The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant evolution.The nature and t...The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant evolution.The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages.In this study,we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family,focusing on the proteins typically associated with RNA editing,which show the most spectacular variation in numbers and domain composition across the plant kingdom.We characterize over 2250000 PPR motifs in over 400000 proteins.In lycophytes,polypod ferns,and hornworts,nearly 10%of expressed protein-coding genes encode putative PPR editing factors,whereas they are absent from algae and complex-thalloid liverworts.We show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity.We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors.Finally,using the sequence variations across the datasets,we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors,given their phylogenetic distribution and sequence characteristics.展开更多
Even after 30 years of active research, RNA editing in plant organelles remains an enigma. Why do most plants post- transcriptionally alter hundreds or thousands of nucleotides in organellar transcripts？ How do they ...Even after 30 years of active research, RNA editing in plant organelles remains an enigma. Why do most plants post- transcriptionally alter hundreds or thousands of nucleotides in organellar transcripts？ How do they achieve such an effective and targeted process？ What is known is that in almost all plants, RNA editing is essential for correct synthesis of the photosynthetic and respiratory machinery in mitochondria and chloroplasts. The sites to be edited are defined by a large class of sequence-specific RNA binding proteins： pentatricopeptide repeat （PPR） proteins （Barkan and Small, 2014）. However, genetic and biochemical evidence has long suggested that other factors must be involved too. Two recent papers in Proceedings of the National Academy of Sciences USA provide exciting new evidence for protein complexes implicated in RNA editing using known mitochondrial or piastid PPR editing factors as bait in pull-down assays （Andres-Colás et al., 2017; Guillaumot et al., 2017）.展开更多
基金supported by the Australian Research Council(grant numbers FL140100179 to I.D.S.,DP150102692 to C.S.B.and I.D.S.,CE140100008 to I.D.S.,DE150101484 to B.G.)the German Research Foundation(DFG grant number SCHA1952/2-1 to M.S.-R.).
文摘The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant evolution.The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages.In this study,we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family,focusing on the proteins typically associated with RNA editing,which show the most spectacular variation in numbers and domain composition across the plant kingdom.We characterize over 2250000 PPR motifs in over 400000 proteins.In lycophytes,polypod ferns,and hornworts,nearly 10%of expressed protein-coding genes encode putative PPR editing factors,whereas they are absent from algae and complex-thalloid liverworts.We show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity.We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors.Finally,using the sequence variations across the datasets,we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors,given their phylogenetic distribution and sequence characteristics.
文摘Even after 30 years of active research, RNA editing in plant organelles remains an enigma. Why do most plants post- transcriptionally alter hundreds or thousands of nucleotides in organellar transcripts？ How do they achieve such an effective and targeted process？ What is known is that in almost all plants, RNA editing is essential for correct synthesis of the photosynthetic and respiratory machinery in mitochondria and chloroplasts. The sites to be edited are defined by a large class of sequence-specific RNA binding proteins： pentatricopeptide repeat （PPR） proteins （Barkan and Small, 2014）. However, genetic and biochemical evidence has long suggested that other factors must be involved too. Two recent papers in Proceedings of the National Academy of Sciences USA provide exciting new evidence for protein complexes implicated in RNA editing using known mitochondrial or piastid PPR editing factors as bait in pull-down assays （Andres-Colás et al., 2017; Guillaumot et al., 2017）.
