Reassessing the evolution of the 1-deoxy-D-xylulose 5-phosphate synthase family suggests a possible novel function for the DXS class 3 proteins

The methylerythritol 4-phosphate (MEP) pathway is of paramount importance for generating plastidial isoprenoids. The first enzyme of the MEP pathway, 1-deoxy-D-xylulose-5-phosphate synthase (DXS), catalyzes a flux-controlling step. In plants the DXS gene family is composed of three distinct classes with non-redundant functions. Although the DXS1 and DXS2 subfamilies have been well characterized, the DXS3 subfamily has been considerably understudied. Here, we carried out in silico and functional analyses to better understand the DXS3 class. Our phylogenetic analysis showed high variation in copy number among the different DXS classes, with the apparent absence of DXS1 class in some species. We found that DXS3 subfamily emerged later than DXS1 and DXS2 and it is under less intense purifying selection. Furthermore, in the DXS3 subfamily critical amino acids positions in the thiamine pyrophosphate binding pocket are not conserved. We demonstrated that the DXS3 proteins from Arabidopsis, Maize, and Rice lack functional DXS activity. Moreover, the Arabidopsis DXS3 protein displayed distinctive sub-organellar chloroplast localization not observed in any DXS1 or DXS2 proteins. Coexpression analysis of the DXS3 from Arabidopsis showed that, unlike DXS1 and DXS2 proteins, it coexpresses with genes related to post-embryonic development and reproduction and not with primary metabolism and isoprenoid synthesis.

Automated summary

The DXS3 subfamily plays a crucial role in the MEP pathway in generating plastidial isoprenoids and shows unique evolution and functionality compared to DXS1 and DXS2 subfamilies. DXS3 proteins lack functional activity in Arabidopsis, Maize, and Rice, and display distinct sub-organellar chloroplast localization. DXS3 coexpresses with genes related to post-embryonic development and reproduction, indicating a different role compared to DXS1 and DXS2 proteins in primary metabolism and isoprenoid synthesis.