Ecotype analysis for functional domain mapping of plant RNA editing proteins
Plant Physiology
Final Report Abstract
In the present project, we have made progress in the functional domain mapping of RNA editing in plant mitochondria and plastids. This process converts specific C nucleotides to U mostly in mRNAs. So far several RNA editing factors have been isolated including PLS type PPR proteins. PPR type RNA editing factors consist of a N-terminal PPR domain, which has a sequence specific RNA binding activity and C-terminal E and DYW domains. Nucleotide specificity of PPR domain can be basically explained by a PPR-code, in which an amino acid combination at two specific positions in P and S type PPR motif confers its binding nucleotide identity. In bioinformatic investigations of the correlations between the target RNA and sequence-specific PPR editing proteins, we extend the PPR code to the L domain that has been considered as only a spacer between P and S type PPR motifs. This PPR code allows us to design sequence specific RNA binding proteins, which will be applicable to process or label specific RNAs in any organism. Although the current PPR code is very useful, it does not always fit with the target specificity in all RNA editing factors and requires further improvement. To elucidate such significant amino acid positions that are not yet identified, at first, we identified several PPR proteins, which are required for editing sites in mitochondria as specific factors through comparison of natural ecotype variations. Comparison of PPR editing factors between the ecotypes in Arabidopsis deduced some candidate amino acid residues, which likely affect RNA editing extents. MORF proteins (multiple organellar RNA editing factor) are a novel protein family involved in RNA editing process in flowering plants. The MORF proteins appear to interact with PPR site-specific trans-factors and thereby to facilitate the RNA editing reaction, suggesting the requirement of complex RNA editosomes in plant organelles. Structural analysis of MORF1 and MORF9 revealed that MORFs form a dimer at the central part of the conserved MORF domain. Using this information, we could predict residues important for their editing function. Further functional analysis of MORF proteins in RNA editosomes will be conduced by introducing specific point mutations in MORF proteins or by searching for SNPs at the positions in different ecotypes and analyzing their effect.
Publications
- (2013) Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS ONE 8, e65343
Takenaka, M., Zehrmann, A.,Brennicke, A., Graichen, K.
(See online at https://doi.org/10.1371/journal.pone.0065343) - (2013) MEF10 is required for RNA editing at nad2-842 in mitochondria of Arabidopsis thaliana and interacts with MORF8. Plant Mol. Biol. 81, 337-346
Härtel, B., Zehrmann, A., Verbitskiy, D., van der Merwe, J. A., Brennicke, A., Takenaka, M.
(See online at https://doi.org/10.1007/s11103-012-0003-2) - (2014) How Complex are the Editosomes in Plant Organelles? Mol. Plant 7(4):582-585
Takenaka, M.
(See online at https://doi.org/10.1093/mp/sst170) - (2014) The pentatricopeptide repeat protein MEF26 participates in RNA editing in mitochondrial cox3 and nad4 transcripts. Mitochondrion 19 Pt B:126-134
Arenas-M, A., Zehrmann, A., Moreno, S., Gómez, I., Takenaka, M., Jordana, X.
(See online at https://doi.org/10.1016/j.mito.2014.08.006) - (2015) MEF13 requires MORF3 and MORF8 for RNA editing at eight targets in mitochondrial mRNAs in Arabidopsis thaliana. Mol. Plant 8, 1466-77
Glass, F., Härtel, B., Zehrmann, A., Verbitskiy, D., Takenaka, M.
(See online at https://doi.org/10.1016/j.molp.2015.05.008) - (2015) The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana. PLoS One. 10(10):e0140680
Brehme N., Bayer-Császár E., Glass F., Takenaka M.
(See online at https://doi.org/10.1371/journal.pone.0140680) - (2016) A PPR protein in the PLS subfamily stabilizes the 5’-end of processed rpl16 mRNAs in maize chloroplasts. Nucleic Acids Res. 44, 4278-4288
Hammani, K. Takenaka M. Miranda, R. Barkan, A.
(See online at https://doi.org/10.1093/nar/gkw270) - (2017) Crystal structures of the Arabidopsis organellar RNA editing factors MORF1 and MORF9. Nucleic Acids Res. 45, 4915–4928
Haag, S., Schindler, M., Berndt, L., Brennicke, A., Takenaka, M., Weber, G.
(See online at https://doi.org/10.1093/nar/gkx099) - (2017) The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors, BBA Gene Regul. Mech. 1860:813-828
Bayer-Császár E., Haag, S., Jörg A., Glass F., Härtel, B., Obata, T., Meyer, E. H., Brenncike, A., Takenaka, M.
(See online at https://doi.org/10.1016/j.bbagrm.2017.05.004)
