Transposable elements (TEs) drive genome evolution in all branches of life. TE insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1’), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains but little is known about what controls its copy number. Here, we provide evidence that a novel gene from an exapted Ty1’ sequence, Domesticated Restriction of Ty1’ relic 2 (DRT2), encodes a restriction factor that inhibits Ty1’ movement. DRT2 arose through domestication of a Ty1’ GAG gene and contains the C-terminal domain of capsid (CA-CTD), which in the related Ty1 canonical (Ty1c) subfamily functions as a self-encoded restriction factor. Bioinformatic analysis reveals the widespread nature of DRT2, its evolutionary history, and pronounced structural variation at the Ty1’ relic 2 locus. Ty1’ retromobility analyses demonstrate DRT2 restriction factor functionality, and northern blot and RNA-seq analysis indicate that DRT2 is transcribed in multiple strains. Velocity co-sedimentation profiles indicate an association between Drt2 and Ty1’ virus like particles (VLPs) or assembly complexes. Chimeric Ty1’ elements containing DRT2 retain retromobility, suggesting an ancestral role of productive Gag CA-CTD functionality is present in the sequence. Unlike Ty1c, Ty1’ retromobility increases with copy number, suggesting that CA-CTD based restriction is not limited to the Ty1c subfamily self-encoded restriction factor and drove the endogenization of DRT2. The discovery of an exapted Ty1’ restriction factor provides insight into the evolution of the Ty1 family, evolutionary hot-spots, and host-TE interactions.

中文翻译：

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通过酵母逆转录转座子的驯化来进化限制因子

转座元件 (TE) 驱动生命所有分支的基因组进化。TE 插入通常对其宿主有害，因此需要改进控制机制来限制其传播。长末端重复反转录转座子 Ty1 prime (Ty1') 是 Ty1 家族的一个亚家族，存在于许多酿酒酵母菌株中，但人们对控制其拷贝数的因素知之甚少。在这里，我们提供的证据表明，来自延伸的 Ty1' 序列的新基因，即 Ty1' 遗迹 2 (DRT2) 的驯化限制，编码了抑制 Ty1' 运动的限制因子。DRT2 通过 Ty1' GAG 基因的驯化产生，并包含衣壳的 C 末端结构域 (CA-CTD)，该结构域在相关的 Ty1 规范 (Ty1c) 亚家族中充当自编码限制因子。生物信息分析揭示了 DRT2 的广泛性质、其进化历史以及 Ty1' 遗迹 2 基因座的显着结构变异。Ty1' 逆转录分析证明了 DRT2 限制因子的功能，Northern 印迹和 RNA-seq 分析表明 DRT2 在多个菌株中转录。速度共沉降曲线表明 Drt2 和 Ty1' 病毒样颗粒 (VLP) 或组装复合物之间存在关联。含有 DRT2 的嵌合 Ty1' 元件保留了逆转录性，表明序列中存在生产性 Gag CA-CTD 功能的祖先作用。与 Ty1c 不同，Ty1' 的逆转录性随着拷贝数的增加而增加，这表明基于 CA-CTD 的限制并不限于 Ty1c 亚家族自编码限制因子，并且驱动了 DRT2 的内源化。延伸的 Ty1' 限制因子的发现提供了对 Ty1 家族进化、进化热点和宿主-TE 相互作用的深入了解。