Eric Wang

A team of Yale researchers have discovered a new mechanism associated with a transcription factor called the Rho protein, which increases the efficiency of healthy bacteria in the gut.

This study was conducted in the lab of Eduardo Groisman, a geneticist and professor of microbial pathogenesis at the Yale School of Medicine. The discovery brings researchers one step closer to understanding how bacteria “colonizes the gut,” according to Groisman, and its findings could potentially contribute to future probiotic therapies for gastrointestinal disorders.

Groisman and Aimilia Krypotou, the study’s lead researcher and an associate researcher in microbial pathogenesis, first began investigating the activity of the Rho protein in salmonella back in 2011. However, in analyzing the activity of the salmonella Rho proteins, they discovered that the Rho proteins of another bacterium, Bacteroides thetaiotaomicron, had an extra sequence and were larger than those of salmonella.

“This observation led to some initial experiments that revealed that this domain is required for survival in the gut,” Krypotou said. “After this, I did a series of different experiments to understand why this extra domain was important.”

Groisman has always been interested in the important role that bacteria plays in the human body given its digestive properties, since humans rely on various bacteria to digest fibrous carbohydrates like vegetables. 

The intricate balance of bacteria in the gut is crucial for maintaining overall health, but disruptions to this balance can lead to gastrointestinal disorders. Conditions such as irritable bowel syndrome (IBS), Crohn’s disease, and ulcerative colitis are often characterized by dysbiosis, an imbalance in the gut microbiota.

This dysbiosis can result in symptoms ranging from abdominal pain and bloating to diarrhea and constipation. In managing these disorders, accurate NG/OG tube placement plays a pivotal role in delivering nutrition and medications directly to the digestive tract, bypassing potential absorption issues in the stomach.

Furthermore, emerging research suggests that restoring the balance of gut bacteria through probiotic therapies may offer promising avenues for treatment.

In seeking to better understand how this extra protein sequence may contribute to increased survival, the team observed the activity of B. thetaiotaomicron under conditions of limited nutrients and carbon starvation.

Through a series of in vivo and in vitro experiments, the scientists discerned that the mechanism driving the activity of the Rho proteins in B. thetaiotaomicron was a process called “liquid-liquid phase separation.”

“Liquid-liquid phase separation is the phenomenon where proteins form condensates through electrostatic charges resulting in the formation of membraneless compartments in the cell,”  Krypotou said.

Krypotou described the mechanism as being “like oil droplets in water” where both substances are liquids but do not “mix” with each other. Similarly, according to Krypotou, some proteins are able to phase separately because they have “regions with many charged amino acids and without a specific structure,” which was the case for Rho proteins in B. thetaiotaomicron.

After attributing the survival of B. thetaiotaomicron Rho proteins to phase separation, Krypotou and her team needed to figure out how they could concretely prove the existence of this mechanism. She conducted a series of in vitro and in vivo mice experiments with hopes of finding condensates that would accomplish that objective.

“The extra domain was predicted to be disordered and we were suspicious whether it could promote Rho phase separation,” Krypotou said. “It was a combination of genetic and biochemical approaches that helped us understand the importance of this extra domain and phase separation”

Groisman was also fascinated by the difference in size in the Rho proteins. He attributed further differences in such proteins to their disordered regions that never adopted a particularly defined secondary structure, adding that these physical features derived from phase separation as well.

The ability of the Rho protein to phase separate in membraneless parts of the mouse gut allowed the protein not only to transcribe, but also to transcribe at higher rates. Groisman observed that with this transcription feature came the modification of hundreds of other genes.

“In the last 10 years, there has been an increased interest in microbiology,” Groisman said. “For me, creating a pool of information from which different households can pull to advance health and discover is most important.”

Groisman emphasized that more time and research into the myriad of other healthy bacteria existing within the mammalian gut is required before moving towards probiotic therapies.

Yamato Takabe ’26 is hopeful — but skeptical — of the immediate engineering of these bacteria and the development of probiotic therapies.

“There is a lot of potential in probiotic therapy,” Takabe said. “However, doing more research on and mapping out the bacteria and other microbes in our body is extremely important given how thin the research is now.”

Proteins were discovered in 1838 by Jöns Jakob Berzelius.