Sequence and Spacing of TATA Box Elements Are Critical for Accurate Initiation from the β-Phaseolin Promoter

Abstract

The ␤-phaseolin (phas) gene, which encodes one of the major seed storage proteins of P. vulgaris, is tightly regulated at the transcription level resulting in strict tissuespecific and spatial expression during embryonic development. The phas proximal promoter contains a complex arrangement of core promoter elements including three TATA boxes as well as several putative initiator elements. To delineate the respective contributions of the core promoter elements to transcription initiation we have performed site-directed mutagenesis of the phas promoter. In vivo expression studies were performed on transgenic Arabidopsis harboring phas promoter mutants driving expression of the ␤-glucuronidase (gus) reporter gene. Quantitative assessment of GUS activity in seeds bearing the promoter mutants indicated that both sequence and spacing of the TATA elements influenced the efficiency of transcription. Substitution, insertion or deletion mutations had no effect on histochemical staining patterns indicating that strict spacing requirements are not essential for correct spatial expression of phas during embryogenesis. Further evaluation of the phas promoter by in vitro transcription analysis revealed the presence of multiple TATA-dependent transcription initiation start sites. The distance between TATA elements and transcription start sites was maintained in insertion and deletion mutants through the creation of novel initiation sites, indicating that positioning of the TATA elements rather than DNA sequence was the primary determinant of start site location. We conclude that, while dispensable for proper spatial distribution, the complex architecture of the phas promoter is required to ensure high levels of accurate phas transcription initiation in the developing embryo.The proximal promoter region of a gene contains core promoter elements that determine the basal transcription activity of the gene and typically direct the positioning of the transcription initiation start site. Three different classes of transcription initiation elements have been identified in eukaryotes: TATA boxes, initiator (Inr) 1 elements and downstream promoter elements (DPE). To date, only TATA boxes and Inr elements have been identified in plant promoters. All three elements utilize similar mechanisms of initiation requiring RNA polymerase II and sequence-specific binding of transcription factor IID (1). However, mechanistic differences exist between the different initiation elements. TATA-containing promoters can function in the absence of an Inr, whereas DPE promoters are Inr-dependent; TATA box directed transcription occurs on average 25-30 bp downstream of the TATA box while Inr driven transcription typically originates at the adenosine residue in the ϩ1 position of the Inr element itself (2). Sequence analysis of the Drosophila and human genomes indicates that only a minority of promoters contain the classical arrangement of one TATA box and one Inr element (3, 4). The remaining promoters contain varying combinations of TATA, Inr, and DPE ele...

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

“…Evolutionary fate of rhizome-specific genes anaerobic genes (AAACAAA; Mohanty et al, 2005) showed significantly higher abundance in S. bicolor than the other species. The promoters of S. bicolor genes were enriched relative to those of O. sativa for three additional cis-elements, À300 element (Thomas and Flavell, 1990), À10 promoter element (Thum et al, 2001) and TATA box (Grace et al, 2004). By contrast, two promoters, polyA signal (O'Nell et al, 1990) and pro-or hypo-osmolarity element found in the promoter of proline dehydrogenase (Satoh et al, 2002) were more abundant in the promoters of S. bicolor than S. propinquum alleles.…”

“…Five additional cis-acting regulatory elements, such as CRT/DRE motif (Xue, 2003), (CA) n element in storage protein genes (Ellerstrom et al, 1996), TATA box (Grace et al, 2004), the CCA1-binding element related to regulation by phytochrome (Wang et al, 1997), and pyrimidine box required for gibberellic acid (GA) induction (Cercos et al, 1999), were also more abundant in S. propinquum than either S. bicolor or O. sativa alleles (Table 3).…”

Expression of Rice (Oryza sativa L.) Genes Involved in High-Affinity Nitrate Transport during the Period of Nitrate Induction

“…Several putative TATA boxes were found in OsNRT2.1, OsNRT2.2 and OsNRT2.4. TATABOX2 (Grace et al 2004) was found at −152 and at −124 in OsNRT2.1 and OsNRT2.2, respectively. TATABOXOSPAL (Zhu et al 2002) was found at −156 in OsNRT2.4.…”

Phaseolin: Structure and Evolution

“…Three TATA box sequences are located upstream from the mRNA cap at positions -28, -37 and -39. Slightom et al [25] postulated that the sequence at -28 was likely to be the most important in driving high expression from the phas promoter; this was later confirmed by Grace et al [40] who used an in vitro transcription system that revealed that the sequence and spacing of the TATA box elements are critical for accurate initiation from the -phaseolin promoter. The A+T content of the introns is similar to that in soybean proteins, but is considerably higher than those of non-plant species.…”