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Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures.

bioRxiv : the preprint server for biology·2025
Same author

A riboswitch-controlled TerC family transporter Alx tunes intracellular manganese concentration in <i>Escherichia coli</i> at alkaline pH.

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Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures.

Christine Stephen1, Danea E Palmer1, Clarisa Bautista1

  • 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States.

Nucleic Acids Research
|June 11, 2025
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Summary
This summary is machine-generated.

Manganese riboswitches protect bacteria from toxicity. This study reveals how these RNA sensors fold and detect manganese, even during synthesis, and respond to pH changes.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Microbiology

Background:

  • Manganese riboswitches regulate bacterial manganese homeostasis by controlling the expression of manganese exporters.
  • Existing structural data of isolated aptamers do not fully explain ligand-induced conformational changes and communication with the expression platform.

Purpose of the Study:

  • To investigate the folding dynamics and manganese-sensing mechanisms of two distinct manganese riboswitches (mntP and alx) in Escherichia coli.
  • To elucidate the role of pH in modulating riboswitch function.
  • To understand how these riboswitches differentiate between manganese concentration and pH as environmental cues.

Main Methods:

  • Co-transcriptional RNA chemical probing was employed to visualize dynamic RNA folding intermediates.
  • Single-nucleotide resolution analysis was used to pinpoint the timing of riboswitching events during transcription.
  • Comparative analysis of mntP and alx riboswitches was performed to identify differences in folding and pH-dependence.

Main Results:

  • Manganese ion sampling by the RNA occurs prior to complete aptamer synthesis and folding.
  • The precise transcription window for manganese-dependent riboswitching was identified at single-nucleotide resolution.
  • Key differences in the folding pathways of the alx and mntP riboswitches were uncovered.
  • Riboswitch-specific pH effects were characterized, revealing differential sensing mechanisms.

Conclusions:

  • Bacterial manganese riboswitches exhibit dynamic folding processes, with metal ion binding initiating early in RNA synthesis.
  • The mntP and alx riboswitches display distinct folding mechanisms and respond differently to pH, enabling nuanced environmental sensing.
  • This work provides novel insights into the intricate mechanisms by which bacteria adapt to varying manganese and pH conditions.