title: Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants.
abstract: The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.plantppr.com) that provides open access to these resources for the community.
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China.|BGI-Shenzhen, Shenzhen, 518083, China.|School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Gutmann
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhong
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China.
authors.forename: Yongtao
authors.initials: Y
authors.lastname: Ye
authors.affiliation: School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia.
authors.forename: Mark F
authors.initials: MF
authors.lastname: Fisher
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Fengqi
authors.initials: F
authors.lastname: Bai
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Castleden
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Song
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Song
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Jiaying
authors.initials: J
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China.|School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
authors.forename: Boon L
authors.initials: BL
authors.lastname: Lim
authors.affiliation: School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia.
authors.forename: Charles S
authors.initials: CS
authors.lastname: Bond
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China.
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Small
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019669:Embryophyta / Q000235:genetics* / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism; D008958:Models, Molecular; D008961:Models, Structural; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018087:Plastids / Q000378:metabolism; D021381:Protein Transport; D017393:RNA Editing / Q000235:genetics*; D000067776:RNA Recognition Motif Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins; D000067776:RNA Recognition Motif Proteins; D018749:RNA, Plant
keywords: RNA binding; RNA editing; genome annotation; pentatricopeptide repeat motifs; pentatricopeptide repeat proteins; structural modelling