Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model

We speculate that structures of genes might have been produced not only by the origination of the gene by itself, but also by the combination of several parts of structures from other species, through events, such as gene transfer, fusion of DNA sequences, and rearrangement of DNA sequences, to create new functions in evolution. To study the relationship between the 3D structure and DNA sequence of proteins comprised of multi-domains, six genes in Escherichia coli, including those coding for Flavodoxin (ferredoxin) reductase, Flavin oxidoreductase, Integrase/recombinase xerD, Endonuclease III, Heat shock protein (grpE), and Elongation Factor Tu (tufB), were chosen, since the 3D structures of these proteins had been determined by X-ray crystallography. The DNA sequences were analyzed by probability as calculated by using a species-specific inhomogeneous Markov model and divided into regions. The probability was calculated by the GeneMark program from the third-order matrix of Class III genes (Escherichia coli horizontally transferred genes) produced with the Markov model by Borodovsky M. et al.. The probability indicates the degree of similarity to the DNA sequence of the genes that were used for producing the matrix with the Markov model. Moreover, the probability indicates whether the origin of the divided DNA sequence would be different from that of the Class III genes. The divided regions, except for those of Flavin oxidoreductase, corresponded to the structural domains classified by CATH. Namely, the divided regions, suggested to be of different origins by analysis with the Markov model, showed correspondence to the domains and the gross content of the 3D structure. We can ascertain which DNA sequences would have been incorporated into the structure of a gene as parts of the structure in evolution. We propose a hypothesis that in evolution, the structure of genes might have been arisen by the incorporation of DNA sequences from other species.