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Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria.

Emily A Seward1, Steven Kelly2

  • 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.

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Summary
This summary is machine-generated.

Bacterial genes optimize codon use for both efficiency and cost, with transfer RNA gene copy number influencing this trade-off. This multi-objective selection impacts molecular evolution and gene composition.

Keywords:
BacteriaCodon biasGene evolutionMolecular evolutionNatural selectionSynonymous codon useTranscript optimizationTranslational efficiency

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Synonymous codons are not equally utilized, leading to biased codon usage that varies across organisms.
  • Selection pressures include increasing translational efficiency and decreasing biosynthetic cost, but their interaction and evolutionary impact are unclear.

Purpose of the Study:

  • Investigate the multi-objective selection driving codon use optimization in bacteria.
  • Determine how selection for transcript biosynthetic cost and translational efficiency interact.
  • Understand the effect of these factors on molecular sequence evolution.

Main Methods:

  • Analyzed 1320 bacterial genomes.
  • Examined selection pressures on codon usage.
  • Assessed the influence of transfer RNA gene copy number on codon cost-efficiency trade-offs.

Main Results:

  • Bacterial genes undergo multi-objective selection for codon use, balancing biosynthetic cost and translational efficiency.
  • Transfer RNA gene copy number modifies the cost-efficiency balance, often creating opposing selection pressures.
  • Highly optimized genes exhibit reduced rates of synonymous and non-synonymous mutation.

Conclusions:

  • Selection-driven optimization of codon use provides a mechanistic explanation for gene-specific evolutionary rate variation.
  • Optimization of messenger RNA synthesis resource allocation is crucial for gene evolution and composition.