Unlocking the Secrets of Cellular Flexibility and Survival

In a revelation that may alter our comprehension of cellular resilience and adaptability, scientists at Scripps Research have unveiled the intricate interactions between a primordial inorganic polymer of phosphate termed polyphosphate (polyP), and two essential building blocks of existence: DNA and the element magnesium. These elements formed clusters of minuscule liquid droplets—also referred to as condensates—with flexible and malleable structures.

PolyP and magnesium play crucial roles in numerous biological processes. Therefore, these findings may pave the way for innovative methods to manipulate cellular reactions, which could yield significant implications in translational medicine.

The resulting study, published in Nature Communications on October 26, 2024, unveils a delicate “Goldilocks” zone—a precise magnesium concentration spectrum—where DNA encircles polyP-magnesium ion condensates. Similar to a thin eggshell shielding a liquid-like interior, this seemingly straightforward structure may aid cells in organizing and safeguarding their genetic material.

This endeavor commenced as a partnership between co-senior authors Associate Professor Lisa Racki, PhD, and Professor Ashok Deniz, PhD, both affiliated with the Department of Integrative Structural and Computational Biology at Scripps Research. Racki has been examining these structures in bacterial cells, while Deniz’s adjacent laboratory has delved into the physical chemistry of biomolecular condensates for the past decade. They realized that collaboration was essential to unlock these ancient interactions.

“We were aware that DNA was in close vicinity to the magnesium-rich polyP condensates in cells, yet we were entirely astonished by the beautiful spheres of DNA that illuminated under the microscope,” Racki expresses.

As molecular detectives, witnessing these structures raised thrilling inquiries about the physics and mathematics of the DNA shells and their potential influence on polyP condensates.”

Professor Ashok Deniz, PhD, Department of Integrative Structural and Computational Biology at Scripps Research

The microscopy visuals demonstrated that DNA entwines itself around a condensate, forming a fragile eggshell-like barrier. This shell could impact molecular transport and also impede fusion: the phenomenon where two condensates amalgamate into one. In the absence of DNA shells, polyP-magnesium ion condensates easily fused—akin to how oil droplets and vinegar combine in a salad dressing container upon shaking.

However, a meticulous analysis indicated that fusion overall decelerated to differing extents, based on the DNA length. The researchers hypothesized that longer DNA resulted in increased entanglement on condensate surfaces—resembling how long hair tangles more than shorter hair.

DNA measures over 1,000 times thinner in diameter compared to condensates, making molecular details challenging to visualize. Fortunately, the infrastructure for capturing such imaging has been established by two other faculty members at Scripps Research: Assistant Professor Danielle Grotjahn, PhD, and Scripps Fellow Donghyun Raphael Park, PhD.

Collaborating with Park, with assistance from Grotjahn, the researchers employed cryo-electron tomography to meticulously scrutinize the condensate surfaces. Utilizing electrons in lieu of light, this method acquires three-dimensional, high-resolution images of specimens that were swiftly frozen to conserve their structures. The newfound images revealed that DNA forms filaments extending from condensate surfaces, resembling tangled locks of hair.

Another pivotal revelation: DNA shell formation only transpired within a defined magnesium concentration range—too much or too little, and the shell would not form. This “Goldilocks” effect underscores how cells can manage condensate structure, size, and function merely by adjusting control parameters.

“While we often consider cellular interfaces as boundaries, they simultaneously create a new landscape by providing a surface for molecules to organize,” observes Racki. “DNA may not merely be a jumbled mess at the surface but is instead orchestrated by these condensates.”

In this milieu, Deniz and Racki are particularly keen on deciphering DNA supercoiling—how DNA twists like a spring to fit within cells.

“Cells must regulate their DNA curls,” Racki elucidates. “Interestingly, the mathematics of DNA supercoiling leads to ‘action-at-a-distance’ effects—similar to how twisting a rope can generate coils far from where one is gripping it.”

The researchers suspect that DNA interactions with polyP condensates within cells might transmit local changes in DNA supercoiling across extensive distances, resulting in wider changes in gene expression and cellular functionality. Studying this effect is one of the team’s subsequent objectives.

“We are enthused by the potential of utilizing these discoveries to create novel tools for cellular control—possibly simpler, more cost-efficient methods to manage biomatter for biomedicine,” expresses Deniz.