Diversity Of Translation Initiation Regulation In E.coli

Translation initiation regulation of prokaryotes is a central challenge in bioinformatics. An important step in this challenge is how ribosomes correctly combine on mRNA and effectively identity translation initiation codon. It is also the key of gene expression level regulation. Based on some genes which own SD sequence, Shine-Dalgarno region are identified and sorted by the method of self-consistent information clustering in E.coli. Then, ground on three-dimensional and secondary structure, some 16S rRNA segments which may combine with translation initiation regulation sequence are predicted.Self-consistent information clustering is applied to predict the strength of the SD sequence of the protein-coding genes in E.coli and 17 kinds of base correlation modes which are contained in strong SD sequence are shown. All SD sequences are classified into three classes by different strength, such as strong, medium and weak SD sequences. It is found that different SD classes are characterized by different preferential modes. For example, the most preferential mode in the weak SD sequences is GGAGG, whereas it is AAGGA in the strong SD sequences. The distances between the bases in particular modes and translation initiation codons vary among different SD classes. For example, the base A in GGAG mode occurs mostly at position -8 in strong SD sequences, however, it occurs more often at position -7 or -9 in weak SD sequence. On average, the base which the most frequently occurs at position -9 is base G, but the least frequently occurs at position -9 is base C. The results also show that the stronger SD sequences correlate the higher gene expression level and the weak SD sequences correlate the lower gene expression level. The recognition of translation initiation codon and translation efficiency is affected by the SD sequence matches the anti-SD sequence and the relative position of SD sequence.16S rRNA is separated into different loop or helix segments according as its secondary structure in E.coli. Then, translation initiation regulation sequences are aligned with these 16S rRNA segments. According to the scores of alignment, the correlating analysis is done between CAI (Codon Adaptation Index) and the scores. The positive correlated 16S rRNA segments are filtered by ribosomal protein binding site on 16S rRNA and translation initiation regulation sequence bordered upon 16S rRNA region. The result is that anti-SD sequence, the right stem 5 and the right stem 18 can interact with translation initiation regulation sequence to promote translation initiation. Different positional relation between anti-SD and the right stem 5 or the right stem 18 on SD sequence are analyzed, the results indicate: in the process of regulation of translation initiation, anti-SD sequence acts as dominant effect. When anti-SD sequence away from translation initiation codon, the right stem 5 or the right stem 18 assist translation initiation regulation to accelerate gene expression.