Comparative proteomics analysis of MRSA under different experimental conditions

The ability of methicillin-resistant Staphylococcus aureus (MRSA) to adapt to environmental stressors is crucial for its survival and persistence. This study used shotgun proteomics to analyze the protein profiles of MRSA strains ST398 and JE2 under three experimental conditions: EC1 (control, 37 °C, pH 7), EC2 (35 °C, pH 6), and EC3 (35 °C, pH 6 with 5% NaCl). Proteins were extracted and digested with trypsin using filter-aided sample preparation (FASP), followed by LC-MS/MS analysis. Raw data were analyzed using Proteome Discoverer software with label-free quantification (LFQ), identifying an average of 2640 ± 70 and 2832 ± 154 proteins in ST398 and JE2, respectively. Qualitative and quantitative differences in protein expression were observed between strains and conditions. Under EC2, ABC transporters increased and arginine metabolism was upregulated, suggesting metabolic adaptation to acidic stress. Purine metabolism was downregulated, indicating a metabolic shift. Under EC3 condition, NaCl addition induced glycine-betaine biosynthesis and proteins involved in potassium limitation. JE2 exhibited a more pronounced oxidative and stress response under salt stress, indicating a strain-specific adaptation. These findings highlight strain-specific proteomic responses in MRSA, highlighting the roles of arginine, glycine-betaine, and purine metabolism, along with stress-response proteins, in coping with environmental stressors.