Codon usage influences fitness through RNA toxicity.
Codon usage influences fitness through RNA toxicity.
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DOI：
10.1073/pnas.1810022115
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发表时间：
2018-08-21
影响因子：
11.1
通讯作者：
Kudla G
中科院分区：
文献类型：
--
作者：
Mittal P;Brindle J;Stephen J;Plotkin JB;Kudla G
基因的同义突变不会改变蛋白质序列，但可能会影响基因表达和细胞功能。在这里，我们描述了大肠杆菌中同义突变的一个意想不到的毒性效应，对细菌生理学和进化具有潜在的重大影响。与之前研究的同义突变的影响不同，我们发现的影响与翻译无关，但它依赖于有毒mRNA分子的产生。我们假设，我们确定的机制通过对基因组中出现的同义突变施加选择性限制，影响细菌内源基因的进化。对生物技术和合成生物学感兴趣的是，我们鉴定了能够减轻RNA毒性的细菌菌株和生长条件，从而允许高效地过度表达异源蛋白质。许多生物体受到选择压力的影响，这会导致同义密码子的不平等使用，即密码子偏向。为了实验地剖析同义位点上的选择机制，我们在大肠杆菌中表达了数百个GFP基因的同义变体，并使用定量生长和活力分析来评估细菌的适合性。出乎意料的是，我们发现了许多表达对大肠杆菌有毒的同义变体。与之前研究的同义突变的影响不同，我们发现的影响与翻译无关，但它依赖于有毒mRNA分子的产生。我们确定了毒性的RNA序列决定因素，并进化出能够耐受有毒GFP变体表达的抑制菌株。对这些抑制株的基因组测序显示，一组启动子突变通过降低mRNA水平来防止毒性。我们得出结论，非翻译依赖的RNA毒性是细菌基因表达的一个以前未被认识到的障碍。
Synonymous mutations in genes do not change protein sequence, but they may affect gene expression and cellular function. Here we describe an unexpected toxic effect of synonymous mutations in Escherichia coli, with potentially large implications for bacterial physiology and evolution. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We hypothesize that the mechanism we identified influences the evolution of endogenous genes in bacteria by imposing selective constraints on synonymous mutations that arise in the genome. Of interest for biotechnology and synthetic biology, we identify bacterial strains and growth conditions that alleviate RNA toxicity, thus allowing efficient overexpression of heterologous proteins. Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To experimentally dissect the mechanisms of selection on synonymous sites, we expressed several hundred synonymous variants of the GFP gene in Escherichia coli, and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic to E. coli. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We identified RNA sequence determinants of toxicity and evolved suppressor strains that can tolerate the expression of toxic GFP variants. Genome sequencing of these suppressor strains revealed a cluster of promoter mutations that prevented toxicity by reducing mRNA levels. We conclude that translation-independent RNA toxicity is a previously unrecognized obstacle in bacterial gene expression.
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原核生物和真核生物翻译起始位点附近 mRNA 稳定性降低的普遍趋势
影响因子：
4.3
作者：
Gu W;Zhou T;Wilke CO
通讯作者：
Wilke CO
影响因子：
10.7
作者：
Knöppel A;Näsvall J;Andersson DI
通讯作者：
Andersson DI
影响因子：
4.6
作者：
Kwon SK;Kim SK;Lee DH;Kim JF
通讯作者：
Kim JF
DOI：
10.1038/nrg2899
发表时间：
2011-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
64.8
作者：
Jain A;Vale RD
通讯作者：
Vale RD