Pan Yu-Hang, Shan Lin, Zhang Yu-Yao, Yang Zheng-Hu, Zhang Yuan, Cao Shi-Meng, Liu Xiao-Qi, Zhang Jun, Yang Li, Chen Ling-Ling
State Key Laboratory of RNA Innovation, Science and Engineering, New Cornerstone Science Laboratory, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
Nature. 2025 Jul 23. doi: 10.1038/s41586-025-09412-1.
The multilayered nucleolus is the primary site of ribosome biogenesis, where successive maturation of small (SSU) and large (LSU) ribosomal subunit precursors occurs. However, the spatiofunctional relationship between pre-rRNA processing and nucleolar substructures and how this adapts to changing cellular physiological demands have remained incompletely understood. Here our spatiotemporal analyses revealed a compartment-specific ribosomal subunit processing in human nucleoli, with SSU processomes maintained in fibrillar centre (FC)-dense fibrillar component (DFC)-periphery dense fibrillar component (PDFC) domains while LSU pre-rRNAs largely transited to PDFC-granular component regions. Slowly proliferating cells exhibited unexpected 5' external transcribed spacer (5' ETS)-centred SSU processing impairment, accompanied by structural remodelling of FC-DFC units and retarded SSU outflux. Direct 5' ETS processing perturbation at least partially recapitulated these FC-DFC unit alterations, supporting the functional interdependence between SSU processing and nucleolar architecture. Notably, anamniote bipartite nucleoli with merged FC-DFC compartments exhibited distinct 5' ETS distribution and slower pre-rRNA flux compared with multilayered nucleoli in amniotes. Introducing a FC/DFC interface to bipartite nucleoli enhanced processing efficiency, indicating that the evolutionary emergence of nested FC-DFC units may have optimized pre-rRNA processing. Collectively, depicting the spatiotemporal distribution of pre-rRNAs reveals an essential role of 5' ETS-centred processing in maintaining nucleolar substructures and suggests a possible evolutionary advantage of the multilayered structure in amniotes.
多层核仁是核糖体生物发生的主要场所，小（SSU）和大（LSU）核糖体亚基前体在此连续成熟。然而，前体rRNA加工与核仁亚结构之间的时空功能关系以及这种关系如何适应不断变化的细胞生理需求，仍未完全明了。在这里，我们的时空分析揭示了人类核仁中特定区室的核糖体亚基加工过程，SSU加工体维持在纤维中心（FC）-致密纤维组分（DFC）-外周致密纤维组分（PDFC）结构域，而LSU前体rRNA主要转移到PDFC-颗粒组分区域。缓慢增殖的细胞表现出意想不到的以5'外部转录间隔区（5' ETS）为中心的SSU加工受损，同时伴有FC-DFC单元的结构重塑和SSU流出延迟。直接的5' ETS加工扰动至少部分重现了这些FC-DFC单元的改变，支持了SSU加工与核仁结构之间的功能相互依存关系。值得注意的是，与羊膜动物的多层核仁相比，具有融合FC-DFC区室的无羊膜动物二分核仁表现出不同的5' ETS分布和较慢的前体rRNA通量。在二分核仁中引入FC/DFC界面提高了加工效率，表明嵌套的FC-DFC单元的进化出现可能优化了前体rRNA加工。总的来说，描绘前体rRNA的时空分布揭示了以5' ETS为中心的加工在维持核仁亚结构中的重要作用，并暗示了羊膜动物多层结构可能具有的进化优势。
