The chemistry of lifes origin and genes evolution
Introduction: Genes are general biomarkers for the origin and evolution of all living species. Since it was cracked down five decades ago, the molecular basis for the genetic code shared by all organisms remains a conceptual challenge to scientific endeavors and has fascinated scientists across numerous disciplinary fields, although three early hypothesis including frozen accident, stereochemical principle(Crick, 1968)1 physicochemical principle(Woese, 1965) 2 and co-evolution (Wong, 1975) 3 are available concerning its origin and evolution. As one of the major components in the Natures complexity and integrity, it is an amalgamation of the concepts mat provide the foundation for the disciplines of physical science, mathematics and engineering, and offer ample opportunity for exchanging opinions with experts in heterogeneous areas. In this study, an organic chemistry approach is introduced aiming at elucidating the organizational features, the molecular versus atomic information logic underlying the genetic coding contents, and their intrinsic relations to the origin and evolution of the genetic code and life (Yang, 2001, 2004,2005).4-7Methods: First, physical organic chemistry principle combined with synthetic organic chemistry principle are applied to explore how chemical structures of both nucleobases and amino acids may have played a role in shaping the genetic code (Tab.1).Upon a systematic analysis of the structural regularity in RNA nucleobases, we invoked the chemical parameters, I,e., the covalent bonding sp2 hybrid of the nitrogen atoms, which are U(0), C(1), G(2) and A(3), as a distinct determinative measure for empirical stereo-electronic property in listing the genetic code in the UCGA succession. Results revealed that amino acid hydropathy correlates strongly with the sp2 nitrogen atom numbers in nucleobases rather than with the overall electronic property such as redox potentials of the bases, reflecting that stereo-electronic property of bases may play a role. In the rearranged code table, five simple but stereo-structurally distinctive amino acids (Gly, Pro, Val, Thr and Ala) and their codon quartets form a crossed intersection core. Secondly, a re-categorization of the amino acids according to their β-carbon stereochemistry, verified by charge density (at β-carbon) calculation using quantum mechanics, results in five groups of stereo-structurally distinctive amino acids, the group leaders of which are Gly, Pro, Val. Thr and Ala, remarkably overlapping the above core. These two observations provide empirical arguments for a contention that a frozen core could have formed at a certain evolutionary stage. The possible existence of this primordial codon core is in conformity with a previous evolutionary model whereby stereochemical interactions may have shaped the code (Tab.1).Based on the above newly suggested primordial codon core, novel three-dimensional displays and Hamilton graphs for the genetic code framework in a UCGA succession were invented using 16 vertices (nodes) to represent the 16 genetic code doublets, a 16-vertex genetic network comprising of 32 arcs linking 16 vertices of order 4 was obtained. Subsequently, a topological method was carried out for a solid geometric investigation to examine the atom contents and organizational properties of the system, revealing a molecular versus atomic information logic behind the genetic coding contents, which are constrained by two evolutionary axes and the Fibonacci-lucas sequence.Results: (1) The first identification of the polyhedral D2h spherical symmetry (viral symmery) AB4C6B4A inherent in the genetic code. From its isoform Hamiltonian graph display, topological transformations allowed us to have established that the internal relation within the 64 genetic codons and the degeneracy of codons can be explicitly described within the unprecedented framework of a quasi-28-gon, its symmetry is similar to simple spherical viruses (Fig. 1).(2) Combining their group graph features with chemical structural properties of both nucleobases and amino acid side chains lead to the discovery of two evolutionary axes (from simple to complex, from symmetry to symmetry breaking) as displayed by bom the function and structural diversity of amino acids, and coding degeneracy), which are consistent with two distinct classes of 20 aminoacyl-tRNA synthetases (AARS) used in protein translation. A comprehensive study of the carbon atom numbers in the amino acid side chains revealed that the quasi-28-gon organization is inherently associated with two evolutionary axes, evidently from simple to complex, and the side-chain carbon-atom numbers (2, 1, 3, 4 and 7) in the overwhelming majority of the amino acids recognized by each of the two classes of AARS are constrained by a mathematical relationship, the Lucas series (Ni = Ni-1+Ni-2 , which is similar to Fibonacci series). A stepwise co-evolutionary selection logic of the amino acids is hence suggested.(3) Based on the rotational symmetric arrangement of the 20 amino acids in the genetic code, analyses of the organization of the genetic code system together with their intrinsic relation to the two classes of AARS are further investigated. The studies revealed that the two evolutionary axes within the genetic code overlap the symmetry axes within the two classes of AARS.(4) Symmetry breaking, codon assignment variations and evolutionary distinctiveness: It is observable that the mitodrondria genetic codes in Yeast, Filamentous fungi and Trypanosome retain more symmetric features than animals and higher plants. Higher plants and some Yeasts started to carry abnormal codons at the initial evolutionary stage along the secondary (horizontal) evolutionary axis. For higher plants, Arg coded by CGG is changed to Trp; for Yeasts Saccharomyces cerevisiae and Torulopsis glabrata, Thr is replaced by Leu at the CUN position (N = U, C, G, or A). More interestingly, it is evident that most of the codon variations occur within the Class Ⅰ AARS. Moreover, these variations rarely occur at the first stage (or in the primordial codon core region) along the primary evolutionary axis (Fig. 2).Conclusions: The novel identification of the unprecedented quasi-28-gonal D2h symmetricfeature (simple viral structure), the two evolutionary axes, a primordial codon core, together with the Fibonacci-Lucas sequence-restricted non-random selection of the amino acid side chains underlying the synchronous genetic network (Fig. 1, 2), may help advance our understanding of this biological principle, origin of primitive life and gene evolution. 4-7
genes origin of life evolution viruses symmetry amino acid nucleobase stereochemistry genetic code evolutionary axis.
Chi Ming Yang
Physical Organic Chemistry and System Biology, Nankai University, Tianjin 300071, China
国际会议
杭州
英文
79-81
2007-06-06（万方平台首次上网日期，不代表论文的发表时间）