Systematic strategies for developing phage resistant Escherichia coli strains

Xuan Zou, Xiaohong Xiao, Ziran Mo, Yashi Ge, Xing Jiang, Ruolin Huang, Mengxue Li, Zixin Deng, Shi Chen (), Lianrong Wang () and Sang Yup Lee ()
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Xuan Zou: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Xiaohong Xiao: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Ziran Mo: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Yashi Ge: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Xing Jiang: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Ruolin Huang: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Mengxue Li: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Zixin Deng: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Shi Chen: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Lianrong Wang: Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
Sang Yup Lee: Korea Advanced Institute of Science and Technology

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract Phages are regarded as powerful antagonists of bacteria, especially in industrial fermentation processes involving bacteria. While bacteria have developed various defense mechanisms, most of which are effective against a narrow range of phages and consequently exert limited protection from phage infection. Here, we report a strategy for developing phage-resistant Escherichia coli strains through the simultaneous genomic integration of a DNA phosphorothioation-based Ssp defense module and mutations of components essential for the phage life cycle. The engineered E. coli strains show strong resistance against diverse phages tested without affecting cell growth. Additionally, the resultant engineered phage-resistant strains maintain the capabilities of producing example recombinant proteins, D-amino acid oxidase and coronavirus-encoded nonstructural protein nsp8, even under high levels of phage cocktail challenge. The strategy reported here will be useful for developing engineered E. coli strains with improved phage resistance for various industrial fermentation processes for producing recombinant proteins and chemicals of interest.

Date: 2022
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DOI: 10.1038/s41467-022-31934-9

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