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MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing

Nature Plants volume 3, Article number: 17037 (2017) Cite this article

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Abstract

RNA editing is a post-transcriptional process that modifies the genetic information on RNA molecules. In flowering plants, RNA editing usually alters cytidine to uridine in plastids and mitochondria. The PLS-type pentatricopeptide repeat (PPR) protein and the multiple organellar RNA editing factor (MORF, also known as RNA editing factor interacting protein (RIP)) are two types of key trans-acting factors involved in this process. However, how they cooperate with one another remains unclear. Here, we have characterized the interactions between a designer PLS-type PPR protein (PLS)3PPR and MORF9, and found that RNA-binding activity of (PLS)3PPR is drastically increased on MORF9 binding. We also determined the crystal structures of (PLS)3PPR, MORF9 and the (PLS)3PPR–MORF9 complex. MORF9 binding induces significant compressed conformational changes of (PLS)3PPR, revealing the molecular mechanisms by which MORF9-bound (PLS)3PPR has increased RNA-binding activity. Similarly, increased RNA-binding activity is observed for the natural PLS-type PPR protein, LPA66, in the presence of MORF9. These findings significantly expand our understanding of MORF function in plant organellar RNA editing.

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Figure 1: Structural overview of the designer (PLS)3PPR.
Figure 2: Crystal structure of MORF9.
Figure 3: MORF9 interacts with (PLS)3PPR and increases its RNA-binding activity.
Figure 4: Crystal structure of (PLS)3PPR in complex with MORF9.
Figure 5: Structural alignment of free (PLS)3PPR with MORF9-bound (PLS)3PPR.
Figure 6: Proposed working model of MORF9 in plant plastid RNA editing.

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Acknowledgements

We thank the staff from BL17U/BL19U1/beamline of the National Centre for Protein Sciences Shanghai (NCPSS) at the Shanghai Synchrotron Radiation Facility for assistance during data collection, and research associates at the Centre for Protein Research, Huazhong Agricultural University, for technical support. This work was supported by funds from the Ministry of Science and Technology (grant 2015CB910900), the Fok Ying-Tong Education Foundation (grant 151021), the National Science Foundation of China (grant 91535301), the Fundamental Research Funds for the Central Universities (programme no. 2014PY026, no. 2015PY219 and no. 2014JQ001), Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (programme no. 2013RC013) and the China Postdoctoral Science Foundation (grant 2015M572163).

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  1. Junjie Yan and Qunxia Zhang: These authors contributed equally to this work.

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China

    Junjie Yan, Qunxia Zhang, Zeyuan Guan, Qiang Wang, Li Li, Fengying Ruan, Tingting Zou & Ping Yin

  2. Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

    Rongcheng Lin

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Contributions

J.Y., Q.Z., R.L., T.Z. and P.Y. designed all experiments. J.Y., Q.Z., L.L. and F.R. performed protein expression, purification and crystallization. Z.G. determined all of the structures. J.Y., Q.Z. and Q.W. carried out biochemical assays. J.Y. and P.Y. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Ping Yin.

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Supplementary Figures 1–10, Supplementary Table 1. (PDF 1690 kb)

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Yan, J., Zhang, Q., Guan, Z. et al. MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing. Nature Plants 3, 17037 (2017). https://doi.org/10.1038/nplants.2017.37

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