RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages

IF 14.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Cell Pub Date : 2024-09-10 DOI:10.1016/j.molcel.2024.08.023
Teodorus Theo Susanto, Victoria Hung, Andrew G. Levine, Yuxiang Chen, Craig H. Kerr, Yongjin Yoo, Juan A. Oses-Prieto, Lisa Fromm, Zijian Zhang, Travis C. Lantz, Kotaro Fujii, Marius Wernig, Alma L. Burlingame, Davide Ruggero, Maria Barna
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Abstract

Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including Dhx30 and Llph, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed that RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts.

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RAPIDASH:无标记核糖体相关蛋白富集揭示胚胎组织、癌细胞和巨噬细胞中的组成动态
核糖体正在成为基因表达的直接调节器,核糖体相关蛋白(RAPs)使核糖体能够调节翻译。然而,由于缺乏在不同样本类型中富集 RAPs 的技术,因此无法对 RAP 的特性、动态和功能进行系统分析。我们开发了一种名为 RAPIDASH 的无标记方法,可从任何样本中富集核糖体和 RAPs。我们将 RAPIDASH 应用于小鼠胚胎组织,发现了数百个潜在的 RAPs,包括 Dhx30 和 Llph 这两个对神经发育很重要的前脑 RAPs。我们确定了 LLPH 在神经发育中的关键作用,它与长编码序列基因的翻译有关。此外,我们还发现 RAPIDASH 可以识别癌细胞中核糖体的变化。最后,我们描述了免疫细胞活化过程中核糖体组成重塑的特点,并观察到刺激后的广泛变化。因此,RAPIDASH 能够发现多种细胞类型、组织和刺激下的 RAPs,并能适应多种情况下核糖体重塑的特征。
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来源期刊
Molecular Cell
Molecular Cell 生物-生化与分子生物学
CiteScore
26.00
自引率
3.80%
发文量
389
审稿时长
1 months
期刊介绍: Molecular Cell is a companion to Cell, the leading journal of biology and the highest-impact journal in the world. Launched in December 1997 and published monthly. Molecular Cell is dedicated to publishing cutting-edge research in molecular biology, focusing on fundamental cellular processes. The journal encompasses a wide range of topics, including DNA replication, recombination, and repair; Chromatin biology and genome organization; Transcription; RNA processing and decay; Non-coding RNA function; Translation; Protein folding, modification, and quality control; Signal transduction pathways; Cell cycle and checkpoints; Cell death; Autophagy; Metabolism.
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