Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli.
Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli.
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转录终止衰减剂的鉴定：对大肠杆菌RNA调控的影响。
DOI：
10.1128/mbio.02371-22
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发表时间：
2022-12-20
期刊：
影响因子：
6.4
通讯作者：
Gottesman, Susan
中科院分区：
文献类型：
--
作者：
Morita, Teppei;Majdalani, Nadim;Miura, Masahiro C.;Inose, Rerina;Oshima, Taku;Tomita, Masaru;Kanai, Akio;Gottesman, Susan
许多细菌小RNA（sRNA）的调节功能需要RNA伴侣分子Hfq与sRNA内在终止子的3′端结合，因此sRNA信号可能通过调节其终止子来调节。在这里，使用多拷贝屏幕开发的终止子sRNA SgrS，我们确定了一个sRNA基因（cyaR）和三个蛋白质编码基因（cspD，ygjH，和rof），衰减SgrS终止在大肠杆菌。CyaR和YgjH（一种假定的tRNA结合蛋白）的分析表明CyaR活性是间接的，YgjH的作用是中等的。蛋白质衰减剂CspD和Rof的过度产生导致SgrS和另外两种sRNA的终止子处的更频繁的通读，并且SgrS对靶mRNA的调节减少。双环霉素或rho突变体模拟了已知Rho抑制剂Rof的作用，表明Rho在sRNA终止中具有意想不到的作用。CspD是冷休克蛋白家族的一员，结合终止和通读转录本，稳定它们并减弱终止。通过对CspD过表达菌株的RNA测序分析，我们发现CspD对一些终止位点的基因表达具有全局影响。我们进一步证明了内源性CspD在cspD高度表达的缓慢生长条件下的作用。这些发现提供了内在终止效率变化的证据，证实这是sRNA信号调节的另一层。
The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 3′ portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate. Overproduction of the protein attenuators CspD and Rof resulted in more frequent readthrough at terminators of SgrS and two other sRNAs, and regulation by SgrS of target mRNAs was reduced. The effect of Rof, a known inhibitor of Rho, was mimicked by bicyclomycin or by a rho mutant, suggesting an unexpected role for Rho in sRNA termination. CspD, a member of the cold shock protein family, bound both terminated and readthrough transcripts, stabilizing them and attenuating termination. By RNA sequencing analysis of the CspD overexpression strain, we found global effects of CspD on gene expression across some termination sites. We further demonstrated effects of endogenous CspD under slow growth conditions where cspD is highly expressed. These findings provided evidence of changes in the efficiency of intrinsic termination, confirming this as an additional layer of the regulation of sRNA signaling.
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影响因子：
3.5
作者：
CHEREPANOV, PP;WACKERNAGEL, W
通讯作者：
WACKERNAGEL, W
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.6
作者：
Johansen, Jesper;Eriksen, Maiken;Valentin-Hansen, Poul
通讯作者：
Valentin-Hansen, Poul
影响因子：
3.9
作者：
Holmqvist E;Wagner EGH
通讯作者：
Wagner EGH