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Codon influence on protein expression in E. coli correlates with mRNA levels.

Grégory Boël1,2,3, Reka Letso1,2, Helen Neely1,2

  • 1Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.

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Genetic code degeneracy influences protein expression by modulating mRNA degradation and protein elongation kinetics. Codon content, not just usage frequency, impacts gene expression levels in Escherichia coli.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • The genetic code's degeneracy allows multiple DNA sequences to code for the same protein, influencing gene expression.
  • The precise mechanisms by which synonymous codons affect protein and mRNA levels remain incompletely understood.

Purpose of the Study:

  • To investigate sequence features, particularly codon content, that influence protein expression levels.
  • To develop a metric for codon influence on gene expression and compare it with mRNA folding parameters.

Main Methods:

  • Analysis of 6,348 experiments using bacteriophage T7 polymerase for mRNA synthesis in Escherichia coli.
  • Application of logistic regression to derive a novel codon-influence metric.
  • Comparison of codon influence with genomic codon usage and mRNA folding parameters.

Main Results:

  • A new codon-influence metric showed weak correlation with codon usage but strong correlation with protein and mRNA concentrations and lifetimes.
  • Codon content was a stronger determinant of protein expression than mRNA folding, except for the initial ~16 codons.
  • Redesigned genes showed similar transcription but enhanced in vitro translation, with native inefficient sequences exhibiting reduced in vivo mRNA levels.

Conclusions:

  • Codon content significantly modulates protein expression by affecting the balance between protein elongation and mRNA degradation.
  • This kinetic competition is a key aspect of Escherichia coli physiology and translational regulation.