Biology subjects

Broder, Y.

Publications and source records attributed to Broder, Y..

3 recordsLinked to original sources

bioRxiv2026

Lysosome-Related Organelles Orchestrate Guanine Crystal Formation in Pigment Cells

Iridosomes, the guanine crystal-forming organelles of pigment-producing iridophores, are among the most versatile, visually striking yet mechanistically uncharacterized organelles in vertebrate biology. Lysosome-related organelles (LROs) support cell type-specific functions by adapting endolysosomal pathways for specialized roles. Here, we show that iridosomes represent a previously unrecognized subtype of LROs. Using transcriptomic profiling of zebrafish iridophores, CRISPR-Cas9-mediated gene disruption, and cryogenic transmission electron microscopy, we define the molecular program underlying iridosome biogenesis. Iridosomes have evolved unique adaptations for crystal growth while retaining core features of other LROs. Key regulators, including RAB32a, AP3M2, and HPS5, are essential for crystal formation, with gene knockouts causing reduced crystal number, altered morphology, and distinct maturation defects. We further identify hallmark LRO features in iridosomes, including intraluminal vesicles and pH-regulated developmental transitions. Cross-species transcriptomic analysis confirms that iridosomes share an LRO signature across vertebrates, including teleost fish and reptiles, suggesting ancient evolutionary origins. These findings establish iridosomes as crystalline LROs and as a model for investigating how cells construct structurally specialized organelles through coordinated trafficking, acid-base regulation, and crystallization, with implications for LRO evolution and human disease.

developmental biology↗

bioRxiv2025

Global DNA signatures of temperature and nutrient limitation in prokaryotes

Microorganisms adapt to their environment through changes in both their genes and overall genome composition. However, identifying universal principles of genomic adaptation remains challenging because different environments present multiple, overlapping selective pressures. To overcome this challenge, we analyzed DNA composition patterns across diverse environments using machine learning. By examining tetranucleotide frequencies from 1,112 marine and soil metagenomic samples, we discovered that environmental temperature can be accurately predicted from DNA composition alone (R2=0.82). This temperature signal remained robust even when analyzing individual bacterial phyla and classes, suggesting a fundamental adaptive response. To examine this adaptation mechanism, we analyzed GC content relationships with temperature and found opposing relationships in different environments: positive correlations in soil but negative correlations in marine samples. We show that this inverse relationship in marine environments is driven by nutrient availability, as GC content increases with nutrient levels while nutrients decrease with temperature in marine ecosystems. Despite these contrasting GC patterns, we identified specific tetranucleotides composed of equal numbers of GC and AT bases (50% GC content) that showed consistent temperature correlations across all environments. These findings reveal a complex interplay between temperature adaptation and nutrient limitation in shaping microbial genomes.

microbiology↗

bioRxiv2024

Controlled pH Alteration Enables Guanine Accumulation and Drives Crystallization within Iridosomes

Many animals exhibit remarkable colors produced by the constructive interference of light reflected from arrays of intracellular guanine crystals. These systems are utilized for various purposes, including vision, camouflage, communication, and thermal regulation. Each guanine crystal forms within a membrane-bound organelle called an iridosome, where precise control over crystal formation occurs. While the presence of guanine crystals in iridosomes is well-documented, the mechanisms facilitating the accumulation of water-insoluble guanine and driving its crystallization remain unclear. Here, we employ advanced imaging and spectroscopy techniques to characterize the maturation of iridosomes in zebrafish iridophores during development. Using cryo-electron microscopy, we found that amorphous guanine accumulates in early-stage iridosomes. Synchrotron-based soft X-ray microscopy studies revealed that, unlike mature crystals, the accumulated guanine is initially in its protonated state. Live imaging with a pH sensor demonstrated that early-stage iridosomes are acidic and that their pH gradually approaches neutrality during maturation. Additionally, the application of a V-ATPase inhibitor reduced the acidity of iridosomes and significantly decreased crystal formation, suggesting the involvement of V-ATPase in regulating the organelle pH. Our findings reveal new insights into the molecular mechanisms facilitating guanine accumulation and crystallization within iridosomes, emphasizing the pivotal role of pH alternations in the precise formation of biogenic crystals.

cell biology↗