Selected recent publications


1.  Nakamura, M., Tsunoda, T. and Obokata, J. (2002) Photosynthesis nuclear genes generally lack

  TATA boxes: a tobacco PhotosystemI gene responds to light through an initiator. Plant J.



  1. 2. Miyamoto,T., Obokata,J. and Sugiura,M. (2002) Recognition of RNA editing sites is directed by

  unique proteins in chloroplasts: Biochemical identification of cis-acting elements and trans-

  acting factors involved in RNA editing in tobacco and pea chloroplasts.

  Mol Cell Biol 22:6726-6734


3.  Matsuo,M.and Obokata,J. (2002) Dual roles of photosynthetic electron transport in Photosystem I

    biogenesis: Light induction of mRNAs and a chlomatic regulation at post-mRNA level.

    Plant Cell Physiol. 43:1189-1197


4. Sherameti, I., Nakamura, M., Yamamoto, Y.Y., Pfannschmidt, T., Obokata, J. and Oelmueller, R.

   (2002) Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by the

    photosynthetic electron transport: A crucial cis-element in the spinach PsaD gene is located

   in the 5'-untranslated region. Plant J. 32:631-639

5. Hasegawa,K., Yukawa,Y., Obokata, J. and Sugiura, M. (2003) The tRNALeu-like sequence within

  the promoter of an Arabidopsis clock-regulated gene is functional: efficient transcription by RNA

     polymerase-III dependent in vitro transcription system. Gene 307:133-139


6. Sasaki,T.,Yukawa,Y., T.Miyamoto, J.Obokata and Sugiura, M. (2003)Identificatioin of RNA editing

   sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana

   tabacum) :comparative analysis shows the involvement of distinct trans-factors for ndhB editing.

   Molecular Biology and Evolution 20:1028-1035


7. Nakamura, T., Furuhashi, Y., Hasegawa, K., Hashimoto, H., Watanabe, K., Obokata, J., Sugita, M.

    and Sugiura, M. (2003) Array-based analysis on tobacco plastid transcripts: preparation of a

  genomic microarray containing all genes and intergenic regions. Plant Cell Physiol 44:861-867


8. Nagao, I. and Obokata, J. (2003) Poly(U) motif in the 5' untranslated region enhances the

    translational efficiency of the b-glucuronidase mRNA in transgenic tobacco.

    Plant Science 165:621-626


9. Miyamoto,T., Obokata,J. and Sugiura,M. (2004) A site-specific factor interacts directly with

  its cognate RNA editing site in chloroplast transcripts. Proc Natl Acad Sci USA 101:48-52


10. Nagao, I., Masuyama, K. and Obokata, J. (2004) In vitro evolution of translational regulatory cis-

    elements. Endocytobiosis Cell Res 15: 385-389


11. Nakamura, M., Tsunoda, T., Yoshitsugu, T. and Obokata, J. (2004) Core promoter diversity and

    photosynthesis gene regulation. Endocytobiosis Cell Res 15: 300-308


12. Hirose, T., Miyamoto, T., Obokata, J. and Sugiura, M. (2004) In vitro editing system from higher

   plant chloroplasts. Methods in Molecular Biology 265: 333-344


13. Matsuo, M., Ito, Y., Yamauchi, R. and Obokata,J.(2005) Rice nuclear genome continuously

    integrates shuffles and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux.

    Plant Cell 17:665-675


14. Nagao,I. and Obokata,J.(2006) In vitro selection of translational regulatory elements. 

    Anal Biochem 354:1-7


15. Matsuo,M. and Obokata,J.(2006) Remote control of photosynthetic genes by the mitochondrial

    respiratory chain. Plant J  47:873-882


16. Yamamoto,YY.,Ichida,H,,Matsui,M,,Obokata,J,,Sakurai,T,,Satou,M,,Seki,M,,Shinozaki,K,,Abe, T.

    (2007) Identification of plant promoter constituents by analysis of local dstribution of short

    sequences.BMC Genomics 8:67


17. Yamamoto, YY., Ichida, H.,Abe, T., Suzuki, Y., Sugano, S. and Obokata, J.(2007)   

    Differentiation of core promoter architecture between plants and mammals revealed by LDSS

      analysis. Nucleic Acid Res 35:6219-6226


18. Kobayashi, Y., Matsuo, M., Sakamoto, K., Wakasugi, T., Yamada, K. and Obokata, J.(2008)

     Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by

     an identical site-recognition protein in tobacco chloroplasts. Nucleic Acid Res

     Nucleic Acids Res 36:311-318

19. Yamamoto, YY. and Obokata, J. (2008)

  ppdb: a plant promoter database. Nucleic Acids Res 36(database issue):D977-981

20. Shikanai, T. and Obokata, J. (2008) Machinery of RNA editing  in plant organelles. In Frontiers

      of RNA and DNA Editing (ed. by Harold C. Smith) Wiley Press

  1. 21.Takabayashi,A.,Ishikawa,N., Obayashi,T., Ishida,S., Obokata,J.,Endo,T. and Sato, F.,(2008)  Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches.  Plant J. 57:207-219

  1. 22.Yamamoto, YY., Yoshitsugu, T., Sakurai, T., Seki, M., Shinozaki, K. and Obokata, J. (2009) heterogeneity of Arabidopsis core promoters revealed by high density TSS analysis Plant J.  60:350-362

  1. 23.Yamamoto, YY., Yusa, Y., Yamamoto, S,. Hirano, Y., Hirano Y., Motomura, T., Tanemura, T. and Obokata, J. (2009) Identification of photosynhetic sacoglossans from Japan. Endocytobiosis Cell Res 19:112-119

  1. 24.Matsuo, M., Hachisu, R., Tabata, S., Fukuzawa, H. and Obokata, J.(2010) Transcriptome analysis of respiration-responsive genes in Chlamydomonas reinhardtii: Mitochondrial retrograde signaling coordinates the genes for cell proliferation with energy-producing metabolisms. Plant Cell Physiol  doi:10.1093/pcp/pcq192