Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and Shadowing

• Published in: The Plant cell Vol. 15; no. 6; pp. 1296 - 1309
• Main Authors: Hong, Ray L., Hamaguchi, Lynn, Busch, Maximilian A., Weigel, Detlef
• Format: Journal Article
• Language: English
• Published: United States American Society of Plant Biologists 01-06-2003
• Subjects: AGAMOUS Protein, Arabidopsis - genetics; AGAMOUS Protein, Arabidopsis - metabolism; Apical meristems; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Base Sequence; Binding sites; Biological taxonomies; Brassicaceae - genetics; Brassicaceae - metabolism; Cucumbers; Cucumis sativus - genetics; Cucumis sativus - metabolism; Flowers - genetics; Flowers - metabolism; Gene Expression Regulation, Plant; Genes, Homeobox - genetics; Genes, Homeobox - physiology; Genomes; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Introns; Molecular Sequence Data; Phylogenetics; Phylogeny; Plant cells; Plant Proteins - genetics; Plant Proteins - metabolism; Plants; Polymerase chain reaction; Sequence Homology, Nucleic Acid; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1040-4651; 1532-298X; 1532-298X
• DOI: 10.1105/tpc.009548

In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3-kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae species, several other motifs, but not the LFY and WUS binding sites identified previously, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for the activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection but also demonstrate that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.