The maize INDETERMINATEI flowering time regulator defines a highly conserved zinc finger protein family in higher plants

Background: The maize INDETERMINATE1 gene, IDI, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain ( IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that IDI binds to DNA suggests that members of this gene family are involved in transcriptional regulation. Results: Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that IDI is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of IDI suggest that it is a divergent member of the maize IDD family. Although no clear IDI ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize IDI, form a group separate from other IDD genes. In contrast to IDI mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with IDI protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only. Conclusion: Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific IDI expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative IDI protein orthologs from rice and sorghum. These similarities between IDI and closely related genes in other grasses point to possible similarities in function.