A Unified Theory on Construction and Evolution of the Genetic Code

A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1,the redundancy distribution of codons in the genetic code obeys MD minimization principle; 2, the hydrophilic-hydrophobic distribution of amino acids on the code table is global MD (GMD) minimal; 3, the standard genetic code can be deduced from the adaptive minimization of GMD; 4, the variants of the standard genetic code can be explained quantitatively by use of GMD formalism and the general trend of the evolution is GMD non-increasing which reflects the selection on the code. We have demonstrated that the redundancy distribution of codons and the hydrophobic-hydrophilic (H-P) distribution of amino acids are robust in the code relative to the mutational parameter, and indicated that the GMD can be looked as a non-fitness function on the adaptive landscape. Finally, an important aspect on the symmetry of the code construction, the Yin-Yang duality is investigated. The Yin-Yang duality among codons affords a sound basis for understanding the H-P structure in the genetic code. The approximate universality of the canonical genetic code and the discoveries of various deviant codes in a wide range of organisms strongly reveal that the genetic code is still evolving. Several mechanisms on code evolution were proposed, for example, the codon capture and the ambiguous decoding by tRNA [Knight et al, 2001; Santos et al, 2004]. However, a unified theory still lacks for a full explanation of the genetic code evolution both in its high universality and various deviations. Evidently, the point is closely related to the construction of the code. The construction of the genetic code obeys some general rules that afford a basis for understanding the universality and changeability of the code. On the other hand, the error minimization property of the genetic code was analyzed by several authors [Di Giuilo et al, 1994; Freeland & Hurst, 1998]. But it is still unclear why the canonical genetic code takes the standard form with error non-minimized and what are the evolutionary constraints for deducing the standard code. In the article we emphasize the unified understanding of the code construction and code evolution. We shall indicate that the unification between code construction and code evolution can be achieved through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism for MD minimization. The materials are organized in the article as follows. In the first section we will review the mutational deterioration theory on the redundancy distribution in the genetic code. Then the adaptive minimization of global mutational deterioration and the accuracy of the genetic code will be discussed in the second section. Next, in the third section, we will study the