Junichi Obokata

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Plant promoter architecture is important for understanding regulation and evolution of the promoters, but our current knowledge about plant promoter structure, especially with respect to the core promoter, is insufficient. Several promoter elements including TATA box, and several types of transcriptional regulatory elements have been found to show local(More)
The c o m p l e t e n u c i e o t i d e sequence [155 ,844 bp) o f t o b a c c o ( N i c o t i a n a tabecum v a r . B r i g h t y e l l o w 4) c h l o r o p l a s t DNA [ S h i n o z a k i e t e l . 1986) is p r e s e n t e d . The c i r c u l a r DNA [see F ig . 1) i8 i nea r zed by c u t t i n g a t the j u n c t i o n JLA between IR A and LSC JLA is d e(More)
ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are(More)
Plastid DNA fragments are often found in the plant nuclear genome, and DNA transfer from plastids to the nucleus is ongoing. However, successful gene transfer is rare. What happens to compensate for this? To address this question, we analyzed nuclear-localized plastid DNA (nupDNA) fragments throughout the rice (Oryza sativa ssp japonica) genome, with(More)
Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also found in plant promoters, it is not known if CpG-type promoters exist in plants. Plant promoters contain Y Patches (pyrimidine patches) in the core promoter region,(More)
The promoter architecture of the nuclear-encoded photosystem I genes was studied using a tobacco gene, psaDb, as a model case. Linker scanning mutations revealed that the psaDb promoter does not have a TATA box. Instead, pyrimidine-rich Initiator (Inr) elements that overlap the transcription start sites are essential for light-responsive transcription of(More)
Chloroplastic NAD(P)H dehydrogenase (NDH) plays a role in cyclic electron flow around photosystem I to produce ATP, especially in adaptation to environmental changes. Although the NDH complex contains 11 subunits that are homologous to NADH:ubiquinone oxidoreductase (complex I; EC, recent genetic and biological studies have indicated that NDH also(More)
Expression of the psbB gene cluster in tobacco chloroplasts has been studied. This cluster contains the genes for the 51 kDa chlorophyll a apoprotein (psbB) and the 10 kDa phosphoprotein (psbH) of photosystem II, and cytochrome b6 (petB) and subunit IV (PetD) of the cytochrome b/f complex in this order. Northern blot hybridization and reverse transcription(More)
RNA editing alters genomic nucleotide sequences at the transcript level. In higher plant chloroplasts, C-to-U conversion is known to occur at around 30 specific sites. The tobacco cultivar Nicotiana tabacum is an amphidiploid derived from ancestors of N. sylvestris (maternal) and N. tomentosiformis (paternal). The chloroplast genome of N. tabacum is(More)
Our limited understanding of plant promoters does not allow us to recognize any core promoter elements for the majority of plant promoters. To understand the promoter architecture of Arabidopsis, we used the combined approach of in silico detection of novel core promoter elements and large-scale determination of transcription start sites (TSSs). To this(More)