A Natural Variation in Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development.

The modification of tRNA is important for accurate, efficient protein translation. A number of tRNA-modifying enzymes were found to influence various developmental processes in distinct organisms. However, few genetic or molecular studies have focused on genes encoding tRNA-modifying enzymes in green plant organelles. Here, we discovered that , a natural variation allele of (), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice into the rice () cv 187R. Map-based cloning revealed that encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of was further confirmed by genetic complementation experiments and mutant analysis. mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD forms homodimers and has strong GTPase activity, whereas PDD fails to form homodimers and has weak GTPase activity. Liquid chromatography-coupled tandem quadrupole mass spectrometry revealed that PDD is associated with the 5-methylaminomethyl-2-thiouridine modification of chloroplast tRNA. Furthermore, compared to 187R, NIL- has severely reduced levels of proteins involved in photosynthesis and ribosome biogenesis but increased levels of plastid-encoded RNA polymerase subunits. Finally, we demonstrate that the defect due to alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.