DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins      

Abstract

LONG HYPOCOTYL5 (HY5) is a bZIP (basic leucine zipper) transcription factor that activates photomorphogenesis and root development in Arabidopsis (Arabidopsis thaliana). Previously, STF1 (soybean [Glycine max] TGACG-motif binding factor 1), a homologous legume protein with a RING-finger motif and a bZIP domain, was reported in soybean. To investigate the role of STF1, the phenotypes of transgenic Arabidopsis plants overexpressing STF1 and HY5 were compared. In addition, the DNA-binding properties of STF1 and HY5 were extensively studied using random binding site selection and electrophoretic mobility shift assay. Overexpression of STF1 in the hy5 mutant of Arabidopsis restored wild-type photomorphogenic and root development phenotypes of short hypocotyl, accumulation of chlorophyll, and root gravitropism with partial restoration of anthocyanin accumulation. This supports that STF1 is a homolog of HY5 with a role in light and hormone signaling. The DNA-binding properties of STF1 and HY5 are shown to be similar to each other in recognizing many ACGT-containing elements with a consensus sequence motif of 5#-( G / A )( G / A ) TGACGT( C /G/ A )( A /T/ G )-3#. The motif represents a characteristically strong preference for flanking sequence to TGACGT and a larger sequence than the sequences recognized by the G-box binding factor and TGA protein families. The finding of C-box, hybrid C/G-, and C/A-boxes as high-affinity binding sites over the G-box and parameters associated with HY5 recognition define the criteria of HY5/STF1 protein-DNA interaction in the promoter regions. This study helps to predict the precise in vivo binding sites of the HY5 protein from the vast number of putative HY5 genomic binding sites analyzed by chromatin immunoprecipitation on chip.

Light Regulation of Gibberellin Biosynthesis in Pea Is Mediated through the COP1/HY5 Pathway

“…Like the divergent HY5 orthologs previously identified in other legume species, LONG1 is distinguished from HY5 by the presence of an additional N-terminal domain with close similarity to the N-terminal RING-type Zn-finger domain of the cellulose synthase A subunit (Nishimura et al, 2002b;Song et al, 2008). Despite this structural difference, however, LONG1 and HY5 appear to have largely similar functions in photomorphogenesis.…”

“…A mutant for the L. japonicus LONG1 ortholog ASTRAY shows increased hypocotyl elongation and reduced chlorophyll and anthocyanin content (Nishimura et al, 2002a). Expression of the soybean ortholog STF1 in transgenic Arabidopsis complemented the hy5 mutant phenotype with respect to these three traits (Song et al, 2008). In addition, STF1 and HY5 have a similar DNA binding repertoire (Song et al, 2008).…”

“…Expression of the soybean ortholog STF1 in transgenic Arabidopsis complemented the hy5 mutant phenotype with respect to these three traits (Song et al, 2008). In addition, STF1 and HY5 have a similar DNA binding repertoire (Song et al, 2008). Although more detailed comparisons of the legume genes with Arabidopsis HY5 are needed, there is little evidence so far that the additional N-terminal domain of the legume HY5-like genes has any additional role.…”

Phytochrome and phytohormone interplay in tomato: impacts on fruit physiology and quality traits

“…and degenerate AuxRE (TGTGNC) motifs (Martıńez-Garcıá et al, 2000;Song et al, 2008;Chaabouni et al, 2009). …”

“…Typical 3 kb upstream from the initial codon ATG was analyzed for the presence of PBEbox (CACATG), G-box (CACGTG), CA-hybrid (GACGTA) and CG-hybrid (GACGTG) motifs, which are recognized by HY5 and/or PIFs (Martıńez-Garcıá et al, 2000;Song et al, 2008), as well as the presence of canonical AuxRE (TGTGTC) and degenerate AuxRE (TGTGNC), which are recognized by ARFs (Chaabouni et al, 2009). …”