Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

Applying a novel bioinformatic algorithm, we demonstrate on a genome-wide scale that singular motifs or composite modules of AuxREs, ZREs, MREs but also of MYC2 related elements are significantly enriched in promoters of auxin-inducible genes. Despite considerable, species-specific differences in the genome structure in terms of the GC content, this enrichment is generally conserved in dicot (Arabidopsis thaliana) and monocot (Oryza sativa) model plants. Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families. Consistently, a bipartite module, which encompasses a bZIP-associated G-box Related Element (GRE) and an AuxRE motif, has been found to be highly enriched. Making use of transient reporter studies in protoplasts, these findings were experimentally confirmed, demonstrating that GREs functionally interact with AuxREs in regulating auxin-mediated transcription.Using genome-wide bioinformatic analyses, evolutionary conserved motifs have been defined which potentially function as AuxRE-dependent coupling elements to establish auxin-specific expression patterns. Based on these findings, experimental approaches can be designed to broaden our understanding of combinatorial, auxin-controlled gene regulation.Auxin is a major plant hormone that regulates concerted plant growth as it is involved in diverse plant developmental processes [1] such as apical dominance [2], root formation [3] and growth-related tropisms [4]. In general, the manifestation of auxin-mediated responses is ascribed to the encoded activity of auxin responsive genes [5].The transcriptional response to auxin is primarily mediated through cis-regulatory Auxin Response Elements (AuxREs) [6]. These elements are bound by Auxin Response Factors (ARFs) [7] that act with Aux/IAA proteins to regulate auxin dependent gene transcription, whereby Aux/IAA proteins repress ARF activity at low cellular auxin concentrations [8-10]. Auxin mediates the interaction