Exploiting spatial dimensions to enable parallelized continuous directed evolution. Issue 9 (21st September 2022)

• Record Type: Journal Article
• Authors: Wei, Ting; Lai, Wangsheng; Chen, Qian; Zhang, Yi; Sun, Chenjian; He, Xionglei; Zhao, Guoping; Fu, Xiongfei; Liu, Chenli
• Is Part Of: Molecular systems biology. Volume 18:Issue 9(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-09-21
• Subjects: bacteriophage -- directed evolution -- range expansion -- spatial competition -- virus spreading; Molecular biology -- Periodicals; Systems biology -- Periodicals; 572.8
• DOI: 10.15252/msb.202210934
• Languages: English
• ISSNs: 1744-4292

Abstract

Abstract: Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid‐controlling system or robotic platforms, which limits their popularization and application in general laboratories. Inspired by our previous study on bacterial range expansion, in this study, we report a system termed SPACE for rapid and extensively parallelizable evolution of biomolecules by introducing spatial dimensions into the landmark phage‐assisted continuous evolution system. Specifically, M13 phages and chemotactic Escherichia coli cells were closely inoculated onto a semisolid agar. The phages came into contact with the expanding front of the bacterial range, and then comigrated with the bacteria. This system leverages competition over space, wherein evolutionary progress is closely associated with the production of spatial patterns, allowing the emergence of improved or new protein functions. In a prototypical problem, SPACE remarkably simplified the process and evolved the promoter recognition of T7 RNA polymerase (RNAP) to a library of 96 random sequences in parallel. These results establish SPACE as a simple, easy to implement, and massively parallelizable platform for continuous directed evolution in general laboratories. Synopsis: The spatial competition among phages that infect range‐expanding host bacteria is exploited to develop a spatial continuous directed evolution system that is simple, easy to implement, and massively parallelizable. SPACE is a system for rapid and parallelizable evolution of biomolecules, which introduces spatial dimensions into the phage‐assisted continuous evolution system. The system leverages competition over space, wherein evolutionary progress is closely associated with the production of spatial patterns, allowing the emergence of improved or new protein functions. SPACE is applied to evolve the promoter recognition of T7 RNA polymerase to a library of 96 random sequences in parallel. Abstract : The spatial competition among phages that infect range‐expanding host bacteria is exploited to develop a spatial continuous directed evolution system that is simple, easy to implement, and massively parallelizable.