A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks

In bacteria, natural transposon mobilization can drive adaptive genomic rearrangements. Here, we build on this capability and develop an inducible, self-propagating transposon platform for continuous genome-wide mutagenesis and the dynamic rewiring of gene networks in bacteria. We first use the platform to study the impact of transposon functionalization on the evolution of parallel E. coli populations towards diverse carbon source utilization and antibiotic resistance phenotypes. We then develop a modular, combinatorial assembly pipeline for the functionalization of transposons with synthetic or endogenous gene regulatory elements (e.g., inducible promoters) as well as DNA barcodes. We compare parallel evolutions across alternating carbon sources, and demonstrate the emergence of inducible, multi-genic phenotypes and the ease with which barcoded transposons can be tracked longitudinally to identify the causative rewiring of gene networks. This work establishes a synthetic transposon platform that can be used to optimize strains for industrial and therapeutic applications, e.g., by rewiring gene networks to improve growth on diverse feedstocks, as well as help address fundamental questions about the dynamic processes that have sculpted extant gene networks.

在细菌中，天然转座子（transposon）的转座活动可驱动适应性基因组重排。本研究基于这一特性，开发了一套可诱导、自我增殖的转座子平台，能够在细菌中实现全基因组范围的持续诱变，并对基因网络进行动态重构。
我们首先利用该平台，探究转座子功能化对平行大肠杆菌（E. coli）种群向多种碳源利用与抗生素耐药表型演化的影响。
随后，我们开发了一套模块化组合组装流程，可利用合成或内源基因调控元件（如可诱导启动子）以及DNA条形码对转座子进行功能化改造。
我们对比了交替碳源条件下的平行演化实验，证实可诱导多基因表型的出现，且条形码转座子可便捷地实现纵向追踪，以此确定介导基因网络重连的关键动因。
本研究构建的合成转座子平台，既可用于工业与治疗相关的菌株优化（例如通过重连基因网络以提升菌株在多种原料底物上的生长性能），也可助力解答关于塑造现存基因网络的动态过程的基础科学问题。