title: Liquid-based iterative recombineering method tolerant to counter-selection escapes.
abstract: Selection-based recombineering is a flexible and proven technology to precisely modify bacterial genomes at single base resolution. It consists of two steps of homologous recombination followed by selection/counter-selection. However, the shortage of efficient counter-selectable markers limits the throughput of this method. Additionally, the emergence of 'selection escapees' can affect recombinant pools generated through this method, and they must be manually removed at each step of selection-based recombineering. Here, we report a series of efforts to improve the throughput and robustness of selection-based recombineering and to achieve seamless and automatable genome engineering. Using the nucleoside kinase activity of herpes simplex virus thymidine kinase (hsvTK) on the non-natural nucleoside dP, a highly efficient, rapid, and liquid-based counter-selection system was established. By duplicating hsvtk gene, combined with careful control of the population size for the subsequent round, we effectively eliminated selection escapes, enabling seamless and multiple insertions/replacement of gene-size fragments in the chromosome. Four rounds of recombineering could thus be completed in 10 days, requiring only liquid handling and without any need for colony isolation or genotype confirmation. The simplicity and robustness of our method make it broadly accessible for multi-locus chromosomal modifications.
authors.affiliation: Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Tominaga
authors.affiliation: Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan.
authors.forename: Shigeko
authors.initials: S
authors.lastname: Kawai-Noma
authors.affiliation: Department of Frontier Bioscience, Hosei University, 3-7-2, Koganei, Tokyo 184-8584, Japan.
authors.forename: Ikuro
authors.initials: I
authors.lastname: Kawagishi
authors.affiliation: Department of Frontier Bioscience, Hosei University, 3-7-2, Koganei, Tokyo 184-8584, Japan; Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Tokyo 184-8584, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sowa
authors.affiliation: Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan.
authors.forename: Kyoichi
authors.initials: K
authors.lastname: Saito
authors.affiliation: Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Umeno
mesh_terms: D003001:Cloning, Molecular / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics*; D060847:Metabolic Engineering / Q000379:methods*; D018139:Simplexvirus / Q000201:enzymology / Q000235:genetics*; D013937:Thymidine Kinase / Q000235:genetics* / Q000378:metabolism
chemical_list: D013937:Thymidine Kinase