Convergent MurJ flippase inhibition by phage lysis proteins
Article Date: 25 February 2026
Article URL: https://www.nature.com/articles/s41586-026-10163-w
Article Image: none provided
Summary
This Nature paper shows that small phage-encoded single-gene lysis proteins (Sgls) from diverse single-stranded RNA phages converge on the bacterial lipid II flippase MurJ. Using cryo-EM, the authors solved three Sgl–MurJ complex structures (Sgl M–MurJ, Sgl PP7–MurJ and Sgl CJ3–MurJ) and found that Sgls bind within MurJ’s transmembrane region and trap it in inactive conformations, blocking lipid II flipping and causing cell lysis. Mutational and physiological assays identify key contact residues and MurJ variants that confer resistance; heterologous expression of a Bacillus flippase (Amj) rescues lysis, confirming target specificity. Structural and functional data (PDB: 9NU4, 9NU5, 9NU8; EMDB: EMD-49796, EMD-49797, EMD-49798) support a convergent evolutionary strategy by phages to exploit a conserved vulnerability in Gram-negative cell-wall biogenesis.
Key Points
- Three high-resolution cryo-EM structures reveal Sgls from different phages bind the MurJ flippase and block its conformational cycle.
- Sgl binding occludes the MurJ transmembrane cavity and prevents lipid II translocation, leading to bacterial lysis.
- Site-directed mutagenesis of Sgls and MurJ mapped key contact residues; specific MurJ mutants provide resistance.
- Heterologous expression of Amj (a non-homologous lipid II flippase) suppresses lysis, confirming MurJ is the direct target.
- Data and coordinates are publicly deposited (PDB and EMDB accession codes listed in the paper) and microscopy/code resources are available on GitHub.
- Results highlight MurJ as a conserved and exploitable weak spot for ‘protein antibiotic’ action and a promising structural target for novel antimicrobials.
Content summary
The authors purified and co-expressed MurJ with three different phage Sgl proteins, solved cryo-EM structures of each complex, and combined structural analysis with mutational lysis assays and microscopy. Structural comparisons show Sgls occupy overlapping binding regions in MurJ and stabilise conformations incompatible with lipid II flipping. Functional assays (lysis curves, western blots, microscopy) and suppression experiments with alternative flippases corroborate the structural mechanism. The paper includes extensive extended data and supplementary materials (mutational scans, cryo-EM processing, microscopy analyses) and deposits coordinates and maps in public databases.
Context and relevance
Bacterial cell-wall assembly is a validated antibiotic target and MurJ is essential for lipid II translocation in many Gram-negative bacteria. With rising antimicrobial resistance, structurally validated vulnerabilities like MurJ are especially important. This work connects phage biology and structural membrane-protein biology to reveal naturally evolved ‘protein antibiotics’ that could inspire new antibacterial strategies or molecular scaffolds to inhibit MurJ. It also advances understanding of phage lysis evolution and single-gene lysis mechanisms across diverse phages.
Why should I read this
Short version: if you care about new antibiotic ideas, phage biology, or membrane-protein structure — this paper is worth ten minutes. It gives atomic-level evidence of how tiny phage proteins jam an essential bacterial machine, points to real rescue/suppression experiments, and lays out clear leads for drug discovery or engineered phage tools. Handy if you want to skip sifting through supplementary piles — these authors did the heavy lifting for you.
Author
Punchy take: This is a must-read for researchers in antimicrobial discovery and phage therapeutics. The structures and functional validation are convincing and immediately useful for anyone thinking of MurJ as a drug target or of harnessing phage-derived protein inhibitors.