Uno Reina, Nakayama Yoichi, Tomita Masaru
Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0014, Japan.
Gene. 2006 Sep 15;380(1):30-7. doi: 10.1016/j.gene.2006.05.013. Epub 2006 Jun 2.
Chi sequences (5'-GCTGGTGG-3') are cis-acting 8 bp sequence elements that enhance homologous recombination promoted by the RecBCD pathway in Escherichia coli. The genome of E. coli K-12 MG1655 contains 1009 Chi sequences and this frequency far exceeds the expected value for occurrence of an 8 bp sequence in a genome of this size. It is generally thought that the over-representation of Chi sequences indicates that they have been selected for during evolution because of their function in recombination. The genes from three E. coli strains (K-12, O157 and CFT) were classified into three categories (island, match to other E. coli, and backbone). Island genes have a different base composition and codon usage in comparison with those in the backbone genes, therefore they were relatively new and not yet adapted to the base composition patterns and codon usage typical of the recipient genome. The over-representation of Chi sequences was examined by comparing Chi frequencies and codon frequencies between island and backbone genes. The difference in the CTGGTG di-codon frequency between the backbone and island genes was correlated with the frequency of Chi sequences which were translated in the Leu-Val (-G/CTG/GTG/G-) reading frame in the K-12 strain. These results suggest that the main reading frame of Chi sequences increased as a result of the di-codon CTG-GTG increasing under a genome-wide pressure for adapting to the codon usage and base composition of the E. coli K-12 strain, and that the RecBCD recombinase might adjust its recognition sequence to a frequently occurring oligomer such as G-CTG-GTG-G.
Chi序列（5'-GCTGGTGG-3'）是顺式作用的8碱基对序列元件，可增强大肠杆菌中RecBCD途径促进的同源重组。大肠杆菌K-12 MG1655的基因组包含1009个Chi序列，这一频率远远超过在这种大小的基因组中出现8碱基对序列的预期值。一般认为，Chi序列的过度存在表明它们在进化过程中因其在重组中的功能而被选择。来自三种大肠杆菌菌株（K-12、O157和CFT）的基因被分为三类（岛状、与其他大肠杆菌匹配和主干）。与主干基因相比，岛状基因具有不同的碱基组成和密码子使用情况，因此它们相对较新，尚未适应受体基因组典型的碱基组成模式和密码子使用情况。通过比较岛状基因和主干基因之间的Chi频率和密码子频率，研究了Chi序列的过度存在情况。主干基因和岛状基因之间CTGGTG双密码子频率的差异与K-12菌株中在亮氨酸-缬氨酸（-G/CTG/GTG/G-）阅读框中翻译的Chi序列的频率相关。这些结果表明，在全基因组压力下，由于双密码子CTG-GTG增加以适应大肠杆菌K-12菌株的密码子使用和碱基组成，Chi序列的主要阅读框增加，并且RecBCD重组酶可能将其识别序列调整为频繁出现的寡聚物，如G-CTG-GTG-G。
