Genome-wide identification, classification, and analysis of two-component signal system genes in maize

Cytokinins play many vital roles in plant development and physiology. In plants, cytokinin signals are sensed and transduced by the two-component signal system. This signaling cascade is typically composed of three proteins: a sensory histidine kinase, a histidine phosphotransfer protein, and a response regulator. Through a comprehensive genome-wide analysis of the maize (Zea mays) genome, 48 genes were identified, including 11 ZmHKs, 9 ZmHPs, and 28 ZmRRs (21 A-type ZmRRs and 7 B-type ZmRRs). Using maize genome sequence databases, we analyzed conserved protein motifs and established phylogenetic relationships based on gene structure, homology, and chromosomal location. The duplication of these two-component system genes in the maize genome corresponded to the clusters of these genes in the phylogenetic trees. Sequence analysis of the duplicate genes demonstrated that one gene may be in gene duplication, and that there was significant variation in the evolutionary history of the different gene families. We assessed the expression levels of all ZmRRs in the leaves and roots by reverse transcription PCR; they were all found to be active. Our results provide a foundation for functional and evolutionary studies on maize two-component signal system proteins.