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

The Mar, Sox, and Rob Systems

Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.

The new epoch of structural insights into radical SAM enzymology

The Radical SAM (RS) superfamily of enzymes catalyzes a wide array of enzymatic reactions. The majority of these enzymes employ an electron from a reduced [4Fe-4S]+1 cluster to facilitate the reductive cleavage of S-adenosyl-l-methionine, thereby producing a highly reactive 5'-deoxyadenosyl radical (5'-dA⋅) and l-methionine. Typically, RS enzymes use this 5'-dA⋅ to extract a hydrogen atom from the target substrate, starting the cascade of an expansive and impressive variety of chemical transformations. While a great deal of understanding has been gleaned for 5'-dA⋅ formation, because of the chemical diversity within this superfamily, the subsequent chemical transformations have only been fully elucidated in a few examples. In addition, with the advent of new sequencing technology, the size of this family now surpasses 700,000 members, with the number of uncharacterized enzymes and domains also rapidly expanding. In this review, we outline the history of RS enzyme characterization in what we term "epochs" based on advances in technology designed for stably producing these enzymes in an active state. We propose that the state of the field has entered the fourth epoch, which we argue should commence with a protein structure initiative focused solely on RS enzymes to properly tackle this unique superfamily and uncover more novel chemical transformations that likely exist.

Intramolecular electron transfer from biopterin to FeII-O2 complex in nitric oxide synthases occurs at very different rates between bacterial and mammalian enzymes: Direct observation of a catalytically active intermediate

Nitric oxide synthase (NOS) is a cytochrome P450-type mono‑oxygenase that catalyzes the oxidation of L-arginine to nitric oxide. We previously observed that intramolecular electron transfer from biopterin to Fe²⁺-O₂ in Deinococcus radiodurans NOS (DrNOS) using pulse radiolysis. However, the rate of electron transfer in DrNOS (2.2 × 10³ s^-1) contrasts with a reported corresponding rate (11 s^-1) in a mammalian NOS determined using rapid freeze-quench (RFQ) EPR. We applied pulse radiolysis to Bacillus subtilis NOS (bsNOS) and to rat neural NOS oxygenase domain NOS (mNOS). Concurrently, RFQ EPR was used to trap a pterin radical during single-turnover enzyme reactions of the enzymes. By using the pulse radiolysis method, hydrated electrons (e_aq^-) reduced the heme iron of NOS enzymes. Subsequently, ferrous heme reacted with O₂ to form a Fe²⁺-O₂ intermediate. In the presence of pterin, the intermediate of bsNOS was found to convert to other intermediate in the time range of milliseconds. A similar process was determined to have occurred after pulse radiolysis of the pterin-bound mNOS, though the rate was much slower. The intermediates of all of the NOS enzymes further converted to the original ferric form in the time range of seconds. When using the RFQ method, pterin radicals were formed very rapidly in both DrNOS and bsNOS in the time range of milliseconds. In contrast, the pterin radical in mNOS was observed to form slowly, at a rate of ∼20 s^-1.

Exposure to stressors and antimicrobials induces cell-autonomous ultrastructural heterogeneity of an intracellular bacterial pathogen

Despite their clonality, intracellular bacterial pathogens commonly show remarkable physiological heterogeneity during infection of host cells. Physiological heterogeneity results in distinct ultrastructural morphotypes, but the correlation between bacterial physiological state and ultrastructural appearance remains to be established. In this study, we showed that individual cells of Salmonella enterica serovar Typhimurium are heterogeneous in their ultrastructure. Two morphotypes based on the criterion of cytoplasmic density were discriminated after growth under standard culture conditions, as well as during intracellular lifestyle in mammalian host cells. We identified environmental conditions which affect cytoplasmic densities. Using compounds generating oxygen radicals and defined mutant strains, we were able to link the occurrence of an electron-dense ultrastructural morphotype to exposure to oxidative stress and other stressors. Furthermore, by combining ultrastructural analyses of Salmonella during infection and fluorescence reporter analyses for cell viability, we provided evidence that two characterized ultrastructural morphotypes with electron-lucent or electron-dense cytoplasm represent viable cells. Moreover, the presence of electron-dense types is stress related and can be experimentally induced only when amino acids are available in the medium. Our study proposes ultrastructural morphotypes as marker for physiological states of individual intracellular pathogens providing a new marker for single cell analyses.

Synthetic biology and bioelectrochemical tools for electrogenetic system engineering

Synthetic biology research and its industrial applications rely on deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and electrodes), allowing for the direct integration of electronics with biological processes. However, the use of electrogenetic systems is limited by poor activity, tunability, and standardization. In this work, we developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Last, we demonstrated electrochemical activation of gene expression under aerobic conditions using a novel, modular bioelectrochemical device. These genetic and electrochemical tools facilitate the design and improve the performance of electrogenetic systems. Furthermore, the genetic design strategies used can be applied to other redox-responsive promoters to further expand the available tools for electrogenetics.

Interaction of Periplasmic Fab Production and Intracellular Redox Balance in Escherichia coli Affects Product Yield

Antibody fragments such as Fab's require the formation of disulfide bonds to achieve a proper folding state. During their recombinant, periplasmic expression in Escherichia coli, oxidative folding is mediated by the DsbA/DsbB system in concert with ubiquinone. Thereby, overexpression of Fab's is linked to the respiratory chain, which is not only immensely important for the cell's energy household but also known as a major source of reactive oxygen species. However, the effects of an increased oxidative folding demand and the consequently required electron flux via ubiquinone on the host cell have not been characterized so far. Here, we show that Fab expression in E. coli BL21(DE3) interfered with the intracellular redox balance, thereby negatively impacting host cell performance. Production of four different model Fab's in lab-scale fed-batch cultivations led to increased oxygen consumption rates and strong cell lysis. An RNA sequencing analysis revealed transcription activation of the oxidative stress-responsive soxS gene in the Fab-producing strains. We attributed this to the accumulation of intracellular superoxide, which was measured using flow cytometry. An exogenously supplemented ubiquinone analogue improved Fab yields up to 82%, indicating that partitioning of the quinone pool between aerobic respiration and oxidative folding limited ubiquinone availability and hence disulfide bond formation capacity. Combined, our results provide a more in-depth understanding of the profound effects that periplasmic Fab expression and in particular disulfide bond formation has on the host cell. Thereby, we show new possibilities to elaborate cell engineering and process strategies for improved host cell fitness and process outcome.

Bacterial MerR family transcription regulators: activationby distortion

Transcription factors (TFs) modulate gene expression by regulating the accessibility of promoter DNA to RNA polymerases (RNAPs) in bacteria. The MerR family TFs are a large class of bacterial proteins unique in their physiological functions and molecular action: they function as transcription repressors under normal circumstances, but rapidly transform to transcription activators under various cellular triggers, including oxidative stress, imbalance of cellular metal ions, and antibiotic challenge. The promoters regulated by MerR TFs typically contain an abnormal long spacer between the -35 and -10 elements, where MerR TFs bind and regulate transcription activity through unique mechanisms. In this review, we summarize the function, ligand reception, DNA recognition, and molecular mechanism of transcription regulation of MerR-family TFs.

Mediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transfer

Biology and electronics are both expert at receiving, analyzing, and responding to information, yet they use entirely different information processing paradigms. Biology processes information using networks that are intrinsically molecular while electronics process information through circuits that control the flow of electrons. There is great interest in coupling the molecular logic of biology with the electronic logic of technology, and we suggest that redox (reduction-oxidation) is a uniquely suited modality for interfacing biology with electronics. Specifically, redox is a native biological modality and is accessible to electronics through electrodes. We summarize recent advances in mediated electrochemistry to direct information transfer into biological systems intentionally altering function, exposing it for more advanced interpretation, which can dramatically expand the biotechnological toolbox.

Role of phenazine-enzyme physiology for current generation in a bioelectrochemical system

Pseudomonas aeruginosa produces phenazine-1-carboxylic acid (PCA) and pyocyanin (PYO), which aid its anaerobic survival by mediating electron transfer to distant oxygen. These natural secondary metabolites are being explored in biotechnology to mediate electron transfer to the anode of bioelectrochemical systems. A major challenge is that only a small fraction of electrons from microbial substrate conversion is recovered. It remained unclear whether phenazines can re-enter the cell and thus, if the electrons accessed by the phenazines arise mainly from cytoplasmic or periplasmic pathways. Here, we prove that the periplasmic glucose dehydrogenase (Gcd) of P. aeruginosa and P. putida is involved in the reduction of natural phenazines. PYO displayed a 60-fold faster enzymatic reduction than PCA; PCA was, however, more stable for long-term electron shuttling to the anode. Evaluation of a Gcd knockout and overexpression strain showed that up to 9% of the anodic current can be designated to this enzymatic reaction. We further assessed phenazine uptake with the aid of two molecular biosensors, which experimentally confirm the phenazines' ability to re-enter the cytoplasm. These findings significantly advance the understanding of the (electro) physiology of phenazines for future tailoring of phenazine electron discharge in biotechnological applications.

Fields, biochemistry fast autooxidation of a Bis-Histidyl-ligated globin from the anhydrobiotic tardigrade, ramazzottius varieornatus, by molecular oxygen

Tardigrades, a phylum of meiofaunal organisms, exhibit extraordinary tolerance to various environmental conditions, including extreme temperatures (-272 to 151 °C) and exposure to ionizing radiation. Proteins from anhydrobiotic tardigrades with homology to known proteins from other organisms are new potential targets for structural genomics. Recently, we reported spectroscopic and structural characterization of a hexacoordinated hemoglobin (Kumaglobin [Kgb]) found in an anhydrobiotic tardigrade. In the absence of its exogenous ligand, Kgb displays hexacoordination with distal and proximal histidines. In this work, we analyzed binding of the molecular oxygen ligand following reduction of heme in Kgb using a pulse radiolysis technique. Radiolytically generated hydrated electrons (eaq-) reduced the heme iron of Kgb within 20 µs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediate with a second-order rate constant of 3.0 × 106 M-1 s-1. The intermediate was rapidly (within 0.1 s) autooxidized to the ferric form. Redox potential measurements revealed an E'0 of -400 mV (vs. SHE) in the ferric/ferrous couple. Our results suggest that Kgb may serve as a physiological generator of O2·- via redox signaling and/or electron transfer.

MarA, RamA, and SoxS as Mediators of the Stress Response: Survival at a Cost

To survive and adapt to changing environments, bacteria have evolved mechanisms to express appropriate genes at appropriate times. Exposure to antimicrobials triggers a global stress response in Enterobacteriaceae, underpinned by activation of a family of transcriptional regulators, including MarA, RamA, and SoxS. These control a program of altered gene expression allowing a rapid and measured response to improve fitness in the presence of toxic drugs. Increased expression of marA, ramA, and soxS up regulates efflux activity to allow detoxification of the cell. However, this also results in trade-offs in other phenotypes, such as impaired growth rates, biofilm formation and virulence. Here, we review the current knowledge regarding the trade-offs that exist between drug survival and other phenotypes that result from induction of marA, ramA, and soxS. Additionally, we present some new findings linking expression of these regulators and biofilm formation in Enterobacteriaceae, thereby demonstrating the interconnected nature of regulatory networks within the cell and explaining how trade-offs can exist between important phenotypes. This has important implications for our understanding of how bacterial virulence and biofilms can be influenced by exposure to antimicrobials.

MarA, RamA, and SoxS as Mediators of the Stress Response: Survival at a Cost

To survive and adapt to changing environments, bacteria have evolved mechanisms to express appropriate genes at appropriate times. Exposure to antimicrobials triggers a global stress response in Enterobacteriaceae, underpinned by activation of a family of transcriptional regulators, including MarA, RamA, and SoxS. These control a program of altered gene expression allowing a rapid and measured response to improve fitness in the presence of toxic drugs. Increased expression of marA, ramA, and soxS up regulates efflux activity to allow detoxification of the cell. However, this also results in trade-offs in other phenotypes, such as impaired growth rates, biofilm formation and virulence. Here, we review the current knowledge regarding the trade-offs that exist between drug survival and other phenotypes that result from induction of marA, ramA, and soxS. Additionally, we present some new findings linking expression of these regulators and biofilm formation in Enterobacteriaceae, thereby demonstrating the interconnected nature of regulatory networks within the cell and explaining how trade-offs can exist between important phenotypes. This has important implications for our understanding of how bacterial virulence and biofilms can be influenced by exposure to antimicrobials.

Gene networks that compensate for crosstalk with crosstalk

Crosstalk is a major challenge to engineering sophisticated synthetic gene networks. A common approach is to insulate signal-transduction pathways by minimizing molecular-level crosstalk between endogenous and synthetic genetic components, but this strategy can be difficult to apply in the context of complex, natural gene networks and unknown interactions. Here, we show that synthetic gene networks can be engineered to compensate for crosstalk by integrating pathway signals, rather than by pathway insulation. We demonstrate this principle using reactive oxygen species (ROS)-responsive gene circuits in Escherichia coli that exhibit concentration-dependent crosstalk with non-cognate ROS. We quantitatively map the degree of crosstalk and design gene circuits that introduce compensatory crosstalk at the gene network level. The resulting gene network exhibits reduced crosstalk in the sensing of the two different ROS. Our results suggest that simple network motifs that compensate for pathway crosstalk can be used by biological networks to accurately interpret environmental signals.

Crosstalk between genetic circuits is a major challenge for engineering sophisticated networks. Here the authors design networks that compensate for crosstalk by integrating, not insulating, pathways.

Redox Is a Global Biodevice Information Processing Modality

Biology is well-known for its ability to communicate through (i) molecularly-specific signaling modalities and (ii) a globally-acting electrical modality associated with ion flow across biological membranes. Emerging research suggests that biology uses a third type of communication modality associated with a flow of electrons through reduction/oxidation (redox) reactions. This redox signaling modality appears to act globally and has features of both molecular and electrical modalities: since free electrons do not exist in aqueous solution, the electrons must flow through molecular intermediates that can be switched between two states - with electrons (reduced) or without electrons (oxidized). Importantly, this global redox modality is easily accessible through its electrical features using convenient electrochemical instrumentation. In this review, we explain this redox modality, describe our electrochemical measurements, and provide four examples demonstrating that redox enables communication between biology and electronics. The first two examples illustrate how redox probing can acquire biologically relevant information. The last two examples illustrate how redox inputs can transduce biologically-relevant transitions for patterning and the induction of a synbio transceiver for two-hop molecular communication. In summary, we believe redox provides a unique ability to bridge bio-device communication because simple electrochemical methods enable global access to biologically meaningful information. Further, we envision that redox may facilitate the application of information theory to the biological sciences.

NADPH-related processes studied with a SoxR-based biosensor in Escherichia coli

NADPH plays a crucial role in cellular metabolism for biosynthesis and oxidative stress responses. We previously developed the genetically encoded NADPH biosensor pSenSox based on the transcriptional regulator SoxR of Escherichia coli, its target promoter P_soxS and eYFP as fluorescent reporter. Here, we used pSenSox to study the influence of various parameters on the sensor output in E. coliduring reductive biotransformation of methyl acetoacetate (MAA) to (R)-methyl 3-hydroxybutyrate (MHB) by the strictly NADPH-dependent alcohol dehydrogenase of Lactobacillus brevis (LbAdh). Redox-cycling drugs such as paraquat and menadione strongly activated the NADPH biosensor and mechanisms responsible for this effect are discussed. Absence of the RsxABCDGE complex and/or RseC caused an enhanced biosensor response, supporting a function as SoxR-reducing system. Absence of the membrane-bound transhydrogenase PntAB caused an increased biosensor response, whereas the lack of the soluble transhydrogenase SthA or of SthA and PntAB was associated with a strongly decreased response. These data support the opposing functions of PntAB in NADP⁺ reduction and of SthA in NADPH oxidation. In summary, the NADPH biosensor pSenSox proved to be a useful tool to study NADPH-related processes in E. coli.

Connecting Biology to Electronics: Molecular Communication via Redox Modality

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues.

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.

DNA Charge Transport: from Chemical Principles to the Cell

The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.

Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

Members of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP- and dRNA-seq with in vitro biochemistry to characterize a putative NsrR homologue in Streptomyces venezuelae. ChIP-seq analysis revealed that rather than regulating the nitrosative stress response like Streptomyces coelicolor NsrR, Sven6563 binds to a conserved motif at a different, much larger set of genes with a diverse range of functions, including a number of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the putative target genes are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator.

Integrated High-Content Quantification of Intracellular ROS Levels and Mitochondrial Morphofunction

Oxidative stress arises from an imbalance between the production of reactive oxygen species (ROS) and their removal by cellular antioxidant systems. Especially under pathological conditions, mitochondria constitute a relevant source of cellular ROS. These organelles harbor the electron transport chain, bringing electrons in close vicinity to molecular oxygen. Although a full understanding is still lacking, intracellular ROS generation and mitochondrial function are also linked to changes in mitochondrial morphology. To study the intricate relationships between the different factors that govern cellular redox balance in living cells, we have developed a high-content microscopy-based strategy for simultaneous quantification of intracellular ROS levels and mitochondrial morphofunction. Here, we summarize the principles of intracellular ROS generation and removal, and we explain the major considerations for performing quantitative microscopy analyses of ROS and mitochondrial morphofunction in living cells. Next, we describe our workflow, and finally, we illustrate that a multiparametric readout enables the unambiguous classification of chemically perturbed cells as well as laminopathy patient cells.

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens.

IMPORTANCE

By protecting microbes against reactive oxygen insults, SODs aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling, and murine infection experiments. We identified virulence determinants common to the two homologs, assembly differences, and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and a basis for SOD-specific drug design and an extension of immunogen design to target two important pathogens that continue to pose global health threats.

[Genetically Encoded Fluorescent Redox Sensors]

Redox processes play a key role in cells of all.organisms. These processes imply directed flows of electrons via so-called redox pairs: substances that exist in both reduced and oxidized states simultaneously within the cell. Examples of redox pairs are NAD+/NADH, NADP+/NADPH, GSSG/2GSH. Until recently, studies of redox processes in the living cells were challenged by the lack of suitable methods. Genetically encoded fluorescent biosensors provide a new way to study biological processes including redox ones. Biosensors allow real-time detection of messengers, metabolites and enzymatic activities in living systems of different complexity from cultured cells to transgenic animals. In this review, we describe the main types of known redox biosensors with examples of their use.

Reflections on the Theories of Aging, of Oxidative Stress, and of Science in General. Is It Time to Abandon the Free Radical (Oxidative Stress) Theory of Aging?

SIGNIFICANCE

Aging and oxidative stress are complex phenomena, and their understanding is of enormous theoretical and practical significance.

RECENT ADVANCES

Numerous hypotheses and theories that attempt to explain these phenomena have been developed. These hypotheses and theories compete with each other, with each claiming to be the correct one, while significantly contradicting each other.

CRITICAL ISSUES

It is important to develop a maximally correct theory that may then trigger significant practical breakthroughs.

FUTURE DIRECTIONS

None of these theories is entirely correct or close enough to the truth. However, most of them contain many correct elements (CE). Finding these CE is possible by analysis of these theories. Once the CE are found, they can be merged by synthesis in a better new theory. An analysis of some of the theories of aging followed by synthesis is attempted.

Transcription Factors That Defend Bacteria Against Reactive Oxygen Species

Bacteria live in a toxic world in which their competitors excrete hydrogen peroxide or superoxide-generating redox-cycling compounds. They protect themselves by activating regulons controlled by the OxyR, PerR, and SoxR transcription factors. OxyR and PerR sense peroxide when it oxidizes key thiolate or iron moieties, respectively; they then induce overlapping sets of proteins that defend their vulnerable metalloenzymes. An additional role for OxyR in detecting electrophilic compounds is possible. In some nonenteric bacteria, SoxR appears to control the synthesis and export of redox-cycling compounds, whereas in the enteric bacteria it defends the cell against the same agents. When these compounds oxidize its iron-sulfur cluster, SoxR induces proteins that exclude, excrete, or modify them. It also induces enzymes that defend the cell against the superoxide that such compounds make. Recent work has brought new insight into the biochemistry and physiology of these responses, and comparative studies have clarified their evolutionary histories.

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.

Configurational changes of heme followed by cytochrome c folding reaction

Although the folding kinetics of cytochrome c (Cyt-c), ferric or ferrous Cyt-c, has been extensively investigated as a paradigm for a protein folding reaction using various time-resolved spectroscopic techniques, the configurational change of heme associated with the folding reaction from a ferric Cyt-c to a ferrous Cyt-c induced by one-electron reduction has not been elucidated. To address this issue, we investigated the configurational change of heme in the Cyt-c folding process induced by one-electron reduction using a combination of time-resolved resonance Raman spectroscopy and pulse radiolysis. The results presented herein reveal that the reduction of ferric Cyt-c and the ligation of Met80 occur simultaneously within a timescale of approximately 2 μs, and that the ligand binding and exchange of heme depend on the initial configuration of the heme. The rapid ligation of Met80 observed in this study may be attributed to the intramolecular diffusion of Met80 into ferrous Cyt-c with a 5-coordinated high-spin configuration. Conversely, the ligand exchange of a ferrous Cyt-c with a 6-coordinated low-spin configuration was significantly slower.

[Compartmentalization of ROS-mediated signal transduction]

The localization of signaling molecules close to their targets is the central principle of cell signaling. The colocalization of multicomponent signaling complexes is realized through protein scaffolds that provide better specificity than undirected diffusion ofthe same components. ROS-generating complexes have been suggested to follow this principle by specific intracellular localization of ROS production and the limitation of ROS diffusion distances. However, the lack of adequate methods did not allow direct detection of local ROS production to confirm the model ofredox signaling compartmentalization. Nevertheless, evidences of local ROS production and restriction of diffusion were provided by kinetic modeling and data on the subcellular localization of NADPH-oxidase isoforms, their adapter proteins and local restriction of ROS diffusion. Here we shall discuss the properties of antioxidant system which prevents uncontrolled ROS diffusion from the sites of generation to the adjacent subcellular compartments; the current data of the specific localization NADPH-oxidases activity and its influence on intracellular processes; the recent evidences of the ROS diffusion restriction.

An overview of mechanisms of redox signaling

A principal characteristic of redox signaling is that it involves an oxidation-reduction reaction or covalent adduct formation between the sensor signaling protein and second messenger. Non-redox signaling may involve alteration of the second messenger as in hydrolysis of GTP by G proteins, modification of the signaling protein as in farnesylation, or simple non-covalent binding of an agonist or second messenger. The chemistry of redox signaling is reviewed here. Specifically we have described how among the so-called reactive oxygen species, only hydroperoxides clearly fit the role of a second messenger. Consideration of reaction kinetics and cellular location strongly suggests that for hydroperoxides, particular protein cysteines are the targets and that the requirements for redox signaling is that these cysteines are in microenvironments in which the cysteine is ionized to the thiolate, and a proton can be donated to form a leaving group. The chemistry described here is the same as occurs in the cysteine and selenocysteine peroxidases that are generally considered the primary defense against oxidative stress. But, these same enzymes can also act as the sensors and transducer for signaling. Conditions that would allow specific signaling by peroxynitrite and superoxide are also defined. Signaling by other electrophiles, which includes lipid peroxidation products, quinones formed from polyphenols and other metabolites also involves reaction with specific protein thiolates. Again, kinetics and location are the primary determinants that provide specificity required for physiological signaling although enzymatic catalysis is not likely involved. This article is part of a Special Issue entitled "Redox Signalling in the Cardiovascular System".

F-box and leucine-rich repeat protein 5 (FBXL5): sensing intracellular iron and oxygen

Though essential for many vital biological processes, excess iron results in the formation of damaging reactive oxygen species (ROS). Therefore, iron metabolism must be tightly regulated. F-box and leucine-rich repeat protein 5 (FBXL5), an E3 ubiquitin ligase subunit, regulates cellular and systemic iron homeostasis by facilitating iron regulatory protein 2 (IRP2) degradation. FBXL5 possesses an N-terminal hemerythrin (Hr)-like domain that mediates its own differential stability by switching between two different conformations to communicate cellular iron availability. In addition, the FBXL5-Hr domain also senses O2 availability, albeit by a distinct mechanism. Mice lacking FBXL5 fail to sense intracellular iron levels and die in utero due to iron overload and exposure to damaging levels of oxidative stress. By closely monitoring intracellular levels of iron and oxygen, FBLX5 prevents the formation of conditions that favor ROS formation. These findings suggest that FBXL5 is essential for the maintenance of iron homeostasis and is a key sensor of bioavailable iron. Here, we describe the iron and oxygen sensing mechanisms of the FBXL5 Hr-like domain and its role in mediating ROS biology.

SoxR as a single-cell biosensor for NADPH-consuming enzymes in Escherichia coli

An ultra-high-throughput screening system for NADPH-dependent enzymes, such as stereospecific alcohol dehydrogenases, was established. It is based on the [2Fe-2S] cluster-containing transcriptional regulator SoxR of Escherichia coli that activates expression of soxS in the oxidized but not in the reduced state of the cluster. As SoxR is kept in its reduced state by NADPH-dependent reductases, an increased NADPH demand of the cell counteracts SoxR reduction and increases soxS expression. We have taken advantage of these properties by placing the eyfp gene under the control of the soxS promoter and analyzed the response of E. coli cells expressing an NADPH-dependent alcohol dehydrogenase from Lactobacillus brevis (LbAdh), which reduces methyl acetoacetate to (R)-methyl 3-hydroxybutyrate. Under suitable conditions, the specific fluorescence of the cells correlated with the substrate concentration added and with LbAdh enzyme activity, supporting the NADPH responsiveness of the sensor. These properties enabled sorting of single cells harboring wild-type LbAdh from those with lowered or without LbAdh activity by fluorescence-activated cell sorting (FACS). In a proof-of-principle application, the system was used successfully to screen a mutant LbAdh library for variants showing improved activity with the substrate 4-methyl-2-pentanone.

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.

Comparative study of SoxR activation by redox-active compounds

SoxR from Escherichia coli and related enterobacteria is activated by a broad range of redox-active compounds through oxidation or nitrosylation of its [2Fe-2S] cluster. Activated SoxR then induces SoxS, which subsequently activates more than 100 genes in response. In contrast, non-enteric SoxRs directly activate their target genes in response to redox-active compounds that include endogenously produced metabolites. We compared the responsiveness of SoxRs from Streptomyces coelicolor (ScSoxR), Pseudomonas aeruginosa (PaSoxR) and E. coli (EcSoxR), all expressed in S. coelicolor, towards natural or synthetic redox-active compounds. EcSoxR responded to all compounds examined, whereas ScSoxR was insensitive to oxidants such as paraquat (Eh -440 mV) and menadione sodium bisulphite (Eh -45 mV) and to NO generators. PaSoxR was insensitive only to some NO generators. Whole-cell EPR analysis of SoxRs expressed in E. coli revealed that the [2Fe-2S](1+) of ScSoxR was not oxidizable by paraquat, differing from EcSoxR and PaSoxR. The mid-point redox potential of purified ScSoxR was determined to be -185 ± 10 mV, higher by approximately 100 mV than those of EcSoxR and PaSoxR, supporting its limited response to paraquat. The overall sensitivity profile indicates that both redox potential and kinetic reactivity determine the differential responses of SoxRs towards various oxidants.

Antimicrobial strategies centered around reactive oxygen species--bactericidal antibiotics, photodynamic therapy, and beyond

Reactive oxygen species (ROS) can attack a diverse range of targets to exert antimicrobial activity, which accounts for their versatility in mediating host defense against a broad range of pathogens. Most ROS are formed by the partial reduction in molecular oxygen. Four major ROS are recognized comprising superoxide (O2•-), hydrogen peroxide (H2O2), hydroxyl radical (•OH), and singlet oxygen ((1)O2), but they display very different kinetics and levels of activity. The effects of O2•- and H2O2 are less acute than those of •OH and (1)O2, because the former are much less reactive and can be detoxified by endogenous antioxidants (both enzymatic and nonenzymatic) that are induced by oxidative stress. In contrast, no enzyme can detoxify •OH or (1)O2, making them extremely toxic and acutely lethal. The present review will highlight the various methods of ROS formation and their mechanism of action. Antioxidant defenses against ROS in microbial cells and the use of ROS by antimicrobial host defense systems are covered. Antimicrobial approaches primarily utilizing ROS comprise both bactericidal antibiotics and nonpharmacological methods such as photodynamic therapy, titanium dioxide photocatalysis, cold plasma, and medicinal honey. A brief final section covers reactive nitrogen species and related therapeutics, such as acidified nitrite and nitric oxide-releasing nanoparticles.

The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium

Oxic environments are hazardous. Molecular oxygen adventitiously abstracts electrons from many redox enzymes, continuously forming intracellular superoxide and hydrogen peroxide. These species can destroy the activities of metalloenzymes and the integrity of DNA, forcing organisms to protect themselves with scavenging enzymes and repair systems. Nevertheless, elevated levels of oxidants quickly poison bacteria, and both microbial competitors and hostile eukaryotic hosts exploit this vulnerability by assaulting these bacteria with peroxides or superoxide-forming antibiotics. In response, bacteria activate elegant adaptive strategies. In this Review, I summarize our current knowledge of oxidative stress in Escherichia coli, the model organism for which our understanding of damage and defence is most well developed.

ompW is cooperatively upregulated by MarA and SoxS in response to menadione

OmpW is a minor porin whose biological function has not been clearly defined. Evidence obtained in our laboratory indicates that in Salmonella enterica serovar Typhimurium the expression of OmpW is activated by SoxS upon exposure to paraquat and it is required for resistance. SoxS belongs to the AraC family of transcriptional regulators, like MarA and Rob. Due to their high structural similarity, the genes under their control have been grouped in the mar/sox/rob regulon, which presents a DNA-binding consensus sequence denominated the marsox box. In this work, we evaluated the role of the transcription factors MarA, SoxS and Rob of S. enterica serovar Typhimurium in regulating ompW expression in response to menadione. We determined the transcript and protein levels of OmpW in different genetic backgrounds; in the wild-type and Δrob strains ompW was upregulated in response to menadione, while in the ΔmarA and ΔsoxS strains the induction was abolished. In a double marA soxS mutant, ompW transcript levels were lowered after exposure to menadione, and only complementation in trans with both genes restored the positive regulation. Using transcriptional fusions and electrophoretic mobility shift assays with mutant versions of the promoter region we demonstrated that two of the predicted sites were functional. Additionally, we demonstrated that MarA increases the affinity of SoxS for the ompW promoter region. In conclusion, our study shows that ompW is upregulated in response to menadione in a cooperative manner by MarA and SoxS through a direct interaction with the promoter region.

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.