A natural variation in pleiotropic developmental defects uncovers a crucial role for chloroplast tRNA modification in translation and plant development

Hui Liu, Ding Ren, Ling Jiang, Xiaojing Li, Yuan Yao, Limin Mi, Wanli Chen, Aowei Mo, Ning Jiang, Jinshui Yang, Peng Chen, Hong Ma, Xiaojin Luo, Pingli Lu

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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 PDDOL, a natural variation allele of PLEIOTROPIC DEVELOPMENTAL DEFECTS (PDD), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice Oryza longistaminata into the rice (Oryza sativa) cv 187R. Map-based cloning revealed that PDD encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of PDD was further confirmed by genetic complementation experiments and mutant analysis. PDD mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD187R forms homodimers and has strong GTPase activity, whereas PDDOL 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-PDDOL 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 PDDOL alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.

Original languageEnglish (US)
Pages (from-to)2345-2366
Number of pages22
JournalPlant Cell
Volume32
Issue number7
DOIs
StatePublished - Jul 2020

All Science Journal Classification (ASJC) codes

  • Plant Science
  • Cell Biology

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