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Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.

Shira Fisher1, Hanah Margalit2

  • 1Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.

RNA (New York, N.Y.)
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PubMed
Summary
This summary is machine-generated.

Bacterial small RNAs (sRNAs) regulate genes by binding to messenger RNAs (mRNAs). This study found that conserved sRNA binding sites within coding sequences favor frequent codons, suggesting evolutionary selection for efficient gene regulation.

Keywords:
base-pairingconservationreading framesmall RNA

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Bacterial small RNAs (sRNAs) are key regulators of gene expression, primarily through base pairing with target mRNAs.
  • While initially studied in 5' untranslated regions, sRNA binding sites are now recognized within protein-coding sequences, indicating novel regulatory roles.
  • The evolutionary maintenance and frameshifting of these intragenic sRNA binding sites remain poorly understood.

Purpose of the Study:

  • To investigate the evolutionary pressures and frameshifting mechanisms governing bacterial small RNA binding sites within coding sequences.
  • To identify conserved, functionally important positions within these intragenic sRNA binding sites.
  • To explore the interplay between codon usage bias, evolutionary conservation, and sRNA-mRNA interactions.

Main Methods:

  • Utilized RIL-seq data to identify prime sRNA binding positions within coding sequences, defined by high conservation (≥95%) within binding site motifs.
  • Analyzed the relationship between prime binding positions, reading frame, and codon usage frequency.
  • Performed cross-genome conservation analysis across Enterobacterales to assess the maintenance of base pairing interactions.

Main Results:

  • Prime sRNA binding positions within coding sequences were found to align with the reading frame and correspond to frequently used codons, exceeding random expectations.
  • Codon usage bias and evolutionary pressures appear to influence the establishment and maintenance of these intragenic binding sites.
  • While some positions showed conservation of base pairing, degeneracy of the genetic code sometimes necessitated compensation by other positions to maintain sufficient base pairing interactions.

Conclusions:

  • Intragenic sRNA binding sites are shaped by evolutionary selection, favoring frequent codons to enhance sRNA-mRNA encounter probability.
  • The maintenance of sRNA-target interactions relies on a combination of conserved interacting positions and sufficient overall base pairing, despite challenges posed by genetic code degeneracy.
  • Distinct interacting positions and an adequate number of base pairs are crucial for sustaining functional sRNA-target interactions within bacterial coding sequences.