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Coding-sequence determinants of gene expression in Escherichia coli.

Grzegorz Kudla1, Andrew W Murray, David Tollervey

  • 1Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.

Science (New York, N.Y.)
|April 11, 2009
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Summary

Synonymous mutations impact gene expression by altering messenger RNA (mRNA) folding near the ribosomal binding site, not by codon bias. This mRNA folding stability significantly influences protein levels and translation initiation rates.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Synonymous mutations, which do not change the amino acid sequence of a protein, can still affect gene expression levels.
  • The precise mechanisms by which synonymous mutations influence gene expression are not fully understood.
  • Investigating these mechanisms is crucial for understanding gene regulation and protein production.

Purpose of the Study:

  • To investigate how synonymous mutations influence gene expression.
  • To determine the factors that contribute to variations in protein levels despite identical amino acid sequences.
  • To elucidate the roles of mRNA stability, folding, and codon bias in gene expression.

Main Methods:

  • Engineered a synthetic library of 154 genes encoding the same green fluorescent protein (GFP) with random synonymous mutations.
  • Expressed the synthetic gene library in Escherichia coli.
  • Measured GFP protein levels, messenger RNA (mRNA) levels, mRNA degradation rates, and bacterial growth rates.
  • Analyzed correlations between gene expression, mRNA folding stability, codon bias, and translation initiation.

Main Results:

  • GFP protein levels varied 250-fold across the library.
  • Significant variations were observed in mRNA levels, degradation patterns, and bacterial growth rates.
  • Codon bias did not correlate with gene expression levels.
  • mRNA folding stability near the ribosomal binding site explained over 50% of the variation in protein levels.
  • mRNA folding and translation initiation rates were identified as predominant factors in shaping individual gene expression.

Conclusions:

  • Synonymous mutations significantly impact gene expression through mechanisms beyond codon bias.
  • mRNA folding stability near the ribosomal binding site is a key determinant of protein levels.
  • Translation initiation rates, influenced by mRNA structure, play a predominant role in gene expression.
  • While codon bias affects global translation efficiency and cellular fitness, mRNA folding is critical for individual gene expression levels.