Proteomic and Network Analysis of Bacillus cereus Adaptation: Impact of Plasmid on Cytosolic and Secretome Profiles

The emergence of new pathogen bacteria is often the consequence of horizontal gene transfer (HTF) which enables adaptation to a new ecological niche. The emetic lineage of B. cereus, a foodborne pathogen, harbors the pXO1-like mega-plasmid pCER270 that encodes the structural genes ces for the non-ribosomal biosynthesis of the emetic toxin cereulide. Here, we evaluate the effect of pCER270 and ces deletion on adaptation and virulence using protein-protein interaction (PPI) network analysis. In the first condition, the pCER270 plasmid was removed from the emetic B. cereus reference strain F4810/72 (aka AH187) using plasmid curing techniques. In contrast, in the second condition, the ces genes located on the plasmid were knocked out, retaining the rest of the plasmid's genomic content. TMT-based high-pH offline 2D-RPLC-MS/MS (Exploris 480/FAIMS) identified differentially abundant proteins, which were mapped onto a whole genome data-based PPI network to investigate network topology changes. Network analysis revealed functional interactions between plasmid-encoded and chromosomal pathways, demonstrating how acquiring the pCER270 plasmid reshapes the overall cellular network. Plasmid deletion disrupts protein clusters critical for maintaining cell surface integrity, transcriptional regulation, sporulation, and metabolism. In contrast, ces gene deletion leads to more localized changes. These findings show how HTF influences bacterial virulence and ecological adaptability.