulation. Thus, regulatory RNA pairing in coding sequences can locally slow translation elongation, likely impacting co-translational protein folding and allowing improved incorporation of co-factors or more optimal folding under specific conditions.

Keywords: ArcZ; DNA damage; DNA ligase; HemK; Hfq; co-factor incorperation; protein folding; regulatory RNAs; translation elongation.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

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