Distribution and evolution of sequence characteristics in the E. coli genome.
Distribution and evolution of sequence characteristics in the E. coli genome.
复制标题
大肠杆菌基因组中序列特征的分布和进化。
DOI：
10.1080/07391102.1986.10506347
复制
发表时间：
1986
影响因子：
4.4
通讯作者：
Earley,S
中科院分区：
文献类型：
--
作者：
Blake,RD;Earley,S
已发表DNA序列的平均(G+C)组成(51.0%)和标准差(±3.8%)占E的10%。大肠杆菌基因组与高分辨率熔解确定的主要总体分布非常一致。虽然碱基和邻近特征的差异在基因组的所有区域中很小且一致，但发现序列的 (G+C) 含量在对应于编码 (53% G+C) 和非编码 (46% G+C) 区域的边界内以分段方式变化；后者的差异比编码区大六倍。不同区域的方差对该区域的（G+C）含量表现出强烈的负相关性，反映了A-T和G-C碱基对分别是A-T和C-G对的优选邻居的情况；偏差随着 (G+C) 含量的减少而增加。邻域分析表明，最极端的正偏差发生在所有区域的 AA、TT、GC 和 CG 中，特别是在非编码区域。 (A)n 等的寡聚串数量异常多，是这种偏差的进一步结果。这些和其他特征表明在复制或修复过程中施加的相邻频率存在固有偏差，这反过来又反映了突变过程中的相邻影响。格兰瑟姆和其他人指出的密码子使用偏差在一定程度上是由于编码序列通过选择同义密码子来适应这种微环境，从而保留固有的邻近偏差。
The mean (G+C) composition (51.0%) and standard deviation (±3.8%) of published DNA sequences accounting for 10% of theE. coligenome is in excellent agreement with the principal overall distribution determined by high resolution melting. While differences in base and neighbor characteristics are small and uniform throughout all regions of the genome, it is found that the (G+C) content of sequences varies in segmented fashion within boundaries corresponding to coding (53% G+C) and noncoding (46% G+C) regions; with variances in the latter being six-fold greater than in coding regions. The variance in different regions shows a strong negative dependence on (G+C) content of the region, reflecting the condition that A-T and G-C base pairs are preferred neighbors of A-T and C-G pairs, respectively; with the bias increasing with decreasing (G+C) content. Neighbor analysis indicates the most extreme positive biases occur in AA, TT, GC and CG throughout all regions, but particularly in noncoding regions. Extraordinary numbers of oligomeric strings of (A)n, etc., are the further consequence of this bias. These and other characteristics point to the existence of inherent biases in neighbor frequencies levied during replication or repair, and which reflect, in turn, neighbor influences during mutation. The bias in codon usage noted by Grantham and others is seen here as due, in part, to the adaptation of coding sequences to this microenvironment through selection among synonymous codons so as to preserve inherent neighbor biases.