Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests The authors declare no competing interests.

References

    1. Duval M, Simonetti A, Caldelari I, and Marzi S (2015). Multiple ways to regulate translation initiation in bacteria: mechanisms, regulatory circuits, dynamics. Biochimie 114, 18–29. doi: 10.1016/j.biochi.2015.03.007. - DOI - PubMed
    1. Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, and Puglisi JD (2018). How messenger RNA and nascent chain sequences regulate translation elongation. Annu. Rev. Biochem 87, 421–449. doi: 10.1146/annurev-biochem-060815-014818. - DOI - PMC - PubMed
    1. Chaney JL, and Clark PL (2015). Roles for synonymous codon usage in protein biogenesis. Annu. Rev. Biophys 44, 143–166. doi: 10.1146/annurev-biophys-060414-034333. - DOI - PubMed
    1. Stein KC, and Frydman J (2019). The stop-and-go traffic regulating protein biogenesis: How translation kinetics controls proteostasis. J. Biol. Chem 294, 2076–2084. doi: 10.1074/jbc.REV118.002814. - DOI - PMC - PubMed
    1. Samatova E, Daberger J, Liutkute M, and Rodnina MV (2021). Translational control by ribosome pausing in bacteria: how a non-uniform pace of translation affects protein production and folding. Front. Microbiol 11, 619430. doi: 10.3389/fmicb.2020.619430. - DOI - PMC - PubMed

MeSH terms

LinkOut - more resources