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<p>Current methods for protein engineering are constrained by limited understanding of sequence–function relationships, the difficulty of designing complex properties by artificial intelligence methods and labor-intensive directed evolution. Here, to enable continuous and scalable protein evolution and systematic exploration of protein adaptive landscapes, we established an industrial-grade automation platform featuring high throughput, high efficiency, enhanced reliability and minimal human intervention (operational for ~1 month). We then developed new genetic circuits for the OrthoRep continuous evolution system to achieve growth-coupled evolution for proteins with diverse and complex functionalities. This included improving lactate sensitivity of LldR via dual selection and increasing operator selectivity for LmrA using the NIMPLY circuit. We integrated these components into an all-in-one laboratory, iAutoEvoLab, and evolved proteins from inactive precursors to fully functional entities, such as a T7 RNA polymerase fusion protein CapT7 with mRNA capping properties, which can be directly applied to in vitro mRNA transcription and mammalian systems. Our system represents a versatile tool for protein engineering and expands the scope for investigating the origins and evolutionary trajectories of protein functions.</p><p></p>

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An industrial automated laboratory for programmable protein evolution

  • 期刊论文

  • 发表日期：

    2025年11月19日

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  • Da Shen,
  • Xin Wang,
  • Yuan Gao,
  • Wei Wang,
  • Yuchao Li,
  • He Chen,
  • Yushuai Guo,
  • Shuaihua Cao,
  • Yuqing Huang,
  • Yan Zhang,
  • Chengzhi Wang,
  • Shuyi Zhang

摘要

Current methods for protein engineering are constrained by limited understanding of sequence–function relationships, the difficulty of designing complex properties by artificial intelligence methods and labor-intensive directed evolution. Here, to enable continuous and scalable protein evolution and systematic exploration of protein adaptive landscapes, we established an industrial-grade automation platform featuring high throughput, high efficiency, enhanced reliability and minimal human intervention (operational for ~1 month). We then developed new genetic circuits for the OrthoRep continuous evolution system to achieve growth-coupled evolution for proteins with diverse and complex functionalities. This included improving lactate sensitivity of LldR via dual selection and increasing operator selectivity for LmrA using the NIMPLY circuit. We integrated these components into an all-in-one laboratory, iAutoEvoLab, and evolved proteins from inactive precursors to fully functional entities, such as a T7 RNA polymerase fusion protein CapT7 with mRNA capping properties, which can be directly applied to in vitro mRNA transcription and mammalian systems. Our system represents a versatile tool for protein engineering and expands the scope for investigating the origins and evolutionary trajectories of protein functions.