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Nucleotide composition affects codon usage toward the 3'-end.

Fouad Zahdeh1,2, Liran Carmel1

  • 1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.

Plos One
|December 5, 2019
PubMed
Summary
This summary is machine-generated.

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Scientists found a universal trend of AT-rich codons at the 3' gene end across 91 species. This codon usage bias likely prevents RNA secondary structures that could hinder translation termination.

Area of Science:

  • Genetics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • The 3'-end of coding sequences exhibits codon usage bias.
  • Factors like translation efficiency, accuracy, and RNA folding are proposed causes.
  • The universality and primary drivers of this bias remain debated.

Purpose of the Study:

  • To quantify codon usage bias at gene ends across diverse species.
  • To investigate the universality of this bias and its underlying factors.
  • To determine the main determinants of 3'-end codon usage bias.

Main Methods:

  • Developed a novel measure for quantifying 3'-end codon usage bias.
  • Analyzed codon bias in 91 species from all three domains of life.
  • Characterized codons by features related to proposed influencing factors.

Related Experiment Videos

Main Results:

  • A universal trend favors AT-rich codons towards the gene's 3'-end.
  • This bias was observed across a wide range of species.
  • The observed trend correlates with avoiding RNA secondary structures near the stop codon.

Conclusions:

  • The 3'-end codon usage bias is a universal phenomenon.
  • Avoidance of RNA secondary structures near the stop codon is the likely explanation.
  • This mechanism likely optimizes translation termination efficiency.