Evidence map›Paper›PMID 40199319›Full record

ArticleMolecular cell2025

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

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026
    Review
  2. Article
  3. Article
  4. Review
  5. Origin and adaptive evolutionary trajectory of the 3' UTR-derived sRNA UhpU in Enterobacteriaceae.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Narumon ThongdeeDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Miranda M AlanizDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Ekaterina SamatovaMax Planck Institute for Multidisciplinary Sciences, Department of Physical Biochemistry, 37077 Göttingen, Germany.
Aoshu ZhongDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Caroline EsnaultBioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Hongen ZhangBioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Ryan K DaleBioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
Marina V RodninaMax Planck Institute for Multidisciplinary Sciences, Department of Physical Biochemistry, 37077 Göttingen, Germany.
Gisela StorzDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA. Electronic address: storzg@mail.nih.gov.

Funding

Small Regulatory RNAsZIAHD001608 · NICHD · EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT · PI STORZ, GISELA · 2009 to 2025
$16.9M
Small, Noncoding RNAs and Small ORFSZ01HD001608 · NICHD · EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT · PI STORZ, GISELA · 1991 to 2008
$2.3M
Intramural NIH HHS Z01 HD001608Intramural NIH HHS ZIA HD001608
6 · The paper itself

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.

Indexed as

Escherichia coliEscherichia coli ProteinsOpen Reading FramesRNA, BacterialRNA, MessengerRNA, Small UntranslatedBase PairingBinding SitesDNA DamageGene Expression Regulation, BacterialNucleic Acid ConformationProtein BiosynthesisRibosomesEscherichia coli ProteinsRNA, BacterialRNA, MessengerRNA, Small UntranslatedArcZco-factor incorperationDNA damageDNA ligaseHemKHfqprotein foldingregulatory RNAstranslation elongation

Identifiers

PMID40199319
PMCPMC12051397

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.