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Omics-guided bacterial engineering of Escherichia coli ER2566 for recombinant protein expression
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  • Liz Zhou,
  • Yue Ma,
  • Kaihang Wang,
  • Tingting Chen,
  • Yang Huang,
  • Liqin Liu,
  • Yuqian Li,
  • Jie Sun,
  • Yisha Hu,
  • Tingting Li,
  • Yingbin Wang,
  • Qingbing Zheng,
  • Qinjian Zhao,
  • Jun Zhang,
  • Ying Gu,
  • Hai Yu,
  • Shaowei Li,
  • Ningshao Xia
Liz Zhou
Xiamen University
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Yue Ma
Xiamen University
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Kaihang Wang
Zhejiang University First Affiliated Hospital Department of Hematology
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Tingting Chen
Xiamen University
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Yang Huang
Xiamen University
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Liqin Liu
Xiamen University
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Yuqian Li
Xiamen University
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Jie Sun
Xiamen University
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Yisha Hu
Xiamen University
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Tingting Li
Xiamen University
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Yingbin Wang
Xiamen University
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Qingbing Zheng
Xiamen University
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Qinjian Zhao
Xiamen University
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Jun Zhang
Xiamen University
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Ying Gu
Xiamen University
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Hai Yu
Xiamen University
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Shaowei Li
Xiamen University

Corresponding Author:[email protected]

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Ningshao Xia
National Institute of Diagnostics and Vaccine Development in Infectious Diseases
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Abstract

The production of exogenous recombinant proteins is constrained by the complexity of the connections between cellular physiology and recombinant protein synthesis. Here, we developed a rational and highly efficient approach to improve bacterial engineering, using HPV16-L1 as a protein candidate. Comparing the transcriptomic profiles of the strain under leaky expression and low temperature-induced stress, we found that leaky expression accelerated host energy metabolism and altered ribosome synthesis assembly, and inducing overexpression of the heterologous protein under low-temperature conditions led to an upregulation in polysaccharide transport, and cell motility, and a downregulation in oxidation-reduction, and anaerobic respiration. Subsequently, we selected and knocked out 36 hub genes to determine the potential impact of these genes on protein production. Deletion of bluF, cydA, mngR, and udp led to a significant decrease in soluble recombinant protein production. Moreover, knocking out several motility-related DEGs (ER2666-ΔflgH-ΔflgL, ER2666-ΔflgH-ΔflgL-ΔflgK) simultaneously improved the protein yield by 1.5-fold at 24°C or 37°C induction. This study highlights a rational and efficient strategy to increase the yield of recombinant proteins in model or non-model organisms, and lays a solid foundation for the engineering of bacterial strains for recombinant technological advances.