SummaryIn response to sublethal concentrations of antibiotics, bacteria often induce an adaptive response that can contribute to antibiotic resistance. We report the response of Bacillus subtilis to bacitracin, an inhibitor of cell wall biosynthesis found in its natural envi-

The quorum sensing disrupter (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone (furanone) of the alga Delisea pulchra was previously found by us (Environ Microbiol 3:731-736, 2001) to inhibit quorum sensing in Escherichia coli via autoinducer-2 (AI-2, produced by LuxS). In this study, DNA microarrays were used to study the genetic basis of this natural furanone inhibition of AI-2 signaling (significant values with p < 0.05 are reported). Using DNA microarrays, the AI-2 mutant Escherichia coli DH5alpha was compared with the AI-2 wild-type strain, E. coli K12, to determine how AI-2 influenced gene expression. Escherichia coli K12 was also grown with 0 and 60 microg/mL furanone to study the inhibition of quorum sensing gene expression. It was found that 166 genes were differentially expressed by AI-2 (67 were induced and 99 were repressed) and 90 genes were differentially expressed by furanone (34 were induced and 56 were repressed). Importantly, 79% (44 out of 56) of the genes repressed by furanone were induced by AI-2, which indicated that furanone inhibited AI-2 signaling and influenced the same suite of genes as a regulon. Most of these genes have functions of chemotaxis, motility, and flagellar synthesis. Interestingly, the aerotaxis genes aer and tsr were discovered to be induced by AI-2 and repressed by furanone. Representative microarray results were confirmed by RNA dot blotting. Furthermore, the E. coli air-liquid interface biofilm formation was repressed by furanone, supporting the results that taxis and flagellar genes were repressed by furanone. The autoinducer bioassay indicated that 100 microg/mL furanone decreased the extracellular concentration of AI-2 2-fold, yet luxS and pfs transcription were not significantly altered. Hence, furanone appeared to alter AI-2 signaling post-transcriptionally.

Bacillus subtilis can grow under anaerobic conditions, either with nitrate or nitrite as the electron acceptor or by fermentation. A DNA microarray containing 4,020 genes from this organism was constructed to explore anaerobic gene expression patterns on a genomic scale. When mRNA levels of aerobic and anaerobic cultures during exponential growth were compared, several hundred genes were observed to be induced or repressed under anaerobic conditions. These genes are involved in a variety of cell functions, including carbon metabolism, electron transport, iron uptake, antibiotic production, and stress response. Among the highly induced genes are not only those responsible for nitrate respiration and fermentation but also those of unknown function. Certain groups of genes were specifically regulated during anaerobic growth on nitrite, while others were primarily affected during fermentative growth, indicating a complex regulatory circuitry of anaerobic metabolism.In recent years, Bacillus subtilis has been shown to be a facultative bacterium capable of growing with nitrate or nitrite as the electron acceptor or growing by fermentation in the absence of oxygen (22). The process of dissimilatory reduction of nitrate to ammonia is carried out by two enzymes, the membrane-bound nitrate reductase and the NADH-dependent nitrite reductase (8,9,19). The nitrate reductase is encoded by the narGHJI operon, which is controlled by FNR, an anaerobic regulator (12). The nitrite reductase is encoded by the nasDEF operon, which is not controlled by FNR, since no effect on anaerobic growth on nitrite has been observed in fnr mutant strains. Both fnr and nasDEF regions are regulated by the two-component signal transduction system ResDE, which also controls the expression of the resABC, qcrABC, and cta regions (16,23,28). Furthermore, the ResDE Ϫ mutant requires six-carbon sugars for normal growth. These results indicate that ResDE plays a global role in both aerobic and anaerobic respiration.In the absence of nitrate and nitrite, B. subtilis grows poorly on glucose under anaerobic conditions (18). Efficient fermentative growth can be obtained if pyruvate is provided. Lactates, acetate, and ethanol are found to be the end products of fermentation. Fermentative growth requires the ftsH gene but does not require the FNR gene. In addition, resD and resDE mutations have a moderate effect on fermentative growth. These results suggest that nitrate respiration and fermentation are governed by divergent regulatory pathways (18).Recent advances in functional genomic technologies such as DNA microarray construction provide a unique way to explore the metabolic and genetic control of gene expression on a genomic scale (6). The fact that the complete sequence of B. subtilis is available (14) makes it feasible to apply these functional genomic technologies. To investigate the global changes in gene expression associated with anaerobiosis in B. subtilis, we constructed DNA microarrays containing 4,020 open reading frames (ORFs). These microarrays...

SummaryMetal ion homeostasis is regulated principally by metalloregulatory proteins that control metal ion uptake, storage and efflux genes. We have used transcriptional profiling to survey Bacillus subtilis for genes that are rapidly induced by exposure to high levels of

The Bacillus subtilis zinc uptake repressor (Zur) regulates genes involved in zinc uptake. We have used DNA microarrays to identify genes that are derepressed in a zur mutant. In addition to members of the two previously identified Zur-regulated operons (yciC and ycdHI-yceA), we identified two other genes, yciA and yciB, as targets of Zur regulation. Electrophoretic mobility shift experiments demonstrated that all three operons are direct targets of Zur regulation. Zur binds to an ϳ28-bp operator upstream of the yciA gene, as judged by DNase I footprinting, and similar operator sites are found preceding each of the previously described target operons, yciC and ycdHI-yceA. Analysis of a yciA-lacZ fusion indicates that this operon is induced under zinc starvation conditions and derepressed in the zur mutant. Phenotypic analyses suggest that the YciA, YciB, and YciC proteins may function as part of the same Zn(II) transport pathway. Mutation of yciA or yciC, singly or in combination, had little effect on growth of the wild-type strain but significantly impaired the growth of the ycdH mutant under conditions of zinc limitation. Since the YciA, YciB, and YciC proteins are not obviously related to any known transporter family, they may define a new class of metal ion uptake system. Mutant strains lacking all three identified zinc uptake systems (yciABC, ycdHI-yceA, and zosA) are dependent on micromolar levels of added zinc for optimal growth.

We examined the effects of nitric oxide (NO) and sodium nitroprusside (SNP) on Bacillus subtilis physiology and gene expression. In aerobically growing cultures, cell death was most pronounced when NO gas was added incrementally rather than as a single bolus, suggesting that the length of exposure was important in determining cell survival. DNA microarrays, Northern hybridizations, and RNA slot blot analyses were employed to characterize the global transcriptional response of B. subtilis to NO and SNP. Under both aerobic and anaerobic conditions the gene most highly induced by NO was hmp, a flavohemoglobin known to protect bacteria from NO stress. Nitric oxide (NO) is a lipophilic, freely diffusible radical that can inhibit enzymes, damage DNA, initiate lipid peroxidation, and exacerbate peroxide-induced damage (49,53,66). NO chemistry can be divided into those reactions that occur between NO and biomolecules (direct effects) and those reactions that can only occur subsequent to NO reacting with oxygen or superoxide to form reactive nitrogen oxide species (RNOS) (indirect effects). Direct effects of NO include the formation of metal-nitrosyl complexes (63) and reactions with lipid-derived (50) and other high-energy radicals (34). For example, NO coordinates free or enzyme-bound Fe(II) to form Fe-NO as described for cytochrome P450 (36, 43, 64). Fe nitrosylation leads to altered activity of at least two bacterial metalloregulatory proteins: Fur and Fnr (13,14). Indirect effects occur after NO reacts with either oxygen to generate N 2 O 3 or superoxide to generate the highly reactive oxidant peroxynitrite (OONO Ϫ ). Peroxynitrite rapidly decomposes to form nitrate (NO 3 Ϫ ), hydroxyl radical ( ⅐ OH), and nitrogen dioxide radical ( ⅐ NO 2 ). Some RNOS have the propensity to react with thiol groups and amines to form S-nitrosothiols and nitrosamines.Bacteria encounter NO from a variety of sources. Macrophages of the mammalian immune system generate NO with an inducible NO synthase as part of their arsenal employed against microbial pathogens (38,57). NO synthases have also been identified in some bacteria, including Bacillus subtilis (1, 2), although their function in many cases remains elusive.Denitrifying bacteria produce NO as an intermediate in the reduction pathway from nitrate to dinitrogen (33). B. subtilis is not capable of denitrification, yet it coexists with denitrifying bacteria in subsurface environments. It is therefore likely that B. subtilis has developed a targeted response to exogenously and perhaps endogenously produced NO.Several bacterial enzymes can alleviate NO stress. The Escherichia coli flavohemoglobin Hmp has NO reductase activity under anaerobic conditions (31) and NO dioxygenase (22) or denitrosylase activity (25) under aerobic conditions; however, only the aerobic Hmp activities appear to confer NO stress resistance (20). In addition, both E. coli and Salmonella enterica hmp mutants are hypersensitive to NO (41,56,57). Nakano showed that B. subtilis hmp is regulated by ResDE, a two-comp...

SummaryWe have used DNA microarrays to monitor the global transcriptional response of Bacillus subtilis to changes in manganese availability. Mn(II) leads to the MntR-dependent repression of both the mntH and mntABCD operons encoding Mn(II) uptake systems.

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