Computational analysis of the evolution of the structure and function of 1-deoxy-D-xylulose-5-phosphate synthase, a key regulator of the mevalonate-independent pathway in plants.

We investigated molecular evolution of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), an important regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Sequence alignment showed that some regions, likely to be functionally important, were highly conserved among all of the plant DXS sequences analysed. Phylogenetic trees were inferred using DXS sequences from 11 species of Angiosperms and showed the division of the sequences into two classes. Clustering of DXS sequences did not correspond to phylogenetic relationships among the plant species studied. There was no consistency in the similarity of the variable regions in the secondary structure of the DXS functional protein except for Capsicum and Lycopersicon, both members of the Solanaceae. Hydrophobicity plots for the functional region of DXS revealed great similarity in their hydrophobic structure, consistent with the phylogenetic trees inferred, and with eight prominent hydrophilic and hydrophobic peaks. We also observed a consistent set of features common to the DXS transit peptides studied. These features were the same hydrophobic slope, a hydrophobic region in residues 35-45, and, in eight of 12 sequences, a Pro-Pro-Thr sequence at the C-terminal end. The transit sequences are likely bipartite and contain features that suggest the DXS protein is not only targeted to the chloroplast, but also to the thylakoid. To our knowledge this is the first suggestion that DXS is located specifically in the chloroplast thylakoid.