Periodic Reporting for period 1 - CRYSTALCELL (Unraveling the molecular mechanisms underlying intracellular crystal formation)
Reporting period: 2022-12-01 to 2025-05-31
Many animals use molecular crystals for an astonishing variety of optical functions, from vision to the production of structural colors in fish and chameleons. These intracellular molecular crystals play vital roles in the function of cells and the ecology of different organisms. Thus, failure of the mechanisms controlling crystal formation can be highly deleterious to the organism and may result in pathologies, such as gout and kidney stones in humans.
The orchestrated precipitation of organic materials, which produces crystals with unique morphologies and properties at ambient conditions, occurs within specialized crystal-forming cells, such as the light-reflecting iridophores. Inside iridophores, guanine crystals develop in an organelle dubbed iridosome, where exquisite control over crystal size, shape and assembly is exerted using strategies exceeding the synthetic state-of-the-art. Understanding the capacity of cells to generate a compartmentalized organelle capable of such intricate chemical and biological processes has thus far been limited by the technical inability to study this complex organelle, thus representing an underexplored avenue in cell biology.
Crystal formation involves a sequence of events that predominately occurs early in the life cycle of the iridophore. It starts with the synthesis and trafficking of vast quantities of precursor molecules into the iridosome, followed by their concentration within the iridosome lumen and, ultimately, culminating in the formation of bio-organic crystals with controlled properties. The resulting product, a precisely shaped and sized crystal, is then placed within ordered crystal arrays, which are often tunable. The mechanisms underlying the molecular and cellular biology of the iridosome have remained largely unknown, leaving many important unresolved questions: How are iridosomes formed? Which machinery is involved in the crystal formation process? How conserved are these processes between different species? This project is focused on answering these fundamental questions using an interdisciplinary set of skills, merging chemistry, crystallography, and cell biology. For that, we have developed new approaches and applied methodologies that have sufficiently matured in recent years. Our ultimate goal is to provide a mechanistic understating of the processes and principles governing the controlled formation of molecular crystals.
The orchestrated precipitation of organic materials, which produces crystals with unique morphologies and properties at ambient conditions, occurs within specialized crystal-forming cells, such as the light-reflecting iridophores. Inside iridophores, guanine crystals develop in an organelle dubbed iridosome, where exquisite control over crystal size, shape and assembly is exerted using strategies exceeding the synthetic state-of-the-art. Understanding the capacity of cells to generate a compartmentalized organelle capable of such intricate chemical and biological processes has thus far been limited by the technical inability to study this complex organelle, thus representing an underexplored avenue in cell biology.
Crystal formation involves a sequence of events that predominately occurs early in the life cycle of the iridophore. It starts with the synthesis and trafficking of vast quantities of precursor molecules into the iridosome, followed by their concentration within the iridosome lumen and, ultimately, culminating in the formation of bio-organic crystals with controlled properties. The resulting product, a precisely shaped and sized crystal, is then placed within ordered crystal arrays, which are often tunable. The mechanisms underlying the molecular and cellular biology of the iridosome have remained largely unknown, leaving many important unresolved questions: How are iridosomes formed? Which machinery is involved in the crystal formation process? How conserved are these processes between different species? This project is focused on answering these fundamental questions using an interdisciplinary set of skills, merging chemistry, crystallography, and cell biology. For that, we have developed new approaches and applied methodologies that have sufficiently matured in recent years. Our ultimate goal is to provide a mechanistic understating of the processes and principles governing the controlled formation of molecular crystals.
Genetic Regulation of Crystal Morphology: We demonstrated that crystal shape is dictated by its chemical composition, which is genetically controlled through tissue-specific expression of specialized paralogs with remarkable substrate selectivity. This genetic orchestration allows organisms to produce diverse crystal morphologies and functionalities.
Amyloid-Like Scaffolds: We have identified previously undescribed amyloid-like protein-based fibers that template the nucleation of molecular crystals, regulating their size and shape. This discovery advances our understanding of the molecular regulation of biogenic crystal formation and has significant implications for designing crystals where morphology is crucial to functionality.
pH as a Driver for Molecular Crystallization: We revealed how organelle pH modulation drives guanine accumulation and crystallization. By employing live-cell imaging, cryo-electron microscopy, and synchrotron spectroscopy, we demonstrated how pH transitions regulate crystal formation in iridophores, offering critical insights into organelle function and maturation.
Cross-Species Comparisons in Crystal Formation: Through comparative studies of zebrafish and medaka, we uncovered conserved and divergent genetic pathways regulating crystal formation. By integrating transcriptomics, metabolomics, and ultrastructural analyses, our work provided evolutionary insights into the molecular regulation of biogenic crystals.
Amyloid-Like Scaffolds: We have identified previously undescribed amyloid-like protein-based fibers that template the nucleation of molecular crystals, regulating their size and shape. This discovery advances our understanding of the molecular regulation of biogenic crystal formation and has significant implications for designing crystals where morphology is crucial to functionality.
pH as a Driver for Molecular Crystallization: We revealed how organelle pH modulation drives guanine accumulation and crystallization. By employing live-cell imaging, cryo-electron microscopy, and synchrotron spectroscopy, we demonstrated how pH transitions regulate crystal formation in iridophores, offering critical insights into organelle function and maturation.
Cross-Species Comparisons in Crystal Formation: Through comparative studies of zebrafish and medaka, we uncovered conserved and divergent genetic pathways regulating crystal formation. By integrating transcriptomics, metabolomics, and ultrastructural analyses, our work provided evolutionary insights into the molecular regulation of biogenic crystals.
Our work advances the understanding of biogenic crystal formation, revealing both shared and specialized pathways that underlie these processes. The discovery of pH regulation as a key factor in guanine crystallization represents a significant step forward, with potential implications for controlling crystal growth in synthetic systems. Similarly, our findings on uric acid crystallization in leucophores provide a new perspective on how cellular processes evolve to meet specific functional needs.
Beyond biology, these results offer a foundation for developing bio-inspired materials that mimic the optical properties of these crystals. Specifically, the precise control of crystal morphology and assembly observed in zebrafish cells could guide innovations in photonics or nanotechnology. Furthermore, the biosynthetic pathways identified for guanine and uric acid could be harnessed for the bioengineering of biofactories, such bacteria and yeast for the production of these important metabolites. To fully realize these applications, further research is needed to translate these biological principles into scalable and practical technologies.
By addressing the fundamental mechanisms of biogenic crystal formation, this project bridges the gap between biology and materials science, showcasing how nature’s designs can inspire cutting-edge solutions to human challenges.
Beyond biology, these results offer a foundation for developing bio-inspired materials that mimic the optical properties of these crystals. Specifically, the precise control of crystal morphology and assembly observed in zebrafish cells could guide innovations in photonics or nanotechnology. Furthermore, the biosynthetic pathways identified for guanine and uric acid could be harnessed for the bioengineering of biofactories, such bacteria and yeast for the production of these important metabolites. To fully realize these applications, further research is needed to translate these biological principles into scalable and practical technologies.
By addressing the fundamental mechanisms of biogenic crystal formation, this project bridges the gap between biology and materials science, showcasing how nature’s designs can inspire cutting-edge solutions to human challenges.