Research  Papers

70. Bayer-Császár, E., Jörg, A., Härtel, B., Brennicke, A., Takenaka, M. (2023)  The Gating Domain of MEF28 is Essential for Editing Two Contiguous Cytidines in nad2 mRNA in Arabidopsis thaliana. Plant Cell Physiol. 2023 Aug 2:pcad087. doi: 10.1093/pcp/pcad087. Epub ahead of print. PMID: 37530742.

69. Yang, Y., Oldenkott, B., Ramanathan, S., Lesch, E., Takenaka, M., Schallenberg-Rüdinger, M. and Knoop, V. (2023), DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection. Plant J. 116: 840-854.,https://doi.org/10.1111/tpj.16412

68. Jung, L., Schleicher, S., Alsaied Taha, F., Takenaka, M., Binder, S. (2023), The MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4) is essential for the accumulation of dicistronic rpl5-cob mRNAs in Arabidopsis thaliana. Plant J. 113(2), 375–386. https://doi.org/10.1111/tpj.16053

67. Toma-Fukai S., Sawada Y., Maeda A., Shimizu H., Shikanai T., Takenaka M., Shimizu T. (2023) Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation. Plant Cell. 29;35(6):1888-1900. doi: 10.1093/plcell/koac318.

66. Maeda A, Takenaka S, Wang T, Frink B, Shikanai T, Takenaka M. (2022) DYW deaminase domain has a distinct preference for neighboring nucleotides of the target RNA editing sites. Plant J. 111(3), 756–767. https://doi.org/10.1111/tpj.15850

65. Nakazato, I., Okuno, M. , Zhou, C., Itoh, I., Tsutsumi, N., Takenaka, M., Arimura, S. (2022) Targeted base editing in the mitochondrial genome of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 119(20), e2121177119. https://doi.org/10.1073/pnas.2121177119

64. Takenaka M. (2022) Quantification of Mitochondrial RNA Editing Efficiency Using Sanger Sequencing Data. In: Van Aken O., Rasmusson A.G. (eds) Plant Mitochondria. Methods in Molecular Biology, vol 2363. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1653-6_18

63. Takenaka, M., Takenaka, S., Barthel, T., Frink, B., Haag, S., Verbitskiy, D., Oldenkott, B., Schallenberg-Rüdinger, M., Feiler, C.G., Weiss, M.S., Palm, G.J., Weber, G. (2021) DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis. Nature Catalysis 4, 510–522. https://doi.org/10.1038/s41929-021-00633-x

62. Yamagishi, H., Jikuya, M., Okushiro, K., Hashimoto, A., Fukunaga, A., Takenaka, M., Terachi, T. (2021) A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility 

Mol. Genet. and Genom. https://doi.org/10.1007/s00438-021-01777-y

61. Higashi, H., Kato, Y., Fujita, T., Iwasaki, S., Nakamura, M., Nishimura, Y., Takenaka, M., Shikanai, T. (2021). The pentatricopeptide repeat protein PGR3 is required for the translation of petL and ndhG by binding their 5'UTRs. Plant Cell Physiol., pcaa180. Advance online publication. https://doi.org/10.1093/pcp/pcaa180

60. Oldenkott, B. Burger, M. Hein, AC., Jörg, A., Senkler, J., Braun, HP. Knoop, V., Takenaka, M.  Schallenberg-Rüdinger, M., (2020) One C-to-U RNA Editing Site and Two Independently Evolved Editing Factors: Testing Reciprocal Complementation with DYW-type PPR Proteins from the Moss Physcomitrium (Physcomitrella) Patens and the Flowering Plants Macadamia integrifolia and Arabidopsis thaliana. Plant Cell 32, 2997-3018. DOI: https://doi.org/10.1105/tpc.20.00311

59. Brehme, N., Glass,F., Jörg, A., Takenaka, M. (2020) MEF46 and MEF47 are novel specificity factors for RNA editing sites in mitochondrial nad transcripts. Mitochondrion, 53, 121-127. https://doi.org/10.1016/j.mito.2020.05.002.

58. Marchetti, F., Cainzos, M., Shevtsov, S., Córdoba, J. P., Sultan, L. D., Brennicke, A., Takenaka, M., Pagnussat, G., Ostersetzer-Biran, O., & Zabaleta, E. (2020). Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana. Plant Cell Physiol., 61, 1080-1094. https://doi.org/10.1093/pcp/pcaa028

57. Malbert, B., Burger, M., Lopez-Obando, M., Baudry, K., Launay-Avon, A., Härtel, B., Verbitskiy, D., Jörg, A., Berthomé, R., Lurin, C., Takenaka, M., Delannoy, E. (2020) The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins. Plants 9, 280. https://doi.org/10.3390/plants9020280

56. Glass F., Takenaka M. (2018) The Yeast Three-Hybrid System for Protein Interactions. In: Oñate-Sánchez L. (eds) Two-Hybrid Systems. Methods Mol. Biol., vol 1794. Humana Press, New York, NY

55. Arenas-M, A., González-Durán, E., Gómez, I., Burger, M., Brennicke, A., Takenaka, M., Jordana, X., (2017) The Pentatricopeptide Repeat Protein MEF31 is Required for Editing at Site 581 of the tatC Transcript and Indirectly Influences Editing at Site 586 of the Same Transcript. Plant and Cell Physiol., pcx190, https://doi.org/10.1093/pcp/pcx190

54. Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J.(2017) Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell. 2017 Oct 5;171(2):287-304.e15. doi: 10.1016/j.cell.2017.09.030.

53. Andrés-Colás, N., Zhu, Q., Takenaka, M., De Rybel, B., Weijers, D., Van Der Straeten, D. (2017) Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids. Proc. Natl. Acad. Sci. USA. doi: 10.1073/pnas.1705815114.

52. Guillaumot, D., Lopez-Obando, M., Baudry, K., Avon, A., Rigaill, G., Falcon de Longevialle, A., Broche, B., Takenaka, M., Berthomé, R., De Jaeger, G., Delannoy, E., Lurin, C. (2017) Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc. Natl. Acad. Sci. USA. doi: 10.1073/pnas.1705780114. 

51. Bayer-Császár E., Haag, S., Jörg A., Glass F., Härtel, B., Obata, T., Meyer, E. H., Brennicke, A., Takenaka, M.  (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.

50. Haag, S.,  Schindler, M., Berndt, L., Brennicke, A., Takenaka, M., Weber, G. (2017) Crystal structures of the Arabidopsis organellar RNA editing factors MORF1 and MORF9. Nucleic Acids Res. 45, 4915–4928

49. Hammani, K. Takenaka M. Miranda, R. Barkan, A. (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.

48. Lin, P.C., Lu, C.W., Shen, B.N., Lee, G.Z., Bowman, J.L., Arteaga-Vazquez, M.A., Liu, L.Y.D., Hong, S.F., Lo, C.F., Su, G.M., Kohchi, T., Ishizaki, K., Zachgo, S., Althoff, F., Takenaka, M., Yamato, K.T., Lin, S.S. (2016) Identification of miRNAs and their targets in the liverwort Marchantia polymorpha by integrating RNA-Seq and degradome analyses. Plant Cell Physiol. 57, 339-358. 

47. Brehme N., Bayer-Császár E., Glass F., Takenaka M. (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. doi: 10.1371/journal.pone.0140680. 

46. Glass, F., Härtel, B., Zehrmann, A., Verbitskiy, D., Takenaka, M. (2015) MEF13 requires MORF3 and MORF8 for RNA editing at eight targets in mitochondrial mRNAs in Arabidopsis thaliana. Mol. Plant 8, 1466-77. doi.org/10.1016/j.molp.2015.05.008

45. Zehrmann, A., Härtel, B., Glass, F., Bayer-Csaszar, E., Obata, T., Meyer, E., Brennicke, A., Takenaka, M. (2015) Selective homo- and heteromer interactions between the multiple organellar RNA editing factor (MORF) proteins in Arabidopsis thaliana. J. Biol. Chem. 290:6445-6456

44. Arenas-M, A., Zehrmann, A., Moreno, S., Gómez, I., Takenaka, M., Jordana, X. (2014) The pentatricopeptide repeat protein MEF26 participates in RNA editing in mitochondrial cox3 and nad4 transcripts. Mitochondrion 19 Pt B:126-134

43. Brehme, N., Zehrmann, A., Verbitskiy, D., Härtel, B., Takenaka, M. (2014) Mitochondrial RNA editing PPR proteins can tolerate proteintags at E as well as at DYW domain termini. Front. Plant Sci. 5:127

42. Härtel, B., Zehrmann, A., Verbitskiy, D., Takenaka, M. (2013) The longest mitochondrial RNA editing PPR protein MEF12 in Arabidopsis thaliana requires the full length E domain. RNA Biol. 10, 1337-1342 

41. Takenaka, M., Zehrmann, A.,Brennicke, A., Graichen, K.(2013) Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS ONE 8, e65343.

40. Arenas-M, A., Takenaka, M., Moreno, S., Gómez, I., Jordana, X. (2013) Contiguous RNA editing sites in the mitochondrial nad1 transcript of Arabidopsis thaliana are recognized by different proteins. FEBS Lett. 587, 887-891

39. Härtel, B., Zehrmann, A., Verbitskiy, D., van der Merwe, J. A., Brennicke, A., Takenaka, M. (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

38. Takenaka, M., and Brennicke, A. (2012) Using multiplex single-base extension typing to screen for mutants defective in RNA editing. Nat Protoc. 7, 1931-1945 

37. Verbitskiy, D., Zehrmann, A., Härtel, B., Brennicke, A.,Takenaka, M. (2012) Two related RNA editing proteins target the same sites in mitochondria of Arabidopsis thaliana. J. Biol. Chem. 287, 38064-38072 

36. Zhu, Q., Dugardeyn, J., Zhang, C., Takenaka, M., Kühn, K., Craddock, C., Smalle, J., Karampelias, M., Denecke, J., Peters, J., Gerats, T., Brennicke, A., Eastmond, P., Meyer, EH., Van Der Straeten, D. (2012) SLO2, a mitochondrial PPR protein affecting several RNA editing sites, is required for energy metabolism. Plant J. 71, 836-849 

35. Takenaka, M., Zehrmann, A., Härtel, B., Kugelmann, M., Verbitskiy, D., Brennicke, A. (2012) MORF family proteins are required for RNA editing in mitochondria and plastids of plants. Proc. Natl. Acad. Sci. USA 109, 5104-5109

34. Sosso, S., Mbelo, S. , Vernoud, V., Gendrot, G., Dedieu, A., Chambrier, P., Dauzat, M., Heurtevin, L., Guyon, V., Takenaka, M. and Rogowsky, P. M. (2012), PPR2263, a DYW-subgroup pentatricopeptide repeat protein, is required for mitochondrial nad5 and cob transcript editing, mitochondrion biogenesis and maize growth. Plant Cell 24, 676-691

33. Zehrmann, A., van der Merwe, J. A., Verbitskiy, D., Härtel, B., Brennicke, A., Takenaka, M. (2012) The DYW-class PPR protein MEF7 is required for RNA editing at four sites in mitochondria of Arabidopsis thaliana. RNA Biol. 9, 1-7

32. Verbitskiy, D., van der Merwe, J. A., Zehrmann, A., Härtel, B., Takenaka, M. (2012) The E-class PPR Protein MEF3 of Arabidopsis thaliana can Function in Mitochondrial RNA editing also with an Additional DYW Domain. Plant Cell Physiol. 53, 358-367

31. Hammani, K., Takenaka, M., Tanz, S.K., Okuda, K., Shikanai, T., Brennicke, A., Small, I. (2011) The pentatricopeptide repeat protein OTP87 is essential for RNA editing of nad7 and atp1 transcripts in Arabidopsis mitochondria. J. Biol. Chem. 286, 21361-21371. 

30. Zehrmann, A., Verbitskiy, D., Härtel, B., Brennicke, A., Takenaka, M. (2011) PPR proteins network as site-specific RNA editing factors in plant organelles. RNA Biol. 8, 67-70 

29. Verbitskiy, D., Zehrmann, A., Härtel, B., Brennicke, A., Takenaka, M. (2011) The DYW-E-PPR protein MEF14 is required for RNA editing at site matR-1895 in mitochondria of Arabidopsis thaliana. FEBS Lett. 585, 700-704

28. Zehrmann, A., Verbitskiy, D., Härtel, B., Brennicke, A., Takenaka, M. (2010) RNA editing competence of trans-factor MEF1 is modulated by ecotype-specific differences but requires the DYW domain. FEBS Lett. 584, 4181-4186

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

26. Takenaka, M. (2011) Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing. In: RNA and DNA editing. (R. Aphasizhev, ed.) Humana Press, Springer, Heidelberg, pp. 151-161

25. Takenaka, M., and Zehrmann, A. (2011) Complementation of Mutants in Plant Mitochondrial RNA Editing by Protoplast Transfection. In: RNA and DNA editing. (R. Aphasizhev, ed.) Humana Press, Springer, Heidelberg, pp. 163-169

24. Verbitskiy, D., Zehrmann, A., Brennicke, A., Takenaka, M. (2010) A truncated MEF11 protein shows site-specific effects on mitochondrial RNA editing. Plant Signal. Behav. 5, 558-560

23. Takenaka, M. (2010) MEF9, an E subclass PPR protein, is required for an RNA editing event in the nad7 transcript in mitochondria of Arabidopsis thaliana. Plant Physiol. 152, 939-947

22. Verbitskiy, D., Zehrmann, A., van der Merwe, J. A., Brennicke, A., Takenaka, M. (2009) The PPR-protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana. Plant J. 61, 446-455 

21. Zehrmann, A., Verbitskiy, D., van der Merwe, J. A., 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

20. 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

19. Zehrmann, A., van der Merwe, J. A., Verbitskiy, D., Brennicke, A., Takenaka, M. (2008) Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana.  Mitochondrion 8, 319-327

18. Verbitskiy, D., van der Merwe, J. A., Zehrmann, A., Brennicke, A., Takenaka, M. (2008) Multiple specificity-recognition motifs enhance RNA editing in plant mitochondria. J. Biol. Chem. 283, 24374-24381

17. Takenaka, M., Verbitskiy, D., van der Merwe, J. A., Zehrmann, A., Plessmann, U., Urlaub, H., Brennicke, A. (2007) In vitro RNA editing in plant mitochondria does not require energy. FEBS Lett. 58, 2743-2747

16. Yamato, K., Ishizaki, K., Fujisawa, M., Okada, S., Nakayama, S., Fujishita, M., Bando, H., Yodoya, K., Hayashi, K., Bando, T., Hasumi, A., Nishio, T., Sakata, R., Yamamoto, M., Yamaki, A., Kajikawa, M., Yamano, T., Nishide, T., Choi, S.-H., Shimizu-Ueda, Y., Hanajiri, T., Sakaida, M., Kohno, K., Takenaka, M., Yamaoka, S., Kuriyama, C., Kohzu, Y., Nishida, H., Brennicke, A., Shin-I, T., Kohara, Y., Kohchi, T., Fukuzawa, H., Ohyama, K. (2007) Gene organization of the Y chromosome in the haploid dioecious liverwort, Marchantia polymorpha L. Proc. Natl. Acad. Sci. USA 104, 6472-6477

15. Takenaka, M., Brennicke, A. (2007) RNA editing in plant mitochondria: assays and biochemical approaches. Meth. Enzymol. 424, 437-458

14. Verbitskiy, D., Takenaka, M., Neuwirt, J., van der Merwe, J.A., Brennicke, A. (2006) Partially edited RNAs are intermediates of RNA editing in plant mitochondria. Plant J. 47, 408-416

13. van der Merwe, J. A., Takenaka, M., Neuwirt, J., Verbitskiy, D., Brennicke, A. (2006) RNA editing sites in plant mitochondria can share cis-elements. FEBS Lett. 580, 268-272

12. Neuwirt, J., Takenaka, M., van der Merwe, J. A., Brennicke, A. (2005) An in vitro RNA editing system from cauliflower mitochondria: Editing site recognition parameters can vary in different plant species. RNA 11, 1563-1570

11. Takenaka, M., Neuwirt, J. Brennicke, A. (2004) Complex cis-elements determine an RNA editing site in pea mitochondria. Nucleic Acids Res. 32, 4137-4144

10. Yamaoka, S., Takenaka, M., Hanajiri, T., Shimizu-Ueda, Y., Nishida, H., Yamato, K. T., Fukuzawa, H. Ohyama, K. (2004) A mutant with constitutive sexual organ development in Marchantia polymorpha L. Sex. Plant Reprod. 16, 253-257

9. Takenaka, M., Brennicke, A. (2003) In vitro RNA editing pea mitochondria requires NTP or dNTP, suggesting involvement of an RNA helicase. J. Biol. Chem. 278, 47526-47533

8. Okada, S., Sone, T., Fujisawa, M., Nakayama, S., Takenaka, M., Ishizaki, K., Kono, K., Shimizu-Ueda, Y., Hanajiri, T., Yamato, K. T., Fukuzawa, H. Brennicke, A. Ohyama, K. (2001) The Y chromosome in the liverwort Marchantia polymorpha has accumulated unique repeat sequences harboring a male-specific gene. Proc. Natl. Acad. Sci. USA 98, 9454-9459

7. Okada, S., Fujisawa, M., Sone, T., Nakayama, S., Nishiyama, R., Takenaka, M., Yamaoka, S., Sakaida, M., Kono, K., Takahama, M., Yamato, K. T., Fukuzawa, H., Brennicke, A. Ohyama, K. (2000). Construction of male and female PAC genomic libraries suitable for identification of Y-chromosome-specific clones from the liverwort, Marchantia polymorpha. Plant J. 24, 421-428

6. Takenaka, M., Yamaoka, S., Hanajiri, T., Shimizu-Ueda, Y., Yamato, K. T., Fukuzawa, H. Ohyama, K. (2000). Direct transformation and plant regeneration of the haploid liverwort Marchantia polymorpha L. Transgenic Res. 9, 179-185

5. Nishiyama, R., Yamato, K. T., Miura, K., Sakaida, M., Okada, S., Kono, K., Takahama, M., Sone, T., Takenaka, M., Fukuzawa, H. Ohyama, K. (2000). Comparison of expressed sequence tags from male and female sexual organs of Marchantia polymorpha. DNA Res. 7, 165-174

4. Sone, T., Fujisawa, M., Takenaka, M., Nakagawa, S., Yamaoka, S., Sakaida, M., Nishiyama, R., Yamato, K. T., Ohmido, N., Fukui, K., Fukuzawa, H. Ohyama, K. (1999). Bryophyte 5S rDNA was inserted into 45S rDNA repeat units after the divergence from higher land plants. Plant Mol. Biol. 41, 679-685

3. Nishiyama, R., Mizuno, H., Okada, S., Yamaguchi, T., Takenaka, M., Fukuzawa, H. Ohyama, K. (1999). Two mRNA species encoding calcium-dependent protein kinases are differentially expressed in sexual organs of Marchantia polymorpha through alternative splicing. Plant Cell Physiol. 40, 205-212

2. Akashi, K., Takenaka, M., Yamaoka, S., Suyama, Y., Fukuzawa, H. Ohyama, K. (1998). Coexistence of nuclear DNA-encoded tRNAVal(AAC) and mitochondrial DNA-encoded tRNAVal(UAC) in mitochondria of a liverwort Marchantia polymorpha. Nucleic Acids Res. 26, 2168-2172

1. Akashi, K., Hirayama, J., Takenaka, M., Yamaoka, S., Suyama, Y., Fukuzawa, H. Ohyama, K. (1997). Accumulation of nuclear- encoded tRNAThr (AGU) in mitochondria of the liverwort Marchantia polymorpha. Biochim. Biophys. Acta. 1350, 262-266