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Evolutionary switches between two serine codon sets are driven by selection.

Igor B Rogozin1, Frida Belinky1, Vladimir Pavlenko1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.

Proceedings of the National Academy of Sciences of the United States of America
|November 2, 2016
PubMed
Summary
This summary is machine-generated.

Serine codon evolution involves two nucleotide substitutions, often via threonine or cysteine intermediates, driven by purifying selection. This process leads to frequent amino acid replacement reversals and homoplasy at short evolutionary distances.

Keywords:
homoplasypositive selectionpurifying selectionserine codon setstandem nucleotide substitutions

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genetics

Background:

  • Serine is unique, encoded by two disjoint codon sets requiring double nucleotide substitutions for switching.
  • Prior research suggested simultaneous double nucleotide substitutions for conserved serine codons.

Purpose of the Study:

  • To reconstruct the genome-wide evolution of serine codons across diverse prokaryotes and eukaryotes.
  • To investigate the mechanisms and selective pressures driving serine codon set switches.

Main Methods:

  • Genome-wide reconstruction of serine codon evolution.
  • Analysis of codon usage in triplets of closely related prokaryotic and eukaryotic species.

Main Results:

  • Most serine codon set switches occur via two consecutive nucleotide substitutions, not simultaneous ones.
  • These switches proceed through threonine or cysteine intermediates and are selection-driven.
  • Purifying selection favors an initial deleterious substitution followed by a compensatory one.

Conclusions:

  • Serine codon evolution is shaped by strong purifying selection, involving sequential, compensatory nucleotide substitutions.
  • This mechanism results in frequent reversals of amino acid replacements and widespread homoplasy.
  • Understanding these evolutionary dynamics is crucial for interpreting protein evolution and genetic data.