Paukstelis Paul J, Chen Jui-Hui, Chase Elaine, Lambowitz Alan M, Golden Barbara L
Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
Nature. 2008 Jan 3;451(7174):94-7. doi: 10.1038/nature06413.
The 'RNA world' hypothesis holds that during evolution the structural and enzymatic functions initially served by RNA were assumed by proteins, leading to the latter's domination of biological catalysis. This progression can still be seen in modern biology, where ribozymes, such as the ribosome and RNase P, have evolved into protein-dependent RNA catalysts ('RNPzymes'). Similarly, group I introns use RNA-catalysed splicing reactions, but many function as RNPzymes bound to proteins that stabilize their catalytically active RNA structure. One such protein, the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (TyrRS; CYT-18), is bifunctional and both aminoacylates mitochondrial tRNA(Tyr) and promotes the splicing of mitochondrial group I introns. Here we determine a 4.5-A co-crystal structure of the Twort orf142-I2 group I intron ribozyme bound to splicing-active, carboxy-terminally truncated CYT-18. The structure shows that the group I intron binds across the two subunits of the homodimeric protein with a newly evolved RNA-binding surface distinct from that which binds tRNA(Tyr). This RNA binding surface provides an extended scaffold for the phosphodiester backbone of the conserved catalytic core of the intron RNA, allowing the protein to promote the splicing of a wide variety of group I introns. The group I intron-binding surface includes three small insertions and additional structural adaptations relative to non-splicing bacterial TyrRSs, indicating a multistep adaptation for splicing function. The co-crystal structure provides insight into how CYT-18 promotes group I intron splicing, how it evolved to have this function, and how proteins could have incrementally replaced RNA structures during the transition from an RNA world to an RNP world.
“RNA世界”假说认为，在进化过程中，最初由RNA承担的结构和酶促功能被蛋白质取代，导致后者在生物催化中占据主导地位。这种演变在现代生物学中仍然可见，例如核糖体和核糖核酸酶P等核酶已演变成依赖蛋白质的RNA催化剂（“核糖核蛋白酶”）。同样，I类内含子利用RNA催化的剪接反应，但许多I类内含子作为与蛋白质结合的核糖核蛋白酶发挥作用，这些蛋白质可稳定其具有催化活性的RNA结构。一种这样的蛋白质，即粗糙脉孢菌线粒体酪氨酰-tRNA合成酶（TyrRS；CYT-18），具有双重功能，既能使线粒体tRNA（Tyr）氨酰化，又能促进线粒体I类内含子的剪接。在这里，我们确定了与具有剪接活性、羧基末端截短的CYT-18结合的Twort orf142-I2 I类内含子核酶的4.5埃共晶体结构。该结构表明，I类内含子通过一个新进化出的RNA结合表面跨同二聚体蛋白的两个亚基结合，该表面不同于结合tRNA（Tyr）的表面。这个RNA结合表面为内含子RNA保守催化核心的磷酸二酯主链提供了一个延伸的支架，使该蛋白质能够促进多种I类内含子的剪接。相对于非剪接细菌TyrRS，I类内含子结合表面包括三个小插入片段和其他结构适应性变化，表明其剪接功能经历了多步适应性变化。该共晶体结构为CYT-18如何促进I类内含子剪接、它如何进化出这种功能以及在从RNA世界向核糖核蛋白世界的转变过程中蛋白质如何逐步取代RNA结构提供了深入见解。
