Large-scale proteomic methods are essential for the functional characterization of proteins in their native cellular context. However, proteomics has lagged far behind genomic approaches in scalability, standardization, and cost. Here, we introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem. In vivo-expressed proteins are coupled with their encoding messenger RNAs (mRNAs) via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity by next generation DNA sequencing. We have generated a high-coverage in vivo mRNA display library of the Saccharomyces cerevisiae proteome and demonstrated its potential for characterizing subcellular localization and interactions of proteins expressed in their native cellular context. In vivo mRNA display libraries promise to circumvent the limitations of mass spectrometry-based proteomics and leverage the exponentially improving cost and throughput of DNA sequencing to systematically characterize native functional proteomes.

大规模蛋白质组学方法对于蛋白质在其天然细胞环境中的功能表征至关重要。然而，蛋白质组学在可扩展性、标准化和成本方面远远落后于基因组方法。在这里，我们介绍体内 mRNA 展示，这是一种将各种蛋白质组学应用转化为 DNA 测序问题的技术。体内表达的蛋白质通过高亲和力茎环 RNA 结合域相互作用与其编码信使 RNA (mRNA) 偶联，从而能够通过下一代 DNA 测序以高灵敏度和特异性高通量鉴定蛋白质。我们已经生成了酿酒酵母蛋白质组的高覆盖率体内 mRNA 展示文库，并证明了其在表征其天然细胞环境中表达的蛋白质的亚细胞定位和相互作用的潜力。体内 mRNA 展示文库有望规避基于质谱的蛋白质组学的局限性，并利用 DNA 测序成本和通量呈指数级提高的优势来系统地表征天然功能蛋白质组。