Acid derivatives transport 20.01.17 nucleotide/nucleoside/nucleobase transport 20.01.27 drug/toxin transport 20.03 transport facilities 20.03.02 carrier (electrochemical potential-driven transport) 20.03.02.02 symporter 20.03.02.02.01 proton driven symporter 20.03.02.02.02 sodium driven symporter 20.09 transport routes 20.09.18 cellular import 32 CELL RESCUE, DEFENSE, AND VIRULENCE 32.01 stress response 32.01.01 oxidative stress response 32.07 detoxification 32.07.05 detoxification by export 32.07.07 oxygen and radical detoxification 32.07.07.01 catalase reaction 34 INTERACTION WITH 25033180 THE ENVIRONMENT 34.01 homeostasis 34.01.01 homeostasis of cations 70.30 prokaryotic cytoplasmic membrane doi:10.1371/journal.pone.0050003.tP VALUE 7.69E-03 5.21E-03 1.94E-02 1.94E-02 3.01E-03 1.52E-03 1.34E-07 2.98E-02 7.69E-03 9.41E-04 1.19E-05 4.51E-03 1.22E-03 1.62E-02 2.73E-02 2.77E-02 1.97E-02 1.98E-02 7.36E-04 5.60E-04 7.85E-03 1.63E-02 3.51E-04 7.13E-04 6.00E-04 7.49E-06 4.62E-03 8.33E-04 1.55E-02 1.61E-04 1.72E-02 4.61E-02 1.12E-03 3.22E-04 1.40E-using 2 independent assays (BacLight assay and transcriptome profiling) and various antibiotic concentrations (0.6 to 46 MIC) at which the MoA of fusaricidin is likely to involve membrane damage. The function of differentially expressed genes could be divided into 2 categories: one is involved in the function of cell membrane (yceD, ymcC, yuaFG, ythP, and yojB), and the other is mainly related to detoxification, multidrug resistance, and cell protection (yceE, ydjP, and yeaA). yceD is involved in biofilm formation and was overexpressed by 3-fold after fusaricidin treatment, suggesting that accelerated biofilm formation may contribute to the resistance to toxins [14]. In Escherichia coli, the methionine sulfoxide reductase YeaA has an important function in protecting cells from oxidative damage [15]. It acts on free methionine sulfoxide (MetSO) and proteins that contain MetSOresidues. Phenotypic analysis of an E. coli strain lacking a functional copy of msrB revealed its importance in cadmium resistance. Cadmium is a potential carcinogen and damages cells in several ways, including via the catalysis of AOS production [16]. YmcC is considered to be a lipoprotein and may therefore contribute to the membrane protection [17]. Most of the genes that were altered 5 min after the fusaricidin addition are involved in detoxification. The relationship among these rapid-response genes was determined using string analysis and is shown in Figure 2. ybdK-ybdJ, kinA-spo0F, kinB-spo0F, and kinC were closely correlated with the rapidresponse phase. kinA-spo0F 
and kinB-spo0F are functionally important for bacterial spore formation. KinC is JWH 133 chemical information suggested to regulate gene expression during the stable phase, whereas the function of YbdK-YbdJ is currently unknown. As shown inMechanisms of Fusaricidins to Bacillus subtilisFigure 5. Changes in nucleotide metabolism. The expression of genes related to nucleotide metabolism are schematically presented. The 3 bars from left to right represent the fold changes of the gene expressions in response to the 3 time points (5, 20, and 170 min). The red bars represent an upregulation; 
the green bars, a downregulation; and the gray bars, the messages that did not significantly change relative to our cutoff (3-fold increase in expression). doi:10.1371/journal.pone.0050003.gFigure 2, KinB-Spo0F did not affect YdjPQ and YuaFGI directly, but KapB may function as an intermediate purchase JW-74 between them. The transm.Acid derivatives transport 20.01.17 nucleotide/nucleoside/nucleobase transport 20.01.27 drug/toxin transport 20.03 transport facilities 20.03.02 carrier (electrochemical potential-driven transport) 20.03.02.02 symporter 20.03.02.02.01 proton driven symporter 20.03.02.02.02 sodium driven symporter 20.09 transport routes 20.09.18 cellular import 32 CELL RESCUE, DEFENSE, AND VIRULENCE 32.01 stress response 32.01.01 oxidative stress response 32.07 detoxification 32.07.05 detoxification by export 32.07.07 oxygen and radical detoxification 32.07.07.01 catalase reaction 34 INTERACTION WITH 25033180 THE ENVIRONMENT 34.01 homeostasis 34.01.01 homeostasis of cations 70.30 prokaryotic cytoplasmic membrane doi:10.1371/journal.pone.0050003.tP VALUE 7.69E-03 5.21E-03 1.94E-02 1.94E-02 3.01E-03 1.52E-03 1.34E-07 2.98E-02 7.69E-03 9.41E-04 1.19E-05 4.51E-03 1.22E-03 1.62E-02 2.73E-02 2.77E-02 1.97E-02 1.98E-02 7.36E-04 5.60E-04 7.85E-03 1.63E-02 3.51E-04 7.13E-04 6.00E-04 7.49E-06 4.62E-03 8.33E-04 1.55E-02 1.61E-04 1.72E-02 4.61E-02 1.12E-03 3.22E-04 1.40E-using 2 independent assays (BacLight assay and transcriptome profiling) and various antibiotic concentrations (0.6 to 46 MIC) at which the MoA of fusaricidin is likely to involve membrane damage. The function of differentially expressed genes could be divided into 2 categories: one is involved in the function of cell membrane (yceD, ymcC, yuaFG, ythP, and yojB), and the other is mainly related to detoxification, multidrug resistance, and cell protection (yceE, ydjP, and yeaA). yceD is involved in biofilm formation and was overexpressed by 3-fold after fusaricidin treatment, suggesting that accelerated biofilm formation may contribute to the resistance to toxins [14]. In Escherichia coli, the methionine sulfoxide reductase YeaA has an important function in protecting cells from oxidative damage [15]. It acts on free methionine sulfoxide (MetSO) and proteins that contain MetSOresidues. Phenotypic analysis of an E. coli strain lacking a functional copy of msrB revealed its importance in cadmium resistance. Cadmium is a potential carcinogen and damages cells in several ways, including via the catalysis of AOS production [16]. YmcC is considered to be a lipoprotein and may therefore contribute to the membrane protection [17]. Most of the genes that were altered 5 min after the fusaricidin addition are involved in detoxification. The relationship among these rapid-response genes was determined using string analysis and is shown in Figure 2. ybdK-ybdJ, kinA-spo0F, kinB-spo0F, and kinC were closely correlated with the rapidresponse phase. kinA-spo0F and kinB-spo0F are functionally important for bacterial spore formation. KinC is suggested to regulate gene expression during the stable phase, whereas the function of YbdK-YbdJ is currently unknown. As shown inMechanisms of Fusaricidins to Bacillus subtilisFigure 5. Changes in nucleotide metabolism. The expression of genes related to nucleotide metabolism are schematically presented. The 3 bars from left to right represent the fold changes of the gene expressions in response to the 3 time points (5, 20, and 170 min). The red bars represent an upregulation; the green bars, a downregulation; and the gray bars, the messages that did not significantly change relative to our cutoff (3-fold increase in expression). doi:10.1371/journal.pone.0050003.gFigure 2, KinB-Spo0F did not affect YdjPQ and YuaFGI directly, but KapB may function as an intermediate between them. The transm.