Does the Genetic Code Have A Eukaryotic Origin?  

作　　者：Zhang Zhang Jun Yu 

机构地区：[1]CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences

出　　处：《Genomics, Proteomics & Bioinformatics》2013年第1期41-55,共15页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by grants from the National Basic Research Program (973 Program) (Grant No. 2011CB944100and 2011CB944101);National Natural Science Foundation of China (Grant No. 90919024);the Special Foundation Work Program, the Ministry of Science and Technology (Grant No.2009FY120100);the "100-Talent Program" of Chinese Academy of Sciences (Grant No. Y1SLXb1365);the National Programs for High Technology Research and Development(863 Program;Grant No. 2012AA020409) by the Ministry of Science and Technology of China

摘　　要：In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core ＂house-keeping＂ functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mech- anism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables^C and purine contents--of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity （% usage） is plotted as a function of CJC content variation. The analysis leads to a new pattern--the symmetric pattern--where the sensitivity ofpurine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN （valine） and CAN （CAR for asparagine and CAY for aspartic acid） and the most biased amino acid is valine （always over-estimated） followed by alanine （always under-estimated）. The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core ＂house-keeping＂ functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mech- anism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables^C and purine contents--of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity （% usage） is plotted as a function of CJC content variation. The analysis leads to a new pattern--the symmetric pattern--where the sensitivity ofpurine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN （valine） and CAN （CAR for asparagine and CAY for aspartic acid） and the most biased amino acid is valine （always over-estimated） followed by alanine （always under-estimated）. The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.

关 键 词：Genetic code Purine content Sensitivity CODON Amino acid 

分 类 号：Q343[生物学—遗传学]