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<p>Reconstructing transcription–translation-coupled DNA replication (TTcDR) in artificial systems is crucial for creating synthetic life; however, existing approaches face limitations mainly due to their reliance on purified biological components. Here, we introduce LoopReX, a cell-free system that reconstitutes TTcDR using crude <i>Escherichia coli</i> extracts, offering a more complex native biological environment. LoopReX leverages a minimal machinery composed of phi29 DNA polymerase and T7 RNA polymerase, with the latter facilitating DNA replication initiation through the generation of primer RNAs. Using machine learning, we optimize LoopReX to enhance the efficiency of both DNA replication and protein expression, achieving scalable, sustainable genetic flow and high-yield protein production with robust iterative performance. Furthermore, artificial nucleoids, autonomously formed through CipB-based compartmentalization, improve DNA spatial organization and support multiple biological functions. This work advances the construction of artificial life by reconstituting TTcDR within a single, scalable, and functionalized system, opening exciting possibilities for synthetic biology, biotechnology, and bio-hybrid applications.</p>

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Reconstituting transcription–translation-coupled DNA replication within complex in vitro biological systems

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月15日

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  • Xiao Zheng,
  • Wenli Gao,
  • Wan-Qiu Liu,
  • Yufei Zhang,
  • Shuhui Huang,
  • Xiangyang Ji,
  • Yicong Lu,
  • Yifan Liu,
  • Shengjie Ling,
  • Jian Li

摘要

Reconstructing transcription–translation-coupled DNA replication (TTcDR) in artificial systems is crucial for creating synthetic life; however, existing approaches face limitations mainly due to their reliance on purified biological components. Here, we introduce LoopReX, a cell-free system that reconstitutes TTcDR using crude Escherichia coli extracts, offering a more complex native biological environment. LoopReX leverages a minimal machinery composed of phi29 DNA polymerase and T7 RNA polymerase, with the latter facilitating DNA replication initiation through the generation of primer RNAs. Using machine learning, we optimize LoopReX to enhance the efficiency of both DNA replication and protein expression, achieving scalable, sustainable genetic flow and high-yield protein production with robust iterative performance. Furthermore, artificial nucleoids, autonomously formed through CipB-based compartmentalization, improve DNA spatial organization and support multiple biological functions. This work advances the construction of artificial life by reconstituting TTcDR within a single, scalable, and functionalized system, opening exciting possibilities for synthetic biology, biotechnology, and bio-hybrid applications.