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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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Estimating translational selection in eukaryotic genomes.

Mario dos Reis1, Lorenz Wernisch

  • 1School of Crystallography, Birkbeck College, London, UK. mdosrei@nimr.mrc.ac.uk

Molecular Biology and Evolution
|November 27, 2008
PubMed
Summary
This summary is machine-generated.

Natural selection influences codon usage bias across eukaryotic genomes, with selection strength linked to gene expression levels. Population size plays a key role in translational selection efficiency.

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Area of Science:

  • Population genetics
  • Genomics
  • Molecular evolution

Background:

  • Natural selection impacts codon usage bias in prokaryotic and eukaryotic genomes.
  • Estimating selection on codon usage is challenging due to small selection coefficients.

Purpose of the Study:

  • To measure the strength of selected codon usage bias (S) in 10 eukaryotic genomes using a population genetics model.
  • To investigate the relationship between selection strength, gene expression, and population size.

Main Methods:

  • Employed a population genetics model to estimate selection coefficients (S) for codon usage bias.
  • Analyzed 10 eukaryotic genomes, classifying orthologous genes by expression levels.
  • Compared estimated S values with empirical population size estimates.

Main Results:

  • Selection strength (S) is strongly correlated with gene expression levels.
  • Fungi genomes exhibit the highest S values, followed by invertebrates and plants.
  • Mammalian genomes (human, mouse) show low S values for highly expressed genes, potentially due to methodological limitations.

Conclusions:

  • Reliable estimation of codon usage selection requires analyzing genes with similar expression levels.
  • Population size significantly influences the effectiveness of translational selection.
  • Codon usage bias varies across eukaryotic lineages, with fungi showing the strongest selection.