RNA metabolic regulation plays diverse roles in nutrient-dependent seedling growth in Arabidopsis

Plants continuously respond to changes in nutrient availability by adjusting their growth and development. However, the role of RNA metabolism in this process is unclear. We performed seedling growth assays using Arabidopsis thaliana mutants defective in RNA metabolism. When grown on full-strength Murashige and Skoog (MS) medium containing 1% sucrose, all mutants had shorter primary roots than the wild type, suggesting the importance of RNA metabolic regulation for seedling growth under nutrient-rich conditions. Primary root growth exhibited distinct responses to the presence of sucrose in the following mutants: ccr4a ccr4b, with defects in the deadenylases CARBON CATABOLITE REPRESSOR4a (CCR4a) and CCR4b, which function in poly(A) tail degradation; mtr4-2, with a mutation in the exosome co-factor mRNA TRANSPORT4 (MTR4), which is required for 3'-5' RNA degradation; and rid1-1, with a defect in the RNA helicase ROOT INITIATION DEFECTIVE1 (RID1), which functions in pre-mRNA splicing. Whereas the ccr4a ccr4b seedlings did not exhibit sucrose-dependent changes in root growth, the mtr4-2 and rid1-1 seedlings exhibited more pronounced growth inhibition in response to a lack of sucrose and reduced MS salt and vitamin concentrations, respectively, compared to the wild type. When grown on 0.1×MS medium without sucrose, upf3-1 seedlings, which lack functional UP-FRAMESHIFT3 (UPF3), a component of nonsense-mediated mRNA decay (NMD), were larger than the wild type, suggesting the importance of NMD in regulating seedling growth under nutrient-limited conditions. Therefore, different RNA metabolic pathways play distinct roles in the nutrient-dependent regulation of plant growth, adjusting plant fitness to different environments.