A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin

Colomer-Winter, C.; Nair, Z. J.; Chua, J.; Jabli, S.; Roch, M.; Cazenave-Gassiot, A.; Sierra, R.; Andrey, D. O.; Chng, S.-S.; Kline, K. A.

doi:10.1101/2025.11.16.688641

bioRxiv · 10.1101/2025.11.16.688641

A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin

Colomer-Winter, C.·Nair, Z. J.·Chua, J.·Jabli, S.·Roch, M.·Cazenave-Gassiot, A.·Sierra, R.·Andrey, D. O.·Chng, S.-S.·Kline, K. A.

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Abstract

Daptomycin is a last resort antibiotic used to treat vancomycin-resistant enterococcal infections, but daptomycin resistance (DAPR) arises quickly during treatment. Resistance is due to sequential acquisition of point mutations in the two-component system LiaFSR and in cardiolipin synthases and is associated with alteration of phospholipid and glycolipid membrane composition. The molecular mechanisms underlying these lipid changes are currently unknown. Similarly, it is unclear why mutations in liaFSR occur prior to mutations in cls. We discovered that Enterococcus faecalis remodels membrane composition as a phenotypic response to daptomycin that parallels the membrane composition of DAPR strains. The enrichment in glycolipids that follows antibiotic exposure is due to LtaS1, the main LTA synthase of E. faecalis. Moreover, LtaS1 activity is governed by a network of two-component systems formed by LiaFSR, SapRS, and BsrRS that couple antibiotic sensing with membrane lipid remodeling. Together, our results provide a unifying mechanism that drives phenotypic membrane fortification in a Gram-positive pathogen which simultaneously predisposes the cell to acquire genetic high-level daptomycin resistance. Significance StatementDaptomycin is the preferred alternative to treat vancomycin-resistant Enterococcus infections. However, the efficacy of daptomycin is limited by the acquisition of daptomycin resistance. Alterations in lipid membrane composition represent a conserved strategy to fortify the Gram-positive membrane. We discovered that E. faecalis phenotypically remodels membrane composition in response to daptomycin and that the enrichment in glycolipids is dependent on LTA synthesis. We expand our limited knowledge of enterococcal LTA synthases, confirming LtaS1 as the main LTA synthase and placing LTA biogenesis under control of a network of antibiotic-responsive two-component systems. Our work provides a molecular explanation for the sequential evolution of daptomycin resistance and may support the use of existing LtaS inhibitors to prevent acquisition of daptomycin resistance.

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Colomer-Winter, C., Nair, Z. J., Chua, J., Jabli, S., Roch, M., Cazenave-Gassiot, A., Sierra, R., Andrey, D. O., Chng, S.-S., Kline, K. A.. 2025-11-17. A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin. https://doi.org/10.1101/2025.11.16.688641

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