Jiménez-Montaño Miguel Angel
Division of Mathematics, Science, and Technology, Parker Building, Nova Southeastern University, Fort Lauderdale, FL 33314-7796, USA.
Biosystems. 2009 Nov;98(2):105-14. doi: 10.1016/j.biosystems.2009.07.006. Epub 2009 Jul 28.
We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.
我们描述了一种遗传密码的紧凑表示形式,它将密码表分解为四重奏。它代表了遗传语言的“最小语法”。它由RNA碱基和密码子双峰的克莱因四元群结构证明是合理的。碱基列向量与相应行向量V(T)=(C G U A)的外积矩阵,被视为信号向量,具有由作用于双峰AA的KxK碱基变换群的四个陪集组成的块结构。这个矩阵,转换为弱/强(W/S)和嘌呤/嘧啶(R/Y)核苷酸类别,会导致一个在不同区域有混合和非混合家族的密码表。它们之间的一个基本区别是非可交换的(R/Y)双峰:AC/CA、GU/UG。我们用模乘法群描述了标准密码中的简并性和异常密码中的系统变化。我们说明了表征四重奏中突变的二进制子码。我们引入了一个决策树来预测对应于每个密码子的tRNA识别模式,并将我们的结果与Jestin和Soulé [Jestin, J.-L., Soulé, C., 2007. 遗传密码中碱基替换的对称性预测tRNA的2'或3'氨酰化。J. Theor. Biol. 247, 391 - 394] 的相关发现,以及Delarue [Delarue, M., 2007. 密码子分配中的不对称基本规则:通过连续二进制选择快速早期进化遗传密码的可能线索。RNA 13, 161 - 169] 和Rodin与Rodin [Rodin, S.N., Rodin, A.S., 2008. 关于遗传密码的起源:其在tRNA和氨酰 - tRNA合成酶中的原始互补性特征。Heredity 100, 341 - 355] 对密码表的重新排列进行比较。