Punicalagin inhibits Staphylococcus aureus growth and biofilm formation: integrated omics reveals potential mechanisms

Punicalagin (Pun), a major polyphenolic compound derived from pomegranate (Punica granatum), has demonstrated promising antibacterial activity against a range of pathogenic bacteria, including Staphylococcus aureus. However, its precise mode of action at the molecular level remains largely unexplored. Therefore, we implemented a multi-omics strategy integrating differential proteomic and transcriptomic analyses, in conjunction with electron microscopy and in vitro anti-biofilm assays, to elucidate the potential molecular mechanisms underlying Pun’s antibacterial effects on S. aureus. We determined Pun’s minimum inhibitory concentration (MIC) against S. aureus to be 64 µg/mL and revealed that Pun disrupted S. aureus cell membrane integrity. Notably, Pun significantly inhibited S. aureus biofilm formation even at 1/8 MIC. Omics analysis identified 710 differentially expressed proteins (DEPs, 340 upregulated, 370 downregulated) and 601 differentially expressed genes (DEGs, 234 upregulated, 367 downregulated) in response to Pun treatment. Further analysis of the integrated DEPs and DEGs revealed that Pun disrupted bacterial growth by impairing cell membrane integrity through inhibition of key fatty acid synthesis enzymes, including ACC, BCCP, and FabH, and by inhibiting biofilm formation through suppression of adhesion-related proteins, including ClfA, SdrCDE, Eap, and Ebps. Additionally, Pun treatment led to the downregulation of multiple TCS-related genes, suggesting a potential interference with TCS transduction pathways, which may contribute to reduced S. aureus resistance to antimicrobial agents. Furthermore, Pun upregulated iron acquisition-related proteins and ABC transporters, suggesting a broader impact on bacterial physiology. Our findings provide valuable insights into the potential molecular mechanisms underlying Pun’s antibacterial activity against S. aureus, laying a foundation for its potential application as an antimicrobial agent.