Improved bacterial recombineering by parallelized protein discovery

Timothy M. Wannier, Akos Nyerges, Helene M. Kuchwara, Márton Czikkely, Dávid Balogh, Gabriel T. Filsinger, Nathaniel C. Borders, Christopher J. Gregg, Marc J. Lajoie, Xavier Rios, Csaba Pál, George M. Church

Research output: Article

1 Citation (Scopus)

Abstract

Exploiting bacteriophage-derived homologous recombination processes has enabled precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we introduce a highthroughput method for SSAP discovery that we call "serial enrichment for efficient recombineering" (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli, while PapRecT enables efficient recombineering in Pseudomonas aeruginosa, a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.

Original languageEnglish
Pages (from-to)13689-13698
Number of pages10
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number24
DOIs
Publication statusPublished - jún. 16 2020

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    Wannier, T. M., Nyerges, A., Kuchwara, H. M., Czikkely, M., Balogh, D., Filsinger, G. T., Borders, N. C., Gregg, C. J., Lajoie, M. J., Rios, X., Pál, C., & Church, G. M. (2020). Improved bacterial recombineering by parallelized protein discovery. Proceedings of the National Academy of Sciences of the United States of America, 117(24), 13689-13698. https://doi.org/10.1073/pnas.2001588117