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Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those

Keiichi Homma1, Tamotsu Noguchi2, Satoshi Fukuchi3

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Codon usage in eukaryotic genes is less optimized in intrinsically disordered regions (IDRs) compared to structural domains (SDs). This suggests IDRs can tolerate more translational errors due to their lack of fixed structure.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Highly expressed genes typically exhibit optimized codon usage, potentially enhancing translational accuracy.
  • Eukaryotic proteins contain intrinsically disordered regions (IDRs) lacking fixed structures, contrasting with structured domains (SDs).

Purpose of the Study:

  • To investigate whether codon usage differs between intrinsically disordered regions (IDRs) and structural domains (SDs) in eukaryotic proteins.
  • To determine if the structural flexibility of IDRs influences codon optimization and translational error tolerance.

Main Methods:

  • Analyzed codon usage across all genes in seven eukaryotes using tRNA adaptation index and codon adaptation index.
  • Accounted for varying amino acid compositions in different protein regions when calculating expected adaptation indices.
  • Compared observed codon adaptation indices with expected values for both IDRs and SDs.

Main Results:

  • Codon usage is significantly less optimized in gene regions encoding IDRs than in regions encoding SDs.
  • This pattern holds true regardless of the location of IDRs within the protein (N-terminus, middle, or C-terminus).
  • The findings were consistent across two different algorithms used for predicting intrinsically disordered regions.

Conclusions:

  • Intrinsically disordered regions (IDRs) exhibit less optimized codon usage than structural domains (SDs).
  • This difference supports the hypothesis that IDRs are more tolerant of translational errors due to their lack of structural constraints.
  • Codon usage patterns in eukaryotes are influenced by protein structural properties and their impact on translation fidelity.