Selective RNA Processing and Stabilization are Multi-Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli.
Selective RNA Processing and Stabilization are Multi-Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli.
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DOI：
10.1002/advs.202301459
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发表时间：
2023-11
期刊：
影响因子：
15.1
通讯作者：
Huang, Ranran
中科院分区：
文献类型：
--
作者：
Liu, Daixi;Lv, Haibo;Wang, Yafei;Chen, Jinyu;Li, Dexin;Huang, Ranran
关键词：
选择性RNA加工和稳定化（SRPS）促进多顺反子操纵子中多个基因的差异表达。然而，SRPS相关酶的协调作用如何影响化学计量调节仍不清楚。在本研究中，首次报道了大肠杆菌中这些酶的全基因组靶向组分析，采用单核苷酸分辨率。在RNA焦磷酸水解酶加工比率和分配给初级转录物的前三个核苷酸的分数之间观察到严格的线性关系。与PNIPs靶向体相关的茎-环显示出与PNIPs在3′端的终止率负相关的折叠自由能。5′非翻译区（UTR）中超过十分之一的RNase E加工位点形成不同的茎环，影响核糖体结合和翻译效率。使用双荧光报告系统验证SRPS元件的有效性。这些发现突出了一种多层和定量调控方法，用于优化细菌中基因的化学计量表达，并促进SRPS在合成生物学中的应用。选择性RNA加工和稳定（SRPS）有助于多顺反子操纵子中多个基因的差异表达。这一发现提出了一种多层、定量和普遍存在的转录后调控机制以及精确优化基因表达化学计量的元素。此外，这一发现提出了一种新的策略，“多顺反子操纵子加SRPS元件”，以解决挑战的“平衡表达的底盘细胞中的多个基因”在合成生物学。
Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS‐related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome‐wide targetome analysis is reported of these enzymes in Escherichia coli, at a single‐nucleotide resolution. A strictly linear relationship is observed between the RNA pyrophosphohydrolase processing ratio and scores assigned to the first three nucleotides of the primary transcript. Stem‐loops associated with PNPase targetomes exhibit a folding free energy that is negatively correlated with the termination ratio of PNPase at the 3′ end. More than one‐tenth of the RNase E processing sites in the 5′‐untranslated regions（UTR） form different stem‐loops that affect ribosome‐binding and translation efficiency. The effectiveness of the SRPS elements is validated using a dual‐fluorescence reporter system. The findings highlight a multi‐layer and quantitative regulatory method for optimizing the stoichiometric expression of genes in bacteria and promoting the application of SRPS in synthetic biology. The selective RNA processing and stabilization (SRPS) facilitate differential expression of multiple genes in polycistronic operons. The discovery presents a multilayer, quantitative, and ubiquitous posttranscriptional regulatory mechanism as well as elements to precisely optimize gene expression stoichiometry. Moreover, this finding suggests a novel strategy of ‘polycistronic operon plus SRPS elements’ to address the challenge of ‘balanced expression of multiple genes in chassis cells’ in synthetic biology.
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影响因子：
11.1
作者：
Hui MP;Foley PL;Belasco JG
通讯作者：
Belasco JG
DOI：
10.1126/science.1191652
发表时间：
2010-10-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ajikumar PK;Xiao WH;Tyo KE;Wang Y;Simeon F;Leonard E;Mucha O;Phon TH;Pfeifer B;Stephanopoulos G
通讯作者：
Stephanopoulos G
影响因子：
14.9
作者：
Dar D;Sorek R
通讯作者：
Sorek R
影响因子：
56.9
作者：
Caputi, Lorenzo;Franke, Jakob;O'Connor, Sarah E.
通讯作者：
O'Connor, Sarah E.
影响因子：
16.6
作者：
Broglia, Laura;Lecrivain, Anne-Laure;Charpentier, Emmanuelle
通讯作者：
Charpentier, Emmanuelle