Genomewide bioinformatic analysis negates any specific role for Dof, GATA and Ag/cTCA motifs in nitrate responsive gene expression in Arabidopsis.

Nitrate response at the plant level is mediated by the transcriptional regulation of several hundreds of genes, but no common cis-acting nitrate-responsive elements (NREs) have been identified so far. Earlier, we bioinformatically ruled out the possibility that the previously published [(a/t)7Ag/cTCA] motif could act as NRE on its own (Das et al., 2007, Mol. Genet. Genomics, 278: 519-525). In the present study, we examined other motifs such as Dof and GATA binding elements in homologous as well as heterologous pairwise combinations in the Arabidopsis genome in silico. None of the above three motifs revealed any unique association with nitrate responsive genes or their subsets in any combination, either within their ORFs or 1 kb flanking sequences on either side. Additionally, twelve new, top-scoring candidate motifs that were generated using different online motif samplers were analyzed in silico using a subset of 21 'early' nitrate responsive genes, but did not reveal any specificity of occurence. These results underscore the need to continue the search for novel candidate NREs, as possible sites of intervention to understand/improve nitrate-responsive gene expression and nitrate use efficiency.