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Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for

Alexander L Cope1, Robert L Hettich2, Michael A Gilchrist3

  • 1Genome Science and Technology, University of Tennessee, Knoxville, United States of America.

Biochimica Et Biophysica Acta. Biomembranes
|October 4, 2018
PubMed
Summary

Signal peptides in E. coli do not show a preference for inefficient codons, contrary to previous hypotheses. Accounting for gene expression and amino acid usage reveals codon usage patterns are similar to cytoplasmic proteins.

Keywords:
AdaptationistCodon usage biasProtein secretionProtein synthesisSignal peptides

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genetics

Background:

  • The Sec secretion pathway is essential for protein transport across cellular membranes in all life forms.
  • Signal peptides, located at the N-terminus of secreted proteins, possess unique physicochemical properties.
  • Previous studies suggested signal peptides use translationally inefficient codons, potentially optimizing protein secretion.

Purpose of the Study:

  • To investigate codon usage bias (CUB) in *E. coli* signal peptides.
  • To test the hypothesis that inefficient codons in signal peptides enhance protein secretion efficiency.
  • To differentiate between selection and mutation bias in shaping CUB.

Main Methods:

  • Analysis of *E. coli* signal peptides using Codon Adaptation Index (CAI) and tRNA Adaptation Index (tAI).
  • Application of the Ribosomal Overhead Cost formulation of the Stochastic Evolutionary Model of Protein Production Rates (ROC-SEMPPR).
  • Simulations to control for amino acid usage and gene expression effects.

Main Results:

  • CAI and tAI analyses initially suggested inefficient codon usage in signal peptides compared to cytoplasmic proteins.
  • Simulations indicated these differences disappeared when accounting for amino acid usage and gene expression.
  • ROC-SEMPPR analysis revealed CUB in signal peptides is indistinguishable from 5'-ends of cytoplasmic proteins.
  • CUB is weaker at the 5'-ends of genes compared to later segments.

Conclusions:

  • The hypothesized preference for inefficient codons in signal peptides is not supported when accounting for confounding factors.
  • Population genetics models like ROC-SEMPPR are crucial for accurate interpretation of CUB data.
  • Failure to consider mutation bias and gene expression effects can lead to misinterpretation of codon usage patterns.