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Explore our cutting edge research, world-class patient care, career opportunities and more.
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Cell biology is governed by the same underlying physical properties that cause dew to form on cool mornings, prevent oil from mixing with water, and shape soap bubbles into spheres.
In recent years, scientists have demonstrated how cells tap into these physical properties, which emerge from the collective behavior of many molecules, to organize proteins, DNA, and RNA into liquid-like compartments, like oil droplets in water. This phenomenon, called biomolecular phase separation, drives the spontaneous formation of concentrated “droplets” called condensates that help coordinate essential biological processes. The fundamental roles of condensates in cells mean that when something goes wrong with their behavior, diseases may follow. St. Jude researchers are mapping the condensate landscape within cells to understand their roles in biological function and illuminate the wider impact of these dynamic droplets.
Teasing apart competing transcription models
Condensates have been closely associated with transcription, the process of copying a DNA segment into a complementary strand of messenger RNA. However, scientists were unclear about what really matters: the phase-separated droplets containing the transcriptional machinery or the soluble complexes they form that coexist with the droplets.
To address this question, co-corresponding authors Tanja Mittag, PhD, Department of Structural Biology, and Aseem Ansari, PhD, Department of Chemical Biology & Therapeutics chair, focused on the yeast transcription factor Gcn4 and its transcriptional binding partner, Med15, to compare the role of small, soluble protein complexes against that of larger, phase-separated droplets.
“We wanted to identify what is actually functional in gene regulation versus what is simply a consequence of the inherent stickiness of the sequences that tend to form networked structures,” Ansari said. “We found that it wasn’t ‘this or that.’ It was ‘this and that.’ It’s a lesson that these mechanisms are not mutually exclusive.”
Published in Molecular Cell, they found that smaller soluble complexes and phase-separated condensates share driving forces for their formation. They also revealed that both mechanisms can mediate transcription, and phase separation does not necessarily offer increased activity. In fact, Gcn4 variants with high affinities for Med15 were seen to have a lower activity in the resulting condensates relative to what would be expected for soluble complexes. In these cases, condensates may dampen activity.
“In general, we think condensates and complexes act very similarly,” said Mittag. “However, if we generate condensates that rely on very high affinities, their internal properties are likely not well suited for promoting biochemical activity.”
It’s important to know whether stress granules are supportive of fibril formation or protective. This information will aid in deciding how to develop potential treatments against a whole spectrum of neurodegenerative diseases.
Department of Structural Biology
How stress granules shape neurodegenerative disease
A collaborative effort between Mittag and researchers from Washington University in St. Louis, also published in Molecular Cell, focused on the interactions driving neurodegenerative disease. Amyloid fibrils, the hallmark of many such diseases, have been previously suggested to originate within condensates, prompting the researchers to investigate this association systematically.
Under stress conditions, such as heat, cells form condensates called stress granules that halt energy-intensive processes, such as protein production, temporarily. When the stress has lifted, the granules disassemble, and normal processes resume. Mutations in key stress granule proteins such as hnRNPA1 prolong the lifetime of stress granules and drive the formation of insoluble protein threads called amyloid fibrils, which accumulate over time, causing neurodegeneration.
The researchers showed that while fibril formation can be initiated on condensate surfaces, the condensates’ interiors suppress fibril formation. This implies that condensate interiors are not microenvironments that drive neurodegenerative diseases such as amyotrophic lateral sclerosis or frontotemporal dementia, as was previously considered.
“It’s important to know whether stress granules are supportive of fibril formation or protective,” said co-corresponding author Mittag. “This information will aid in deciding how to develop potential treatments against a whole spectrum of neurodegenerative diseases.”
Cancer-causing condensates rely on disordered protein regions
When the interactions behind condensate formation are unchecked, the resulting droplets may not always serve protective or productive roles, but they may offer therapeutic potential. A study published in Nature Cell Biology by co-corresponding authors Richard Kriwacki, PhD, Department of Structural Biology, and Stephen Mack, PhD, Department of Developmental Neurobiology, showed that interactions between disordered regions of the ZFTA–RELA fusion oncoprotein helped form condensates essential for the development of ependymoma, a common childhood brain tumor.
When the disordered protein region (located on the RELA part of the fusion) was absent, condensates did not form, and ependymoma did not develop. However, when the scientists swapped the RELA disordered domain with other unrelated disordered protein domains, the novel fusions regained their ability to form condensates.
By combining with the ZFTA part of the fusion protein, which locates and binds to oncogenes, ZFTA–RELA condensates promote oncogene expression leading to brain tumor development.
“Our findings strengthen the view that condensate formation should be considered a driving mechanism for oncogenic fusion proteins in general,” said Kriwacki. “Instead of focusing on this fusion protein, we can now start identifying its interacting partners within condensates, examining which are essential for tumor formation and targeting those.”
While the work was done in ependymoma, other cancers driven by fusion proteins may have a similar vulnerability. “We discovered a novel mechanism for assembling molecules that underlies the formation of a deadly brain tumor,” said Mack. “By understanding these aberrant condensates, we may have found a new place to look for therapeutic interventions for cancers driven by fusion oncoproteins.”
Charting a path across the condensate landscape
These studies show that understanding the physical properties of biomolecules driving condensate formation is essential to understanding how these dynamic droplets influence fundamental cellular functions. St. Jude researchers are clarifying the interactions and networks within condensates, and in doing so are creating a dynamic map of condensate biology within cells that will guide the way for future research endeavors.