Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

The Plant Journal : for Cell and Molecular Biology
Shifeng ChengIan D Small

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 ...Continue Reading

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Citations

May 3, 2016·The Plant Journal : for Cell and Molecular Biology·Géraldine BonnardPhilippe Giegé
Oct 31, 2016·Trends in Plant Science·Tao SunMaureen R Hanson
Oct 25, 2016·Scientific Reports·Joanna MelonekIan Small
Dec 9, 2016·International Journal of Molecular Sciences·Yuzhe SunBoon Leong Lim
Dec 28, 2016·Genes·Mizuho Ichinose, Mamoru Sugita
Nov 30, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Huamin ZhangLugang Zhang
Feb 1, 2018·The Plant Journal : for Cell and Molecular Biology·Navot GalpazNurit Katzir
Aug 2, 2017·Proceedings of the National Academy of Sciences of the United States of America·Damien GuillaumotClaire Lurin
Oct 3, 2018·The Plant Journal : for Cell and Molecular Biology·Joanna MelonekIan Small
Nov 6, 2018·The New Phytologist·Hannes RuwePeter Kindgren
Jan 4, 2019·Plant & Cell Physiology·Takehito KobayashiTakahiro Nakamura
Mar 8, 2019·The Plant Journal : for Cell and Molecular Biology·Rosalind Williams-CarrierAlice Barkan
Feb 28, 2019·Physiologia Plantarum·Aleix Gorchs Rovira, Alison G Smith
Jul 10, 2019·Genome Biology and Evolution·Evan S ForsytheDaniel B Sloan
Oct 17, 2017·The Plant Journal : for Cell and Molecular Biology·Thiruvenkadam ShanmugamSang-Bong Choi
Oct 19, 2017·The Plant Journal : for Cell and Molecular Biology·Timothée VincentAnne-Marie Duchêne
Nov 5, 2019·Wiley Interdisciplinary Reviews. RNA·Carl R ShotwellJ Andrew Berglund
Sep 15, 2019·The Plant Journal : for Cell and Molecular Biology·Philippe FuchsMarkus Schwarzländer
Aug 24, 2019·The Plant Journal : for Cell and Molecular Biology·Kwanuk LeeHunseung Kang
Jan 12, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zhenghai ZhangLihao Wang
Oct 21, 2019·The Plant Journal : for Cell and Molecular Biology·Ian D SmallOren Ostersetzer-Biran

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