title: Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes.
abstract: BACKGROUND
  Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported.
  
  
  RESULTS
  Based on an informatics method (SCUO) we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC3)2 + 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC3)2 + 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation.
  
  
  CONCLUSIONS
  The synonymous codon usage bias could be simply expressed as 1+ (p/2)log2(p/2) + ((1-p)/2)log2((l-p)/2), where p = GC3. The software we developed for measuring SCUO (codonO) is available at http://digbio.missouri.edu/~wanx/cu/codonO.
authors.affiliation: Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. wanx@missouri.edu
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Andris
authors.initials: A
authors.lastname: Kleinhofs
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D001482:Base Composition / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation / Q000706:statistics & numerical data; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D020862:GC Rich Sequence / Q000235:genetics; D005815:Genetic Code / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008957:Models, Genetic
chemical_list: D003062:Codon; D019641:DNA, Archaeal; D004269:DNA, Bacterial