Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks

Nobuhiko Muramoto, Arisa Oda (), Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa () and Kunihiro Ohta ()
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Nobuhiko Muramoto: Toyota Central R&D Laboratories, Inc.
Arisa Oda: The University of Tokyo
Hidenori Tanaka: Toyota Central R&D Laboratories, Inc.
Takahiro Nakamura: The University of Tokyo
Kazuto Kugou: The University of Tokyo
Kazuki Suda: The University of Tokyo
Aki Kobayashi: The University of Tokyo
Shiori Yoneda: The University of Tokyo
Akinori Ikeuchi: Toyota Central R&D Laboratories, Inc.
Hiroki Sugimoto: Toyota Central R&D Laboratories, Inc.
Satoshi Kondo: Toyota Motor Corporation
Chikara Ohto: Toyota Motor Corporation
Takehiko Shibata: RIKEN Advanced Science Institute
Norihiro Mitsukawa: Toyota Central R&D Laboratories, Inc.
Kunihiro Ohta: The University of Tokyo

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: Abstract DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.

Date: 2018
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DOI: 10.1038/s41467-018-04256-y

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