title: A content-centric organization of the genetic code.
abstract: The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively. For prokaryotic genomes, when the genomic GC content increases, their amino acid contents tend to be restricted to the GC-rich quarter and the purine-content insensitive half, where all codons are fourfold degenerate and relatively mutation-tolerant. Conversely, when the genomic GC content decreases, most of the codons retract to the AU-rich quarter and the purine-content sensitive half; most of the codons not only remain encoding physico-chemically diversified amino acids but also vary when transversion (between purine and pyrimidine) happens. Amino acids with sixfold-degenerate codons are distributed into all four quarters and across the two halves; their fourfold-degenerate codons are all partitioned into the purine-insensitive half in favorite of robustness against mutations. The features manifested in the rearranged codon table explain most of the intrinsic relationship between protein coding sequences (the informational content) and amino acid compositions (the functional content). The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physico-chemical properties.
authors.affiliation: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China. junyu@genomics.org.cn
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000596:Amino Acids / Q000235:genetics; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D004247:DNA / Q000235:genetics; D005815:Genetic Code / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D009154:Mutation / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D000596:Amino Acids; D003062:Codon; D004247:DNA