Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling
Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling
复制标题
DOI：
10.1371/journal.pgen.0030153
复制
发表时间：
2007-09-01
期刊：
影响因子：
4.5
通讯作者：
El Karoui, Meriem
中科院分区：
文献类型：
--
作者：
Halpern, David;Chiapello, Helene;El Karoui, Meriem
细菌在物种水平上的生物多样性，就基因的获取或丢失而言，是如此巨大，以至于它提出了一个问题，即如何使必要的染色体区域免于不受控制的重排。基因组的保护可能取决于特定的DNA基序，这些基序对经历重组的区域施加限制。尽管大多数这样的基序仍未确定，但根据它们的基因组分布特性，它们在理论上是可以预测的。我们检查了“交叉热点启动子”或CHI在大肠杆菌中的分布，发现它的异常分布仅限于三个菌株共同的核心基因组。然后，我们制定了一套标准，并将其纳入统计模型，以搜索核心基因组中可能涉及其他物种基因组稳定性的基序。我们的策略使我们识别并生物学验证了两种不同的具有CHI特性的七聚体，一个在金黄色葡萄球菌中，另一个在几种链球菌中。这一策略为大规模发现区分核心基因组和菌株可变区的其他重要功能非编码基序铺平了道路。
Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements. Protection of the genome likely depends on specific DNA motifs that impose limits on the regions that undergo recombination. Although most such motifs remain unidentified, they are theoretically predictable based on their genomic distribution properties. We examined the distribution of the ``crossover hotspot instigator,'' or Chi, in Escherichia coli, and found that its exceptional distribution is restricted to the core genome common to three strains. We then formulated a set of criteria that were incorporated in a statistical model to search core genomes for motifs potentially involved in genome stability in other species. Our strategy led us to identify and biologically validate two distinct heptamers that possess Chi properties, one in Staphylococcus aureus, and the other in several streptococci. This strategy paves the way for wide-scale discovery of other important functional noncoding motifs that distinguish core genomes from the strain-variable regions.