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Codon usage bias and environmental adaptation in microbial organisms.

Davide Arella1, Maddalena Dilucca2, Andrea Giansanti3,4

  • 1Department of Physics, Sapienza University of Rome, 00185, Rome, Italy. davidearella@gmail.com.

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Microbial codon usage bias influences cellular fitness and adaptation. Organisms with diverse lifestyles show reduced translational efficiency, highlighting strong translational selection shaping codon choices to match tRNA availability.

Keywords:
AdaptationArchaeaBacteriaCodon biasEnvironmenttRNA

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Area of Science:

  • Microbial Ecology
  • Genomics
  • Molecular Evolution

Background:

  • Synonymous codons are not used equally within genomes, a phenomenon termed codon usage bias.
  • Codon usage bias is linked to cellular fitness and the ecological strategies of microbes.

Purpose of the Study:

  • To investigate the relationship between codon usage bias, microbial lifestyles, and habitats.
  • To explore the role of translational efficiency in microbial adaptation to diverse environments.

Main Methods:

  • Analyzed codon usage bias (RSCU) and tRNA gene copy number (tGCN) in 615 microbial genomes.
  • Utilized Principal Component Analysis (PCA) to correlate traits with codon preferences.
  • Measured average tRNA adaptation index (tAI) to assess translational efficiency.

Main Results:

  • Species with similar traits and environments exhibit similar codon preferences and tRNA availability spectra.
  • Organisms thriving in multiple habitats, facultative microbes, mesophiles, and pathogens display reduced translational efficiency.
  • Synonymous codon choices are strongly influenced by translational selection to match tRNA availability based on lifestyle.

Conclusions:

  • Codon usage bias and translational efficiency are key factors in microbial adaptation to environmental conditions.
  • This study provides the first large-scale examination of codon bias and translational efficiency in microbial environmental adaptation.