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Transposon-plasmid nesting enables fast response to fluctuating environments

Yuanchi Ha,Rohan Maddamsetti,Xiaoli Chen,E. Şimşek,Dongheon Lee,Hye-in Son,Charlotte T. Lee,E. Kussell,Lingchong You

Published 2025 in bioRxiv

ABSTRACT

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.

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