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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.

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Life Sciences
Inferred from text
RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 9 field assertions
SourceKeyLast seenRaw
NCBI GEOGSE32537115 d agoJSON v1
FieldAssertionExtractorEvidence
access_levelsource · NCBI GEOconnector:ncbi_geo@1.0.0
concepts[field].local:field:life-sciencesmapping · NCBI GEOconnector:ncbi_geo@1.0.0
concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencingsource · NCBI GEOconnector:ncbi_geo@1.0.0/gdstype
concepts[modality].local:modality:rna-seqenrichment · NCBI GEOkeyword-concept-rules@1.0.0title+description (75%)
concepts[modality].local:modality:sequencingenrichment · NCBI GEOkeyword-concept-rules@1.0.0title+description (75%)
concepts[modality].local:modality:single-cell-rna-seqenrichment · NCBI GEOkeyword-concept-rules@1.0.0title+description (65%)
descriptionsource · NCBI GEOconnector:ncbi_geo@1.0.0/summary
publication_datesource · NCBI GEOconnector:ncbi_geo@1.0.0
titlesource · NCBI GEOconnector:ncbi_geo@1.0.0/title