大肠杆菌mRNA编码区长度、形成二级结构倾向与密码子偏好性的关系

从GenBank获得大肠杆菌K-12MG1655株的全基因组序列,计算了与基因密码子偏好性相关的多个参数(Nc、CAI、GC、GC3s),对其mRNA编码区长度、形成二级结构倾向与密码子偏好性之间的关系进行了统计学分析,发现虽然翻译效率(包括翻译速度和翻译精度)是制约大肠杆菌高表达基因的密码子偏好性的主要因素,同时,mRNA编码区长度及其形成二级结构的倾向也是形成这种偏好性的不可忽略的原因,而且对偏好性有一定程度的削弱。另外对mRNA编码区形成二级结构倾向的生物学意义进行了讨论分析。

Insight into relationship among mRNA coding region length, folding tendency and codon usage bias in Escherichia coli

Escherichia coli has been regarded as a model organism in the study of codon usage bias. Most studies in this organism regarding this topic have focused their mind on translation efficiency (translation speed and translation precision). However, some genes with low codon usage bias and high expression can not be explained by translation efficiency. And some evidence of local RNA secondary structure in coding region of Escherichia coli genes have been given. All of these need explanation from a new point of view. The genomic sequence of Escherichia coli K_12 MG 1655 was obtained from GenBank. Several parameter (Nc,CAI,GC,GC3s) of 4199 genes on codon usage bias were computed. Folding tendency of mRNA coding region was represented by its average energy of 50 nucleotides. And then, relationship among mRNA coding region length, folding tendency and codon usage bias in Escherichia coli were studied. It is argued that though translation efficiency is a primary cause that shapes the codon usage bias of highly expressed genes in Escherichia coli, mRNA coding region length and folding tendency are also unneglectable factor for codon usage bias and weakening of bias. In addition, biological significance of folding tendency in mRNA coding regions was discussed.