Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains |
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Authors: | Dong Shuyun Wang Yang Cassidy-Amstutz Caleb Lu Gang Bigler Rebecca Jezyk Mark R Li Chunhua Hall Traci M Tanaka Wang Zefeng |
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Institution: | Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. |
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Abstract: | Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence. |
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Keywords: | Protein Domains Protein Motifs RNA RNA Metabolism RNA Splicing RNA-Protein Interaction Protein Design Protein Engineering |
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