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Lysosome-Related Organelles Orchestrate Biogenic Crystal Formation in Pigment Cells

ABSTRACT: Lysosome-related organelles (LROs) enable cell-type-specific functions by adapting endolysosomal pathways for specialized roles. Here, we show that iridosomes - optically active, guanine crystal-forming organelles in zebrafish iridophores - constitute a previously unrecognized class of LROs. Using transcriptomic profiling of purified iridophores, CRISPR-Cas9 gene perturbation, and cryogenic transmission electron microscopy, we identify a conserved molecular program governing iridosome biogenesis. Key LRO regulators, including rab32a, ap3M2, and hps5, are required for crystal formation, with gene disruptions leading to reduced organelle number and distorted crystal morphology. We also observe hallmark LRO features such as intraluminal vesicles and dynamic pH regulation during maturation. Cross-species transcriptomic analysis reveals that the LRO identity of iridosomes is conserved in vertebrates including fish and reptiles, suggesting ancient evolutionary roots. These findings expand the LRO paradigm to include organelles dedicated to crystalline assembly and establish iridophores as a model for investigating how cells build structurally specialized organelles through coordinated trafficking, acid-base regulation, and biomineralization.

ORGANISM(S): Danio rerio

PROVIDER: GSE297759 | GEO | 2026/03/19

REPOSITORIES: GEO

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Project description:Soil salinization is a primary constraint on global agricultural productivity. 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). 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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Lysosome-Related Organelles Orchestrate Biogenic Crystal Formation in Pigment Cells

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