The redox status of the cytoplasm is under physiological conditions in a reduced state. Thus, most cysteines are present as free thiols (
6). Because aerobic organisms have to cope with oxidative stress caused by ROS, such as superoxide anions, hydrogen peroxide, or hydroxyl radicals, they need to employ effective mechanisms that maintain the reduced state. In gram-negative bacteria, the thiol-disulfide balance is accomplished by the glutathione (GSH) system, a thiol-based redox buffer. The GSH system consists of glutaredoxin (Grx), GSH (γ-glutamylcysteinyl glycine), GSH reductase, and GSH peroxidase (
34). Reduction of disulfides occurs via sequential electron transfer from glutaredoxin and reduced GSH; oxidized GSH (GSSG) is reduced by the NADPH-dependent GSH reductase. GSH peroxidase enables the direct detoxification of ROS by GSH oxidation.
Besides ROS and reactive nitrogen species, so-called “reactive electrophilic species” (RES) affect the thiol redox balance. RES include different chemical compounds such as aldehydes, quinones, and the azo compound diamide (
2,
43,
45,
46,
53,
66). Quinones and aldehydes have electron-deficient centers that result in thiol-(S) alkylation of cysteine. Exposure of cells to diamide induces the oxidative as well as the electrophile stress response in
B. subtilis (
43,
45,
53). The toxicity of diamide is based on disulfide bond formation (
40), which was recently visualized in
B. subtilis and
S. aureus by the fluorescence alkylation of oxidized thiols (FALKO) assay (
32,
64). It was thought that the formation of nonnative inter- and intramolecular disulfide bonds results in damage of proteins.
Cysteine, BSH, and CoA are also dominant LMW thiols in
S. aureus (
52). In this study, we have investigated in more detail the extents of S thiolations and inter- and intramolecular disulfide bond formation of
B. subtilis and
S. aureus in response to disulfide stress. The results showed that exposure to diamide leads to S thiolations in
S. aureus. Using a nonreducing/reducing sodium dodecyl sulfate (SDS) diagonal electrophoresis approach, proteins with intermolecular disulfide bonds could be distinguished from proteins with intramolecular disulfide bonds (
57). The results support that the majority of reversible thiol oxidations are based on S thiolations rather than disulfide bonds between proteins. Depletion of the free cysteine pool in
B. subtilis after exposure to diamide supports this finding. To assess if GSH may have a bearing on the thiol redox buffer of
B. subtilis, the
gshF gene of
Listeria monocytogenes (
gshFLm ) was expressed in
B. subtilis, enabling GSH biosynthesis (
29). Although GSH production does not enhance the resistance to oxidative stress in
B. subtilis, it participates in the formation of S thiolations.
MATERIALS AND METHODS
Bacterial strains and growth conditions.
The bacterial strains used were
B. subtilis 168 (
trpC2) (
1) and a
B. subtilis strain expressing
gshFLm (
trpC2 amyE::
lacI gshF Spec
r). All
B. subtilis strains were cultivated in a synthetic medium (
60) at 37°C under vigorous agitation.
S. aureus UAMS-1 (
28) was cultivated in a synthetic medium described earlier (
26). However, MOPS (morpholinepropanesulfonic acid) and glycine were omitted and all amino acids were at 1 mM. If needed, cysteine was substituted by 1 mM Na
2S
2O
3. Spectinomycin was used for
B. subtilis gshFLm at 100 μg/ml. GSH production in the
B. subtilis gshFLm strain was induced with 40 μM IPTG (isopropyl-β-
d-thiogalactopyranoside) at an optical density at 500 nm (OD
500) of 0.2. All strains were grown to the exponential growth phase (OD
500 of 0.5) and exposed to 1 mM (
B. subtilis) or 2 mM (
S. aureus) diamide. The
B. subtilis gshFLm strain was exposed to 50 μM Paraquat and 100 μM H
2O
2. Controls were taken at an OD
500 of 0.5.
Growth curves, survival tests, and DCW.
Growth curves were performed by measuring OD500 at different time points. For survival tests, samples from bacterial cultivations were diluted and 100 μl was plated onto LB agar plates. The plates were incubated over night at 37°C, colonies were counted, and subsequently the weighted arithmetic mean was determined. For calculations of the dry cell weight (DCW), 20 ml of B. subtilis cells was collected by centrifugation at different time points as replicates. At these time points, the OD500 was measured with different dilutions of the culture. The cells were washed twice with distilled water and transferred to a constant-preweight glass vial. The glass vial was dried in an oven (60°C) to constant weight. The OD500 was plotted against the net weight of the glass vials. The analysis of the regression resulted in the following relationship: DCW (mg/ml culture) = 0.2107 × OD500 + 0.0043, with R 2 = 0.995.
Construction of the B. subtilis gshFLm strain.
A 2.43-kb fragment of Listeria monocytogenes EGD-e DNA, containing the gshF gene (lmo2770) including its putative ribosomal binding site, was amplified by PCR employing a forward SphI primer, 5′-TATA GCATGC TTATTTAAAACCCCTGAGGTG-3′, and a reverse SphI primer, 5′-ATAT GCATGC AAATGGTGAAATTGGATTG-3′. The underlined letters show the SphI restriction site. The purified fragment digested with SphI was sequenced to verify identity to the deposited sequence and cloned into SphI sites of the integration vector pDR79 (amyE::PspaC-spc; a gift from Sigal Ben-Yehuda, The Hebrew University, Jerusalem, Israel). The resulting construct, containing a proper PspaC-gshF fusion, was designated pDR79-gshF. A linearized pDR79-gshF DNA was transformed into competent B. subtilis 168 cells and integrated into the amyE gene. Transformants were selected for spectinomycin resistance (100 μg/ml) and designated the B. subtilis gshFLm strain, which contained a disrupted amyE gene with an intact GSH synthase gene fused to the IPTG-inducible PspaC promoter.
HPLC analysis of LMW thiols from B. subtilis.
Cells were cultured as described above. Two milliliters of culture was centrifuged for 1 min and washed with 50 mM Tris-HCl (pH 8.0). The pellet was resuspended in 50 μl extraction buffer (50% [vol/vol] acetonitrile [ACN] in 20 mM Tris-HCl, pH 8.0) containing 2 mM monobromobimane (mBBr; Molecular Probes). As an internal standard, 1 μM penicillamine was added to each sample. The suspension was incubated for 15 min at 60°C in the dark. Control samples were incubated for 10 min with 5 mM
N-ethylmaleimide (NEM; Sigma-Aldrich) under the same conditions before the addition of mBBr (2 mM). The cellular debris was removed by centrifugation, and the reaction was stopped by addition of 5 mM aqueous methane sulfonic acid. Thiol standards were prepared as described previously (
21).
A derivatized sample was separated by high-performance liquid chromatography (HPLC) (
51), and peak recognition was performed with a fluorescence detector (Shimadzu RF-10AXL). Briefly, the CoA method was used, which constituted a tetrabutylammonium phosphate (TBAP; Sigma-Aldrich) ion-pairing protocol designed for the separation of CoA-bimane derivatives (
51). A C
8 RP column (AccQ-Tag, 3.0 μm, 150 mm; Waters) at a flow rate of 0.8 ml min
−1 was used in a column oven at 25°C. The chromatographic protocol employed the following solvents and gradients: solvent A, 10% (vol/vol) methanol, 0.25% (vol/vol) acetic acid, and 10 mM TBAP, pH 3.4; solvent B, 90% (vol/vol) methanol, 0.25% (vol/vol) acetic acid, and 10 mM TBAP. At time zero, 0% solvent B was used, followed by 30 min with 40% solvent B, 40 min with 75% solvent B, and 50 min with 100% solvent B.
Analysis of total LMW and protein thiol amounts (DTNB method).
Cells were grown and treated with diamide as described above. To determine the amounts of LMW thiols, 50 ml of the culture was centrifuged and the pellet was resuspended in 600 μl extraction buffer. The suspension was incubated for 10 min at 60°C, and subsequently the cell debris was removed by centrifugation. Five hundred microliters of supernatant was mixed with 10 μl 100 mM 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) in dimethyl sulfoxide. The pellet was again incubated with 600 μl extraction buffer, as described above, and 500 μl was added to the same tube used before. The A 412 was measured, and the LMW thiol content was calculated.
To determine the amount of protein thiols, the pellet harvested from 50 ml of culture was resuspended in 1,000 μl denaturing buffer, consisting of 8 M urea, 1% CHAPS {3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate}, 1 mM EDTA, 200 mM Tris-HCl (pH 8.0), and 10 μl of 100 mM DTNB was added directly. The suspension was incubated for 15 min and centrifuged. The supernatant was diluted, A 412 was measured, and the protein thiol content was calculated.
Determination of the GSH/GSSG-ratio in the B. subtilis gshFLm strain.
Cells were cultured and treated with diamide as described above. Forty milliliters of the culture was centrifuged, and the pellet was resuspended in 400 μl extraction buffer. For GSSG determination, the buffer contained 3% scavenger reagent (GSH/GSSG assay kit from Oxford Biomedical Research). The suspension was incubated for 15 min at 60°C, and subsequently the cell debris was removed by centrifugation. Different dilutions were used for the assay according to the manufacturer's instructions.
Protein isolation and alkylation of thiol groups.
Cells were harvested by centrifugation at 10,000 × g for 10 min at 4°C. The pellet was resuspended in denaturing buffer containing 100 mM iodoacetamide (IAM). Cells were disrupted by sonication, and the lysate was incubated in the dark for 20 min to allow alkylation of thiol groups. Proteins were precipitated in a fourfold volume of pure acetone. The resulting pellet was washed twice with acetone, dried in a SpeedVac, and resuspended in denaturing buffer without IAM.
FALKO assay.
The two-dimensional (2D) gel-based FALKO assay was performed as described by Hochgräfe et al. (
32). Proteins were isolated with alkylated thiol groups as described above. The protein concentration was measured according to Bradford et al. (
9), and equal protein amounts of stressed and control samples were used. All reversible thiol modifications (disulfide bonds and mixed disulfides) were reduced with Tris-(2-carboxyethyl-)-phosphine (TCEP; Molecular Probes) and subsequently labeled with the fluorescence dye BODIPY FL C
1-IA [
N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-
s-indacene-3-yl)-methyl)-iodoacetamide; Molecular Probes] as described previously (
32). The labeling reaction was stopped by centrifugation through a Bio-Rad Micro Bio-Spin 6 column. 2D polyacrylamide gel electrophoresis (PAGE), gel imaging, data analysis, and protein identification were performed as described elsewhere (
32).
Diagonal nonreducing/reducing SDS gel electrophoresis.
Proteins were isolated with alkylated thiol groups as described above. The concentration of protein was measured according to Bradford et al. (
9), and equal protein amounts of all samples were applied. Samples were separated by SDS-PAGE under nonreducing conditions. The lanes of the SDS gel were cut and incubated in sample buffer (2% SDS, 62.5 mM Tris-HCl, pH 8.0) containing 50 mM dithiothreitol to reduce disulfide bonds. Subsequently, the lanes were incubated in sample buffer containing 100 mM IAM or 100 μM BODIPY FL C
1-IA, respectively. Each lane of the SDS gel was positioned vertically and separated again by SDS-PAGE. The resulting diagonal SDS gels were stained with SYPRO Ruby and scanned. Subsequently, proteins were stained with Coomassie brilliant blue as described previously (
20) and scanned. Proteins that did not migrate on the diagonal were identified as described previously (
20). For control purposes, SDS lanes were separated under reducing conditions in the first and second dimensions. Proteins that did not comigrate with the diagonal were omitted from further studies.
[35S]cysteine monitoring of S thiolations.
The monitoring of S thiolations by [
35S]cysteine was performed as described previously (
33). In brief, protein synthesis was inhibited by addition of chloramphenicol for 30 min (
B. subtilis gshFLm strain) and fusidic acid for 60 min (
S. aureus). The culture was supplemented with [
35S]cysteine for 30 min, and subsequently cells were treated with diamide for 30 min or harvested as control samples. The proteins were isolated as described above. Equal protein amounts of all samples were applied to filter disks, and the radioactivity was measured in a scintillation counter. Aliquots of protein samples were reduced with TCEP prior to filter disk application to prove reducible S thiolations.
Analyses of intracellular metabolites by GC-MS and LC-MS.
Analyses of intracellular metabolites by gas chromatography-mass spectrometry (GC-MS) were performed as described by Liebeke et al. (
46). Briefly, samples were harvested by fast filtration, and subsequently the metabolism was quenched with an ethanol solution and liquid nitrogen. After cell disruption and metabolite extraction, samples were analyzed by GC-MS. Samples to detect possible disulfides and NADP(H) as well as ppGpp were analyzed by liquid chromatography (LC)-MS as described before (
4,
18). An aminopropyl column (Phenomenex Luna NH
2, 250 mm by 2 mm, 5 μm) was used with solvent A (20 mM ammonium acetate, 20 mM ammonium hydroxide, 5% [vol/vol] ACN in water; pH 9.45) and solvent B (pure ACN). The flow rate was 0.2 ml·min
−1, with the following gradient:
t = 0 min, 85% solvent B;
t = 15 min, 0% solvent B;
t = 38 min, 0% solvent B;
t = 40 min, 85% solvent B; and
t = 50 min, 85% solvent B. The mass spectrometer was adjusted as described by Donat et al. (
18).
GeLC-MS analysis.
Gel electrophoresis LC-MS (GeLC-MS) was carried out as described by Hochgräfe et al. (
33). In brief, protein extracts of cells, stressed with diamide for 30 min, were isolated as described above. However, protein precipitation by acetone was omitted. The protein extracts were separated by nonreducing, one-dimensional SDS-PAGE. Gel lanes were sliced and each slice was digested with trypsin. The resulting peptide mixtures were separated by reversed-phase HPLC directly coupled to an LTQ Orbitrap mass spectrometer for subsequent tandem-MS (MS/MS) analysis. Extracts of
B. subtilis ghsFLm cells were searched against database of
B. subtilis 168 extracted from SubtiList (
http://genolist.pasteur.fr/SubtiList ). Extracts of
S. aureus UAMS-1 cells were searched against a fusion protein database of all accessible
S. aureus strains, including phage proteins and plasmid-encoded proteins.
DISCUSSION
Lithgow et al. showed that inactivation of the cysteine synthase CysM in
S. aureus SH1000 results in decreased resistance against oxidative stress (
48). Furthermore, they detected a depleted cysteine pool in the
cysM-lacking mutant. The diminished oxidative stress resistance is probably linked to this depletion. Here we provide evidence that cysteine participates in the formation of S thiolations in
S. aureus, as revealed by the [
35S]cysteine assay and the GeLC-MS approach. Thus, it is likely that cysteine functions as thiol redox buffer in
S. aureus and
B. subtilis. BSH, another abundant cysteine-derived thiol in both organisms, is most likely also a key player in this buffer (
52). CoA may also contribute to this buffer, which is an abundant thiol in
S. aureus (
49). Moreover,
S. aureus possesses a CoA-disulfide reductase which strengthens a possible role of CoA as thiol redox-buffer (
14,
15).
Using the diagonal gel electrophoresis, we confirmed that redox-active enzymes, such as AhpC and Tpx, form disulfide bonds during their catalytic cycle. AhpC forms homomeric or heteromeric intermolecular disulfide bonds with its redox partner protein, AhpF (
38). In contrast, the thiol-dependent peroxidade Tpx forms intramolecular disulfide bonds (
5).
NrdE, a subunit of the class Ib ribonucleotide reductase, seems to undergo increased intermolecular disulfide bond formation with a redoxin in response to diamide (
22,
31). FabF, the β-ketoacyl carrier protein synthase II, forms an intermolecular disulfide bond under disulfide stress. FabF in
Streptococcus pneumoniae possesses an active-site thiolate and occurs in
E. coli as a homodimer (
25,
36). These observations suggest that active-site cysteines of FabF lead to intermolecular, homodimeric disulfide bond formation under diamide stress due to their sterical proximity. FabHB, the β-ketoacyl carrier protein synthase III, catalyzes the same reactions as FabF (
63) and is induced in diamide-treated
B. subtilis cells (
45). These findings suggest a reduced activity of FabF which could be compensated for by FabHB induction.
In general, the diagonal gel electrophoresis approach of diamide-treated
B. subtilis and
S. aureus cells supports the idea that the majority of disulfide bonds (
32,
64) are mixed disulfides of protein thiols with LMW thiols rather than inter- and intramolecular disulfide bonds. However, we have to consider that some cysteine-containing proteins may be below the detection level of this assay or could have cysteine residues that are not solvent exposed and not accessible for thiol modifications.
The metabolome data revealed depletion of cysteine after exposure to diamide. Under these thiol-specific stress conditions, cysteine biosynthesis is induced by the derepression of the CymR regulon (
19,
45). We found an increase of
O-acetylserine, which leads to dissociation of the CymR-CysK complex and derepression of the CymR regulon (
61). The concentration of serine, the precursor of
O-acetylserine, did not change significantly. However, the concentration of glycine, which is a precursor of serine, is reduced under disulfide stress and the synthesis of the glycyl-tRNA synthetase is also decreased (
45). These results might indicate a fortified provision of glycine for serine synthesis.
The CymR-controlled MccA (YrhA) and MccB (YrhB) proteins participate in the conversion of methionine to cysteine and are induced under disulfide stress (
37,
45). MetE, the cobalamin-independent methionine synthase, is S cysteinylated under diamide stress and less active in the S-thiolated state in
E. coli (
33,
35). We observed that the methionine pool was fourfold decreased in diamide-treated cells. These findings indicate an increased conversion of methionine to cysteine and simultaneously a decreased synthesis of methionine.
Free transition metals such as iron, copper, and zinc can be coordinated by cysteine (
50). Disulfide bond formation in Zn-binding proteins such as RsrA and Hsp33 releases Zn (
44,
54). However, it seems unlikely that diamide leads to depletion of cysteine caused by complexation of released metal ions. We suggest that the cysteine pool is drastically depleted due to formation of S thiolation based on cysteine or related compounds. Thus, cysteine biosynthesis is induced from different precursors after exposure to diamide in
B. subtilis.
After exposure to diamide, the cellular amount of LMW thiols decreased from 5.42 to 1.33 μmol/g DCW (4.09 μmol/g DCW = 75%) and that of protein thiols decreased from 12.89 to 5.26 μmol/g DCW (7.63 μmol/g DCW = 60%). Using GC or LC-MS analyses, no LMW disulfides were detected. It has to be considered that formation of an intra- and intermolecular disulfide bond needs two protein thiols. Taken together, this allows an approximation that about 70% diamide-provoked disulfide bonds consist of S thiolations (see Fig. S6 in the supplemental material). Hansen et al. exposed eukaryotic HEK and HeLa cells to diamide and detected a 300-fold increase in S glutathionylations in these cells, thereby using a third of the GSH pool (
30). Concomitantly, oxidation to GSSG increased fivefold, using 50% of the GSH pool. These results show that a large fraction of LMW thiols is used for S thiolations under disulfide stress.
Furthermore, we detected under disulfide stress an increase in the concentration of threonine, whereas the concentrations of the threonine-derived amino acids, leucine, isoleucine, and valine, were decreased. The ketol-acid reductoisomerase IlvC and the branched-chain amino acid aminotransferase YwaA are involved in the conversion of threonine to leucine, isoleucine, and valine. Both proteins undergo reversible thiol modifications after exposure to diamide (
32). It might be possible that diamide modifies the functionality of YwaA and IlvC and correspondingly affects synthesis of the branched-chain amino acids. IlvC uses NADPH in its reaction, and oxidoreductases use NADPH as well. Thus, the competition for NADPH could be responsible for the decrease of the branched-chain amino acids. However, analysis of NADP
+ and NADPH revealed no significant difference in the redox ratio (see Fig. S7 in the supplemental material). This indicates that the fortified use of NADPH by oxidoreductases does not affect the pool of NADPH and thereby the function of other NADPH-dependent enzymes, such as IlvC.
The depletion of different amino acids can activate the stringent response in
B. subtilis (
62). The alarmon of this adaptation process, ppGpp, was detected during diamide stress, but not during exponential growth. This confirms transcriptome data that diamide triggers the stringent response (
45).
Based on the above studies, we were interested whether in B. subtilis GSH could support cysteine in the maintenance of the thiol redox-buffer. To this end, we analyzed the global thiol oxidation state and S thiolations in a GSH-producing B. subtilis strain. Different approaches used for assaying reversible thiol oxidations failed to reveal any effect of GSH in cells subjected to disulfide stress. An S glutathionylation in YwaA was detected, but no S thiolations by other compounds were identified. This may be related to the increased GSH content in the GSH-producing strain, which leads to a drastic change in the ratio of GSH to other LMW thiols.
Fu et al. (
24) introduced GSH production into
Lactococcus lactis subsp.
cremoris NZ9000. They found that GSH production led to impaired growth due to increased cysteine utilization. Exposure to oxidants (H
2O
2 and the superoxide-generating agent menadione) did not affect the survival of exponentially growing cells with GSH compared to cells without GSH. However, during the transition phase, cells benefit from GSH production: the rate of survival was increased after exposure to oxidants. With the artificial introduction of GSH synthesis, the GSH system was complete in
L. lactis (
24), including GSH reductase, GSH peroxidase, glutaredoxin, and GSH. In contrast to
L. lactis,
B. subtilis lacks the GSH reductase and the GSH peroxidase, suggesting that GSH can be oxidized in
B. subtilis to GSSG but not rereduced to GSH. We cannot exclude that the thioredoxin system is capable of this redox-reaction in
B. subtilis.
In summary, different approaches were used to analyze the nature of reversible thiol oxidations in B. subtilis and S. aureus in response to diamide stress. S thiolation is the major mechanism used to protect cellular protein thiols in both bacteria after exposure to diamide. The decreased amount of the LMW thiol cysteine supports its major role as a thiol redox buffer. However, cysteine is also used for the BSH synthesis, and identified S cysteinylations may be degradation products of previous S bacillithiolations. Thus, future studies will be directed at identifying the precise thiol redox buffer which is used for S thiolations in B. subtilis and S. aureus.