Ha Yuanchi, Maddamsetti Rohan, Chen Xiaoli, Şimşek Emrah, Lee Dongheon, Son Hyein, Lee Charlotte, Kussell Edo, You Lingchong
Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.
Center for Quantitative Biodesign, Duke University, Durham, North Carolina, USA.
bioRxiv. 2025 Jun 8:2025.06.04.657954. doi: 10.1101/2025.06.04.657954.
Mobile genetic elements (MGEs) play a critical role in shaping the response and evolution of microbial populations and communities. Despite distinct maintenance mechanisms, different types of MGEs can form nested structures. Using bioinformatics analysis of 14,338 plasmids in the NCBI RefSeq database, we found transposons to be widespread and significantly enriched on plasmids relative to chromosomes, highlighting the prevalence of transposon-plasmid nesting. We hypothesized that this nested structure provides unique adaptive advantages by combining transposition-driven genetic mobility with plasmid-mediated copy number amplification. Using engineered transposon systems, we demonstrated that nesting enables rapid and tunable responses of transposon-encoded genes in fluctuating environments. Specifically, transposition maintains a reservoir of the encoded genes, while plasmid copy number fluctuations further amplify the dynamic range of gene dosage, thus enhancing the response speed and stability of transposon-encoded traits. Our findings demonstrate an adaptive benefit of transposon-plasmid nesting and provide insights into their ecological persistence and evolutionary success.
可移动遗传元件（MGEs）在塑造微生物种群和群落的反应及进化过程中发挥着关键作用。尽管存在不同的维持机制，但不同类型的MGEs可形成嵌套结构。通过对NCBI RefSeq数据库中14338个质粒进行生物信息学分析，我们发现转座子广泛存在，且相对于染色体而言，在质粒上显著富集，这突出了转座子 - 质粒嵌套的普遍性。我们推测，这种嵌套结构通过将转座驱动的遗传流动性与质粒介导的拷贝数扩增相结合，提供了独特的适应性优势。利用工程化转座子系统，我们证明了嵌套能够使转座子编码的基因在波动环境中做出快速且可调节的反应。具体而言，转座作用维持了编码基因的储备库，而质粒拷贝数的波动进一步扩大了基因剂量的动态范围，从而提高了转座子编码性状的反应速度和稳定性。我们的研究结果证明了转座子 - 质粒嵌套的适应性益处，并为它们的生态持久性和进化成功提供了见解。
