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BACKGROUND 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(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)
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)
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)
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)
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)
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)
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 in higher-plant chloroplasts involves C-to-U conversions at specific sites. Although in vivo analyses have been performed, little is known about the biochemical aspects of chloroplast editing reactions. Here we improved our original in vitro system and devised a procedure for preparing active chloroplast extracts not only from tobacco plants but(More)
The chloroplast genome of higher plants contains 20-40 C-to-U RNA editing sites, whose number and locations are diversified among plant species. Biochemical analyses using in vitro RNA editing systems with chloroplast extracts have suggested that there is one-to-one recognition between proteinous site recognition factors and their respective RNA editing(More)