The nucleotide metabolome of germinating Arabidopsis thaliana seeds reveals a central role for thymidine phosphorylation in chloroplast development

Abstract

Thymidylates are generated by several partially overlapping metabolic pathways in different subcellular locations. This interconnectedness complicates an understanding of how thymidylates are formed in vivo. Analyzing a comprehensive collection of mutants and double mutants on the phenotypic and metabolic level, we report the effect of de novo thymidylate synthesis, salvage of thymidine, and conversion of cytidylates to thymidylates on thymidylate homeostasis during seed germination and seedling establishment in Arabidopsis (Arabidopsis thaliana). During germination, the salvage of thymidine in organelles contributes predominantly to the thymidylate pools and a mutant lacking organellar (mitochondrial and plastidic) thymidine kinase has severely altered deoxyribonucleotide levels, less chloroplast DNA and chlorotic cotyledons. This phenotype is aggravated when mitochondrial thymidylate de novo synthesis is additionally compromised. We also discovered an organellar deoxyuridine-triphosphate pyrophosphatase and show that its main function is not thymidylate synthesis but probably the removal of non-canonical nucleotide triphosphates. Interestingly, cytosolic thymidylate synthesis can only compensate defective organellar thymidine salvage in seedlings but not during germination. This study provides a comprehensive insight into the nucleotide metabolome of germinating seeds and demonstrates the unique role of enzymes that seem redundant at first glance.

Dynamic changes in the levels of metabolites and endogenous hormones during the germination of Zanthoxylum nitidum (Roxb.) DC. Seeds

“… 45 In the process of seed germination, the involvement of purine metabolism in the myriad of bioenergetic processes is required for the mobilization of storage products; moreover, active nucleotide biosynthesis is needed to provide sufficient pyrimidine nucleotides to the embryos to facilitate nucleic acid synthesis. 46 In this study, we observed that some nucleotides (cytosine, CAMP, cytidine, deoxyadenosine and guanosine) involved in the purine metabolism pathway accumulated significantly during the germination of Z. Nitidum seed, consistent with the varying trend of nucleotides during seed germination of common beans, 47 castor, 48 Arabidopsis thaliana 49 and other seeds. This finding indicates that a large number of nucleotides are required for the germination of Z. nitidum seeds in addition to the mobilization of nutrients in cotyledons.…”

An inosine triphosphate pyrophosphatase safeguards plant nucleic acids from aberrant purine nucleotides

“…However, in 7‐d‐old A. thaliana plants, the concentrations of IDP and ITP rose significantly when plants were treated with ribavirin. We hypothesize that this discrepancy is due to a different developmental context, as there is likely more overall nucleotide kinase activity in developing tissues than in fully developed leaves (Niehaus et al ., 2022), which would also increase the rate of spurious IMP phosphorylation.…”