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Transcriptomic analysis of rps6 mutants in Arabidopsis thaliana

ABSTRACT: The eukaryote-specific ribosomal protein of the small subunit eS6 is a target of phosphorylation for the Target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been known and studied for about 50 years, its biochemical and physiological significance remains controversial and poorly understood. To explore the role of eS6 and its phosphorylation we performed RNA-seq on the shoots of 12-day-old seedlings in five Arabidopsis thaliana genotypes. eS6 protein is encoded by two paralogous genes, RPS6A and RPS6B. Our data describe mRNA transcript levels in wild type (ecotype Columbia), two single mutants (rps6a and rps6b), an HA-epitope-tagged transgenic complementation line (rps6a rps6b; eS6A-HA) and a 'phosphonull' transgenic complementation line (rps6a rps6b; eS6A-Δ6SA) with six phosphorylatable residues mutated to alanine. Single mutants showed broad, but moderate changes to mRNA levels with the primary effects encompassing increases in translation and ribosome biogenesis genes and down regulation of photosynthesis. The rps6a rps6b; eS6A-HA plant almost fully complemented defects observed in the single mutants highlighting that the eS6 paralogs are functionally equivalent. Residual mRNA expression defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects, with little or no evidence for gain-of function defects. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE222967 | GEO | 2024/01/24

REPOSITORIES: GEO

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Project description:The eukaryote-specific ribosomal protein of the small subunit eS6 is a target of phosphorylation for the Target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been known and studied for about 50 years, its biochemical and physiological significance remains controversial and poorly understood. Here we report data from Arabidopsis thaliana, which indicate that plants expressing only a largely phospho-deficient isoform of eS6 grow essentially normally under laboratory conditions. The eS6A (RPS6A) paralog of eS6 can functionally rescue double mutations in both rps6a and rps6b when expressed at approximately twice the wild-type dosage. A mutant isoform of eS6A lacking the major six phosphorylatable serine and threonine residues in its carboxyl-terminal tail also rescued the lethality of the double mutant and complemented nearly all mutant phenotypes, including rosette growth, photosynthetic efficiency, polyribosome loading, and the vast majority of gene expression defects at the transcriptome and proteome level. When compared to plants that were rescued with a phospho-enabled version of eS6A, the phospho-deficient seedlings retained a mild pointed-leaf phenotype, and root growth was reduced, and certain cell cycle related mRNAs were misexpressed. The residual mRNA expression defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects, with little or no evidence for gain-of function defects. The proteomes of seedlings rescued with a phospho-enabled and a phospho-deficient isoform of eS6A also had subtle differences suggesting that the P-deficient isoform did not fully reverse the derepression of the ribosome biogenesis regulon that was observed in the single mutants. As expected, the phospho-deficient eS6A also rescued the rps6a and rps6b single mutants; however, phosphorylation of the eS6B paralog was lower than predicted, further underscoring that plants can tolerate phosphodeficiency of eS6 well. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.

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Transcriptomic analysis of rps6 mutants in Arabidopsis thaliana

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