## 2 Results and Discussion  
### General Transcriptome Response of SK-03-92 Treatment  
New drugs to treat _S. aureus_ infections are urgently needed, and SK-03-92 holds considerable promise. SK-03-92 has a stilbenoid backbone [22] and is bactericidal within an hour; however, 10% of the population survives as drug persisters that can grow in media containing up to 32 ug/mL of SK-03-92 but with an MIC equivalent to untreated _S. aureus_ cells. The mechanism of action for SK-03-92 is unknown. To ascertain the effects of SK-03-92 treatment on the transcriptome of _S. aureus_, total RNA was isolated from _S. aureus_ strain MW2 cultures (Table 1) treated for 30 min with 8\(\times\) the MIC of SK-03-92 and untreated MW2 cultures and an RNA microarray was performed. A total of 52 genes were dysregulated by the SK-03-92 drug treatment (Table 2), representing 2% of the total _S. aureus_ transcriptome. This is remarkable because transcriptional profiling of other bactericidal compounds has shown a larger effect on the _S. aureus_ transcriptome, including ortho-phenylphenol (24%) [31], amicoumacin A (20%) [32] and daptomycin (5% to 32%) [33, 34]. Interestingly, the number of downregulated genes (73.1%) greatly surpassed the number of upregulated genes (26.9%). An examination of genes affected by treatment with other stilbene type compounds demonstrates the disparity in their transcript profile compared to treatment with SK-03-92. Pterostilbene, anotherstilbenoid compound, in _Saccharomyces cerevisiae_ showed 1189 genes that were dysregulated: 1007 upregulated (85%) and 182 downregulated (15%) [35]. Microarray analysis with resveratrol treated _Schizosaccharomyces pombe_ showed 480 genes dysregulated, 377 genes that were upregulated and 103 that were downregulated [36]. RNA sequence analysis of resveratrol treated _S. aureus_ cells demonstrated 444 dysregulated genes, 201 upregulated and 243 downregulated [37]. The majority of the genes in our study had a two- to four-fold difference in transcript abundance when comparing SK-03-92 treated vs. untreated _S. aureus_ cultures. Very few genes dysregulated by SK-03-92 were previously shown to be dysregulated by resveratrol (e.g., downregulation of the _purD_, _purH_, _purL_, _lrgA_, and _sdhC_ genes). Only three genes had a 10-fold or higher change in transcript levels, which included two genes annotated to be part of a putative two-component system (TCS) (_SACOL2360_ (annotated as _MW2284_ in MW2 strain) = 14.1-fold lower and _SACOL2361_ (annotated as _MW2285_ in MW2 strain) = 26.9-fold lower) as well as the _glpD_ gene encoding glycerol-3-phosphate dehydrogenase (10-fold higher). Dysregulated genes tied to a potential mechanism of action for SK-03-92 included _glpD_, _adhE_ (_SACOL0135_), _adhP_ (_SACOL0660_), and _sdhC_ (_SACOL1158_). GlpD funnels electrons into the respiratory chain via quinone or menaquinone reduction coupled to the oxidation of glycerol-3-phosphate to glycerone phosphate (dihydroxyacetone phosphate) [40], which can be enzymatically or non-enzymatically transformed into methylglyoxal (MG) [41]. Higher concentrations of MG are thought to halt bacterial growth by damaging proteins by acting as a protein glycating agent that mainly affects arginine residues [42; 43]. In _Candida albicans_, ADH1 catalyzes the NAD+ linked oxidation of MG to pyruvate and disruption of the _adh1_ gene in _C. albicans_ caused accumulation of MG followed by inhibition of growth [44]. The dysregulation of _glpD_ and _adh_ genes suggests that MG was accumulating and glycation was occurring in SK-03-92-treated _S. aureus_. MG glycation of proteins, lipids, and DNA generate advanced glycation end products (AGEs) [43]. Importantly, GlpD has been implicated in drug persistence in _Escherichia coli_[45] and _S. aureus_[34]. A number of genes involved in metabolism were also dysregulated by SK-03-92 treatment, including the _gcvH_ gene that encodes GcvH, which shuttles the methylamine group of glycine from the P-protein to the T-protein via a lipoyl group [46].