Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, NH, USA.
Genome Biol Evol. 2012;4(12):1256-62. doi: 10.1093/gbe/evs099.
It has become clear that different genome regions need not evolve uniformly. This variation is particularly evident in bacterial genomes with multiple chromosomes, in which smaller, secondary chromosomes evolve more rapidly. We previously demonstrated that substitution rates and gene dispensability were greater on secondary chromosomes in many bacterial genomes. In Vibrio, the secondary chromosome is replicated later during the cell cycle, which reduces the effective dosage of these genes and hence their expression. More rapid evolution of secondary chromosomes may therefore reflect weaker purifying selection on less expressed genes. Here, we test this hypothesis by relating substitution rates of orthologs shared by multiple Burkholderia genomes, each with three chromosomes, to a study of gene expression in genomes differing by a major reciprocal translocation. This model predicts that expression should be greatest on chromosome 1 (the largest) and least on chromosome 3 (the smallest) and that expression should tend to decline within chromosomes from replication origin to terminus. Moreover, gene movement to the primary chromosome should associate with increased expression, and movement to secondary chromosomes should result in reduced expression. Our analysis supports each of these predictions, as translocated genes tended to shift expression toward their new chromosome neighbors despite inevitable cis-acting regulation of expression. This study sheds light on the early dynamics of genomes following rearrangement and illustrates how secondary chromosomes in bacteria may become evolutionary test beds.
很明显，不同的基因组区域不需要均匀进化。这种变异在具有多个染色体的细菌基因组中尤为明显，其中较小的次要染色体进化得更快。我们之前已经证明，在许多细菌基因组中，次要染色体上的替代率和基因可 dispensability 更高。在弧菌中，次要染色体在细胞周期中较晚复制，从而降低了这些基因的有效剂量，因此它们的表达量也降低了。因此，次要染色体的快速进化可能反映了较少表达的基因受到的净化选择较弱。在这里，我们通过将多个伯克霍尔德氏菌基因组共享的直系同源物的替代率与对具有主要相互易位的基因组的基因表达研究相关联，来检验这一假说。该模型预测，表达量应该在染色体 1（最大）上最高，在染色体 3（最小）上最低，并且表达量应该从复制起点到末端在染色体上逐渐下降。此外，基因向主染色体的移动应该与表达增加相关，而向次要染色体的移动则会导致表达减少。我们的分析支持了这些预测中的每一个，因为尽管存在表达的顺式调控，但易位基因往往会将表达转移到它们的新染色体邻居。这项研究阐明了基因组在重排后的早期动态，并且说明了细菌中的次要染色体如何成为进化的试验台。
