The evolutionary impact of intragenic FliA promoters in proteobacteria.
The evolutionary impact of intragenic FliA promoters in proteobacteria.
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DOI：
10.1111/mmi.13941
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发表时间：
2018-05
影响因子：
3.6
通讯作者：
Wade JT
中科院分区：
文献类型：
--
作者：
Fitzgerald DM;Smith C;Lapierre P;Wade JT
在大肠杆菌中，一个Sigma因子识别大多数启动子，而六个“替代”Sigma因子识别特定的启动子子集。另一种σ因子FliA（σ28）识别许多鞭毛基因上游的启动子。我们以前的研究表明，大多数E。coli FliA结合位点位于基因内部。然而，尚不清楚这些基因内结合位点是否代表活性启动子。在这里，我们构建和检测转录启动子lacZ融合的所有52个假定的FliA启动子先前确定的ChIP-seq。这些实验，加上已发表的基因组规模的转录数据集的综合分析，强烈表明，大多数基因内FliA结合位点是转录高度不稳定的RNA的活性启动子。此外，我们表明，广泛的基因内FliA依赖的转录可能是一个保守的现象，但特定的启动子本身并不保守。我们的结论是，基因内FliA依赖性启动子和由此产生的RNA不太可能具有重要的调控功能。尽管如此，一个基因内FliA启动子是广泛保守的，并限制重叠的蛋白质编码基因的进化。因此，我们的数据表明，基因内调控元件可以影响细菌蛋白质的进化，并建议基因内调控序列对基因组进化的影响应被更广泛地考虑。最近的研究发现，在意想不到的位置（如基因内部）发现了数千个细菌启动子。在这里，我们调查鞭毛σ因子FliA基因内启动子的功能。我们的数据表明，大多数这些启动子是没有功能的，但一个基因内FliA启动子是广泛保守的，并限制重叠的蛋白质编码基因的进化。我们的数据表明，基因内调控序列显着影响细菌基因组进化。
In Escherichia coli, one Sigma factor recognizes the majority of promoters, and six “alternative” Sigma factors recognize specific subsets of promoters. The alternative Sigma factor FliA (σ28) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved, and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic regulatory elements can influence bacterial protein evolution, and suggest that the impact of intragenic regulatory sequences on genome evolution should be considered more broadly. Recent findings have identified thousands of bacterial promoters in unexpected locations, such as inside genes. Here, we investigate the functions of intragenic promoters for the flagellar sigma factor FliA. Our data suggest that most of these promoters are not functional, but that one intragenic FliA promoter is broadly conserved, and constrains evolution of the overlapping protein-coding gene. Our data suggest that intragenic regulatory sequences significantly impact bacterial genome evolution.