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| Status |
Public on Jan 24, 2024 |
| Title |
Transcriptomic analysis of rps6 mutants in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Pairwise comparisons between 5 RPS6 genotypes: WT, rps6a, rps6b, rps6a rps6b; eS6A-HA, rps6a rps6b; eS6A-Δ6SA
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| Contributor(s) |
von Arnim AG, Enganti R, Urquidi Camacho RA, Dasgupta A |
| Citation(s) |
38250458 |
| |
| Submission date |
Jan 16, 2023 |
| Last update date |
Jan 24, 2024 |
| Contact name |
Elena D Shpak |
| E-mail(s) |
eshpak@utk.edu
|
| Phone |
1-865-974-8383
|
| Organization name |
The University of Tennessee
|
| Department |
Biochemistry, Cellular and Molecular Biology
|
| Lab |
Shpak Lab
|
| Street address |
309 Ken and Blaire Mossman Bldg.
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA924310 |
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