A major challenge in synthetic biology is properly balancing evolved and engineered functions without compromising microbial fitness. Many microbial proteins are not required for growth in regular laboratory conditions, but it is unclear what fraction of the proteome can be eliminated to increase bioproduction and maintain fitness. Here, we investigated the effects of massive genome reduction in E. coli on the expression level and evolutionary stability of a model biosynthetic pathway to produce the pigment protodeoxyviolacein (PDV). We identified an amino acid metabolism imbalance and compromised growth that were correlated with elimination of genes associated with significant proteome fraction. Proteomic profiling suggested that increased amino acid pools are responsible for an alleviation of fitness defects associated with PDV expression. In addition, all strains with genome reductions that significantly affected the proteome exhibited decreased stability of PDV production compared to the wild-type strain under persistent PDV expression conditions despite the alleviation of fitness defects. These findings exhibit the importance of balancing evolved functions with engineered ones to achieve an optimal balance of fitness and bioproduction.

中文翻译：

---

基因组减少的工程化大肠杆菌菌株中的资源重新分配

合成生物学的一个主要挑战是在不损害微生物适应性的前提下，适当平衡进化和工程化的功能。在常规实验室条件下生长不需要许多微生物蛋白，但是尚不清楚可以去除蛋白质组的哪一部分以增加生物产量并保持健康。在这里，我们调查了大肠杆菌中大量基因组减少对表达水平和生产色素原脱氧紫胶素（PDV）的模型生物合成途径的进化稳定性的影响。我们确定了氨基酸代谢失衡和生长受损，这与消除与重要蛋白质组分数相关的基因有关。蛋白质组学分析表明，增加的氨基酸库可减轻与PDV表达相关的适应性缺陷。此外，与基因型减少的所有菌株相比，在持久性PDV表达条件下，尽管减轻了适应性缺陷，但与野生型菌株相比，其显着影响蛋白质组的基因组减少的PDV生产稳定性却下降。这些发现表明平衡进化功能与工程功能以实现健身和生物生产的最佳平衡的重要性。