Changes in relative transcript amounts caused by ∆ftsH in Staphylococcus aureus USA300

Staphylococcus aureus is an important human pathogen causing skin infection and many serious diseases such as pneumonia, sepsis, and toxic shock syndrome. In the bacterium, the membrane-bound protease FtsH plays important roles in the bacterial resistance to various stresses. This study was initiated to explain the strain-specific aggregation of the ftsH-deletion mutant of the Newman strain. To understand the molecular basis of the phenotype, we identified FtsH substrate proteins by comparing the protein contents of two different strains, Newman and USA300, and found that, in the strain Newman, a single nucleotide change in the sensor histidine kinase saeS gene placed the SaeRS two-component system under the control of FtsH, leading to the strain-specific cell-aggregation phenotype. Not only does our study provide a new methodology for protease-substrate determination but it also demonstrates that even a single nucleotide polymorphism can rewire bacterial regulatory network, resulting in a strain-specific phenotype. Our study shows the pitfall of making sweeping conclusion based on experimental results from a single bacterial strain. RNA was prepared from cultures of strains USA300_P23 and USA300_P23_∆ftsH grown late-exponential phage cells in TSB media at 37°C. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.