A Unified Theory on Construction and Evolution of the Genetic Code
📝 Abstract
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.
💡 Analysis
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.
📄 Content
A Unified Theory on Construction and Evolution of the Genetic Code
Liaofu Luo*
Laboratory of Theoretical Biophysics, Faculty of Physical Science and Technology,
Inner Mongolia University, Hohhot 010021, China
*Email address: lolfcm@mail.imu.edu.cn
Abstract
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
1 evolvability of the genetic code from the point of unified mutational deterioration theory. Finally, an important aspect on the symmetry of the code construction, namely, the Yin-Yang duality in the genetic code will be investigated in the last section.
- Mutational deterioration theory on the redundancy distribution in the genetic code
The constancy of the genetic code among different organisms is one of the most striking, interesting, and challenging phenomena in life. The mathematical relation behind the constancy intrigued many biologists and physicists [di Giulio, 1997; Trifonov et al, 1997; Freeland et al, 1998; Maeshiro et al, 1998; Judson et al, 1999; Jimenez-Montano, 1999; Knight et al, 1999; Knight et al, 2000; Freeland et al, 2000; Weberndorfer et al, 2003; Chechetkin, 2003; Copley et al, 2005; Yang, 2005; Goodarzi et al, 2005; Chechetkin, 2006]. Historically, there are two different kinds of theories regarding the origin and evolution of the genetic code [Yockey, 1992; Freeland et al, 2003]. The first approach originated from Gamow [1954]. His “Diamond code” model opened up a way to explain the origin of the universal amino acid code through the stereochemical interactions between codons or anticodons and amino acids [Woese et al, 1966; Woese, 1967; and recently, Knight et al, 2001; Yarus, 2000]. The second approach is called “frozen accident” theory. The term “frozen accident”, used firstly by Crick, means that all living organisms evolved from an ancient single ancestor, and after the evolutionary expansion of the descendants started, changes in the amino acid assignments of codons were not possible [Crick, 1968]. In fact, the two theories can explain part of
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