Viral Mimicry Unveiled: How Ocr Sabotages the BREX System to Outsmart Bacterial Defenses

Bacteriophages are viruses that specialize in infecting bacteria, shaping microbial communities in ways we are still trying to fully understand. Lately, they have been getting a lot of attention as a potential alternative to antibiotics, especially as drug-resistant bacterial infections become a bigger problem. But this is not a one-sided battle—bacteria are constantly evolving new ways to defend themselves, forcing phages to develop clever strategies to fight back. One of these bacterial defense systems is called BREX (Bacteriophage Exclusion), which does not destroy foreign DNA outright like some other immune systems do. Instead, it works through a process called DNA methylation, where bacterial DNA is chemically marked to distinguish it from invading phage DNA. At the core of this system is BrxX, a methyltransferase enzyme that plays a critical role in tagging bacterial DNA and ensuring that the defense system functions properly. Even though BrxX is such an important player in the BREX system, scientists have not fully figured out how it works. Some studies have hinted at its role in modifying bacterial DNA, but details like its precise targets and how it carries out its enzymatic function are still unclear. In contrast, other bacterial defense mechanisms, such as the well-known CRISPR-Cas system or the restriction-modification (R-M) system, have been studied extensively.  To this account, a research team led by Professor Litao Sun from the School of Public Health (Shenzhen) at Sun Yat-sen University published a study in Nucleic Acids Research. They conducted the first in-depth laboratory investigation of BrxX from Escherichia coli, aiming to figure out its biochemical properties—how it binds to DNA, what specific sequences it targets, and how it relies on a co-factor called S-adenosylmethionine (SAM) to do its job. They also turned their attention to Ocr, a phage protein that mimics DNA and is suspected to interfere with the BREX system. Using advanced structural biology techniques like cryo-electron microscopy (cryo-EM), they uncovered how Ocr directly binds to BrxX’s DNA recognition site, effectively shutting down its ability to methylate bacterial DNA.

The research team began by isolating and purifying BrxX from Escherichia coli, aiming to better understand its molecular function. To probe its activity, they conducted DNA methylation assays. The results were revealing: BrxX doesn’t just interact with DNA haphazardly—it specifically targets adenine residues at defined sequence motifs. However, there was a critical caveat. Although BrxX could bind DNA with relatively low sequence specificity, it was unable to methylate it without the presence of SAM, the essential methyl group donor. This observation pointed to a regulatory mechanism. It appeared that BrxX’s catalytic function is tightly coupled to intracellular SAM levels, implying that bacteria might modulate phage defense activity by controlling SAM availability. Next, the researchers turned their attention to Ocr, a protein encoded by the T7 bacteriophage. Given Ocr’s known ability to disrupt bacterial restriction enzymes, they hypothesized it might also interfere with BrxX function. To explore this, they employed electrophoretic mobility shift assays (EMSAs) to test whether Ocr could prevent BrxX from binding to DNA. Their suspicions were confirmed: Ocr formed a complex with BrxX, effectively blocking its access to target DNA sequences. Further methylation assays demonstrated that, in the presence of Ocr, BrxX’s enzymatic activity was completely inhibited. This finding positioned Ocr as more than a passive viral protein—it acts as a potent, direct inhibitor of the BREX system by mimicking DNA and disrupting BrxX’s function. To visualize this interaction at high resolution, the authors turned to cryo-electron microscopy. The resulting structural data revealed that Ocr occupies the DNA-binding cleft of BrxX, precisely where bacterial DNA would typically reside. This mimicry results in a non-functional BrxX-Ocr complex, effectively neutralizing the defense mechanism. Remarkably, this mode of inhibition wasn’t restricted to E. coli. When the researchers expressed BrxX from Bacillus cereus—a Gram-positive bacterium with a genetically distinct BREX system—Ocr still managed to inhibit its activity.

In conclusion, after years of uncertainty around how the BREX system actually works to defend bacteria against phage attacks, Professor Litao Sun and his team have begun to fill in some key gaps. BREX, unlike systems like CRISPR, doesn’t cut foreign DNA. Instead, it chemically modifies the host’s own genome—usually through methylation—essentially tagging it as “self.” Anything without this molecular label is treated as suspicious. The enzyme BrxX plays a central role in this tagging process, but until recently, it wasn’t clear how phages were managing to slip past this line of defense. To tackle that question, Sun’s group focused on a phage-encoded protein called Ocr. What they uncovered is a striking example of viral mimicry in action. Rather than attacking BrxX directly or destroying the BREX system in a brute-force manner, Ocr does something far more elegant—it impersonates DNA. This decoy approach lures BrxX into binding Ocr instead of its intended DNA substrate. Once occupied, BrxX can’t perform its protective function, leaving the host genome unmarked and vulnerable to phage takeover. Digging deeper, the researchers turned to structural analysis to get a close-up view of how this interference actually works. Cryo-EM images revealed that Ocr fits snugly into BrxX’s DNA-binding site—the same physical space that would normally be occupied by bacterial DNA. This isn’t just passive interference; it’s a calculated blockade. With BrxX neutralized by the decoy, the entire BREX defense mechanism is effectively short-circuited.

We believe there are broader implications, for one, it sheds light on a long-overlooked challenge in phage therapy. As interest in using phages to combat antibiotic-resistant infections continues to grow, so does the need to understand why some phages work better than others. BREX systems have been largely invisible in that conversation—but maybe not for much longer. If phage therapy is going to succeed in real-world settings, it will need to account for bacterial defense strategies like BREX. The discovery of Ocr’s role offers a potential roadmap for engineering phages that can dodge those defenses more effectively. Moreover, in industrial microbiology—whether it’s pharmaceutical manufacturing, enzyme production, or biofuel synthesis—phage contamination can wipe out entire batches of engineered bacteria and understanding the ways in which phages evade systems like BREX could help prevent those kinds of costly failures.