Genome-wide identification, classification and expression analysis of GHMP genes family in Arabidopsis thaliana

The GHMP genes family, a unique class of ATP-dependent enzymes, consists of galactokinases, homoserine kinases, mevalonate kinases and phosphomevalonate kinase etc. It was implicated in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. Previous studies mainly focused on the structure, catalytic mechanism or function in abiotic stress signaling. In this study, we integrated the research progress on GHMP genes and identified 12 members (five previously discovered and seven newly identified here) of this family in Arabidopsis thaliana. The gene ontology, phylogenetic relationship, motifs, cis-acting element, expression profiles, structures and protein–protein interaction network of GHMP family were analyzed. The neighbor-joining tree and cluster of gene structures indicated that the 12 members were divided into two classes. The three motifs in the GHMP family were highly conserved among the GHMP family by Multiple EM for Motif Elicitation, providing further proof on their phylogenetic relationship. Additionally, prediction on cis-acting elements indicated that these genes were likely to be involved in multiple responses stimulated by various hormones and abiotic stress. It is roughly consistent with the data of microarray. The identification and bioinformatic analysis of GHMP family in Arabidopsis thaliana could provide reference data for further study on their biological functions, especially in the responsiveness to hormones and stress signaling.