Bioengineers develop roadmap for protein assembly from nature-derived nanobubbles

As far as water equipment goes, floats aren’t exactly high-tech. But the tiny air-filled bubbles that some microorganisms use as flotation devices when they compete for light on the water’s surface are another story.

Known as gas vesicles (GVs), these micrometer-sized bubbles hold great promise for many biomedical applications, including cell imaging, sensing, manipulation, tracking, and more. The problem is, researchers don’t yet know how to make medically useful varieties of GVs in the lab.

Rice University bioengineers have now created a roadmap showing how a group of proteins interact to give rise to the bubbles’ nanoscale shell. By unraveling some of the complex molecular processes that take place during GV assembly, Rice bioengineer George Lu and his team at the Synthetic Macromolecular Assemblies Laboratory are now one step closer to discovering powerful new diagnostics and treatments based on these natural structures.

“GVs are essentially tiny air bubbles, so they can be used with ultrasound to make things inside our bodies visible, like cancer or specific parts of the body,” said Manuel Iburg, a Rice postdoctoral researcher and lead author of a study published in The EMBO Journal. “However, GVs cannot be made in a test tube or on an assembly line, and we cannot make them from scratch.”

The GV family includes some of the smallest bubbles ever created, and they can persist for months. Their long-term stability is due in large part to the special structure of their protein shell, which is permeable to both individual water and gas molecules, but whose inner surface is highly water-repellent, hence the GVs’ ability to retain gas inside even when submerged. And unlike synthetic nanobubbles, which are supplied with gas from the outside, GVs harness gas from the surrounding liquid.

Aquatic photosynthetic bacteria that use GVs to float closer to sunlight have specific genes that encode the proteins that make up this special shell. However, while researchers know exactly what these tiny bubbles look like and why they tend to cluster together, they have yet to understand the protein interactions that enable the process of assembling the structures. Without some understanding of how these protein building blocks work, plans to deploy lab-created GVs in medical applications must be put on hold.

To solve the problem, the researchers focused on a group of 11 proteins that they knew were part of the assembly process and found a way to track how each of them, in turn, interacts with the others inside living parent cells.

“We had to be extremely careful and constantly check whether our cells were still producing GVs,” Iburg says. “In particular, we learned that some GV proteins can be modified without too much difficulty.”

The researchers used this information to add or subtract certain GV proteins during the tests, which allowed them to understand that interactions between certain proteins needed help from other proteins to proceed properly. They also tested whether these individual interactions changed during the GV assembly process.

“Through many permutations and iterations, we created a road map of how all these different proteins must interact to produce a GV inside the cell,” Iburg said. “Our experiments taught us that this road map of GV interactions is very dense and has many interdependent pieces. Some GV proteins form subnetworks that appear to serve a narrower function in the overall process, some must interact with many other parts of the assembly system, and some change their interactions over time.”

“We believe that GVs have great potential to be used in new, rapid and comfortable ultrasound-based diagnostics or even treatment options for patients,” said Lu, an assistant professor of bioengineering at Rice and a researcher at the Cancer Prevention and Research Institute of Texas (CPRIT). “Our findings can also help researchers develop GVs that enable existing treatments to become even more precise, convenient and effective.”