Withers Mike, Wernisch Lorenz, dos Reis Mario
School of Crystallography, Birkbeck College, University of London, UK.
RNA. 2006 Jun;12(6):933-42. doi: 10.1261/rna.2272306. Epub 2006 Apr 17.
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat neglected area of molecular evolution. Escherichia coli, the first phylogenetic species for which more than two different strains have been sequenced, provides an invaluable framework to study the evolution of tRNA genes. In this work, a detailed analysis of the tRNA structure of the genomes of Escherichia coli strains K12, CFT073, and O157:H7, Shigella flexneri 2a 301, and Salmonella typhimurium LT2 was carried out. A phylogenetic analysis of these organisms was completed, and an archaeological map depicting the main events in the evolution of tRNA genes was drawn. It is shown that duplications, deletions, and horizontal gene transfers are the main factors driving tRNA evolution in these genomes. On average, 0.64 tRNA insertions/duplications occur every million years (Myr) per genome per lineage, while deletions occur at the slower rate of 0.30 per million years per genome per lineage. This work provides a first genomic glance at the problem of tRNA evolution as a repetitive process, and the relationship of this mechanism to genome evolution and codon usage is discussed.
从细菌到真核生物，大多数生物体的基因组中转运RNA基因往往以多个拷贝的形式存在。转运RNA基因的进化和基因组结构在分子进化领域一直是一个有些被忽视的方面。大肠杆菌是第一个对两种以上不同菌株进行测序的系统发育物种，为研究转运RNA基因的进化提供了一个宝贵的框架。在这项工作中，对大肠杆菌K12、CFT073和O157:H7菌株、福氏志贺菌2a 301和鼠伤寒沙门氏菌LT2的基因组转运RNA结构进行了详细分析。完成了对这些生物体的系统发育分析，并绘制了一幅描绘转运RNA基因进化主要事件的考古图。结果表明，重复、缺失和水平基因转移是驱动这些基因组中转运RNA进化的主要因素。平均而言，每个基因组每个谱系每百万年（Myr）发生0.64次转运RNA插入/重复，而缺失发生的速率较慢，为每个基因组每个谱系每百万年0.30次。这项工作首次从基因组角度审视了转运RNA进化作为一个重复过程的问题，并讨论了这种机制与基因组进化和密码子使用的关系。
