The Influence Of Synonymous Codon Usage Bias On MRNA Secondary Structure And Its Corresponding Protein Folding Rate

The research on synonymous codon usage bias has always been concerned by biologists. Grantham and others found that codon bias has species differences, and found the different genes with a similar preferences in the early period. With the rapid growth of biological science technology, many datas of codon usage bias research were provided different kinds of large genomic data. The ralated datas were provided from a few or several hundred or even thousands of genomes genomic data, and were used to explore the reason and the rule of evolution for synonymous codon usage bias. In our work, we found that mRNA secondary structure and the protein folding rate have an important relations with the codon usage bias. So the database of mRNA secondary structure and protein folding were established, and the effects of the synonymous codon usage bias on mRNA secondary structure and its corresponding protein folding rate were tried to explore.Firstly, the information of mRNA sequences of 45 kinds of coronaviruses and the nucleoproteins of Escherichia coli was collected. First of all, for every coronavirus?the synonymous codon usage bias of the mRNA sequence of each protein was calculated, the secondary structure of all mRNA sequence was predicted one by one, and the content of mRNA stem or loop structure, folded unit average free energy and the corresponding mRNA specific flexibility four parameters were caculated, thus the database about the information of mRNA secondary structure parameter was founded. Then for the Escherichia coli, each of the nucleoprotein was cut into three peptide segments of a-helices,?-strands and mixed-class according to their secondary structure, the corresponding nucleic acid sequence of each peptide segment was found, the synonymous codon usage bias and the folding rates of corresponding peptide segments were calculated, the database about protein folding rate of the nucleoproteins of Escherichia coli was founded.Secondly, on the bases of our mRNA secondary structure database, the correlation between synonymous codon usage bias and the four kinds of parameters of mRNA secondary structure were analyzed for every mRNA sequence. The results show that, the percents of amino acids which codons significantly correlated with the content of stem structure were reach 90%; the percents of amino acids which codons significantly correlated with the content of loop structure were reach 75%:the percents of amino acids which codons significantly correlated with the average unit folding free energy were reach 90%; the percents of amino acids which codons significantly-correlated with the mRNA specific flexibility were reach 85%. Further analysis found, for the codes of both significantly correlated with the content of stem structure and the content of loop structure, their correlation were completely opposite, the correlation between specific flexibility with synonymous codon usage bias is excellent in all parameters. It means that there are a great relationship between coronavirus of the synonymous codon usage bias and the mRNA secondary structure.Thirdly, based on our database, the correlation between synonymous codon usage bias and the folding rates of three different types of peptide fragment were analyzed. It was found that some of codon usage bias were significantly correlated with the folding rates of segments for each type of the peptide. The results show that the synonymous codon usage bias play an important role in protein folding.