ERC

Unconventional organelles

– biological condensates and crystal biology

 

I study a simple question that turns out to be surprisingly nontrivial:

 

Why do cells build crystals?

 

For more than a century, since Charles Darwin and Ernst Haeckel, intracellular crystals were often regarded as passive waste products or cellular curiosities. My research has shown that these structures can serve as nutrient reservoirs, optical devices, regulators of metabolism, and potentially key players in global biogeochemical cycles.

 

By combining protistology, spectroscopy, microscopy, genetics, structural biology, photonics, and environmental biology, I investigate the formation, function, and evolution of biogenic crystals across microbial eukaryotes.

 

My long-term goal is to establish a unified framework connecting:

genes → molecular self-assembly → crystal formation → cell physiology → ecosystems → global biogeochemical cycles and Earth system processes

 

By understanding why cells build crystals, we may uncover previously hidden principles that shape life across scales, from molecule to structure to organelle to ecosystems

 

 

Research Vision

I am interested in tracking down the chemical and biological nature of unconventional organelles, underexplored cellular inclusions, condensates, and aggregates across diverse biological systems and scales from cellular to ecosystem level. One of the least explored biomaterials is crystalline inclusions. Some of them, purine biocrystals, act as high-dynamic nitrogen storage as well as optical photonic mirrors, and there are as-yet-to-be-tested more predicted functions. This ancient multitool can be one of the oldest biocrystals likely present in the last eukaryotic common ancestor (LECA). I combine diverse imaging and microanalytical techniques with other multi-omics, genetics, systems biology, mineralogy, and oceanography.

 

My work focuses on:

Organic biocrystallization

How and why living cells produce crystals from metabolites, such as nucleobases. Repurposing the ancient core cellular metabolite building DNA.

 

Crystal-based nutrient metabolism

How microbial eukaryotes use crystals as dynamic reservoirs of nitrogen and other elements.

 

Microbial photonics

How crystals manipulate light and contribute to microbial vision, photoreception, and cellular optics.

 

Evolution of crystal biology

How crystal formation evolved across the eukaryotic tree of life and how it shapes ecological success.

 

Environmental significance

How crystal-forming protists influence nutrient cycles in aquatic ecosystems and planetary-scale biogeochemical processes.

 

Research Themes

 

Crystal Biology

I investigate the molecular mechanisms responsible for crystal formation, dissolution, recycling, and inheritance.

Current questions include:

• Which genes control biocrystallization?
• How do cells regulate crystal morphology?
• Why have crystals evolved repeatedly in different lineages?
• Can crystal biology be predicted from genomic information?

 

Nitrogen-Rich Crystals

Purine crystals represent one of the most nitrogen-rich structures known in biology.

Our work suggests that these crystals:

• function as nitrogen storage reservoirs
• participate in nutrient recycling
• contribute to adaptation to nutrient stress
• influence ecosystem nitrogen dynamics

 

Microbial Vision

Recent work from our group revealed a previously unknown role of guanine crystals in microbial vision.

We discovered crystal-based photonic mirrors in the eyespots of Symbiodiniaceae, suggesting that microorganisms evolved sophisticated optical structures using self-assembled organic crystals.

 

Spectroscopy and Chemical Imaging

I use Raman microscopy and complementary spectroscopic techniques for in situ identification of cellular chemistry. This approach allows us to discover previously unknown biological structures without requiring biochemical extraction.

 

Our philosophy:

"Chemistry first discovery-driven approach provides unprecedented potential for finding new phenomena in biology"

 

 

Current Projects

Crystal-Based Vision in Symbiodiniaceae

Photonic mirrors built from guanine crystals

This project investigates newly discovered crystal-based eyespots in marine dinoflagellate symbionts.

Questions:

• How are optical crystals constructed?
• What genes regulate their formation?
• How do microbial cells control light using crystalline materials?
• Did crystal-based photonic systems evolve independently from animal eyes?

 

Molecular Mechanisms of Purine Biocrystallization

Using fungi and protists as experimental systems, we seek to identify the molecular machinery underlying crystal formation.

 

Current model systems:

• Symbiodiniaceae
• Amphidinium carterae
• Candida albicans
• Chromera velia
• Chlamydomonas reinhardtii
• Diverse protists

 

Goals:

• identify crystal-forming genes
• understand crystal turnover
• link metabolism to crystal formation
• establish crystal biology as a new research discipline

Crystal Biology Across Ecosystems

How widespread are crystals in nature?

We are studying:

• marine plankton
• freshwater microorganisms
• coral symbionts
• pathogenic fungi
• environmental protists

The ultimate goal is to understand how crystal biology scales from cells to ecosystems.

 

 

 

Major Research Achievements

 

A Paradigm Shift in Biocrystallization

We demonstrated that purine crystals are widespread throughout eukaryotes and likely more abundant than previously recognized inorganic biominerals.

This finding changed the prevailing view of intracellular crystallization and established a new evolutionary framework for crystal biology.

Pilátová et al. (2022). ISME Journal

Pilátová, J.,* Pánek, T., Oborník, M., Čepička, I., Mojzeš, P. (2022) Revisiting biocrystallization: purine inclusions are widespread in eukaryotes. ISME J, 16:2290–2294. 10.1038/s41396-022-01264-1