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Differences in codon bias cannot explain differences in translational power among microbes.

Les Dethlefsen1, Thomas M Schmidt

  • 1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA. dethlefs@stanford.edu

BMC Bioinformatics
|January 8, 2005
PubMed
Summary
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Codon bias significantly boosts protein synthesis rates in microbes like E. coli, but cannot fully explain large differences in translational power between rapidly and slowly growing species. Other factors in the translational machinery likely play a key role.

Area of Science:

  • Microbiology
  • Molecular Biology
  • Systems Biology

Background:

  • Translational power, the rate of protein synthesis relative to the cellular investment in translation machinery, varies significantly across microbial species.
  • Rapidly growing microbes generally exhibit higher translational power than slowly growing ones.
  • Synonymous codon bias is a known factor influencing translational power, with correlations observed in fast-growing bacteria like E. coli.

Purpose of the Study:

  • To investigate whether differences in codon bias alone can account for the observed variations in translational power among microbes.
  • To quantify the contribution of codon bias to translational rate in E. coli compared to hypothetical strains with varying codon bias.
  • To determine if selection for translational power drives codon bias in all microbial growth conditions.

Related Experiment Videos

Main Methods:

  • Reanalysis of published literature data on microbial translational power and codon bias.
  • Development of an empirically-based mathematical model using codon-specific in vivo translation rates.
  • Comparison of estimated translation rates between E. coli and a hypothetical strain lacking codon bias.

Main Results:

  • Translational power can differ by over five-fold between E. coli and slowly growing microbes.
  • Codon bias in E. coli can increase translation rate by at most 60% under realistic assumptions, and up to double under exaggerated assumptions.
  • The effect of codon bias is insufficient to explain the full range of observed translational power differences.

Conclusions:

  • While codon bias enhances translational power, it is not the sole or primary driver of large differences in this metric across microbial species.
  • Significant variations in translational power suggest underlying differences in the translational machinery itself among microbes.
  • Further research is needed to elucidate the non-codon bias factors contributing to differential translational performance in bacteria and archaea.