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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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A role for REP sequences in regulating translation.

Wenxing Liang1, Kenneth E Rudd2, Murray P Deutscher2

  • 1Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China.

Molecular Cell
|April 21, 2015
PubMed
Summary
This summary is machine-generated.

Repetitive extragenic palindromic (REP) sequences near termination codons downregulate translation by stalling ribosomes. This mechanism, affecting many Escherichia coli genes, impacts mRNA cleavage and trans-translation.

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Area of Science:

  • Molecular Biology
  • Bacterial Genetics
  • Gene Regulation

Background:

  • Repetitive extragenic palindromic (REP) sequences are conserved DNA elements in bacteria, often located downstream of genes.
  • Their precise physiological function, particularly in mRNA regulation, has been largely unknown.
  • These sequences form stable secondary structures in mRNA, suggesting a role in post-transcriptional control.

Purpose of the Study:

  • To elucidate the physiological role of REP sequences in gene expression.
  • To investigate the impact of REP sequence proximity to termination codons on translation.
  • To understand the downstream consequences of REP-mediated translational regulation.

Main Methods:

  • Analysis of mRNA secondary structures formed by REP sequences.
  • Reporter gene assays to measure translational efficiency.
  • Investigating ribosome-mRNA interactions and mRNA cleavage.
  • Genetic manipulation, including overexpression of RNA helicases and UV stress induction.

Main Results:

  • REP sequences downregulate translation when located within 15 nucleotides (nt) of a termination codon.
  • A spacing of 16 nt or more abolished the translational repression effect.
  • REP sequences induce ribosome stalling, leading to mRNA cleavage and activation of trans-translation.
  • Regulation by REP sequences in the nrdAB gene model was sensitive to RNA helicase activity and UV stress.

Conclusions:

  • REP sequences act as a regulatory element that can stall ribosomes near termination codons, thereby downregulating translation.
  • This mechanism is position-dependent, requiring close proximity to the stop codon.
  • The findings reveal a significant regulatory pathway impacting a substantial proportion of Escherichia coli genes, influencing mRNA stability and stress response.