Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters which may constitute up to a third of predicted Escherichia coli promoters. Promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present COdon Restrained Promoter SilEncing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ⁷⁰ promoters embedded within gene coding sequences, with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.

中文翻译：

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一种消除和产生基因内细菌启动子的密码子约束方法

合成生物学的未来应用将需要重构基因序列，在编码序列中没有内部调控元件。这些调控元件包括隐性和基因内启动子，它们可能构成预测的大肠杆菌启动子的三分之一。启动子活性取决于核心碱基与 ​​σ 因子的结构相互作用。合理工程可用于改变与 σ 因子相互作用的关键启动子元件核苷酸并消除下游转录活性。在本文中，我们提出CO别ř estrained P romoter小号IL ëncing (CORPSE)，一种去除基因内启动子的系统。CORPSE 利用 DNA-σ 因子结构关系来破坏嵌入基因编码序列中的σ ⁷⁰启动子，同时将同义密码子更改降至最低。此外，我们提出了一个倒置的 CORPSE 系统 iCORPSE，它可以在基因序列中创建高活性启动子，同时不会干扰修饰基因的功能。