New research published in Nature reports that three small phage proteins from evolutionarily distinct bacteriophages can inhibit the same essential bacterial membrane protein, MurJ. The finding reveals that viruses have repeatedly stumbled on a single weak point in bacterial armor, a convergence that scientists say could guide the design of a new class of antibiotics at a time when drug-resistant infections are a growing global health threat. The work, led by researchers at Caltech, presents cryo-electron microscopy structures showing exactly how each viral protein jams MurJ’s molecular machinery.
Why MurJ Is a Bacterial Lifeline
Every bacterium surrounds itself with a mesh-like shell of peptidoglycan, a giant polymer that keeps the cell from bursting. Building that shell requires ferrying a precursor molecule called lipid II from the inside of the cell membrane to the outside, where it can be stitched into the growing wall. The protein responsible for that transport step is MurJ, a membrane-embedded flippase whose essential role in lipid II flipping was established through chemical-genetic experiments in Escherichia coli. Blocking MurJ can prevent the bacterium from maintaining its protective shell and can lead to cell death.
The identification of MurJ as the missing flippase took years of detective work. Bioinformatic analysis first flagged the protein, then called MviN, as the peptidoglycan precursor transporter, with genetic depletion studies confirming its essentiality. Later structural work captured the crystal structure of E. coli MurJ in an inward-open conformation and mapped functional residues across the protein through large-scale mutagenesis. That structural framework became the reference point for understanding how inhibitors, whether chemical or biological, could shut the flippase down.
Three Viral Proteins, One Shared Target
Small bacteriophages face a packaging problem: their genomes are so tiny that they cannot encode the large, multi-component lysis machines used by bigger viruses to burst open host cells. Instead, they rely on single-gene lysis proteins, or Sgls, compact weapons that each disable a single host target. The new Nature paper shows that three such Sgls, designated SglM, SglPP7, and SglCJ3 (from the predicted phage Changjiang3), all convergently inhibit MurJ despite sharing no detectable sequence similarity. That three evolutionarily distinct phages use the same overall strategy suggests MurJ is a vulnerable point in bacterial physiology.
Genetic screening had already hinted at this convergence. Genome-wide suppressor analysis showed that the PP7 phage Sgl targets MurJ through a mechanism unrelated to SglM, and the same MurJ missense mutations rescued bacteria from both proteins. Those resistance mutations cluster in MurJ’s transmembrane regions, the very segments that undergo conformational changes during the lipid II transport cycle. The pattern suggested that diverse Sgls exploit the same structural vulnerability, a hypothesis the new cryo-EM data supports with high-resolution structural snapshots.
A Molecular Wedge Caught on Camera
To flip lipid II, MurJ must cycle between inward-facing and outward-facing conformations, opening alternately to each side of the membrane. The cryo-EM structures presented in the Nature study capture MurJ bound to each of the three Sgls, revealing how these tiny proteins halt that cycle. Complementary structural work resolved a MurJ–SglM complex at approximately 3.09 angstroms, showing that the phage protein inserts between transmembrane helices 2 and 7 like a wedge, locking MurJ in an outward-facing state. With the transporter frozen mid-cycle, lipid II accumulates on the wrong side of the membrane and peptidoglycan synthesis stalls.
The in vivo consequences match what structural biology predicts. When Sgl genes are expressed in bacteria, cells display phenotypes consistent with cell-wall synthesis failure, including swelling, lysis, and accumulation of lipid II precursors. The wedge model also explains why resistance mutations map to the transmembrane interface where Sgls bind: amino acid substitutions at those positions can loosen the grip of the viral protein without abolishing MurJ’s ability to flip lipid II. That narrow escape route hints at how tightly evolution has optimized MurJ’s structure, leaving bacteria few options to dodge this attack without crippling their own wall-building machinery.
MurJ at the Crossroads of Cell Growth and Antibiotic Design
MurJ is not just a conduit for lipid II; it sits at a regulatory crossroads that links wall construction to overall cell physiology. Studies of peptidoglycan assembly have shown that bacteria carefully coordinate synthesis and remodeling of their sacculus to maintain shape, division, and resistance to osmotic stress. Because MurJ controls the availability of lipid II on the outer face of the membrane, its activity effectively gates when and where new cell-wall material can be inserted. Any perturbation of this step, whether by genetic mutation or viral protein binding, ripples through downstream enzymes that polymerize and cross-link the peptidoglycan network.
Recent work using single-molecule imaging and biochemical reconstitution has illuminated how MurJ’s transport cycle couples to broader cell growth processes, reinforcing the idea that the flippase is both an essential and highly constrained hub. That dual status helps explain why MurJ is such an attractive target for phage Sgls and why convergent evolution has homed in on it multiple times. From a drug-discovery standpoint, it also means that small molecules capable of mimicking the Sgl wedge could exert powerful antibacterial effects with relatively modest changes in binding affinity or kinetics, because even partial inhibition of lipid II flipping can tip the balance toward lethal wall failure.
From Viral Strategy to Antibiotic Blueprint
Most existing antibiotics that target cell-wall synthesis, such as penicillins and vancomycin, act on steps that occur after lipid II has already crossed the membrane. MurJ inhibition blocks an earlier step, which raises the possibility that drugs mimicking Sgl action could complement rather than duplicate current therapies. Caltech researchers describe Sgls as “protein antibiotics,” a framing that highlights their potential as templates for rational drug design. A small molecule engineered to wedge into the same transmembrane groove could, in principle, shut down peptidoglycan biogenesis with the same precision as the viral proteins but with the pharmacological advantages of a traditional drug.
Designing such inhibitors will not be trivial. MurJ is a dynamic membrane protein, and its conformational changes are central to its function, as emphasized by structural and biochemical analyses of lipid II flippases across diverse bacteria. Any candidate compound must not only bind tightly but also bias the transporter toward a nonproductive state, much like the Sgl wedges do. Medicinal chemists will also have to navigate the challenge of reaching MurJ in the inner membrane of Gram-negative pathogens, which are already notorious for their impermeable outer membranes and efflux pumps. Still, the convergent evolution of three distinct viral proteins that all solve this problem in nature offers a powerful roadmap. By decoding and adapting that viral playbook, researchers hope to turn phages’ minimalist lysis strategies into the blueprint for a new generation of antibiotics capable of outmaneuvering resistant bacteria.
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*This article was researched with the help of AI, with human editors creating the final content.
