Sandberg Troy E, Wise Kim S, Dalldorf Christopher, Szubin Richard, Feist Adam M, Glass John I, Palsson Bernhard O
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
J. Craig Venter Institute, San Diego, La Jolla, CA, USA.
iScience. 2023 Jul 28;26(9):107500. doi: 10.1016/j.isci.2023.107500. eCollection 2023 Sep 15.
The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the genome and chemically synthesized . Here, we report the experimental evolution of a syn3.0- derived strain. Ten independent replicates were evolved for several hundred generations, leading to growth rate improvements of > 15%. Endpoint strains possessed an average of 8 mutations composed of indels and SNPs, with a pronounced C/G- > A/T transversion bias. Multiple genes were repeated mutational targets across the independent lineages, including phase variable lipoprotein activation, 5 distinct; nonsynonymous substitutions in the same membrane transporter protein, and inactivation of an uncharacterized gene. Transcriptomic analysis revealed an overall tradeoff reflected in upregulated ribosomal proteins and downregulated DNA and RNA related proteins during adaptation. This work establishes the suitability of synthetic, minimal strains for laboratory evolution, providing a means to optimize strain growth characteristics and elucidate gene functionality.
细菌菌株JCVI-syn3.0是首个拥有最小化合成基因组的活生物体实例，该基因组源自天然基因组并经过化学合成。在此，我们报告了一株源自syn3.0的菌株的实验性进化情况。十个独立的重复样本历经数百代进化，生长速率提高了超过15%。终点菌株平均有8个由插入缺失和单核苷酸多态性组成的突变，具有明显的C/G到A/T颠换偏向。多个基因是独立谱系中反复出现的突变靶点，包括相变可变脂蛋白激活（5个不同的）、同一膜转运蛋白中的非同义替换以及一个未表征基因的失活。转录组分析揭示了在适应过程中核糖体蛋白上调而DNA和RNA相关蛋白下调所反映出的整体权衡。这项工作确立了合成的最小菌株适用于实验室进化，为优化菌株生长特性和阐明基因功能提供了一种手段。
