On the Organizational Dynamics of the Genetic Code  

作　　者：Zhang Zhang Jun Yu 

机构地区：[1]Plant Stress Genomics Research Center, Division of Chemical and Life Sciences and Engineering, King AbduUah University of Science and Technology, Thuwa123955-6900, Saudi Arabia [2]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

出　　处：《Genomics, Proteomics & Bioinformatics》2011年第1期21-29,共9页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by a faculty fund from King Abdullah University of Science and Technology (http://www.kaust.edu.sa) awarded to JY

摘　　要：The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nu- cleotides--adenine, thymine, guanine and cytosine--according to their emergence in evolution, and apply the or- ganizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equiva- lent to a content-centric organization of the code and that codon and amino acid usages under different classifica- tion schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nu- cleotides--adenine, thymine, guanine and cytosine--according to their emergence in evolution, and apply the or- ganizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equiva- lent to a content-centric organization of the code and that codon and amino acid usages under different classifica- tion schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

关 键 词：genetic code CODON GC content purine content organizational dynamics compositional dynamics 

分 类 号：Q755[生物学—分子生物学] S859.796[农业科学—临床兽医学]