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

• DOI: 10.1111/tpj.13121
• Publication Date: 2016-01-14T03:32:34Z
• Authors: Shifeng Cheng; Bernard Gutmann; Xiao Zhong; Yongtao Ye; Mark F. Fisher; Fengqi Bai; Ian Castleden; Yue Song; Bo Song; Jiaying Huang; Xin Liu; Xun Xu; Boon L. Lim; Charles S. Bond; Siu‐Ming Yiu; Ian Small
• Keywords: Pentatricopeptide repeat; Structural motif; Sequence motif; Proteome

Summary 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 an extended binding surface capable sequence‐specific recognition RNA strands. Almost all them post‐translationally targeted to plastids and mitochondria, where they play important roles post‐transcriptional processes including splicing, editing initiation translation. A code describing how recognise their targets promises accelerate research on these proteins, but making use this requires accurate definition annotation various nucleotide‐binding each protein. We have used a structural modelling approach define 10 different variants motif found plant addition putative deaminase is at C‐terminus many ‐editing factors. show super‐helical ‐binding factors potentially longer than previously recognised. redefined develop consistent annotations sequences from 109 genomes. report high error rate gene models public proteomes, due fusions insertions spurious introns. These consistently annotated datasets across wide range species valuable resources for future comparative genomics studies, essential pre‐requisite large‐scale computational predictions targets. created web portal http://www.plantppr.com provides open access community.