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J. Biol. Chem., Vol. 281, Issue 28, 18909-18913, July 14, 2006
Detection of Sulfide Release from the Oxygen-sensing [4Fe-4S] Cluster of FNR* 1![]() ![]() 2
From the
Received for publication, February 22, 2006 , and in revised form, May 4, 2006.
The Escherichia coli FNR protein regulates the transcription of >100 genes in response to environmental O2, thereby coordinating the response to anoxia. Under O2-limiting conditions, FNR binds a [4Fe-4S]2+ cluster through four cysteine residues (Cys20, Cys23, Cys29, Cys122). The acquisition of the [4Fe-4S]2+ cluster converts FNR into the transcriptionally active dimeric form. Upon exposure to O2, the cluster converts to a [2Fe-2S]2+ form, generating FNR monomers that no longer bind DNA with high affinity. The mechanism of the cluster conversion reaction and the nature of the released iron and sulfur are of considerable current interest. Here, we report the application of a novel in vitro method, involving 5,5'-dithiobis-(2-nitrobenzoic acid), for determining the oxidation state of the sulfur atoms released during FNR cluster conversion following the addition of O2. Conversion of [4Fe-4S]2+ to [2Fe-2S]2+ clusters by O2 for both native and reconstituted FNR results in the release of 2 sulfide ions per [4Fe-4S]2+ cluster. This demonstrates that the reaction between O2 and the [4Fe-4S]2+ cluster does not require sulfide oxidation and hence must entail iron oxidation.
Escherichia coli is a facultative anaerobe that adopts different metabolic modes in a hierarchal manner in response to the availability of oxygen (13). This hierarchy reflects the amount of energy that can be harnessed in each metabolic mode and is maintained by transcriptional regulators that monitor either environmental oxygen or the cellular redox state (4). Aerobic respiration, a process that utilizes molecular oxygen (O2) as the terminal electron acceptor, is preferred over anaerobic respiration, which utilizes alternative electron acceptors such as nitrate because of the enormous energetic benefits conferred by aerobic respiration (3). Likewise, anaerobic respiration is preferred over fermentation for similar reasons (3). The global transcriptional regulator FNR (designated due to defects in the utilization of fumarate or nitrate during anaerobic growth in corresponding fnr mutants (5)) activates the expression of genes that encode components of alternative electron transport chains essential for anaerobic respiration (6, 7). Under anaerobic growth conditions, FNR also represses the expression of some genes associated with aerobic respiration (6, 8, 9). FNR shares sequence homology with the cyclic-AMP receptor protein (CRP)3 (10) and, like CRP, consists of two distinct domains that provide DNA binding and sensory functions (11). The C-terminal DNA-binding domain recognizes specific FNR binding sequences within FNR-controlled promoters. The N-terminal sensory domain contains five cysteine residues, four of which (Cys20, Cys23, Cys29, Cys122) are essential (12) and assumed to be capable of binding either a [4Fe-4S]2+ or a [2Fe-2S]2+ cluster (13, 14). A variety of studies have shown that FNR is specifically activated under anaerobic conditions by the acquisition of one [4Fe-4S]2+ cluster per monomer (1517). This promotes dimerization and enhances site specific DNA-binding to target promoters (18, 19). Exposure of the [4Fe-4S]2+ cluster to oxygen or air causes it to undergo a conversion into a [2Fe-2S]2+ cluster, both in vivo and in vitro, resulting in the loss of site specific DNA binding (13, 1922).
Recently we reported that the [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion proceeds through a [3Fe-4S]+ intermediate, leading to production of hydrogen peroxide presumably by a two electron reduction of oxygen and the release of two iron ions (17). The oxidation states of the released iron atoms have yet to be unequivocally established. An alternative [4Fe-4S]2+ to [2Fe-2S]2+ conversion mechanism was recently proposed by Sutton et al. (23). Using Ferene, a strong Fe2+ chelator, release of two Fe2+ ions per cluster was determined, leading to the suggestion that oxidation of released sulfide ions to S0, rather than cluster iron, was taking place. Here we report, using a novel analytical method, direct determination of the amount of cluster sulfide ions released upon in vitro conversion of [4Fe-4S] FNR into [2Fe-2S] FNR. The data demonstrate that cluster sulfur is ejected as sulfide ions and is not, therefore, oxidized upon cluster conversion. The implications of this for the mechanism of oxygen sensing by FNR [4Fe-4S]2+ clusters are discussed.
Purification of [4Fe-4S] FNRNative FNR protein was over-produced in aerobic cultures of JRG5369 (E. coli BL21 DE3 pGS1859). Plasmid pGS1859 was constructed by ligating the fnr gene from pGS199 (24) as a NcoI-BamHI fragment into the corresponding restriction sites within the expression vector pET11d (Stratagene). FNR overproduction was initiated by the addition of isopropyl -D-thiogalactopyranoside. Formation of [4Fe-4S] FNR was promoted, in vivo, by sparging cultures with oxygen-free nitrogen gas at 4 °C, essentially as described by Sutton and Kiley (25). All protein purification and handling was carried out under strictly anaerobic conditions in an anaerobic cabinet (Belle Technology), typically operating at 2.0 ppm O2 by volume, equipped with a specially designed fridge-freezer for anaerobic sample storage and fitted with a liquid nitrogen access port. All buffers were sparged with oxygen-free nitrogen gas for a minimum of 2 h. The purity of isolated FNR was assessed by SDS-PAGE. Full details of the growth conditions and purification of FNR will be published elsewhere.
Purification of Reconstituted [4Fe-4S] FNRGlutathione S-transferase-FNR fusion protein was produced in aerobically grown E. coli BL21
Purification of [2Fe-2S] FNRAn aliquot of native [4Fe-4S] FNR (1 ml,
Quantitative MethodsFNR protein concentrations were determined using the method of Bradford (Bio-Rad), with bovine serum albumin as the standard (26) and a previously determined correction factor of 0.83 (15). FNR iron content was determined in the following way: 0.1 ml of 21.7% HNO3 was added to the same volume of protein and incubated at 95 °C for 30 min. Cooled samples were centrifuged to remove any precipitate, treated with 0.6 ml of 7.5% (w/v) ammonium acetate, 0.1 ml of 12.5% (w/v) ascorbic acid, 0.1 ml of 10 mM Ferene, mixed, and incubated at room temperature for 30 min before absorbance at 593 nm was measured. Iron concentrations were determined by reference to a calibration curve generated from Fe3+ solutions in the range 0200 µM, prepared from SpectrosoL standard iron solution (BDH, Lot OC495679), and treated as described above. Acid-labile sulfide was determined according to the method of Beinert (27). Based on the analyses, both native and reconstituted [4Fe-4S]2+ FNR samples exhibited
Quantitation of Sulfide Released during Cluster ConversionQuantitation of sulfide released from the cluster during the [4Fe-4S]2+ to [2Fe-2S]2+ conversion was carried out using a modified version of the procedure based on DTNB (Ellman's reagent) reported by Nashef and colleagues (29). Briefly, [4Fe-4S] FNR (
Reactive thiol and free sulfide concentrations were calculated by determining the concentration of released TNB anion, using an
We verified that the [4Fe-4S]2+ cluster was stable to the presence of DTNB and Ferene in both buffer systems tested under anaerobic conditions, at least for the duration of the experiment (data not shown). The response of DTNB to sulfide was calibrated using a standard solution of Na2S prepared as described by Beinert (27) and verified by iodometric titration as described by Vogel (28). 0.1 ml of Na2S was added to 2 ml of buffer A containing excess DTNB (2.4 mM) and absorbance at 412 nm measured after 2 min. The amount of TNB anion produced was calculated using a
Since the initial report by Ellman (31) on the thiol-specific reactions of DTNB, the reagent has been used extensively as a means for the quantitation of thiol groups in proteins. However, DTNB may also be used as a colorimetric reagent, as reported by Nashef et al. (29), for the determination of sulfide ions, see Scheme 1. We have suitably modified the published method (29) to quantify sulfide released from FNR during [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion.
The reaction of DTNB with sulfide ion was calibrated against standard Na2S solutions, as described under "Experimental Procedures." These data (data not shown) confirmed that sulfide ions react stoichiometrically with DTNB to yield two TNB anions, as reported previously (29). We also verified that neither the presence of protein nor Fe2+ interferes with the DTNB reaction. From this we concluded that the assay can be used to measure the concentration of sulfide ion in solution. The addition of excess DTNB to [4Fe-4S] FNR under anaerobic conditions causes spectral changes due to the release of TNB anions (Fig. 1A). These arise from the reaction of DTNB with free protein thiol. FNR contains five cysteine residues of which four (Cys20, Cys23, Cys29, Cys122) ligate the [4Fe-4S] cluster. Hence Cys16 should be available for reaction with a modifying reagent such as DTNB, see Scheme 2. In addition, samples of reconstituted and native FNR are not 100% replete with [4Fe-4S] cluster. There is a component of cluster-free (apo-) protein typically ranging from 15 to 30% and 23 to 43% for reconstituted and native FNR, respectively. All five cysteines of apo-FNR are potentially available for reaction with DTNB. However, it has been demonstrated recently (32) that only four out of the five cysteines present in apo-FNR are reactive toward thiol-specific modifying reagents under anaerobic conditions in the presence of denaturants. We have found that the apo-FNR content of samples contains up to three thiols available for modification (see Table 1) depending upon the method used for purification. Under anaerobic denaturing conditions (buffer B containing 6 M guanidine HCl) we have found 4.7 (±0.4) and 4.1 (±0.5) thiols available for modification per monomer in reconstituted and native FNR, respectively (data not shown), consistent with the observations of Achebach and colleagues (32).
The introduction of oxygen causes further substantial changes in the UV-visible spectrum of the FNR DTNB mix due to TNB anion release (Fig. 1B). Since DTNB is inert to oxygen (30), the observed reaction is due to changes in FNR following cluster conversion.
To determine the amount of sulfide ion released during FNR cluster conversion, a correction to the The [2Fe-2S] clusters are believed to have the same cysteine ligands as the [4Fe-4S]2+ clusters (13). To confirm that cluster conversion does not expose any of the [4Fe-4S]2+ cysteine ligands to reaction with thiol modification reagents, [2Fe-2S] FNR was isolated, as described under "Experimental Procedures." Reaction of an aliquot of 5.2 µM [2Fe-2S] FNR (containing 5.2 µM protein, 10.9 µM iron, and 10.2 µM sulfide) with DTNB resulted in a TNB anion concentration of 5.7 µM, indicating the modification of 1.1 (±0.1) thiols per [2Fe-2S] FNR. In the absence of apo-FNR, this is consistent with the modification of Cys16 in each [2Fe-2S] FNR molecule. This supports the conclusion that Cys20, Cys23, Cys29, and Cys122 are the ligands that bind both the [4Fe-4S]2+ and [2Fe-2S]2+ clusters (13). Hence the observed increase in absorbance at 412 nm is not due to further thiol modification. Instead, we ascribe it to the reaction of DTNB with sulfide ions released during cluster conversion.
A series of experiments on both native and reconstituted [4Fe-4S] FNR, in two different buffer systems, all resulted in the detection of 2 sulfide ions per cluster (see Table 1). In addition to two sulfide ions, two iron ions should be released during cluster conversion. We determined iron released during conversion by the introduction of Ferene and ascorbate following the reaction of [4Fe-4S] FNR with oxygen in the presence of excess DTNB. This resulted in a large absorbance band at 593 nm, characteristic of the [Fe(II)(Ferene)3]4 complex (Fig. 1C). Significantly the iron released amounts to 2 iron ions per cluster (Table 1). Therefore, we propose that the reaction observed when the FNR [4Fe-4S]2+ cluster is oxidized by O2 in the presence of DTNB proceeds as in Scheme 3.
The [4Fe-4S]2+ cluster formally consists of two Fe2+ and two Fe3+ ions that are valence delocalised providing an average oxidation state of Fe2.5+ across all four iron ions. The [2Fe-2S]2+ cluster formally contains two Fe3+ ions, therefore ejection of two Fe2+ ions with two sulfide ions from the [4Fe-4S]2+ cluster with formation of a [2Fe-2S]2+ cluster is not oxidative (see Equation 1).
Recently Sutton et al. (23) proposed an alternative mechanism of [4Fe-4S]2+ to [2Fe-2S]2+ conversion that proceeds via the oxidation of cluster S2 ions (here termed sulfide oxidation). This was based on the observation that, in the presence of the strong Fe2+ chelator, Ferene, two Fe2+ ions were detected per cluster following reaction with oxygen. This leads to the possibility of a four-electron reduction of oxygen to water at the expense of cluster sulfide (see Equation 3) (23).
To reconcile the apparent inconsistencies in observations by different workers (compare Equations 3 and 5), Sutton et al. (23) suggested that [4Fe-4S] FNR prepared via in vitro reconstitution, as described by Crack et al. (17), reacts in a significantly different manner to the native [4Fe-4S]2+ FNR following exposure to oxygen. Here, we have used both in vitro reconstituted and native [4Fe-4S] FNR and find no significant differences in the behavior of the proteins (Table 1). This suggests that the same chemistry occurs in vitro upon exposure to oxygen, regardless of whether [4Fe-4S] FNR is generated in vivo or in vitro. In conclusion, our results demonstrate that two sulfide ions are ejected from the FNR [4Fe-4S]2+ cluster in response to oxygen, in vitro, irrespective of whether the [4Fe-4S] FNR is reconstituted or native protein. This is consistent with the idea that the reaction between oxygen and the cluster occurs via metal oxidation, rather than via a sulfide oxidation pathway. The method of sulfide ion determination reported here might be more widely applicable to other studies of iron-sulfur systems that involve cluster conversion or disassembly.
* This work was supported by Biotechnology and Biological Sciences Research Council Grant BB/C500360/1 and by a Wellcome Trust award from the Joint Infrastructure Fund for equipment. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. 1 To whom correspondence may be addressed. Tel.: 44-1603-593830; Fax: 44-1603-592003; E-mail: J.Crack{at}uea.ac.uk. 2 To whom correspondence may be addressed. Tel.: 44-1603-593051; Fax: 44-1603-593045; E-mail: A.Thomson{at}uea.ac.uk.
3 The abbreviations used are: CRP, cyclic-AMP receptor protein; DTNB, 5,5'-dithiobis-(2-nitrobenzoic acid); Ferene, 5,5'(3-(2-pyridyl)-1,2,4-triazine-5,6-diyl)-bis-2-furansulfonate; TNB, 5-thio-2-nitrobenzoate.
We are grateful to Prof. Dennis Dean (Virginia Tech) for plasmid pDB551 and to Belle Technology for their assistance with the anaerobic glove box fridge-freezer.
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