Naturally occurring structural variations (SVs) are a considerable source of genomic variation and can reshape chromosomes 3D architecture. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system has been proved to generate random SVs to impact phenotypes and thus constitutes powerful drivers of directed genome evolution. However, how to reveal the molecular mechanism insights into the interactions between phenotypes and complex SVs, especially inversions and translocations, has so far remained challenging. In this study, we develop a SV-prone yeast strain by using SCRaMbLE with two synthetic chromosomes, synV and synX. An heterologous biosynthesis pathway allowing a high throughput screen for increased yield of astaxanthin is used as readout and a proof of concept for the application of SV in industry. We report here that complex SVs, including a pericentric inversion and a trans-chromosomes translocation between synV and synX, result in two neochromosomes and a 2.7-fold yield of astaxanthin. We demonstrated that inversion and inversion reshaped chromosomes 3D architecture and led to large reorganization of the genetic information nearby the breakpoint of the SVs along the chromosomes. Specifically, the pericentric inversion increased the expression of STE18 and the trans-chromosomic translocation increased the expression of RPS5 and MCM22, which contributed to higher astaxanthin yield. We also used the model learned from the aforementioned random screen and successfully harnessed the precise introduction of trans-chromosomes translocation and pericentric inversions by rational design. Overall, our work provides an effective tool to not only accelerate the directed genome evolution but also reveal mechanistic insight of complex SVs for altering phenotypes.

中文翻译：

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通过受控引入跨染色体结构变异来定向酵母基因组进化

自然发生的结构变异 (SV) 是基因组变异的重要来源，可以重塑染色体 3D 结构。loxP 介导的进化 (SCRaMbLE) 系统的合成染色体重排和修饰已被证明会产生随机 SV 来影响表型，从而构成定向基因组进化的强大驱动力。然而，迄今为止，如何揭示表型与复杂 SV 之间相互作用的分子机制，尤其是倒位和易位，仍然具有挑战性。在这项研究中，我们通过使用具有两个合成染色体 synV 和 synX 的 SCRaMbLE 开发了一种 SV 倾向酵母菌株。允许高通量筛选以提高虾青素产量的异源生物合成途径被用作读数和 SV 在工业中应用的概念证明。我们在此报告了复杂的 SV，包括着丝粒倒位和 synV 和 synX 之间的跨染色体易位，导致两条新染色体和 2.7 倍的虾青素产量。我们证明了倒位和倒位重塑了染色体的 3D 结构，并导致沿染色体的 SV 断点附近的遗传信息进行了大量重组。具体而言，着丝粒倒位增加了 STE18 的表达，而跨染色体易位增加了 RPS5 和 MCM22 的表达，这有助于提高虾青素产量。我们还使用了从上述随机筛选中学到的模型，并通过合理的设计成功地利用了跨染色体易位和中心倒位的精确引入。全面的，