Measurement and modeling of intrinsic transcription terminators.
Measurement and modeling of intrinsic transcription terminators.
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DOI：
10.1093/nar/gkt163
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发表时间：
2013-05
影响因子：
14.9
通讯作者：
Endy D
中科院分区：
文献类型：
--
作者：
Cambray G;Guimaraes JC;Mutalik VK;Lam C;Mai QA;Thimmaiah T;Carothers JM;Arkin AP;Endy D
遗传系统的可靠正向工程仍然受到许多类型的基本遗传元件的临时再利用的限制。虽然一些固有的原核转录终止子被常规使用，但其终止效率还没有得到系统的研究。在这里，我们开发并验证了一种基因架构，该架构能够可靠地测量终端效率。然后，我们收集了61个自然和合成终止子，这些终止子共同编码了大肠杆菌内∼800倍的动态范围内的终止效率。我们模拟了共转录RNA的折叠动力学，以确定可能干扰终止子折叠动力学或影响终止活性的竞争二级结构。我们发现，延伸到核心终止子茎之外的结构可能会增加终止子的活性。通过排除编码这种上下文混淆元素的终止符，我们能够开发出一个线性序列函数模型，该模型可以用于估计终止效率(r=0.9，n=31)，比对所有终止符训练的模型(r=0.67，n=54)更好。由此产生的系统测量的终止子集合应该会改进合成遗传系统的工程，并推进转录终止的定量建模。
The reliable forward engineering of genetic systems remains limited by the ad hoc reuse of many types of basic genetic elements. Although a few intrinsic prokaryotic transcription terminators are used routinely, termination efficiencies have not been studied systematically. Here, we developed and validated a genetic architecture that enables reliable measurement of termination efficiencies. We then assembled a collection of 61 natural and synthetic terminators that collectively encode termination efficiencies across an ∼800-fold dynamic range within Escherichia coli. We simulated co-transcriptional RNA folding dynamics to identify competing secondary structures that might interfere with terminator folding kinetics or impact termination activity. We found that structures extending beyond the core terminator stem are likely to increase terminator activity. By excluding terminators encoding such context-confounding elements, we were able to develop a linear sequence-function model that can be used to estimate termination efficiencies (r = 0.9, n = 31) better than models trained on all terminators (r = 0.67, n = 54). The resulting systematically measured collection of terminators should improve the engineering of synthetic genetic systems and also advance quantitative modeling of transcription termination.
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影响因子：
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