Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Commun Biol. 2024 Nov 4;7(1):1434. doi: 10.1038/s42003-024-07167-5.
The balance between chromosomal and plasmid DNAs determines the genomic plasticity of prokaryotes. Natural selections, acting on the level of organisms or plasmids, shape the abundances of plasmid DNAs in prokaryotic genomes. Despite the importance of plasmids in health and engineering, there have been rare systematic attempts to quantitatively model and predict the determinants underlying the strength of different selection forces. Here, we develop a metabolic flux model that describes the intracellular resource competition between chromosomal and plasmid-encoded reactions. By coarse graining, this model predicts a landscape of natural selections on chromosome/plasmid balance, which is featured by the tradeoff between phenotypic and non-phenotypic selection pressures. This landscape is further validated by the observed pattern of plasmid distributions in the vast collection of prokaryotic genomes retrieved from the NCBI database. Our results establish a universal paradigm to understand the prokaryotic chromosome/plasmid interplay and provide insights into the evolutionary origin of plasmid diversity.
染色体和质粒 DNA 之间的平衡决定了原核生物的基因组可塑性。在生物体或质粒水平上起作用的自然选择决定了原核生物基因组中质粒 DNA 的丰度。尽管质粒在健康和工程方面很重要，但很少有系统的尝试来定量建模和预测不同选择力的基础决定因素。在这里，我们开发了一个代谢通量模型，该模型描述了染色体和质粒编码反应之间的细胞内资源竞争。通过粗粒化，该模型预测了染色体/质粒平衡的自然选择景观，其特征是表型和非表型选择压力之间的权衡。从 NCBI 数据库中检索到的大量原核基因组中观察到的质粒分布模式进一步验证了这一景观。我们的结果建立了一个普遍的范例来理解原核生物的染色体/质粒相互作用，并深入了解质粒多样性的进化起源。
