a combinatorial amino acid code for rna recognition by pentatricopeptide repeat proteins由pentatricopeptide组合氨基酸编码rna识别重复的蛋白质.pdfVIP

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins 1 1 2¤ 3 4 4 Alice Barkan *, Margarita Rojas , Sota Fujii , Aaron Yap , Yee Seng Chong , Charles S. Bond , Ian Small2,3* 1 Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America, 2 Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, Australia, 3 Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia, 4 School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia Abstract The pentatricopeptide repeat (PPR) is a helical repeat motif found in an exceptionally large family of RNA–binding proteins that functions in mitochondrial and chloroplast gene expression. PPR proteins harbor between 2 and 30 repeats and typically bind single-stranded RNA in a sequence-specific fashion. However, the basis for sequence-specific RNA recognition by PPR tracts has been unknown. We used computational methods to infer a code for nucleotide recognition involving two amino acids in each repeat, and we validated this model by recoding a PPR protein to bind novel RNA sequences in vitro. Our results show that PPR tracts bind RNA via a modular recognition mechanism that differs from previously described RNA–protein recognition modes and that underpins a natural library of specific protein/RNA partners of unprecedented size and diversity. These findings provide a significant step toward the prediction of native binding