Label-free quantitative proteomics analysis of antibiotic response in Staphylococcus aureus to oxacillin

Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of fatal bacterial infections in hospitals and has become a global health threat. Although the resistance mechanisms of β-lactam antibiotics have been studied for decades, there are few attempts at systems-wide investigations into how the bacteria respond to antibiotic stress. Spectral counting-based label-free quantitative proteomics has been applied to study global responses in MRSA and methicillin-susceptible S. aureus (MSSA) treated with subinhibitory doses of oxacillin, a model β-lactam antibiotic. We developed a simple and easily repeated sample preparation procedure that is effective for extracting surface-associated proteins. On average, 1025 and 1013 proteins were identified at a false discovery rate threshold of 0.01, for the untreated group of MRSA and MSSA. Upon treatment with oxacillin, 81 proteins (65 up-regulated, 16 down-regulated) were shown differentially expressed in MRSA (p < 0.05). In comparison, 225 proteins (162 up-regulated, 63 down-regulated) were shown differentially expressed in oxacillin-treated MSSA. β-Lactamase and penicillin-binding protein 2a were observed up-regulated uniquely in oxacillin-treated MRSA, which is consistent with the known β-lactam resistance mechanisms of S. aureus. More interestingly, the peptidoglycan biosynthesis pathway and the pantothenate and CoA biosynthesis pathway were found to be up-regulated in both oxacillin-treated MRSA and MSSA, and a series of energy metabolism pathways were up-regulated uniquely in oxacillin-treated MSSA. These new data offer a more complete view of the proteome changes in bacteria in response to the antibiotic. This report is the first in using label-free quantitative proteomics to study β-lactam antibiotic responses in S. aureus.