Omics · study · 2026
SlCAX3 drives the formation of crystal idioblasts for tomato ion compartmentalization under salt stress
Listed in NCBI GEO
Soil salinization is a primary constraint on global agricultural productivity.
Description
While the mechanisms of root ion exclusion and whole-plant long-distance transport are well established, how photosynthetic leaf tissues complexly adapt to high-salinity microenvironments at the spatial and cellular level remains a critical blind spot in plant stress biology. We integrated spatial transcriptomics (ST-seq) and single-nuclei RNA sequencing (snRNA-seq) to construct a high-resolution spatiotemporal transcriptomic atlas of tomato leaves subjected to long-term salt stress (LTSS).
We combined pseudotime trajectory inference, multi-omics deconvolution, elemental analysis, and CRISPR-Cas9-mediated genetic validation to elucidate cellular responses. LTSS induces heterogeneous transcriptional remodeling across leaf tissues, primarily reinforcing vascular structural stability while suppressing mesophyll photosynthesis. Concurrently, LTSS triggers the explosive proliferation and developmental reprogramming of palisade mesophyll cells into highly specialized crystal idioblasts (CIs).
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This cell fate transition is orchestrated by enhanced cell wall remodeling and intensive microenvironmental crosstalk. Genetic analyses establish that the vacuolar transporter SlCAX3 is essential for CI formation. Sequence and structural evaluations indicate that SlCAX3 evolutionarily lost its conserved autoinhibitory N-terminal domain, a structural specialization that may support high-flux ion transport.
Although SlCAX3-driven CI formation does not reduce total foliar Na⁺ content, it facilitates localized ion sequestration within CI vacuoles, which is associated with mitigated oxidative damage and cytotoxicity in adjacent photosynthetic tissues. This study demonstrates that tissue-level salt adaptation in tomato involves spatially coordinated transcriptional responses and localized biomineralization. The identification of SlCAX3's atypical architecture provides a functional supplement to the conserved CAX1/3 transport system in land plants.
Our findings highlight localized cell-state transitions and ion sequestration as an effective tissue-level strategy for mitigating salt stress, offering strategic genetic targets for breeding climate-resilient crops.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE325nnn/GSE325371 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE325371 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1438885 ncbi.nlm.nih.gov/bioproject/PRJNA1438885 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE325371 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |