Compartmentalizing tasks quickly, efficiently, and accurately is the key to any successful organization—including the tiny but complex biological cell.

Vital and at times opposing biochemical tasks are constantly being performed within spherical chambers within the cell that are made of protein and RNA. Although similar to rooms in a house in many respects, they also differ in significant ways. For instance, some chambers within cells do not have membranes—the cellular equivalent of brick-and-mortar walls. Some of these membrane-less rooms in cells form spontaneously while other include rooms within rooms that remodel and reattach to annexes.

These compartments within cells called membraneless organelles (MLOs) or biomolecular condensates take the form of liquid droplets, forming spontaneously, like droplets of oil in water. Sometimes, the droplets are found alone. Other times, one droplet can be found nested inside another. How these droplets reorganize regulates the reactions occurring within them.

In a study titled “Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies,” published in Nature Communications, a team of scientists from the University at Buffalo and Iowa State University explore how MLOs form and organize themselves.

optical microscopy
Study co-authors Taranpreet Kaur (left) and Ibraheem Alshareedah, both physics PhD students at the University at Buffalo, prepare a microfluidic flow chamber for optical microscopy experiments. [Douglas Levere / University at Buffalo]
The authors create simple synthetic MLO systems floating in a buffer to unearth the physical rules that govern their arrangement. They use just three ingredients to create these synthetic MLOs: RNA and two different proteins, a prion-like polypeptide (PLP) and an arginine-rich polypeptide (RRP).

“Different condensates can coexist inside the cells,” says Taranpreet Kaur, a PhD student in physics in the University at Buffalo, College of Arts and Sciences and first author on the study. “They can be detached, attached to another condensate, or completely embedded within one another. So how is the cell controlling this? We found two different mechanisms that allowed us to control the architecture of synthetic membraneless organelles formed inside a test tube. First, the amount of RNA in the mixture helps to regulate the morphology of the organelles. The other factor is the amino acid sequence of the proteins involved.”

“These two factors impact how sticky the surfaces of the condensates are, changing how they interact with other droplets,” says Priya Banerjee, PhD, assistant professor of physics at University at Buffalo, and co-senior author on the paper together with Davit Potoyan, PhD, assistant professor of chemistry at Iowa State University.

“In all, we have shown using a simple system of three components that we can create different kinds of organelles and control their arrangement in a predictive manner. We suspect that such mechanisms may be employed by cells to arrange different MLOs for optimizing their functional output,” says Banerjee.

The next step for the researchers, already underway, is to conduct similar studies inside living cells.

“Going back to our motivations in researching MLOs, the big questions that started the field were questions in cell biology: How do cells organize their internal space?” Banerjee says. “The principles we uncover here contribute to the knowledge base that will improve understanding in this area.”

Numerous interactions between proteins, and proteins and RNA determine the formations of these synthetic MLOs, the study reports. The MLOs form a dense network floating in buffer, competing with each other to form molecular bonds that control their composition and structure.

These findings that provide a set of physical rules that regulate the composition and spatial organization of multicomponent and multiphasic MLOs could lead to advances in fields such as synthetic cell research or new materials for drug delivery. Specifically, the authors show that competition between PLP and RNA for a shared partner RRP, leads to the formation of stable coexisting phases—homogenous PLP MLOs and heterogenous RRP-RNA MLOs.

“We are in the process of learning the biomolecular grammar that may be a universal language used by cells for taming their inner cellular complexity. We hope one day to utilize this knowledge to engineer artificial protocells with custom-designed functionalities inspired by nature,” Potoyan says.