Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein
Songbo Wei, Xiaoxia Dai, Jun Yuan, Shiyang He, Kriti Shah, Shiyuan Guo, Zheng Duan, Jernej Murn, Yinsheng Wang
Abstract
High Resolution Image Download MS PowerPoint Slide Pseudouridine (Ψ) is the most abundant RNA modification in nature; however, not much is known about the biological functions of this modified nucleoside. Employing an unbiased quantitative proteomics method, we identified multiple candidate reader proteins of Ψ in RNA, including a cytoskeletal protein profilin-1 (PFN1). We demonstrated that PFN1 binds directly and selectively to Ψ-containing RNA. Additionally, we discovered approximately 4000 binding sites of PFN1 in human cells, including a known dyskerin (DKC1)-installed Ψ site in TPI1 mRNA, which encodes triosephosphate isomerase. Moreover, we showed that PFN1 and DKC1 are crucial for regulating the stability and translation efficiency of TPI1 mRNA through modulating PFN1-Ψ interaction. Together, we identified PFN1 as a reader protein of Ψ in RNA and illustrated a potential role of PFN1-Ψ interaction in post-transcriptional regulation. These findings provide new insights into the functions of Ψ in RNA biology and in modulating the expression of an important metabolic enzyme.