Organization and regulatory mechanism of the promoters unique to photosynthesis nuclear genes

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Core promoter is a region where preinitiation complex containing RNA polymerase II assembles, and located around the transcription start sites. In plant nuclear genes, core promoters generally contain TATA boxes as an essential element, and are believed to be indispensable for basal transcription but not involved in gene-specific regulation. However, we recently found the case where above assumption is not correct. The core promoter of a tobacco photosystem I gene, psaDb contains a pyrimidine-rich initiator element (Inr) but not a TATA box ; this core promoter architecture is referred to as a TATA-/Inr+ type. Experiments with various chimeric promoters revealed that the light-responsive transcription of psaDb effectively occurs only when the core promoter contains Inr, and TATA box cannot compensate for this Inr. This is the first example in plant genes that the core promoter architecture plays a pivotal role in gene-specific regulation. This finding raised a next question if this selective activation of the core promoter by upstream regulatory elements is unique to psaDb or common to a certain group of plant genes. In this study, we systematically analyzed the core promoter architecture of plant nuclear genes, and demonstrate that PSI genes constitute a unique group in respect to the architecture and function of their core promoters. The core promoters of the PSI gene group are generally TATA-/Inr+ or TATA-/Inr-types, and especially in the latter case, we found no promoter consensus motif so far identified in eukaryotic promoter systems. Swapping experiments of the upstream and core promoters between PSI genes and other TATA-containing plant genes revealed that core promoter requirement of PSI genes is quite different from that of the majority of plant nuclear genes.