Structural basis for the modular recognition of single-stranded RNA by PPR proteins

• Published in: Nature (London) Vol. 504; no. 7478; pp. 168 - 171
• Main Authors: Yin, Ping, Li, Quanxiu, Yan, Chuangye, Liu, Ying, Liu, Junjie, Yu, Feng, Wang, Zheng, Long, Jiafu, He, Jianhua, Wang, Hong-Wei, Wang, Jiawei, Zhu, Jian-Kang, Shi, Yigong, Yan, Nieng
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 05.12.2013; Nature Publishing Group
• Subjects: 631/449/1659; 631/535/1266; 639/638/45/500; 82/16; 82/29; 82/80; 82/83; Amino acids; Binding Sites; Biotechnology; Crystallography, X-Ray; Genetic aspects; Humanities and Social Sciences; letter; Models, Molecular; Molecular genetics; multidisciplinary; Mutation; Physiological aspects; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - metabolism; Protein Binding; Protein Structure, Tertiary; Proteins; RNA; RNA - chemistry; RNA - metabolism; Science; Structure; Zea mays; Zea mays - chemistry; Zea mays - genetics; Zea mays - metabolism; China
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature12651

Although the roles of pentatricopeptide repeat (PPR) proteins in RNA metabolism are well characterised, the mechanism by which they recognise specific single-stranded (ss)RNAs remains ill-understood; here X-ray crystal structures of maize PPR10 in the presence and absence of ssRNA provide details of the PPR10–ssRNA interaction. PPR protein recognition of ssRNA Pentatricopeptide repeat (PPR) proteins are mitochondria- and chloroplast-targeted RNA-binding proteins involved in many aspects of RNA metabolism. The roles of PPR proteins have been well characterized, but how they recognize specific single-stranded RNAs (ssRNAs) is not as well understood. Nieng Yan and colleagues have solved the structure of maize PPR10 in the absence and presence of ssRNA. They find that in the RNA-free form, the 19 repeats make up a superhelical spiral, and that two PPR10 proteins assemble in an antiparallel dimer. Binding of a ssRNA induces strong conformational changes in PPR10, with six repeats each recognizing a single nucleotide in the 6-base-pair core of the target sequence. Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants 1 , 2 , 3 , 4 , 5 , recognize single-stranded RNA (ssRNA) in a modular fashion 6 , 7 , 8 . The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI – ATPH and PSAJ – RPL33 intergenic regions, referred to as ATPH and PSAJ , respectively 9 , 10 . By protecting the target RNA elements from 5′ or 3′ exonucleases, PPR10 defines the corresponding 5′ and 3′ messenger RNA termini 9 , 10 , 11 . Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45 Å, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.