Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate

Cell growth is determined by substrate availability and the cell’s metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can accelerate or slow growth, depending on genetic background and environmental conditions. We evolved a diverse set of Escherichia coli single-gene deletion mutants with a spectrum of growth rates and identified mutations that generally increase growth rate. Despite the metabolic differences between parent strains, mutations that enhanced growth largely mapped to core transcription machinery, including the β and β’ subunits of RNA polymerase (RNAP) and the transcription elongation factor, NusA. The structural segments of RNAP that determine enhanced growth have been previously implicated in antibiotic resistance and in the control of transcription elongation and pausing. We further developed a computational framework to characterize how the transcriptional changes that occur upon acquisition of these mutations affect growth rate across strains. Our experimental and computational results provide evidence for cases in which RNAP mutations shift the competitive balance between active transcription and gene silencing. This study demonstrates that mutations in specific regions of RNAP are a convergent adaptive solution that can enhance the growth rate of cells from distinct metabolic states.细胞生长由底物可获得性，以及细胞将底物同化为生物合成构件的代谢能力共同决定。决定生长速率的代谢基因可发生协同或拮抗相互作用，并可根据遗传背景与环境条件加速或减缓细胞生长。我们通过定向进化获得了一组涵盖不同生长速率表型的多样化大肠杆菌（Escherichia coli）单基因缺失突变体群体，并筛选出可普遍提升生长速率的突变。尽管亲本菌株存在代谢差异，但促生长突变主要定位于核心转录机器，包括RNA聚合酶（RNA polymerase, RNAP）的β与β’亚基，以及转录延伸因子NusA。此前已有研究表明，介导生长提升的RNAP结构区段与抗生素抗性、转录延伸及暂停调控相关。我们进一步开发了一套计算框架，用以解析这些突变获得后引发的转录变化如何在不同菌株中影响生长速率。本研究的实验与计算结果证实，RNAP突变可改变活性转录与基因沉默之间的竞争平衡。本研究表明，RNA聚合酶特定区域的突变是一种趋同适应性策略，可提升不同代谢状态下细胞的生长速率。