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Related Experiment Videos

Tracing specific synonymous codon-secondary structure correlations through evolution.

Matej Oresic1, Michael Dehn, Daniel Korenblum

  • 1Department of Molecular Biology and Genetics, Cornell University, 265 Biotechnology Building, Ithaca, NY 14853, USA.

Journal of Molecular Evolution
|March 29, 2003
PubMed
Summary
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Vertebrate proteins show a preference for GAU codons at alpha-helix N-termini, unlike bacteria, yeast, or plants. This codon bias may aid co-translational folding, suggesting a novel evolutionary mechanism.

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Previous studies identified a preference for GAU over GAC codons for aspartate at alpha-helix N-termini in human proteins, but not in E. coli.
  • This codon bias was specific to the N-termini of alpha-helices.

Purpose of the Study:

  • To investigate if the GAU codon preference at alpha-helix N-termini represents a general difference between eukaryotes and prokaryotes.
  • To analyze codon usage in various organisms, including mammals, vertebrates, S. cerevisiae, and plants.

Main Methods:

  • Comparative analysis of protein and coding sequences across different species.
  • Statistical analysis to assess the correlation between GAU codons and alpha-helix N-termini.
  • Exclusion of proteins known to express correctly in prokaryotic systems to investigate the level of correlation induction.

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Main Results:

  • A strong GAU-alpha-helix correlation was observed in mammalian and vertebrate proteins, similar to human proteins.
  • The correlation was significantly weaker or absent in S. cerevisiae and plant proteins.
  • The correlation was enhanced when excluding proteins expressed in prokaryotic systems, suggesting a post-transcriptional or translational mechanism.
  • Vertebrate correlations were strong enough to potentially improve alpha-helix N-terminus prediction.

Conclusions:

  • The GAU codon preference at alpha-helix N-termini is conserved in vertebrates but not in yeast or plants, indicating a eukaryotic-specific or vertebrate-specific phenomenon.
  • The findings suggest the correlation is induced during protein translation and folding, not at the DNA level.
  • This codon bias may represent a novel evolutionary selection mechanism, potentially facilitating co-translational folding in vertebrates.