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Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes

Abstract

Despite the widespread occurrence of intracellular crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins. Using Raman microscopy, we examined >200 species from all major eukaryotic supergroups. We detected cellular crystalline inclusions in 77% species out of which 80% is composed of purines, such as anhydrous guanine (62%), guanine monohydrate (2%), uric acid (12%) and xanthine (4%). Our findings shifts the paradigm assuming predominance of calcite and oxalates. Purine crystals emerge in microorganisms in all habitats, e.g., in freshwater algae, endosymbionts of reef-building corals, deadly parasites, anaerobes in termite guts, or slime molds. Hence, purine biocrystallization is a general and ancestral eukaryotic process likely present in the last eukaryotic common ancestor (LECA) and here we propose two proteins omnipresent in eukaryotes that are likely in charge of their metabolism: hypoxanthine-guanine phosphoribosyl transferase and equilibrative nucleoside transporter. Purine crystalline inclusions are multifunctional structures representing high-capacity and rapid-turnover reserves of nitrogen and optically active elements, e.g., used in light sensing. Thus, we anticipate our work to be a starting point for further studies spanning from cell biology to global ecology, with potential applications in biotechnologies, bio-optics, or in human medicine.

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Fig. 1: Distribution of purine inclusions identified by Raman microscopy in the eukaryotic tree of life.
Fig. 2: Proposed scheme of guanine inclusions metabolism with emphasis on the transporters potentially involved.

Data availability

All data generated or analysed during this study are included in this published article and its Supplementary Information files.

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Acknowledgements

We express our gratitude to Lukáš Falteisek, Richard Dorrell, Jan Petrášek, Stanislav Volsobě, Kateřina Schwarzerová and Jana Krtková for constructive discussions. English has been kindly corrected by William Bourland. Furthermore, we thank to Dovilė Barcytė, William Bourland, Antonio Calado, Dora Čertnerová, Yana Eglit, Ivan Fiala, Martina Hálová, Miroslav Hyliš, Dagmar Jirsová, Petr Kaštánek, Viktorie Kolátková, Alena Kubátová, Alexander Kudryavtsev, Frederik Leliaert, Julius Lukeš, Jan Mach, Joost Mansour, Jan Mourek, Yvonne Němcová, Fabrice Not, Vladimír Scholtz, Alastair Simpson, Pavel Škaloud, Jan Šťastný, Róbert Šuťák, Daria Tashyreva, Dana Savická, Jan Šobotník, Zdeněk Verner, Jan Votýpka for kindly providing cultures and taxonomic identifications.

Funding

Financial support from the Czech Science Foundation (grants 17–06264 S, 19–19297 S, 20-16549Y, 21-03224S, and 21-26115 S); Grant Agency of Charles University (grant 796217), Charles University Research Center program No. 204069, European Regional Development Fund and the state budget of the Czech Republic, projects no. CZ.1.05/4.1.00/16.0340, CZ.1.05/4.1.00/16.0347, CZ.2.16/3.1.00/21515 and CZ.02.1.01/16_019/0000759, LM2018129.

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JP conceived the study, handled the cell cultures, performed the Raman measurements and data processing, prepared the graphics and videos and wrote the paper; TP and MO performed phylogenetic analyses and profiling; PM conceived the study and corrected the paper; IČ provided the cell cultures and corrected the paper. All authors discussed and approved the paper.

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Correspondence to Jana Pilátová.

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Pilátová, J., Pánek, T., Oborník, M. et al. Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes. ISME J (2022). https://doi.org/10.1038/s41396-022-01264-1

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