Data from: Regulation of vacuole fusion in stomata by dephosphorylation of the HOPS subunit VPS39
Data files
Dec 02, 2025 version files 83.51 GB
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Guard_Cell_enriched_RT_qPCR.xlsx
15.86 KB
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README.md
3.83 KB
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Root_vacuole_data.zip
4.21 GB
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Seedling_qRT_PCR_vps39-2.xlsx
15.59 KB
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Siliques_Data.tar
75.37 GB
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Stomata_Vacuole_Data.zip
3.93 GB
Abstract
Understanding how plants regulate water loss is important for improving crop productivity. Tight control of stomatal opening and closing is essential for the uptake of CO2 while mitigating water vapor loss. The opening of stomata is regulated in part by homotypic vacuole fusion, which is mediated by conserved homotypic vacuole protein sorting (HOPS) and vacuolar SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptors) complexes. HOPS tethers apposing vacuole membranes and promotes the formation of trans-SNARE complexes to mediate fusion. In yeast, HOPS dissociates from the assembled SNARE complex to complete vacuole fusion, but little is known about this process in plants. HOPS-specific subunits VACUOLE PROTEIN SORTING39 (VPS39) and VPS41 are required for homotypic plant vacuole fusion, and a computational model predicted that post-translational modifications of HOPS may be needed for plant stomatal vacuole fusion. Here, we characterized a viable T-DNA insertion allele of VPS39 which demonstrated a critical role of VPS39 in stomatal vacuole fusion. We found that VPS39 has increased levels of phosphorylation at S413 when stomata are closed versus open, and that VPS39 function in stomata and embryonic development requires dynamic changes in phosphorylation. Among all HOPS and vacuolar SNARE subunits, only VPS39 showed differential levels of phosphorylation between open and closed stomata. Moreover, regions containing S413 are not conserved between plants and other organisms, suggesting plant-specific mechanisms. Our data are consistent with VPS39 phosphorylation altering vacuole dynamics in response to environmental cues, similar to well-established phosphorylation cascades that regulate ion transport during stomatal opening.
The methods for this dataset are described in detail in our manuscript. These compressed files contain:
Raw images (.czi) for vacuoles from roots (Root_vacuole_data.zip) used for Figure 1C.
Raw images (.czi) for stomata vacuoles (Stomata_Vacuole_Data.zip) used for Figure 1D-E and Figure 3D-E.
Images (.jpg) of siliques used for quantification of Figure 3A-C (Siliques_Data.tar). Genotypes associated with each plant number on each slide are listed in an Excel file.
qRT-PCR data (.xlsx) from seedlings corresponding to Figure 1B (Seedling_qRT_PCR_vps39-2.xlsx).
qRT-PCR data (.xlsx) from guard cell-enriched tissue corresponding to Figure 1F (Guard_Cell_enriched_RT_qPCR.xlsx).
Description of the data and file structure
Root Vacuole image data files
This includes confocal raw image files captured with a Zeiss LSM980 with Airy scan microscope. Images are organized in folders by date of image acquisition (set 1 to set 6). Within each set, images are organized by genotype (WT, vps39-2 or vps39-2 VPS39-RFP/+). Each image includes green channel for BCECF fluorescence detection and red channel for VPS39-RFP detection.
Stomata vacuole image data files
This includes confocal raw image files captured with a Zeiss LSM980 with an Airy scan microscope. Data is organized in folders based on data of image acquisition. Each folder is subdivided by genotype: wild type (WT), vps39-2 mutant, or vps39-2 mutant complemented with VPS39-S-A-GFP (vps39-2 VPS39-S-A-GFP) or VPS39-S-D-GFP (vps39-2 VPS39-S-A-GFP). Within each genotype, images are sorted by box numbers, where each box corresponds to a leaf fragment from a different plant.
Silique image data
This contains all the images from siliques as captured with a Leica Thunder for Model Organisms dissecting scope. Images are organized in folders by date of data acquisition. Within each date, data is sorted by genotype. Within each genotype, each image includes multiple siliques from 1 or more plants. Each silique is marked with a genotype number as part of the image. An Excel sheet is included to match a plant number to a specific plant genotype for each image.
qRT-PCR files
These files contain raw data from gene expression studies.
Date (when included): Date when qRT-PCR run was performed.
Well: The plate position of the reaction on the qRT-PCR plate.
Fluor: The fluorescence channel used for detection (SYBR GREEN was always used).
Target: Specific gene transcript amplified for that reaction.
Content: The reaction type as designated in the run file (e.g., Unknown sample, Standard, NTC, etc.). This labels the functional role of the well in the experiment, including NTC (no DNA Template Control) or NRT (no RT reaction) controls. This column was not specified for wells containing samples, and therefore, these were marked as "Unkn" by the qPCR machine. All other empty wells (not used) are marked as "Unkn".
Sample: The sample ID corresponding to the biological sample loaded in the well. Genotypes used were either wild type (WT) or vps39-2 mutant (39). For each of these, biological replicates are indicated as A, B, C, and D, and technical replicates with numbers (1-4).
Cq: The quantification cycle (Ct) value is automatically calculated by the instrument. Empty cells indicate that no Ct value was generated due to an unused well. "N/A" indicates that no fluorescence was detected, and these cells correspond to non-template controls.
Other cells left blank correspond to wells intentionally not used in the plate layout (no-template, no-primer, or unassigned wells). These were left blank because the instrument does not output data for unused wells.