Data for: Post-translational regulation of photosynthetic activity via the TOR kinase in plants
Data files
May 28, 2024 version files 203.58 MB
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README.md
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Supplementary_data.zip
Abstract
Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photo-oxidative damage. We have identified a post-translational mechanism linking the eukaryotic Target of Rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity, and photosynthesis in particular. We find that RelA SpoT Homologue 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific N-terminal region which is phosphorylated in a TOR-dependent manner. Downregulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.
README: Data for: Post-translational regulation of photosynthetic activity via the TOR kinase in plants
Summary
This dataset contains underlying data for figure panels in the associated article (D'Alessandro et al.), sequence information, and scripts. Data is organized in folders grouped by figure and figure panel.
Description
Folder: Fig 1
- Subfolder: Fig1B
- Uncropped blots (pptx) and raw image files (tif).
- Subfolder: Fig1C
- "data 1C.xlsx", RSH3/TID peptide spectrum match (PSM) ratios, showing sample origin (Origin), sample ID (ID), and raw data name.
- Raw data files available at ProteomeXchange under accession PXD047124.
- Subfolder: Fig1D
- Uncropped blots (pptx) and raw image files (tif).
- Subfolder: Fig1E
- Uncropped blots (pptx) and raw image files (tif).
- Subfolder: Fig1F
- Uncropped blots (pptx) and raw image files (tif).
- Subfolder: Fig1G
- "Summary of RSH3 phosphopeptides.xlsx", summary of identified RSH3 phosphopeptides with explanatory index.
- "RSH3(39-221) P positions.pptx", peptide spectra supporting phosphopeptides shown in summary.
- Raw data available at ProteomeXchange under accession PXD047124.
- Subfolder: Fig1H
- Uncropped blots (pptx) and raw image files (tif).
Folder: Fig 2
- data 2A.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (CTRL, control or AZD, AZD-8055).
- data 2b.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (CTRL, control or AZD, AZD-8055).
- data 2c.xlsx
- Measured GTP and ppGpp levels in different plant lines (ID) with different treatments (control or AZD, AZD-8055).
- data 2e.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (treatment).
Folder: Fig 3
- data 3A.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (CTRL, control or AZD, AZD-8055).
- data 3C.xlsx
- Quantification of GFP signal in nuclei versus chloroplasts (nuclei on chloroplast ratio) for the N-terminal region of RSH3 (CTP4 P+ and CTP4 P-).
- Subfolder: data 3D
- Uncropped blots (pptx) and raw image files (tif).
Folder: S2
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S2.
Folder: S4B
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S4B.
Folder: S5A
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S5A.
Folder: S6
- Subfolder: IQTREE
- RSH2/3 family full alignments and N-ter region alignments (fasta format, .fas).
- IQTREE phylogenetic tree inference output files including consensus tree (full_length_2_cut_no_col_NTR.fas.contree) and log file (full_length_2_cut_no_col_NTR.fas.log).
Folder: S7
- S7.csv
- Metapredict 2.4 disorder predictions for different RSH proteins.
Folder: S8
- S8.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (AZD 0, AZD 1, and AZD 10).
Folder: S9
- S9B.xlsx
- Measured Fv/Fm ratio (Fv/Fm) in different plant lines (Line) with different treatments (control or AZD).
- S9BC.xlsx
- Measured Fv/Fm ratio (Fv/Fm) and Fv/Fm relative to control conditions for the same line (Relative Fv/Fm) in different plant lines (Line) with different treatments (control or nitrogen starvation (N50)).
Folder: S10
- Subfolder: S10A
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S10A.
- Subfolder: S10B
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S10B.
- S10AB.xlsx
- Calculated ratios (Ratio) for phospho-RPS6 (P-RPS6) signal versus total RPS6 (RPS6) signal from two independent replicates (Rep) in the indicated plant lines (Line) in response to the indicated treatments (Treatment).
Folder: S11
- Uncropped blots (pptx) and raw image files (tif) for Supplementary Figure S11.
- S11.xlsx
- Calculated ratios (Ratio) for phospho-RPS6 (P-RPS6) signal versus total RPS6 (RPS6) signal from two independent replicates (Rep) in the indicated plant lines (Line) in response to the indicated treatments (Treatment).
Folder: script
- Stats_and_Plot.ipynb
- Python script for plotting graphs and statistical testing.
- CLD.py
- Python script for compact letter display (CLD) of statistical test results.
Folder: sequences
- Full plasmid sequences for all constructions created in this study (see Table S3). Sequences are provided in Snapgene format (.dna), and the main features are indicated.
Usage notes
Files are in xlsx, CSV, pptx, jpg, tiff, and png formats.
Sequence data is in Snapgene .dna format. Viewable with free Snapgene viewer.
Scripts are in py and ipynb format for Python.