I. D. Small, O. Rackham, and A. Filipovska, Organelle transcriptomes: Products of a deconstructed genome, Curr. Opin. Microbiol, vol.16, pp.652-658, 2013.

J. M. Gualberto, L. Lamattina, G. Bonnard, J. H. Weil, and J. M. Grienenberger, RNA editing in wheat mitochondria results in the conservation of protein sequences, Nature, vol.341, pp.660-662, 1989.

B. Hoch, R. M. Maier, K. Appel, G. L. Igloi, and H. Kössel, Editing of a chloroplast mRNA by creation of an initiation codon, Nature, vol.353, pp.178-180, 1991.

A. A. Edera, C. L. Gandini, and M. V. Sanchez-puerta, Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria, Plant Mol. Biol, vol.97, pp.215-231, 2018.

F. Grewe, S. Herres, P. Viehöver, M. Polsakiewicz, B. Weisshaar et al., A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii, Nucleic Acids Res, vol.39, pp.2890-2902, 2011.

D. Guillaumot, M. Lopez-obando, K. Baudry, A. Avon, G. Rigaill et al., Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria, Proc. Natl. Acad. Sci, vol.114, pp.8877-8882, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606226

I. D. Small, M. Schallenberg-rüdinger, M. Takenaka, H. Mireau, and O. Ostersetzer-biran, Plant organellar RNA editing: What 30 years of research has revealed, Plant J, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02623566

E. Kotera, M. Tasaka, and T. Shikanai, A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts, Nature, vol.433, pp.326-330, 2005.

I. D. Small and N. Peeters, The PPR motif-A TPR-related motif prevalent in plant organellar proteins, Trends Biochem. Sci, vol.25, pp.45-47, 2000.

J. Colcombet, M. Lopez-obando, L. Heurtevin, C. Bernard, K. Martin et al., Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles, RNA Biol, vol.10, pp.1557-1575, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02645879

P. Yin, Q. Li, C. Yan, Y. Liu, J. Liu et al., Structural basis for the modular recognition of single-stranded RNA by PPR proteins, Nature, vol.504, pp.168-171, 2013.

C. Shen, X. Wang, Y. Liu, Q. Li, Z. Yang et al., Specific RNA recognition by designer pentatricopeptide repeat protein, Mol. Plant, vol.8, pp.667-670, 2015.

P. Kindgren, A. Yap, C. S. Bond, and I. Small, Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis, Plant Cell, vol.27, pp.403-416, 2015.

A. Barkan, M. Rojas, S. Fujii, A. Yap, Y. S. Chong et al., A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins, PLoS Genet, vol.8, 2012.

M. Takenaka, A. Zehrmann, A. Brennicke, and K. Graichen, Improved computational target site prediction for pentatricopeptide repeat RNA editing factors, PLoS ONE, issue.8, 2013.

J. Yan, Y. Yao, S. Hong, Y. Yang, C. Shen et al., Delineation of pentatricopeptide repeat codes for target RNA prediction, Nucleic Acids Res, vol.47, pp.3728-3738, 2019.

T. Kobayashi, Y. Yagi, and T. Nakamura, Comprehensive Prediction of Target RNA Editing Sites for PLS-Class PPR Proteins in Arabidopsis thaliana, Plant Cell Physiol, vol.60, pp.862-874, 2019.

S. Bentolila, W. P. Heller, T. Sun, A. M. Babina, G. Friso et al., RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing, Proc. Natl. Acad. Sci, vol.109, 2012.

S. Bentolila, J. Oh, M. R. Hanson, and R. Bukowski, Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing, PLoS Genet, issue.9, 2013.

M. Takenaka, A. Zehrmann, D. Verbitskiy, M. Kugelmann, B. Hartel et al., Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants, Proc. Natl. Acad. Sci, vol.109, pp.5104-5109, 2012.

E. Bayer-császár, S. Haag, A. Jörg, F. Glass, B. Härtel et al., The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors, Biochim. Biophys. Acta Gene Regul. Mech, vol.1860, pp.813-828, 2017.

J. Yan, Q. Zhang, Z. Guan, Q. Wang, L. Li et al., MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing, vol.3, 2017.

C. Lurin, C. Andrés, S. Aubourg, M. Bellaoui, F. Bitton et al., Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis, Plant Cell, vol.16, pp.2089-2103, 2004.

S. Cheng, B. Gutmann, X. Zhong, Y. Ye, M. F. Fisher et al., Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants, Plant J, vol.85, pp.532-547, 2016.

F. Waltz, T. T. Nguyen, M. Arrivé, A. Bochler, J. Chicher et al., Small is big in Arabidopsis mitochondrial ribosome, Nat. Plants, vol.5, pp.106-117, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02175685

A. Barkan and I. Small, Pentatricopeptide Repeat Proteins in Plants, Annu. Rev. Plant Biol, vol.65, pp.415-442, 2014.

V. Salone, M. Rüdinger, M. Polsakiewicz, B. Hoffmann, M. Groth-malonek et al., A hypothesis on the identification of the editing enzyme in plant organelles, FEBS Lett, vol.581, pp.4132-4138, 2007.

C. Boussardon, A. Avon, P. Kindgren, C. S. Bond, M. Challenor et al., Small, I. The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1, New Phytol, vol.203, pp.1090-1095, 2014.

J. A. Wagoner, T. Sun, L. Lin, and M. R. Hanson, Cytidine deaminase motifs within the DYW domain of two pentatricopeptide repeat-containing proteins are required for site-specific chloroplast RNA editing, J. Biol. Chem, vol.290, pp.2957-2968, 2015.

B. Oldenkott, Y. Yang, E. Lesch, V. Knoop, and M. Schallenberg-rüdinger, Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli, Commun. Biol, vol.2, 2019.

C. Boussardon, V. Salone, A. Avon, R. Berthomé, K. Hammani et al., Two interacting proteins are necessary for the editing of the ndhD-1 site in Arabidopsis plastids, Plant Cell, vol.24, pp.3684-3694, 2012.

N. Andrés-colás, Q. Zhu, M. Takenaka, B. De-rybel, D. Weijers et al., Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids, Proc. Natl. Acad. Sci, vol.114, pp.8883-8888, 2017.

M. Takenaka, D. Verbitskiy, A. Zehrmann, and A. Brennicke, Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of Arabidopsis thaliana, J. Biol. Chem, vol.285, pp.27122-27129, 2010.

K. Leu, M. Hsieh, H. Wang, H. Hsieh, and G. Jauh, Distinct role of Arabidopsis mitochondrial P-type pentatricopeptide repeat protein-modulating editing protein, PPME, in nad1 RNA editing, RNA Biol, vol.13, pp.593-604, 2016.

K. Laluk, S. Abuqamar, and T. Mengiste, The Arabidopsis mitochondria-localized pentatricopeptide repeat protein PGN functions in defense against necrotrophic fungi and abiotic stress tolerance, Plant Physiol, vol.156, pp.2053-2068, 2011.

C. M. Hooper, I. R. Castleden, S. K. Tanz, N. Aryamanesh, and A. H. Millar, SUBA4: The interactive data analysis centre for Arabidopsis subcellular protein locations, Nucleic Acids Res, vol.45, pp.1064-1074, 2017.

B. Gutmann, S. Royan, M. Schallenberg-rüdinger, H. Lenz, I. R. Castleden et al., The expansion and diversification of pentatricopeptide repeat RNA editing factors in plants, Mol. Plant, 2019.

M. Hashimoto, T. Endo, G. Peltier, M. Tasaka, and T. Shikanai, A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis, Plant J, vol.36, pp.541-549, 2003.

K. Hammani, C. C. Des-francs-small, M. Takenaka, S. K. Tanz, K. Okuda et al., Small, I. The pentatricopeptide repeat protein OTP87 is essential for RNA editing of nad7 and atp1 transcripts in Arabidopsis mitochondria, J. Biol. Chem, vol.286, pp.21361-21371, 2011.

F. Glass, B. Härtel, A. Zehrmann, D. Verbitskiy, and M. Takenaka, MEF13 requires MORF3 and MORF8 for RNA editing at eight targets in mitochondrial mRNAs in Arabidopsis thaliana, Mol. Plant, vol.8, pp.1466-1477, 2015.

E. Tasaki, M. Hattori, and M. Sugita, The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript, Plant J, vol.62, pp.560-570, 2010.

M. Ichinose, C. Sugita, Y. Yagi, T. Nakamura, and M. Sugita, 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, vol.54, pp.1907-1916, 2013.

M. F. Diaz, S. Bentolila, M. L. Hayes, M. R. Hanson, and R. M. Mulligan, A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing, Plant J, vol.92, pp.638-649, 2017.

Y. Yagi, S. Hayashi, K. Kobayashi, T. Hirayama, and T. Nakamura, Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants, PLoS ONE, vol.8, 2013.

K. Okuda, H. Shoki, M. Arai, T. Shikanai, I. Small et al., Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing, Plant J, vol.80, pp.870-882, 2014.

A. Chateigner-boutin, C. C. Des-francs-small, E. Delannoy, S. Kahlau, S. K. Tanz et al., Small, I. OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1, Plant J, vol.65, pp.532-542, 2011.

K. Hammani, M. Takenaka, R. Miranda, and A. Barkan, A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts, Nucleic Acids Res, vol.44, pp.4278-4288, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02189760

H. Ruwe, B. Gutmann, C. Schmitz-linneweber, I. Small, and P. Kindgren, The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids, New Phytol, vol.222, pp.218-229, 2019.

J. J. Mcdermott, B. Civic, and A. Barkan, Effects of RNA structure and salt concentration on the affinity and kinetics of interactions between pentatricopeptide repeat proteins and their RNA ligands, PLoS ONE, vol.13, 2018.

R. G. Miranda, M. Rojas, M. P. Montgomery, K. P. Gribbin, and A. Barkan, RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10, RNA, vol.23, pp.586-599, 2017.

R. Williams-carrier, T. Kroeger, and A. Barkan, Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand, RNA, vol.14, 1930.

J. Prikryl, M. Rojas, G. Schuster, and A. Barkan, Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein, Proc. Natl. Acad. Sci, vol.108, pp.415-420, 2011.

P. Armengaud, K. Zambaux, A. Hills, R. Sulpice, R. J. Pattison et al., Integrated software for the fast and accurate measurement of root system architecture, Plant J, vol.57, pp.945-956, 2009.

T. Nakagawa, T. Suzuki, S. Murata, S. Nakamura, T. Hino et al., Improved gateway binary vectors: High-performance vectors for creation of fusion constructs in transgenic analysis of plants, Biosci. Biotechnol. Biochem, vol.71, pp.2095-2100, 2007.

T. Nakagawa, T. Kurose, T. Hino, K. Tanaka, M. Kawamukai et al., Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation, J. Biosci. Bioeng, vol.104, pp.34-41, 2007.

K. Ishizaki, R. Nishihama, M. Ueda, K. Inoue, S. Ishida et al., Development of gateway binary vector series with four different selection markers for the liverwort marchantia polymorpha, PLoS ONE, vol.10, 2015.

B. Malbert, G. Rigaill, V. Brunaud, C. Lurin, and E. Delannoy, Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing, Plastids, vol.1829, 2018.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., Ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

M. D. Curtis and U. Grossniklaus, A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta, Plant Physiol, vol.133, pp.462-469, 2003.