Université de Paris, INSERM U1001, Paris, France.
Université Grenoble Alpes, CNRS UMR5525, Grenoble, France.
PLoS Comput Biol. 2021 Oct 8;17(10):e1009475. doi: 10.1371/journal.pcbi.1009475. eCollection 2021 Oct.
Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time.
由于选择使昂贵的基因回路失活的突变，进化往往是工程稳定生物系统的障碍。基因重叠对序列及其进化产生重要的限制。我们表明，可以利用这些限制来增加昂贵基因的稳定性，清除功能丧失突变。我们结合计算和合成生物学方法，合理设计重叠阅读框，在现有基因内表达必需基因以进行保护。我们的算法成功地在 80%的大肠杆菌基因中创建了重叠阅读框。在实验中，我们对这种重叠构建体的两个基因中的突变进行评分，发现影响保护基因的突变中有很大一部分对必需基因有不利影响。因此，这种重叠通过将这种去除的好处与更大甚至致命的代价联系起来，使昂贵的基因免受自然选择的去除。在我们的合成构建体中，重叠将许多可能的突变体转化为进化死胡同，从而降低系统的进化潜力，从而随着时间的推移增加其稳定性。
