Isopentenyl Phosphate Kinases are Ubiquitous and Copy Numbers are Conserved in Plant Genomes

Abstract Key message: Isopentenyl phosphate kinase (IPK) is a key enzyme in mevalonate pathway in isoprenoid biosynthesis. We analyzed 37 presumptive IPK sequences from 35 plants. An specific evolution model was found in plant IPKs, which can be used as an new target in studying the plant isoprenoids metabilte. Abstract: Isopentenyl phosphate kinase (IPK) is a recently discovered enzyme played key role in mevalonate pathway in isoprenoid biosynthesis. Here, we showed that IPKs are ubiquitously present in plant genomes. All IPKs previously identified had AAK domain. From 35 plant species with genome assembly data available, we extracted all AAK family members. Using OrthoMCL, we identified a group of 37 sequences in which Arabidopsis IPK was included. Further analysis showed that each peptide sequence in this group has a His residue which is a signature of IPK enzyme, indicating that the genes in this group were IPKs. Not like these in other domains of life which showed spotty distribution over the tree of life, virtually all plant genomes we analyzed here had IPK genes. Further, copy numbers of IPKs were very conserved in that no higher than 2 copies remained in each plant genome. Plant IPKs formed a distinctive clade in phylogenetic tree of plant AAK gene family, and had a phylogenetic topology conformed to that of plant species. The IPKs we identified here would provide new molecular targets for characterization of plant mevalonate pathway, and shed light on biochemistry of plant isoprenoids biosynthesis.