Nishida Hiromi
Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan.
Curr Issues Mol Biol. 2013;15:19-24. Epub 2012 Jul 6.
Comparative genomics has revealed that variations in bacterial and archaeal genome DNA sequences cannot be explained by only neutral mutations. Virus resistance and plasmid distribution systems have resulted in changes in bacterial and archaeal genome sequences during evolution. The restriction-modification system, a virus resistance system, leads to avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system. Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated proteins bind DNA regions with low GC content and inhibit the expression of genes contained in those regions. This form of gene repression is another type of virus resistance system. On the other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance systems influence plasmid distribution. Interestingly, the restriction-modification system and nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and genomic signatures do not reflect bacterial and archaeal evolutionary relationships.
比较基因组学研究表明，细菌和古菌基因组DNA序列的变异不能仅用中性突变来解释。病毒抗性和质粒分布系统在进化过程中导致了细菌和古菌基因组序列的变化。限制修饰系统作为一种病毒抗性系统，使得基因组中避免出现回文DNA序列。基因组中发现的成簇规律间隔短回文重复序列（CRISPRs）代表了另一种病毒抗性系统。比较基因组学研究显示，细菌和古菌未能获得任何GC含量高于其染色体GC含量的DNA。因此，水平转移的DNA区域的GC含量低于宿主染色体DNA。一些类核相关蛋白会结合GC含量低的DNA区域，并抑制这些区域所含基因的表达。这种基因抑制形式是另一种病毒抗性系统。另一方面，细菌和古菌利用质粒来获取额外的基因。病毒抗性系统影响质粒分布。有趣的是，限制修饰系统和类核相关蛋白基因是通过质粒进行分布的。因此，GC含量和基因组特征并不能反映细菌和古菌之间的进化关系。
