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

Nobuhiko Muramoto,Norihiro Mitsukawa,Akinori Ikeuchi,Kunihiro Ohta,Takehiko Shibata,Arisa Oda,Hiroki Sugimoto,Takahiro Nakamura,Kazuto Kugou,Aki Kobayashi,Kazuki Suda,Shiori Yoneda,Chikara Ohto,Satoshi Kondo,Hidenori Tanaka

doi:10.1038/s41467-018-04256-y

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.

Highlights

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; it remains unclear about the consequences of massive simultaneous double-strand breaks (DSBs) formation in cells and their resulting phenotypic impact
Based on the degree of broken DNA fragments according to pulse-field gel electrophoresis (PFGE) analysis, we estimated that the DSB frequency was comparable to that in diploid meiotic yeast cells[16], which reportedly produce ~200 DSBs per cell
Our results demonstrated that one-time activation of genomewide multiple DSB formation is sufficient to efficiently induce large-scale genome rearrangements and phenotypic diversification

Summary

Introduction

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. 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. Genome rearrangements are thought to increase phenotypic diversity that provides critical raw materials for evolution Point mutations represent another source of raw genetic materials for natural selection, but provide relatively small changes in DNA sequences and enable rather limited exploration of the sequence space via “fitness–random walk” for adaptation to given environmental changes. Genome rearrangement and WGD might contribute synergistically to genome evolution, but it is difficult to assess the relative impact of DSB induction and genome rearrangements in diploid vs haploid yeast, or tetraploid compared to diploid plants

Methods

Results

Conclusion