title: Gradients in nucleotide and codon usage along Escherichia coli genes.
abstract: The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.
authors.affiliation: Department of Molecular Evolution, EBC, Uppsala University, Norbyvägen 18C, SE-75236, Uppsala, Sweden.
authors.forename: S D
authors.initials: SD
authors.lastname: Hooper
authors.forename: O G
authors.initials: OG
authors.lastname: Berg
mesh_terms: D000596:Amino Acids / Q000032:analysis; D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D003062:Codon; D004926:Escherichia coli / Q000235:genetics*; D016368:Frameshift Mutation; D005798:Genes, Bacterial; D008565:Membrane Proteins / Q000235:genetics; D020125:Mutation, Missense; D009711:Nucleotides / Q000378:metabolism*; D014176:Protein Biosynthesis; D013728:Terminator Regions, Genetic
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D003062:Codon; D008565:Membrane Proteins; D009711:Nucleotides