Genetic code evolution as an initial driving force for molecular evolution

arXiv:0807.1762v2 [q-bio.GN] 15 Mar 2009 Genetic code evolution as an initial driving force for molecular evolution Dirson Jian Li* and Shengli Zhang Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China Abstract There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at molecular level. In absence of evidence, numerous problems in molecular evolution had to fall into a twilight zone of speculation and controversy in the past. Here we show that delicate structures of variations of genomic base compositions and amino acid frequencies resulted from the genetic code evolution. And the driving force of evolution of life also originated in the genetic code evolution. The theoretical results on the variations of amino acid frequencies and genomic base compositions agree with the experimental observations very well, not only in the variation trends but also in some fine structures. Inversely, the genomic data of contemporary species can help reconstruct the genetic code chronology and amino acid chronology in primordial period. Our results may shed light on the intrinsic mechanism of molecular evolution and the genetic code evolution. Keywords: molecular evolution, variation of amino acid frequency, variation of genomic base composition, genetic code evolution 1 1 Introduction The driving force of evolution of life is a core problem in the theory of evolution. A qualified mechanism on driving force should explain the evolutionary trends for both molecular evolution and macroevolution of life. The driving force must be effective persistently from the primordial period through present days. And it had to form at the early stage of evolution of life, by which life evolved from simple to complex consequently. So there must be some relics in genomic properties of contemporary species resulted from such a driving force. We found that rich information is stored in the variation of compositions of proteins and DNAs, which relates to the evolution in early time. The discovery of genetic code helps us understand life at the molecular level [1][2][3][4][5]. A further study of the evolution of genetic code may help us reveal the underlying mechanism in the evolution of life. We found that the genetic code evolution profoundly determined the evolution of amino acid frequencies and genomic base compositions, and it can be taken as the initial driving force in molecular evolution. Inversely, the details of the genetic code evolution can be inferred by the compositions of proteins and DNAs of contemporary species. The organization of the paper is as follows: the experimental observations and theoretical results on the variation of amino acid frequencies are explicated in section 2; the experimental observations and theoretical results on the variation of base compositions are explicated in section 3; their relationships are explicated in section 4. In section 5, we will explain the relationship between genetic code evolution and the variations of the amino acid frequencies and base compositions. All the theoretical results in the sections 2-4 are based on a model, which will be described in details in section 6. The amino acid frequencies are obtained based on two databases: (i) 106 proteomes (85 eubacteria, 12 archaebacteria, 7 eukaryotes and 2 viruses) in Prediction of Entire Proteomes (PEP) 2 (http://cubic.bioc.columbia.edu/pep) [6], and (ii) genomes of 803 microbes in the database in NCBI. Two sets of experimental observations based on PEP and NCBI respectively have been obtained in the paper. Their results agree with each other. So the properties on the variation of amino acid frequencies observed in this paper are universal rules, which is independent of the choice of sample species. The GC contents are obtained from Genome Properties system [7]. These species are representatives of the three domains to study the evolutionary trends of amino acid frequencies and genomic base compositions. Fig. 6a-6d are plotted according to Fig. 9-1, Fig. 9-6, Fig. 9-8 and Fig. 9-7 in [8] respectively; and Fig. S10a-S10c are plotted according to Fig. 9-4 in [8] respectively. The genetic code multiplicity in Fig. S13 is plotted based on Fig. 1 in Ref. [9]. The data of gain-loss of amino acid in Tab. 1 are obtained according to Ref. [10]. 2 Variation of amino acid frequencies 2.1 Experimental observations 2.1.1 Choosing orders of species properly to observe variation trends of amino acid frequencies The amino acid frequencies in species vary slightly, which was routinely assumed to be constant [11][12]. Unfortunately, this is a misleading assumption and resulted in ignorance of studying the mechanism of variation of amino acid frequencies in the past. Actually, it is easy to observe the variation trends of amino acid frequencies if we choose o

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