Lab develops protein assembly roadmap for gas vesicles

Micron-sized bubbles known as gas vesicles (GVs) hold great promise for a range of biomedical applications, including imaging, sensing, cellular manipulation and monitoring, 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 form the bubbles’ nanometer-thin shell. By unraveling some of the complex molecular processes that take place during GV assembly, Rice bioengineer George Lu and his team in the Laboratory of Synthetic Macromolecular Assemblies are now one step closer to unlocking powerful new diagnostics and therapeutics based on these naturally occurring structures.

“GVs are essentially tiny air bubbles, so using them in conjunction with ultrasound may be possible to make things inside our bodies visible, like cancer or specific areas of the body,” says Manuel Iburg, a postdoctoral researcher at Rice and lead author of a study published in the journal Cell Biology. EMBO Magazine. “But GVs can’t be made in a test tube or on an assembly line, and we can’t manufacture them from scratch.”

The GV family contains some of the smallest bubbles ever made, and can persist for months. Their stability over longer periods is largely due to the special structure of their protein shells, which are permeable to both individual water and gas molecules but have an extremely hydrophobic interior — hence the GVs’ ability to retain gas even when submerged. And unlike synthetic nanobubbles, which are fed with gas from the outside, GVs draw gas from the surrounding liquid.

Aquatic photosynthetic bacteria that use GVs to swim closer to sunlight have specific genes that code for proteins that form this specialized shell. But despite knowing what the tiny bubbles look like and even why they tend to clump together, researchers have yet to figure out the protein interactions that enable the structures to assemble. Without some insight into how these protein building blocks work, plans to use lab-designed GVs for medical applications will have to be put on hold.

To solve the problem, the researchers focused on a group of 11 proteins they knew were part of the assembly process and developed a method to track how each of them interacted with others inside living host cells.

“We had to be very meticulous and constantly check to see if our cells were still producing GV,” Iburg said. “One of the things we learned was that some of the GV proteins can be replaced without too much trouble.”

The researchers used this insight to add or remove specific GV proteins when running tests, allowing them to understand which interactions between some proteins needed help from other proteins to occur properly. They also checked whether these individual interactions changed during the GV assembly process.

“Through many such modifications and iterations, we have built a roadmap of how all these different proteins need to interact to produce a GV within the cell,” Iburg said. “We have learned from our experiments that this roadmap of GV interactions is very dense with many interdependent elements. Some of the GV proteins form subnetworks that appear to perform a smaller function in the overall process, some need to interact with many other parts of the assembly system, and some change their interactions over time.”

“We think GVs have great potential to be used for new, rapid, and convenient ultrasound-based diagnostic or even treatment options for patients,” says Lu, an assistant professor of bioengineering at Rice and a fellow at the Cancer Prevention and Research Institute of Texas (CPRIT). “Our findings could also help researchers develop GVs that make existing treatments even more sensitive, convenient, and effective.”