手机体育投注平台

手机体育投注平台Advertisement

Substitutional RNA Editing in Plant Organelles

  • Mizuho IchinoseEmail author
  • Mamoru Sugita
Protocol
  • 51 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2181)

Abstract

RNA editing by cytidine (C) to uridine (U) conversions frequently occurs in land plant mitochondria and plastids. Target cytidines are specifically recognized by nuclear-encoded pentatricopeptide repeat (PPR) proteins in a sequence-specific manner. In the moss Physcomitrella patens, all PPR editing factors possess the DYW-deaminase domain at the C-terminus. Here, we describe methods for the direct sequencing of cDNA to detect RNA editing events and the RNA electrophoresis mobility shift assay (REMSA) to analyze the specific binding of PPR editing factors to their target RNA.

Key words

C-to-U editing Mitochondria Pentatricopeptide repeat Physcomitrella patens Plastid RNA-protein interaction 

References

  1. 1.
    Gott JM, Emeson RB (2000) Functions and mechanisms of RNA editing. Annu Rev Genet 34:499–531
  2. 2.
    Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R, Fligelman ZY, Shoshan A, Pollock SR, Sztybel D, Olshansky M, Rechavi G, Jantsch MF (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22:1001–1005
  3. 3.
    Ichinose M, Sugita M (2017) RNA editing and its molecular mechanism in plant organelles. Genes (Basel) 8:5
  4. 4.
    Cahoon AB, Nauss JA, Stanley CD, Qureshi A (2017) Deep transcriptome sequencing of two green algae, Chara vulgaris and Chlamydomonas reinhardtii, provides no evidence of organellar RNA editing. Genes (Basel) 8:80
  5. 5.
    Kotera E, Tasaka M, Shikanai T (2005) A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433:326–330
  6. 6.
    Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M (2009) A DYW domain–containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell 21:558–567
  7. 7.
    Cheng S, Gutmann B, Zhong X, Ye Y, Fisher MF, Bai F, Castleden I, Song Y, Song B, Huang J, Liu X, Xu X, Lim BL, Bond CS, Yiu SM, Small I (2016) Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J 85:532–547
  8. 8.
    Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A (2013) RNA editing in plants and its evolution. Annu Rev Genet 47:335–352
  9. 9.
    Lenz H, Hein A, Knoop V (2018) Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. BMC Bioinf 19:255
  10. 10.
    Ichinose M, Sugita C, Yagi Y, Nakamura T, Sugita M (2013) Two DYW subclass PPR proteins are involved in RNA editing of ccmFc and atp9 transcripts in the moss Physcomitrella patens: first complete set of PPR editing factors in plant mitochondria. Plant Cell Physiol 54:1907–1916
  11. 11.
    Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C (2007) A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 581:4132–4138
  12. 12.
    Oldenkott B, Yang Y, Lesch E, Knoop V, Schallenberg-Rüdinger M (2019) Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli. Commun Biol 2:85
  13. 13.
    Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, Small I (2012) A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 8:e1002910
  14. 14.
    Yagi Y, Hayashi S, Kobayashi K, Hirayama T, Nakamura T (2013) Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants. PLoS One 8:e57286
  15. 15.
    Takenaka M, Zehrmann A, Brennicke A, Graichen K (2013) Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS One 8:e65343
  16. 16.
    Lo Giudice C, Hernández I, Ceci LR, Pesole G, Picardi E (2019) RNA editing in plants: a comprehensive survey of bioinformatics tools and databases. Plant Physiol Biochem 137:53–61
  17. 17.
    Yan J, Yao Y, Hong S, Yang Y, Shen C, Zhang Q, Zhang D, Zou T, Yin P (2019) Delineation of pentatricopeptide repeat codes for target RNA prediction. Nucleic Acids Res 47:3728–3738
  18. 18.
    Tasaki E, Hattori M, Sugita M (2010) The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript. Plant J 62:560–570
  19. 19.
    Kindgren P, Yap A, Bond CS, Small I (2015) Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis. Plant Cell 27:403–416
  20. 20.
    Hayes ML, Hanson MR (2007) Chapter 21. Assay of editing of exogenous RNAs in chloroplast extracts of Arabidopsis, maize, pea, and tobacco. Methods Enzymol 424:459–482
  21. 21.
    Takenaka M, Brennicke A (2009) Multiplex single-base extension typing to identify nuclear genes required for RNA editing in plant organelles. Nucleic Acids Res 37:e13
  22. 22.
    Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G (2010) Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res 38:4755–4767
  23. 23.
    Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005–1016

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  1. 1.Center for Gene Research, Nagoya UniversityNagoyaJapan
  2. 2.Institute of Transformative Bio-Molecules (ITbM), Nagoya UniversityNagoyaJapan

Personalised recommendations