Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.-猫眼课题宝

在大细菌基因组的不同区域中选择不平等的Sigma70启动子样信号的选择。

DOI：

10.1371/journal.pgen.0020185

发表时间：

2006-11-10

期刊：

PLoS genetics

影响因子：

4.5

通讯作者：

中科院分区：

生物学2区

文献类型：

作者：

Huerta AM;Francino MP;Morett E;Collado-Vides J

来源链接：

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635534/?report=classic

人们对参与基因表达调控的DNA区域的进化过程知之甚少。在大肠杆菌中，我们已经建立了一种区分调节区和非调节区的序列模式。与编码区和位于可转换转录基因之间的区域相比，可被RNA聚合酶识别并可能作为潜在启动子发挥作用的启动子样序列在调节区内的密度很高。此外，即使在调节区内的其他地方存在与RNA聚合酶具有较高结合亲和力的个别位点时，实验确定的功能性启动子位点也经常发现在启动子样信号密度最高的亚区。为了了解这种模式的普遍性，我们分析了属于大多数已建立的细菌门的另外43个基因组。在大多数被分析的基因组中都可以检测到调控区域和非调控区域之间的不同密度，除了那些进化到极端基因组缩减的基因组。因此，这种模式的存在遵循了基因和其他基因组特征的存在，这些基因和其他基因组特征需要弱选择才能有效地保持下去。在此基础上，我们认为寄主限制性病原菌和共生菌的简化基因组中差异密度的丧失是高度结构的小种群中纯化选择效率降低导致基因组退化过程的结果。这意味着在大型细菌基因组中检测到的调控区域和非调控区域之间的启动子样信号的不同分布赋予了显著的、尽管很小的适合性优势。这项研究通过对密切相关的细菌基因组进行更详细的比较分析，为进一步识别影响调控区域的组织和启动子样信号的总体分布的特定类型的选择性限制因素铺平了道路。基因表达调控中最重要的一步是转录的启动。这一过程是通过RNA聚合酶与DNA中存在的特定序列片段(启动子)的结合或特定结合来完成的。启动子位于转录基因的上游区域。人们对参与基因表达调控的DNA区域的进化过程知之甚少。长期以来，σ70启动子的典型图景是由转录起始点(+1)和以+1上游10和35碱基对为中心的两个保守的六核苷酸序列定义的60碱基对区域。作者证明，在大肠杆菌中，启动子以一系列重叠的潜在竞争的RNAP相互作用位点的形式存在。与编码区和位于可转换转录的基因之间的区域相比，大肠杆菌的调节区包含高密度的这些启动子样信号。他们报告说，除了那些经历了严重的基因组退化和大小缩小的基因组外，在大多数真细菌基因组中都可以检测到调节区和非调节区之间的密度差异。这表明，这种模式在大型细菌基因组中的存在赋予了一个显著的、尽管很小的健康优势。

The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes. The most important step in the regulation of genetic expression is the initiation of transcription. This process is accomplished by the association or specific binding of RNA polymerase to particular sequence segments present in the DNA, the promoters. Promoters are located in the upstream regions of the transcribed genes. The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. For a long time, the canonical picture of a σ70 promoter has been a 60 base pair region defined by the transcription start-point (+1) and two conserved hexanucleotide sequences centered 10 and 35 base pairs upstream from the +1. The authors have shown that in Escherichia coli, promoters exist in clusters, as a series of overlapping potentially competing RNAP interaction sites. The E. coli regulatory regions contain high densities of these promoter-like signals, in contrast to coding regions and regions located between convergently transcribed genes. They report that the differential densities between regulatory and nonregulatory regions are detectable in most eubacterial genomes, with the exception of those that have experienced severe genome degradation and size reduction. This suggests that the presence of this pattern in large bacterial genomes confers a significant, although small, fitness advantage.