Integrated transcriptomic and proteomic analysis reveals altered expression of outer membrane proteins in Methionine sulfoxide reductases deleted mutant strain of Salmonella Typhimurium

Methionine residues are highly susceptible to oxidation by host derived reactive oxygen species (ROS) and bacterial methionine sulfoxide reductases (Msrs) are central to reversing this damage. Salmonella enterica serovar Typhimurium encodes five Msrs. Here we examine how complete loss of these repair enzymes (Δ5 msr ) affects the outer membrane proteome. Outer membrane proteins (OMPs) are integral components of the outer membrane involved in nutrient exchange, drug permeability and host interactions that directly influence bacterial stress tolerance, survival and virulence. Loss of the Msr system in the Δ5 msr mutant strain produced a > 3 fold increase ( p  < 0.0001) in ROS levels and altered OMP expression and organization. Using integrated RNA-seq, MALDI-MS proteomics and interactome analyses, we show that the Δ5 msr mutant strain displays coordinated remodelling of multiple OMP classes: induction of substrate-specific porins (LamB), TonB-dependent iron-uptake receptors (CirA) and virulence-associated surface proteins (TraT), coupled with repression of fimbrial and flagellar components (FimD, FliC). Notably, traT emerged as one of the most prominently upregulated outer-membrane–associated genes, with > 78,000-fold induction by RT-qPCR. These transcriptional changes are reflected at the protein level: Sarkosyl extraction and SDS–PAGE revealed a complex banding pattern comprising more than 14 discrete protein bands (~ 120 → ~17 kDa) and MALDI-PMF identified differential band intensities for TraT, Pal and Flagellin in the Δ5 msr mutant strain compared with S. Typhimurium. Network analysis highlights central envelope hubs (OmpA, Pal, TolC) that likely underpin adaptive envelope resilience. Our findings reveal a redox driven strategy by which S. Typhimurium remodels its outer membrane to balance nutrient acquisition, efflux and immune evasion under chronic oxidative stress.