A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli.
A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli.
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DOI：
10.1128/msystems.00021-15
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发表时间：
2016-01
期刊：
影响因子：
6.4
通讯作者：
Vanderpool CK
中科院分区：
文献类型：
--
作者：
Balasubramanian D;Ragunathan PT;Fei J;Vanderpool CK
SRNAs是细菌基因表达的普遍和通用的调节因子。大肠杆菌中的一些特征良好的例子是高度保守的，存在于大肠杆菌的核心基因组中。相比之下，SRNA DicF(在20多年前被发现，但特征仍然很差)是由许多大肠杆菌基因组中存在缺陷的前噬菌体元件携带的基因编码的。在这里，我们对DicF进行表征，以便更好地了解水平获得的sRNA调节因子是如何影响细菌基因表达和生理的。我们的数据证实了长期假设的DicF介导的FtsZ调节，编码细胞分裂所需的细菌微管蛋白同源物。我们进一步揭示了DicF介导的代谢基因表达的转录后控制。异源生产的DicF对大肠杆菌细胞有很高的毒性，但这种毒性不是由于DicF对FtsZ的调节。还需要进一步的工作来揭示DicF和其他由缺陷前驱体编码的产物赋予宿主的生物学作用和好处。在不同的细菌物种中已经发现了数百个小RNA(SRNA)，虽然大多数的功能尚不清楚，但有些调节关键过程，特别是应激反应。SRNA DicF在2500多年前被确定为细胞分裂的抑制剂，但从那时起一直没有特征性。DicF由53个核苷酸组成，由许多大肠杆菌菌株基因组中携带的原噬菌体(Qin)基因编码。我们证明了DicF通过与FtsZ mRNA直接碱基配对来抑制细胞分裂，从而抑制翻译并阻止细菌微管蛋白同源物FtsZ的新合成。利用计算和实验方法进行的系统分析确定了DicF：xylR和PYKA mRNAs的额外mRNA靶标，分别编码木糖吸收和分解代谢调节因子以及丙酮酸激酶。遗传分析表明，DicF直接与这些靶基因发生碱基配对，并抑制这些靶基因的翻译。表达DicF变异体的细胞表型表明，DicF相关的生长抑制不仅仅是由于FtsZ的抑制，这表明DicF介导的调节的生理后果超出了由于FtsZ合成减少而对细胞分裂的影响。重要的是，sRNAs是细菌基因表达的普遍和通用的调节因子。大肠杆菌中的一些特征良好的例子是高度保守的，存在于大肠杆菌的核心基因组中。相比之下，SRNA DicF(在20多年前被发现，但特征仍然很差)是由许多大肠杆菌基因组中存在缺陷的前噬菌体元件携带的基因编码的。在这里，我们对DicF进行表征，以便更好地了解水平获得的sRNA调节因子是如何影响细菌基因表达和生理的。我们的数据证实了长期假设的DicF介导的FtsZ调节，编码细胞分裂所需的细菌微管蛋白同源物。我们进一步揭示了DicF介导的代谢基因表达的转录后控制。异源生产的DicF对大肠杆菌细胞有很高的毒性，但这种毒性不是由于DicF对FtsZ的调节。还需要进一步的工作来揭示DicF和其他由缺陷前驱体编码的产物赋予宿主的生物学作用和好处。
sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to E. coli cells, but the toxicity is not attributable to DicF regulation of ftsZ. Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages. Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over 25 years ago as an inhibitor of cell division but since then has remained uncharacterized. DicF consists of 53 nucleotides and is encoded by a gene carried on a prophage (Qin) in the genomes of many Escherichia coli strains. We demonstrated that DicF inhibits cell division via direct base pairing with ftsZ mRNA to repress translation and prevent new synthesis of the bacterial tubulin homolog FtsZ. Systems analysis using computational and experimental methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. Genetic analyses showed that DicF directly base pairs with and represses translation of these targets. Phenotypes of cells expressing DicF variants demonstrated that DicF-associated growth inhibition is not solely due to repression of ftsZ, indicating that the physiological consequences of DicF-mediated regulation extend beyond effects on cell division caused by reduced FtsZ synthesis. IMPORTANCE sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to E. coli cells, but the toxicity is not attributable to DicF regulation of ftsZ. Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages.