This hypothesis. According to the research of Ludwig [19] and Rezacova [20], CggR appears to respond synergistically to 2 different signals, one being the catabolic signal derived from the presence of sugars and the other being an anabolic signal derived from amino acid metabolism. The presence of the individual signals results in partial derepression of the gapA operon, whereas full induction occurs only if both signals are present. When glucose is absent from the growth medium, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of fructose-1,6-bisphosphate abolishes this interaction, consistent with our previous observations [9]. Increased CggR activity leads to amino acid degradation, which leads to a reduction in the activity of gapA, pgk, tpiA, and eno. Therefore, we suggest that derepression of gluconeogenesis is a mechanism by which additional energy can be UKI-1 chemical information provided to mount a response to fusaricidin. The MIPS analysis revealed significant changes in the genes involved in nucleotide metabolism (Table 1). The genes involved in the nucleotide metabolism pathway are shown in Figure 5, and the PD168393 result of the pathway analysis indicates that the synthesis of purines and pyrimidines is repressed at an early stage. Nucleotide precursor degradation was increased by the fusaricidin treatment, indicating that the antibiotic likely reduced the availability of nucleic acid-related substances in B. subtilis. Transcriptional factors play a central role in the restructuring of the transcriptome in response to environmental signals. The microarray data were subsequently analyzed using the T-profiler to identify the transcriptional factors that mediated the response to fusaricidin. The T-profiler is a computational tool that uses the t test to score changes in the average activity of predefined groups of genes based on the Gene Ontology categorization, upstream matches to a consensus transcription factor-binding motif, or the KEGG pathway [9]. In this study, the gene groups with significant t values (E = 0.05, TF model) are also presented in Table 2. Nine coregulated gene groups were found to be significantly perturbed by fusaricidin after 5 min, including SigW-, CcpA-, SigK-, SigE-, AbrB-, GerE-, FNR-, and SigB-regulated gene groups. As mentioned earlier, SigW probably activates a large stationaryphase regulon that functions in detoxification, production of antimicrobial compounds, or both. SigE and SigK regulate early and late mother cell-specific gene expression, respectively. AbrB 1407003 is the regulon of transition state genes (negative regulation of abrB, aprE, ftsAZ, kinC, motAB, nprE, pbpE, rbs, spoOH, spoVG, tycA, sbo-alb, and yqxM-sipW-tasA, and positive regulation of comK and hpr). Eleven and 13 gene groups were significantly modulated after 20 and 170 min of treatment, respectively. The results showed a strong activation of genes in the SigB regulon after the fusaricidin treatment. SigB is a general stress-response regulator that controls at least 150 genes. Members of the SigB regulon are transientlyMechanisms of Fusaricidins to Bacillus subtilisFigure 6. The transport of cations. 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 t.This hypothesis. According to the research of Ludwig [19] and Rezacova [20], CggR appears to respond synergistically to 2 different signals, one being the catabolic signal derived from the presence of sugars and the other being an anabolic signal derived from amino acid metabolism. The presence of the individual signals results in partial derepression of the gapA operon, whereas full induction occurs only if both signals are present. When glucose is absent from the growth medium, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of fructose-1,6-bisphosphate abolishes this interaction, consistent with our previous observations [9]. Increased CggR activity leads to amino acid degradation, which leads to a reduction in the activity of gapA, pgk, tpiA, and eno. Therefore, we suggest that derepression of gluconeogenesis is a mechanism by which additional energy can be provided to mount a response to fusaricidin. The MIPS analysis revealed significant changes in the genes involved in nucleotide metabolism (Table 1). The genes involved in the nucleotide metabolism pathway are shown in Figure 5, and the result of the pathway analysis indicates that the synthesis of purines and pyrimidines is repressed at an early stage. Nucleotide precursor degradation was increased by the fusaricidin treatment, indicating that the antibiotic likely reduced the availability of nucleic acid-related substances in B. subtilis. Transcriptional factors play a central role in the restructuring of the transcriptome in response to environmental signals. The microarray data were subsequently analyzed using the T-profiler to identify the transcriptional factors that mediated the response to fusaricidin. The T-profiler is a computational tool that uses the t test to score changes in the average activity of predefined groups of genes based on the Gene Ontology categorization, upstream matches to a consensus transcription factor-binding motif, or the KEGG pathway [9]. In this study, the gene groups with significant t values (E = 0.05, TF model) are also presented in Table 2. Nine coregulated gene groups were found to be significantly perturbed by fusaricidin after 5 min, including SigW-, CcpA-, SigK-, SigE-, AbrB-, GerE-, FNR-, and SigB-regulated gene groups. As mentioned earlier, SigW probably activates a large stationaryphase regulon that functions in detoxification, production of antimicrobial compounds, or both. SigE and SigK regulate early and late mother cell-specific gene expression, respectively. AbrB 1407003 is the regulon of transition state genes (negative regulation of abrB, aprE, ftsAZ, kinC, motAB, nprE, pbpE, rbs, spoOH, spoVG, tycA, sbo-alb, and yqxM-sipW-tasA, and positive regulation of comK and hpr). Eleven and 13 gene groups were significantly modulated after 20 and 170 min of treatment, respectively. The results showed a strong activation of genes in the SigB regulon after the fusaricidin treatment. SigB is a general stress-response regulator that controls at least 150 genes. Members of the SigB regulon are transientlyMechanisms of Fusaricidins to Bacillus subtilisFigure 6. The transport of cations. 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 t.
