title: The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins.
abstract: BACKGROUND
  Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding of selective forces and their compositional determinants, the very nature of underlying mutational biases remains unclear.
  
  
  RESULTS
  We explore here a fundamental tradeoff, which analytically describes mutual adjustment of the nucleotide and amino acid compositions and its possible effect on the mutational biases. The tradeoff is determined by the interplay between the genetic code, optimization of the codon entropy, and demands on the structure and stability of nucleic acids and proteins.
  
  
  CONCLUSIONS
  The tradeoff is the unifying property of all prokaryotes regardless of the differences in their phylogenies, life styles, and extreme environments. It underlies mutational biases characteristic for genomes with different nucleotide and amino acid compositions, providing foundation for evolution and adaptation.
authors.affiliation: Computational Biology Unit and Department of Informatics, University of Bergen, N-5008, Bergen, Norway. gonceare@ncbi.nlm.nih.gov.|Current address: Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, USA. gonceare@ncbi.nlm.nih.gov.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goncearenco
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. igorb@bii.a-star.edu.sg.|Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117597, Singapore, Singapore. igorb@bii.a-star.edu.sg.
authors.forename: Igor N
authors.initials: IN
authors.lastname: Berezovsky
mesh_terms: D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D001482:Base Composition; D003062:Codon / Q000235:genetics; D019277:Entropy; D005815:Genetic Code; D016678:Genome; D008957:Models, Genetic; D009154:Mutation; D020543:Proteome
chemical_list: D003062:Codon; D020543:Proteome