DOI: 10.5061/dryad.ghx3ffbtm
title: Data for: Post-translational regulation of photosynthetic activity via the TOR kinase in plants

description: 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.
description: 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.
description: # 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.