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Related Experiment Videos

Codon contexts from weakly expressed genes reduce expression in vivo.

L S Folley1, M Yarus

  • 1Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309.

Journal of Molecular Biology
|October 5, 1989
PubMed
Summary
This summary is machine-generated.

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Codon context near genes influences gene expression levels in Escherichia coli. Specific nucleotide sequences (contexts) near codons are selected to reduce gene expression, impacting protein production.

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Nucleotide sequences surrounding codons in Escherichia coli genes exhibit non-random patterns.
  • These codon context biases are more pronounced in weakly expressed genes compared to highly expressed genes.
  • Previous research suggested these contexts are selected to regulate gene expression levels.

Purpose of the Study:

  • To experimentally compare the expression levels of lacZ genes with different codon contexts.
  • To investigate the mechanism behind context-dependent gene expression regulation.
  • To differentiate between models of translational regulation, including dropoff, interference, and polarity.

Main Methods:

  • Constructed lacZ genes with two variants: a 'low variant' mimicking weak gene contexts and a 'high variant' mimicking strong gene contexts.

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  • Ensured both variants had identical nucleotide and codon composition, differing only in specific nucleotide permutations at codon:codon interfaces.
  • Manipulated ribosome binding sites to alter ribosome density and initiation frequency, and analyzed transcriptional termination.

    • Main Results:

    • The 'low variant' lacZ gene consistently showed significantly lower expression than the 'high variant' across different mRNA contexts.
    • The observed context effect was dependent on the correct translational frame and influenced by other mRNA features like transcriptional pauses.
    • Expression differences were eliminated by altering ribosome initiation frequency, supporting a polarity model where slow translation induces transcriptional termination.

    Conclusions:

    • Codon contexts play a significant role in regulating gene expression levels, potentially through context-induced polarity.
    • The interplay between translational initiation, elongation, and transcriptional elongation rates influences overall gene expression.
    • Context-induced polarity is likely a mechanism employed in genes selected for low and reproducible product levels.