Exploiting RNA Polymerase Vulnerabilities: A New Strategy Against Drug-Resistant Tuberculosis
Key Insights
Rockefeller University researchers have uncovered the atomic-level mechanism by which Mycobacterium tuberculosis (search) develops resistance to rifampicin, the cornerstone TB drug for decades.
The team discovered that rifampicin resistance mutations slow down RNA polymerase (search), and a second mutation compensates—revealing slow transcription as a vulnerability that can be exploited.
Combining two drugs that hit different steps of transcription produced powerful synergy, effectively killing dormant TB bacteria hiding in lung granulomas.
Researchers at The Rockefeller University have mapped, at atomic resolution, how tuberculosis (search) bacteria become resistant to rifampicin—and more importantly, how that very resistance creates a vulnerability that can be exploited with a second drug. The findings, from the laboratory of Elizabeth Campbell at the Laboratory of Molecular Pathogenesis, open a new avenue for treating drug-resistant TB, including the notoriously difficult-to-eradicate dormant infections.
The work centers on RNA polymerase (search) (RNAP), the essential protein complex that transcribes DNA into RNA in every living cell. "RNA polymerase is the protein that copies stretches of genetic code from DNA into an intermediate molecule, RNA, which can later be translated into proteins. This transcription is incredibly important; it's basically the only way a cell can make any proteins and sustain life," Campbell explained. Even dormant Mycobacterium tuberculosis (search) requires a background level of transcription to survive.
How Resistance Reveals a Weakness
Rifampicin has been the backbone of TB treatment for decades, yet the precise mechanism of its action—and of resistance to it—remained incompletely understood. Campbell's team, collaborating with Rockefeller colleague Jeremy Rock, set out to visualize what happens at the atomic scale when rifampicin binds to TB's polymerase.
Their structural studies revealed a critical insight: rifampicin-resistant TB strains carry not just one but co-existing mutations. "When we looked closely at the polymerase, we discovered that the resistance mutation co-exists with other mutations that affect and distort a region of the protein needed to help it move smoothly along a strand of DNA," Campbell said. The first mutation confers rifampicin resistance but slows down the RNA polymerase (search); the second mutation rescues that slowness. This finding established that slow transcription is itself a vulnerability—one that could be targeted.
Synergy Through Rational Combination
Building on this discovery, Campbell and Rock tested whether they could exploit the sluggishness of resistant RNA polymerase (search). They treated drug-resistant TB with a second compound that binds to a different site on RNA polymerase, causing the already struggling enzyme to stop completely and preventing any DNA transcription.
"Combining two drugs resulted in powerful synergy that worked especially well against the dormant bacteria hiding in granulomas—those clusters of immune cells in the lung that contain latent TB infections," Campbell noted. "Being able to treat them and to observe synergy was a significant advance."
The synergy observed in a lung model represents what Campbell describes as "a holy grail for antibiotic therapy"—the combination is more powerful than the sum of its parts. When two different steps of transcription are hit simultaneously, the bacteria cannot compensate for one problem while dealing with the other, making it much harder for resistance to emerge.
A Multi-Step Process, A Multi-Target Opportunity
Transcription is not a single event but a multi-step process encompassing initiation, elongation, and termination—each involving dozens of regulatory proteins that could serve as drug targets. "Rifampicin hits one very specific step: it blocks RNA polymerase (search) very early in the process of transcription. That's enormously effective, which is why it's been the backbone of TB treatment for decades. But it also means that there are a huge number of steps left that we could target," Campbell said.
The lab's methodology combines structural biology—visualizing the exact three-dimensional shape of RNA polymerase (search) in different scenarios—with biochemistry, where individual proteins are purified and tested in vitro with DNA and RNA molecules. "The structures tell you what everything looks like; the biochemistry tells you what each piece does. Together they give us a full picture," Campbell explained.
Beyond Tuberculosis (search): A General Program for Fighting Infectious Disease
The approach extends well beyond TB. During the COVID-19 pandemic, Campbell's lab rapidly pivoted to map the full structure of the coronavirus RNA polymerase (search). The team has also investigated Clostridium difficile (search), one of the most common healthcare-associated infections, demonstrating how an antibiotic can block the polymerase in C. diff without affecting other bacteria—a proof of principle for designing narrow-spectrum, pathogen-specific drugs.
"Every time we understand a new pathogen's transcription machinery in detail, we get a new map of its vulnerabilities," Campbell said. "In that way, I think of our lab's work as building a general program for fighting infectious disease, one pathogen at a time, while at the same time discovering basic scientific principles in bacteria and viruses."