Human mitochondrial gene expression relies on the specific recognition and aminoacylation of mitochondrial tRNAs (mtRNAs) by nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs). Despite their essential role in cellular energy homeostasis, strong mutation pressure and genetic drift have led to an unparalleled sequence erosion of animal mtRNAs. The structural and functional consequences of this erosion are not understood. Here, we present cryo-EM structures of the human mitochondrial seryl-tRNA synthetase (mSerRS) in complex with mtRNA^Ser(GCU). These structures reveal a unique mechanism of substrate recognition and aminoacylation. The mtRNA^Ser(GCU) is highly degenerated, having lost the entire D-arm, tertiary core, and stable L-shaped fold that define canonical tRNAs. Instead, mtRNA^Ser(GCU) evolved unique structural innovations, including a radically altered T-arm topology that serves as critical identity determinant in an unusual shape-selective readout mechanism by mSerRS. Our results provide a molecular framework to understand the principles of mito-nuclear co-evolution and specialized mechanisms of tRNA recognition in mammalian mitochondrial gene expression.

人类线粒体基因表达依赖于核编码线粒体氨酰-tRNA 合成酶 (mt-aaRS) 对线粒体 tRNA (mtRNA) 的特异性识别和氨酰化。尽管它们在细胞能量稳态中发挥着重要作用，但强大的突变压力和遗传漂变导致了动物 mRNA 无与伦比的序列侵蚀。这种侵蚀的结构和功能后果尚不清楚。在这里，我们展示了人类线粒体丝氨酰-tRNA 合成酶 (mSerRS) 与 mtRNA ^Ser(GCU)复合物的冷冻电镜结构。这些结构揭示了底物识别和氨酰化的独特机制。 mtRNA ^Ser(GCU)高度退化，失去了定义典型 tRNA 的整个 D 臂、三级核心和稳定的 L 形折叠。相反，mtRNA ^Ser(GCU)进化出了独特的结构创新，包括彻底改变的 T 臂拓扑，该拓扑在 mSerRS 不寻常的形状选择性读出机制中充当关键的身份决定因素。我们的结果提供了一个分子框架来理解线粒体-核共同进化的原理和哺乳动物线粒体基因表达中 tRNA 识别的特殊机制。