Researchers at Umeå University have identified a key molecular player that helps bacteria survive the hostile environment inside the body. Their study reveals how the protein RfaH acts as a protective shield for bacterial genes — and points to new strategies for fighting persistent infections.
"The human body is a very stressful place for bacteria," says Kemal Avican, research group leader at Department of Molecular Biology and Icelab at Umeå University and leader of the study. "During infection, the immune system attacks, nutrients are scarce, and microbes are exposed to bile salts, acids and heat. We looked at how RfaH helps bacteria deal with that stress by turning on the right survival genes at the right time."
Persistent bacterial infections pose a major challenge in medicine: bacteria can linger in the body long after acute symptoms fade, evading immune defenses and surviving antibiotic treatment. In diseases like tuberculosis, this leads to relapse and makes treatment difficult.
Keeps critical genes switched on
Using Yersinia pseudotuberculosis as a model bacterium that infects the gut, Kemal Avican and his team showed that RfaH is essential for bacterial persistence.
RfaH acts like a molecular bodyguard, ensuring transcription—the step where DNA is copied into a messenger molecule that guides protein production—runs to completion.
"The protein hops onto the transcription machinery and helps it stay on track so the full set of genes is read to the end. This makes RfaH an anti-terminator – it prevents the termination of transcription", explains Kemal Avican.
"When we removed RfaH, the bacteria's ability to establish long-term infection dropped dramatically!" he adds.
Surviving the stress of a hostile environment
The researchers found that RfaH production ramps up precisely when bacteria need it most—in late growth stages and when conditions turn hostile.
In mouse experiments, the difference was stark: nearly all animals became infected with normal bacteria, but only about one in five became infected when bacteria lacked RfaH. This translated to much higher survival rates among the mice.
Many bacterial genes are arranged in long stretches called operons. Without RfaH, the cellular machinery that reads these genes can stall or stop prematurely. RfaH prevents this, ensuring bacteria can produce surface structures, secrete toxins, and resist stress from the body's defenses.
Insights for future antimicrobial therapies
The research revealed that RfaH controls the production of a key component of the surface of bacteria - the O-antigen. Without RfaH, this outer coat becomes defective. But RfaH's influence extends further, activating many "downstream" genes involved in attachment, movement, and nutrient transport.
RfaH itself is present in many bacteria, including harmless members of the microbiota. That is why genes influenced by RfAH through activation or signaling - downstream genes - could provide promising new selective targets to stop persistent infections, the researchers say.
"This antimicrobial approach could disarm pathogenic bacteria without disturbing the beneficial ones", says Joram Kiriga Waititu, postdoctoral fellow at Department of Molecular Biology, and first author of the study.
While Yersinia pseudotuberculosis usually causes an infection in humans that can heal on its own, it serves as a valuable model for gut bacteria that can cause long-term or recurrent disease, such as Escherichia coli, Salmonella and Helicobacter. In this way, the findings could pave the way for new strategies to tackle hard-to-treat gut infections.
The study has been published in the scientific journal mBio and the research was funded in part by the Swedish Research Council, Umeå Centre for Microbial Research (UCMR), the Stress Response Modeling at IceLab Centre of Research Excellence, Kempestiftelserna and the Medical Faculty at Umeå University.
