Protein conformational changes of the oxidative stress sensor, SoxR, upon redox changes of the [2Fe-2S] cluster probed with ultraviolet resonance Raman spectroscopy

Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis

Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.

The Central Role of Redox-Regulated Switch Proteins in Bacteria

Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.

Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site

The redox chemistry of the electron entry/exit site in Escherichia coli hydrogenase-1 is shown to play a vital role in tuning biocatalysis. Inspired by nature, we generate a HyaA-R193L variant to disrupt a proposed Arg-His cation-π interaction in the secondary coordination sphere of the outermost, "distal", iron-sulfur cluster. This rewires the enzyme, enhancing the relative rate of H₂ production and the thermodynamic efficiency of H₂ oxidation catalysis. On the basis of Fourier transformed alternating current voltammetry measurements, we relate these changes in catalysis to a shift in the distal [Fe₄S₄]^2+/1+ redox potential, a previously experimentally inaccessible parameter. Thus, metalloenzyme chemistry is shown to be tuned by the second coordination sphere of an electron transfer site distant from the catalytic center.

Sensing Mechanisms in the Redox-Regulated, [2Fe-2S] Cluster-Containing, Bacterial Transcriptional Factor SoxR

Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster. We have explored the mechanistic and structural basis of SoxR proteins function and determined how the chemistry at the [2Fe-2S] cluster causes the subsequent regulatory response. In this Account, I describe our recent achievements in three different areas using physicochemical techniques, primarily pulse radiolysis. First, redox-dependent conformational changes in SoxR-bound DNA were studied by site-specifically replacing selected bases with the fluorescent probes 2-aminopurine and pyrrolocytosine. X-ray analyses of the DNA-SoxR complex in the oxidized state revealed that the DNA structure is distorted in the center regions, resulting in local untwisting of base pairs. However, the inactive, reduced state had remained uncharacterized. We found that reduction of the [2Fe-2S] cluster in the SoxR-DNA complex weakens the fluorescence intensity within a region confined to the central base pairs in the promoter region. Second, the reactions of NO with [2Fe-2S] clusters of E. coli SoxR were analyzed using pulse radiolysis. The transcriptional activation of SoxR in E. coli occurs through direct modification of [2Fe-2S] by NO to form a dinitrosyl iron complex (DNIC). The reaction of NO with [2Fe-2S] cluster of SoxR proceeded nearly quantitatively with concomitant reductive elimination of two equivalents S⁰ atoms. Intermediate nitrosylation products, however, were too unstable to observe. We found that the conversion proceeds through at least two steps, with the faster phase being the first reaction of the NO molecule with the [2Fe-2S] cluster. The slower reaction with the second equivalent NO molecule, however, was important for the formation of DNIC. Third, to elucidate the differences between the distinct responses of SoxR proteins from two different species, we studied the interaction of E. coli and Pseudomonas aeruginosa SoxR with superoxide anion using a mutagenic approach. Despite the homology between E. coli SoxR and P. aeruginosa SoxR, the function of P. aeruginosa SoxR differs from that of E. coli. The substitution of E. coli SoxR lysine residues, located close to [2Fe-2S] clusters, into P. aeruginosa SoxR dramatically affected the reaction with superoxide anion.

Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via Its Iron-Sulfur Cluster

Human mitoNEET (mNT) is the first identified Fe-S protein of the mammalian outer mitochondrial membrane. Recently, mNT has been implicated in cytosolic Fe-S repair of a key regulator of cellular iron homeostasis. Here, we aimed to decipher the mechanism by which mNT triggers its Fe-S repair capacity. By using tightly controlled reactions combined with complementary spectroscopic approaches, we have determined the differential roles played by both the redox state of the mNT cluster and dioxygen in cluster transfer and protein stability. We unambiguously demonstrated that only the oxidized state of the mNT cluster triggers cluster transfer to a generic acceptor protein and that dioxygen is neither required for the cluster transfer reaction nor does it affect the transfer rate. In the absence of apo-acceptors, a large fraction of the oxidized holo-mNT form is converted back to reduced holo-mNT under low oxygen tension. Reduced holo-mNT, which holds a [2Fe-2S](+)with a global protein fold similar to that of the oxidized form is, by contrast, resistant in losing its cluster or in transferring it. Our findings thus demonstrate that mNT uses an iron-based redox switch mechanism to regulate the transfer of its cluster. The oxidized state is the "active state," which reacts promptly to initiate Fe-S transfer independently of dioxygen, whereas the reduced state is a "dormant form." Finally, we propose that the redox-sensing function of mNT is a key component of the cellular adaptive response to help stress-sensitive Fe-S proteins recover from oxidative injury.

Binding of promoter DNA to SoxR protein decreases the reduction potential of the [2Fe-2S] cluster

The [2Fe-2S] transcriptional factor SoxR, a member of the MerR family, functions as a sensor of oxidative stress in Escherichia coli. The transcriptional activity of SoxR is regulated by the reversible oxidation and reduction of [2Fe-2S] clusters. Electrochemistry measurements on DNA-modified electrodes have shown a dramatic shift in the reduction potential of SoxR from -290 to +200 mV with the promoter DNA-bound [ Gorodetsky , A. A. , Dietrich , L. E. P. , Lee , P. E. , Demple , B. , , Newman , D. K. , and Barton , J. K. ( 2008 ) DNA binding shifts the reduction potential of the transcription factor SoxR , Proc. Natl. Acad. Sci. U.S.A. 105 , 3684 - 3689 ]. To determine the change of the SoxR reduction potential using the new condition, the one-electron oxidation-reduction properties of [2Fe-2S] cluster in SoxR were investigated in the absence and presence of the DNA. The [2Fe-2S] cluster of SoxR was completely reduced by nicotinamide adenine dinucleotide phosphate (NADPH)-cytochrome P450 reductase (CRP) in the presence of a NADPH generating system (glucose 6-dehydrogenase and glucose-6 phosphate), indicating that CRP can serve as an NADPH-dependent electron carrier for SoxR. The reduction potential of SoxR was measured from equilibrium data coupled with NADPH and CRP in the presence of electron mediators. The reduction potentials of DNA-bound and DNA-free states of SoxR were -320 and -293 mV versus NHE (normal hydrogen electrode), respectively. These results indicate that DNA binding causes a moderate shift in the reduction potential of SoxR.

Redox-dependent DNA distortion in a SoxR protein-promoter complex studied using fluorescent probes

The [2Fe-2S] transcriptional factor SoxR, a member of the MerR family, is regulated by the reversible oxidation and reduction of [2Fe-2S] clusters and functions as a sensor of oxidative stress in Escherichia coli. In the oxidized state, distortion of the target DNA promoter region initiates transcription by RNA polymerase, thereby activating transcription. The inactive reduced state of the protein has remained uncharacterized. Here, we directly observed redox-dependent conformational changes in the promoter DNA by site-specifically replacing selected adenine (A) and cytosine (C) bases in the promoter oligonucleotide with the fluorescent probes 2-aminopurine (2Ap) and pyrrolocytosine (pyrrolo-dC), respectively. Reduction of the [2Fe-2S] cluster in the SoxR-DNA complex dramatically weakened the fluorescence intensity of the 2Ap moieties incorporated into the central part of the DNA. In contrast, the fluorescence of 2Ap moieties incorporated at A in other regions and the fluorescence of pyrrolo-dC moieties in the central region of the DNA (C3 and C3') were only slightly decreased by the reduction. These results strongly suggest that the redox change causes a large conformational change within a region confined to the central A-T base pairs in the promoter region of the DNA.

Fe-S proteins that regulate gene expression

Iron-sulfur (Fe-S) cluster containing proteins that regulate gene expression are present in most organisms. The innate chemistry of their Fe-S cofactors makes these regulatory proteins ideal for sensing environmental signals, such as gases (e.g. O2 and NO), levels of Fe and Fe-S clusters, reactive oxygen species, and redox cycling compounds, to subsequently mediate an adaptive response. Here we review the recent findings that have provided invaluable insight into the mechanism and function of these highly significant Fe-S regulatory proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess

Copper and zinc are essential metal ions, but toxic in excess. Bacteria have evolved different strategies to control their intracellular concentrations, ensuring proper supply while avoiding toxicity, including the induction of metal-specific as well as non-specific mechanisms. We compared the transcriptional profiles of Salmonella Typhimurium after exposure to either copper or zinc ions in both rich and minimal media. Besides metal-specific regulatory networks many global stress-response pathways react to an excess of either of these metal ions. Copper excess affects both zinc and iron homeostasis by inducing transcription of these metal-specific regulons. In addition to the control of zinc-specific regulons, zinc excess affects the Cpx regulon and the σ(E) envelope-stress responses. Finally, novel metal-specific upregulated genes were detected including a new copper-detoxification pathway that involves the siderophore enterobactin and the outer-membrane protein TolC. This work sheds light onto the transcriptional landscape of Salmonella after copper or zinc overload, and discloses a new mechanism of copper detoxification.

Oxidative stress sensing by the iron-sulfur cluster in the transcription factor, SoxR

All bacteria are continuously exposed to environmental and/or endogenously active oxygen and nitrogen compounds and radicals. To reduce the deleterious effects of these reactive species, most bacteria have evolved specific sensor proteins that regulate the expression of enzymes that detoxify these species and repair proteins. Some bacterial transcriptional regulators containing an iron-sulfur cluster are involved in coordinating these physiological responses. Mechanistic and structural information can show how these regulators function, in particular, how chemical interactions at the cluster drive subsequent regulatory responses. The [2Fe-2S] transcription factor SoxR (superoxide response) functions as a bacterial sensor of oxidative stress and nitric oxide (NO). This review focuses on the mechanisms by which SoxR proteins respond to oxidative stress.

Analysis of differences in oxygen sensitivity of Fe-S clusters

Many but not all iron-sulphur clusters in metalloproteins are known to be sensitive to molecular oxygen with dramatic consequences for their biological function. We performed a systematic quantum chemical investigation that sheds light on the differences in oxygen sensitivity depending on charge and spin states of these clusters as well as on their spatial fixation by the enzyme's scaffold. We find that significant structural distortions are required to bind O2 exothermically to [Fe2S2] and [Fe3S4] clusters, while only small conformational changes allow for the thermodynamically favorable coordination of molecular oxygen to [Fe4S4] cubanes and [Fe4S3] clusters.

Species-specific residues calibrate SoxR sensitivity to redox-active molecules

In enterics, the transcription factor SoxR triggers a global stress response by sensing a broad spectrum of redox-cycling compounds. In the non-enteric bacteria Pseudomonas aeruginosa and Streptomyces coelicolor, SoxR is activated by endogenous redox-active small molecules and only regulates a small set of genes. We investigated if the more general response in enterics is reflected in the ability of SoxR to sense a wider range of redox-cycling compounds. Indeed, while Escherichia coli SoxR is tuned to structurally diverse compounds that span a redox range of -450 to +80 mV, P. aeruginosa and S. coelicolor SoxR are less sensitive to viologens, which have redox potentials below -350 mV. Using a mutagenic approach, we pinpointed three amino acids that contribute to the reduced sensitivity of P. aeruginosa and S. coelicolor SoxR. Notably these residues are not conserved in homologues of the Enterobacteriaceae. We further identified a motif within the sensor domain that tunes the activity of SoxR from enterics - inhibiting constitutive activity while allowing sensitivity to drugs with low redox potentials. Our findings highlight how small alterations in structure can lead to the evolution of proteins with distinct specificities for redox-active small molecules.

Direct oxidation of the [2Fe-2S] cluster in SoxR protein by superoxide: distinct differential sensitivity to superoxide-mediated signal transduction

The [2Fe-2S] transcription factor SoxR is activated by reversible one-electron oxidation of its [2Fe-2S] cluster, leading to enhanced production of various antioxidant proteins through induction of the soxRS regulon in Escherichia coli. Recently, there has been considerable debate about whether superoxide (O(2)(•)) activates SoxR directly. To elucidate the underlying activation mechanism, we investigated SoxR interaction with O(2)(•) using pulse radiolysis. Radiolytically generated hydrated electrons reduced the oxidized form of the [2Fe-2S] cluster of SoxR within 2 μs. A subsequent increase in absorption in the visible region corresponding to reoxidation of the [2Fe-2S] cluster was observed on a time scale of milliseconds. Addition of human copper/zinc superoxide dismutase inhibited this delayed oxidation in a concentration-dependent fashion (I(50) = 1.0 μm), indicating that O(2)(•) oxidized the reduced form of SoxR directly. The second-order rate constant of this process was estimated to be 5 × 10(8) m(-1) s(-1). A similar result was observed after pulse radiolysis of Pseudomonas aeruginosa SoxR. However, superoxide dismutase inhibited the oxidation of reduced SoxR much more effectively in P. aeruginosa, even at a lower concentration (I(50) = 80 nm), indicating that the soxRS response is much more sensitive to O(2)(•) in E. coli than in P. aeruginosa. These results suggest that SoxR proteins play a distinct regulatory role in the activation of O(2)(•).

Iron sulfur cluster proteins and microbial regulation: implications for understanding tuberculosis

All pathogenic and nonpathogenic microbes are continuously exposed to environmental or endogenous reactive oxygen and nitrogen species, which can critically effect survival and disease. Iron-sulfur [Fe-S] cluster containing prosthetic groups provide the microbial cell with a unique capacity to sense and transcriptionally respond to diatomic gases (e.g. NO and O2) and redox-cycling agents. Recent advances in our understanding of the mechanisms for how the FNR and SoxR [Fe-S] cluster proteins respond to NO and O2 have provided new insights into the biochemical mechanism of action of the Mycobacterium tuberculosis (Mtb) family of WhiB [Fe-S] cluster proteins. These insights have provided the basis for establishing a unifying paradigm for the Mtb WhiB family of proteins. Mtb is the etiological agent for tuberculosis (TB), a disease that affects nearly one-third of the world's population.