Research On Codon Preference Based On DNA Walking

It is well known that biological genetic information contains 64 standard codons.Except for three termination codons,the remaining 61 codons encode 20 common amino acids in organisms.There must be multiple codons corresponding to the same amino acid.Predicated codon bias refers to the phenomenon that different codons encoding the same amino acid occur unequally in different genomes,or in different genes in the same genome,or even in different regions of the same gene.Although the universality of codon bias has long been confirmed,the molecular evolution mechanism and biological effects of codon bias have always been the focus of research.So far,the following facts have been known about codon bias.First,codon bias affects the stability of DNA structure.It is well known that DNA sequence consists of adenine(A),guanine(G),cytosine(C)and thymine(T).Among them,AT pairs form two hydrogen bonds and CG pairs form three hydrogen bonds.If CG-dominant codons have high probability of occurrence,the content of hydrogen bonds in DNA structure is high and its stability is high;on the contrary,the stability is low.Similarly,codon bias also affects the stability of the secondary structure of transcripts(e.g.RNA and tRNA).Secondly,codon bias affects gene expression efficiency.At the same relative concentration of tRNA,the rate of ribosome translation was significantly higher in the dominant codon region of RNA.In addition,codon bias is closely related to the accuracy of gene expression and the accurate folding of amino acid sequences.In this paper,codon bias in typical bacteriophages,bacteria and archaea were studied by DNA walking.The codon bias characteristics of T7 bacteriophage genome and the relationship between T7 bacteriophage and codon bias of its host K12 Escherichia coli genome were discussed and quantitatively characterized.These studies are mainly based on the following facts:1)DNA walking can intuitively display the local and global characteristics of codon bias.2)At present,the research results on codon bias mainly involve a few model organisms,and seldom discuss the bias relationship between viruses and hosts.3)As model organisms,T7 phages and K12 Escherichia coli have relatively reliable and complete data on molecular biology and bioinformatics.By comparing the DNA walking curves corresponding to the "equal probability synonymous nucleotide sequence"(keeping the amino acid sequence unchanged,selecting the nucleotide sequence randomly composed of synonymous codons with equal probability),we found that:l)For the whole genome,there are three different codon bias patterns:strong bias for the third codon,strong bias for the first codon and the third codon,and weak bias for the three codons.2)The codon bias of T7 bacteriophage was significantly different from that of K12 bacterium.3)The codon bias of highly expressed genes in T7 bacteriophage is strong,and the bias characteristics are consistent with those of the genome of E.coli K12.