Synonymous codon usage defines functional gene families

Abstract

The degeneracy of the genetic code is increasingly recognized for roles in regulating translation rate, protein folding, and cell response. However, the functional genomics of codon usage patterns remains poorly defined. We previously showed that prokaryotic and eukaryotic cells respond to individual stresses by uniquely reprogramming the tRNA pool and the dozens of tRNA modifications comprising the tRNA epitranscriptome to cause selective translation of mRNAs from codon-biased stress response genes. Here, we tested the hypothesis that functional gene families have distinct values of codon bias in the Saccharomyces cerevisiae genome by modeling isoacceptor codon distributions using a new approach—analysis of synonymous codon signatures (ASCS).