Structural basis of the redox switch in the OxyR transcription factor

OxyR: a molecular code for redox sensing?

Helmann discusses the controversy surrounding the activation of the bacterial redox-regulated transcription factor OxyR. Evidence from different sources, including crystallographic data, has led to opposing models for the chemical changes that activate OxyR. Is it an intramolecular disulfide-linkage? Is it oxidation of a single cysteine residue to a sulfenic acid? Are there different active forms depending on the type of cysteine modification: intramolecular disulfide bond, sulfenic acid, S-nitrosothiol, or mixed disulfide with glutathione? These issues are discussed in the broader context of transcriptional regulation and how particular regulators may activate distinct genetic programs depending on the precise state of the regulator produced in response to environmental cues.

Glyceraldehyde phosphate dehydrogenase oxidation during cardiac ischemia and reperfusion

OBJECTIVES

Protein S-glutathiolation is a predicted mechanism by which protein thiol groups are oxidized during the oxidative stress of ischaemia and reperfusion. We measured protein S-thiolation during ischaemia and reperfusion and investigated the effect of this oxidative modification on the function of GAPDH.

METHODS

Glutathione was biotinylated (biotin-GSH) and used to probe for protein S-glutathiolation in isolated rat hearts using non-reducing Western blots and streptavidin-HRP. Streptavidin-agarose was used to purify S-glutathiolated proteins and these were identified using N-terminal sequencing and database searching.

RESULTS

Little protein S-glutathiolation occurred in control preparations, but this increased 15-fold during reperfusion. Protein S-glutathiolation was attenuated by the antioxidant mercaptopropionylglycine and was shown to occur only during the firstminutes of reperfusion. Affinity purification of the S-glutathiolated proteins showed 20 dominant S-glutathiolation substrates. A dominant S-thiolated protein was N-terminally sequenced (VKVGVNGFG) and HPLC peptide mapping gave additional sequence nearer the site of oxidation (TGVFTTMEKA). The first sequence was the N-terminus of GAPDH, and the second a peptide from the same protein starting at residue 96. GAPDH was immunopurified from aerobic, ischemic or reperfused hearts. Maleimidofluorescein labeling of purified GAPDH provided an index of its reduced thiol status. In the absence of DTT, ischemia induced a reduction in the number of free thiols on GAPDH that was reversed on reperfusion. When treated with DTT, the free thiol status of GAPDH could be increased in ischemic but not reperfused samples. Ischemia induced a reduction in GAPDH activity that was partially restored by reperfusion. DTT-treatment reactivated ischemic GAPDH, but had little effect on the activity from reperfused tissue. Mass spectra acquired from aerobic GAPDH preparations were relatively simple whereas spectra from ischemic or reperfused preparations were highly complex, possibly indicative of oxidation by multiple oxidants.

CONCLUSIONS

Many proteins, including GAPDH, are targets for S-glutathiolation during cardiac oxidative stress. GAPDH oxidation is associated with a loss in reduced cysteine status that correlates with the inactivation of this enzyme.

Semaphorins: green light for redox signaling?

How semaphorins stimulate plexins to regulate axon steering is an actively investigated question. Ventura and Pelicci discuss new evidence indicating that MICAL, a putative monoxygenase, transmits the signal from the receptor plexin to the actin cytoskeleton through a redox mechanism. MICAL could act either indirectly, causing a local increase in the concentration of reactive oxygen species (ROS), or directly, inducing redox changes in downstream effectors, such as actin and members of the Rho and Rac family of guanosine triphosphatases. Because semaphorin-plexin signaling plays a role in a number of clinically relevant settings, including recovery from spinal cord trauma, regulation of the immune system, and cancer metastasis, these findings could have important therapeutic implications.

Nanotransducers in cellular redox signaling: modification of thiols by reactive oxygen and nitrogen species

The control of signal transduction involves post-translational modification of proteins at key amino acids. Cysteine residues are important in the control of 'redox' cell-signaling pathways, as thiol chemistry offers the possibility of modification by structurally diverse species, including those derived from oxidized lipids, peroxides or nitric oxide. An important and provocative study of the modification of thiols in the transcription factor OxyR recently extended this hypothesis. The findings offer the enticing possibility that the cell can distinguish between different degrees of oxidant and nitrosative exposure by modification at a single site on a signaling molecule.

Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation

Until recently cysteine residues, especially those located extracellularly, were thought to be important for metal coordination, catalysis and protein structure by forming disulfide bonds - but they were not thought to regulate protein function. However, this is not the case. Crucial cysteine residues can be involved in modulation of protein activity and signaling events via other reactions of their thiol (sulfhydryl; -SH) groups. These reactions can take several forms, such as redox events (chemical reduction or oxidation), chelation of transition metals (chiefly Zn(2+), Mn(2+) and Cu(2+)) or S-nitrosylation [the catalyzed transfer of a nitric oxide (NO) group to a thiol group]. In several cases, these disparate reactions can compete with one another for the same thiol group on a single cysteine residue, forming a molecular switch composed of a latticework of possible redox, NO or Zn(2+) modifications to control protein function. Thiol-mediated regulation of protein function can also involve reactions of cysteine residues that affect ligand binding allosterically. This article reviews the basis for these molecular cysteine switches, drawing on the NMDA receptor as an exemplary protein, and proposes a molecular model for the action of S-nitrosylation based on recently derived crystal structures.

Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds

Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent with the chemically reducing environment inside the cells of well-studied organisms. However, recent experiments and new calculations based on genomic data of archaea provide striking contradictions to this pattern. Our results indicate that the intracellular proteins of certain hyperthermophilic archaea, especially the crenarchaea Pyrobaculum aerophilum and Aeropyrum pernix, are rich in disulfide bonds. This finding implicates disulfide bonding in stabilizing many thermostable proteins and points to novel chemical environments inside these microbes. These unexpected results illustrate the wealth of biochemical insights available from the growing reservoir of genomic data.

Inhibition of major histocompatibility complex class II gene transcription by nitric oxide and antioxidants

Interferon (IFN)-gamma facilitates cellular immune response, in part, by inducing the expression of major histocompatibility complex class II (MHC-II) molecules. We demonstrate that IFN-gamma induces the expression of HLA-DRA in vascular endothelial cells via mechanisms involving reactive oxygen species. IFN-gamma-induced HLA-DRA expression was inhibited by nitric oxide (NO) and antioxidants such as superoxide dismutase, catalase, pyrrolidine dithiocarbamate, and N-acetylcysteine. Nuclear run-on assays demonstrated that NO and antioxidants inhibited IFN-gamma-induced HLA-DRA gene transcription. Transient transfection studies using a fully functional HLA-DRA promoter construct ([-300]DR alpha.CAT) showed that inhibition of endogenous NO synthase activity by N(omega)-monomethyl-l-arginine or addition of exogenous hydrogen peroxide (H(2)O(2)) augmented basal and IFN-gamma-stimulated [-300]DR alpha.CAT activity. However, H(2)O(2) and N(omega)-monomethyl-l-arginine could induce HLA-DRA expression suggesting that H(2)O(2) is a necessary but not a sufficient mediator of IFN-gamma-induced HLA-DRA expression. Electrophoretic mobility shift assay and Western blotting demonstrated that NO and antioxidants had little or no effect on IFN-gamma-induced IRF-1 activation or MHC-II transactivator (CIITA) expression but did inhibit IFN-gamma-induced activation of STAT1 alpha (p91) and Y box transcription factors, NF-Y(A) and NF-Y(B). These results indicate that NO and antioxidants may attenuate vascular inflammation by antagonizing the effects of intracellular reactive oxygen species generation by IFN-gamma, which is necessary for MHC-II gene transcription.

Regulation of inducible peroxide stress responses

Bacteria adapt to the presence of reactive oxygen species (ROS) by increasing the expression of detoxification enzymes and protein and DNA repair functions. These responses are co-ordinated by transcription factors that regulate target genes in response to ROS. We compare three classes of peroxide-sensing regulators: OxyR, PerR and OhrR. In all three cases, peroxides effect changes in the redox status of cysteine residues, but the molecular details are distinct. OxyR is converted into a transcriptional activator by the formation of a disulphide bond between two reactive cysteine residues. PerR is a metalloprotein that functions as a peroxide- sensitive repressor. Oxidation is modulated by metal ion composition and may also involve disulphide bond formation. OhrR represses an organic peroxide resistance protein and mediates derepression in response to organic peroxides. Peroxide sensing in this system requires a single conserved cysteine, which is oxidized to form a cysteine-sulphenic acid derivative.

All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade

The mechanism of pI258 arsenate reductase (ArsC) catalyzed arsenate reduction, involving its P-loop structural motif and three redox active cysteines, has been unraveled. All essential intermediates are visualized with x-ray crystallography, and NMR is used to map dynamic regions in a key disulfide intermediate. Steady-state kinetics of ArsC mutants gives a view of the crucial residues for catalysis. ArsC combines a phosphatase-like nucleophilic displacement reaction with a unique intramolecular disulfide bond cascade. Within this cascade, the formation of a disulfide bond triggers a reversible "conformational switch" that transfers the oxidative equivalents to the surface of the protein, while releasing the reduced substrate.

S-thiolation of HSP27 regulates its multimeric aggregate size independently of phosphorylation

HSP27 exists as large aggregates that breakdown after phosphorylation. We show rat cardiac HSP27 is S-thiolated during oxidant stress, and this modification, without phosphorylation, disaggregates multimeric HSP27. Biotinylated cysteine acts as a probe for thiolated proteins, which are detected using non-reducing Western blots probed with streptavidin-horseradish peroxidase. Controls show a low level of S-thiolation, which is increased 3.6-fold during post-ischemic reperfusion. S-thiolated proteins were purified using streptavidin-agarose, and Western immunoblotting showed HSP27 was present. We increased protein S-thiolation 10-fold with 10 microm H2O2 with or without a kinase inhibitor mixture (staurosporine, genistein, bisindolylmaleimide, SB203580, and PD98059). H2O2 alone induced the phosphorylation of HSP27 Ser-86 and Ser-45/Ser-59 of its homologue alphaB crystallin. However, kinase inhibition reduced phosphorylation of these sites below basal. Despite effective kinase inhibition, H2O2 still disaggregated HSP27, but not alphaB crystallin. This is consistent with the lack of an S-thiolation site on alphaB crystallin. Thus, we have demonstrated a novel mechanism of HSP27 multimeric size regulation. S-thiolation must occur at Cys-141, the only cysteine in rat HSP27.

Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation

Phase variation of the outer membrane protein Ag43 in E. coli requires deoxyadenosine methylase (Dam) and OxyR. Previously, it was shown that OxyR is required for repression of the Ag43-encoding gene, agn43, and that Dam-dependent methylation of three GATC target sequences in the regulatory region abrogates OxyR binding. Here we report further characterization of agn43 transcription and its regulation. Transcription was initiated from a sigma(70)-dependent promoter at the G residue of the upstream GATC sequence. Template DNA and RNA polymerase were sufficient to obtain transcription in vitro, but DNA methylation enhanced the level of transcription. Analyses of transcription in vivo of agn'-lacZ with mutated Dam target sequences support this conclusion. Since methylation also abrogates OxyR binding, this indicates that methylation plays a dual role in facilitating agn43 transcription. In vitro transcription from an unmethylated template was repressed by OxyR(C199S), which resembles the reduced form of OxyR. Consistent with this and the role of Dam in OxyR binding, OxyR(C199S) protected from DNase I digestion the agn43 regulatory region from -16 to +42, which includes the three GATC sequences. Deletion analyses of the regulatory region showed that a 101-nucleotide region of the agn43 regulatory region containing the promoter and this OxyR binding region was sufficient for Dam- and OxyR-dependent phase variation

Repression of photosynthesis gene expression by formation of a disulfide bond in CrtJ

Many species of purple photosynthetic bacteria repress synthesis of their photosystem in the presence of molecular oxygen. The bacterium Rhodobacter capsulatus mediates this process by repressing expression of bacteriochlorophyll, carotenoid, and light-harvesting genes via the aerobic repressor, CrtJ. In this study, we demonstrate that CrtJ forms an intramolecular disulfide bond in vitro and in vivo when exposed to oxygen. Mutational and sulfhydryl-specific chemical modification studies indicate that formation of a disulfide bond is critical for CrtJ binding to its target promoters. Analysis of the redox states of aerobically and anaerobically grown cells indicates that they have similar redox states of approximately -200 mV, thereby demonstrating that a change in midpoint potential is not responsible for disulfide bond formation. In vivo and in vitro analyses indicate that disulfide bond formation in CrtJ is insensitive to the addition of hydrogen peroxide but is sensitive to molecular oxygen. These results suggest that disulfide bond formation in CrtJ may differ from the mechanism of disulfide bond formation used by OxyR.

The OhrR repressor senses organic hydroperoxides by reversible formation of a cysteine-sulfenic acid derivative

Reactive oxygen species induce the expression of detoxification and repair genes critical for life in an aerobic environment. Bacterial factors that sense reactive oxygen species use either thiol-disulfide exchange reactions (OxyR, RsrA) or redox labile 2Fe-2S clusters (SoxR). We demonstrate that the reduced form of Bacillus subtilis OhrR binds cooperatively to two adjacent inverted repeat sequences in the ohrA control region and thereby represses transcription. In the presence of organic hydroperoxides, OhrR is inactivated by the reversible oxidation of a single conserved cysteine residue to the corresponding cysteine-sulfenic acid, and perhaps to higher oxidation states.

OxyR: a molecular code for redox-related signaling

Redox regulation has been perceived as a simple on-off switch in proteins (corresponding to reduced and oxidized states). Using the transcription factor OxyR as a model, we have generated, in vitro, several stable, posttranslational modifications of the single regulatory thiol (SH), including S-NO, S-OH, and S-SG, and shown that each occurs in vivo. These modified forms of OxyR are transcriptionally active but differ in structure, cooperative properties, DNA binding affinity, and promoter activities. OxyR can thus process different redox-related signals into distinct transcriptional responses. More generally, our data suggest a code for redox control through which allosteric proteins can subserve either graded (cooperative) or maximal (noncooperative) responses, and through which differential responsivity to redox-related signals can be achieved.

Detection, quantitation, purification, and identification of cardiac proteins S-thiolated during ischemia and reperfusion

We have developed methods that allow detection, quantitation, purification, and identification of cardiac proteins S-thiolated during ischemia and reperfusion. Cysteine was biotinylated and loaded into isolated rat hearts. During oxidative stress, biotin-cysteine forms a disulfide bond with reactive protein cysteines, and these can be detected by probing Western blots with streptavidin-horseradish peroxidase. S-Thiolated proteins were purified using streptavidin-agarose. Thus, we demonstrated that reperfusion and diamide treatment increased S-thiolation of a number of cardiac proteins by 3- and 10-fold, respectively. Dithiothreitol treatment of homogenates fully abolished the signals detected. Fractionation studies indicated that the modified proteins are located within the cytosol, membrane, and myofilament/cytoskeletal compartments of the cardiac cells. This shows that biotin-cysteine gains rapid and efficient intracellular access and acts as a probe for reactive protein cysteines in all cellular locations. Using Western blotting of affinity-purified proteins we identified actin, glyceraldehyde-3-phosphate dehydrogenase, HSP27, protein-tyrosine phosphatase 1B, protein kinase Calpha, and the small G-protein ras as substrates for S-thiolation during reperfusion of the ischemic rat heart. MALDI-TOF mass fingerprint analysis of tryptic peptides independently confirmed actin and glyceraldehyde-3-phosphate dehydrogenase S-thiolation during reperfusion. This approach has also shown that triosephosphate isomerase, aconitate hydratase, M-protein, nucleoside diphosphate kinase B, and myoglobin are S-thiolated during post-ischemic reperfusion.

Constitutive mutations of the OccR regulatory protein affect DNA bending in response to metabolites released from plant tumors

OccR is a LysR-type transcriptional regulator of Agrobacterium tumefaciens that positively regulates the octopine catabolism operon of the Ti plasmid and is also an autorepressor. Positive control of the occ genes occurs in response to octopine, a nutrient released from crown gall tumors. OccR binds to a site upstream of the occQ promoter in the presence and absence of octopine. Octopine causes prebound OccR to undergo a conformational change at the DNA binding site that causes changes in footprint length and DNA bending. To determine the roles of these conformational changes in transcriptional activation, we isolated 22 OccR mutants that were able to activate the occQ promoter in the absence of octopine. Thirteen of these mutants contained single amino acid substitutions, and nine contained two base pair changes resulting in two amino acid substitutions, which in most cases acted synergistically. These mutations spanned the entire length of the protein. Most of these mutant proteins in the absence of octopine displayed DNA binding and bending properties characteristic of transcriptionally active OccR-octopine complexes.

Regulation of receptor protein-tyrosine phosphatase alpha by oxidative stress

The presence of two protein-tyrosine phosphatase (PTP) domains is a striking feature in most transmembrane receptor PTPs (RPTPs). The function of the generally inactive membrane-distal PTP domain (RPTP-D2) is unknown. Here we report that an intramolecular interaction between the spacer region (Sp) and the C-terminus in RPTPalpha prohibited intermolecular interactions. Interestingly, stress factors such as H(2)O(2), UV and heat shock induced reversible, free radical-dependent, intermolecular interactions between RPTPalpha and RPTPalpha-SpD2, suggesting an inducible switch in conformation and binding. The catalytic site cysteine of RPTPalpha-SpD2, Cys723, was required for the H(2)O(2) effect on RPTPalpha. H(2)O(2) induced a rapid, reversible, Cys723-dependent conformational change in vivo, as detected by fluorescence resonance energy transfer, with cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) flanking RPTPalpha-SpD2 in a single chimeric protein. Importantly, H(2)O(2) treatment stabilized RPTPalpha dimers, resulting in inactivation. We propose a model in which oxidative stress induces a conformational change in RPTPalpha-D2, leading to stabilization of RPTPalpha dimers, and thus to inhibition of RPTPalpha activity.

Prokaryotic transcription regulators: more than just the helix-turn-helix motif

Over the past two years, the structures of many prokaryotic transcriptional regulators have been solved, and several of them have revealed the structural mechanism of gene regulation. The crystal structure of BmrR-TPP-DNA reveals a novel mechanism of transcription activation, whereby the drug-bound protein activates the bmr promoter by local DNA unwinding and base pair disruption. Myristoyl-CoA induces FadR by a three-helix pushing mechanism, whereas TetR employs a helical pendulum motion to regulate expression. The structures of AbrB, and DNA complexes of Rob and MuR unveil a novel DNA-binding motif, 'the looped-hinge helix', and new uses of the helix-turn-helix and winged helix motifs in DNA binding.

Reactive nitrogen and oxygen intermediates and bacterial defenses: unusual adaptations in Mycobacterium tuberculosis

The production of reactive oxygen and reactive nitrogen intermediates is an important host defense mechanism mediated in response to infection by bacterial pathogens. Not surprisingly, intracellular pathogens have evolved numerous defense strategies to protect themselves against the damaging effects of these agents. In enteric bacteria, exposure to oxidative or nitrosative stress induces expression of numerous pathways that allow the bacterium to resist the toxic effects of these compounds during growth in the host. In contrast, members of pathogenic mycobacterial species, including the frank human pathogens Mycobacterium tuberculosis and Mycobacterium leprae, are dysfunctional in aspects of the oxidative and nitrosative stress response, yet they remain able to establish and maintain productive acute and persistent infections in the host. This article reviews the current knowledge regarding reactive oxygen and nitrogen intermediates, and compares the adaptative mechanisms utilized by enteric organisms and mycobacterial species to resist the bactericidal and bacteriostatic effects resulting from exposure to these compounds.

Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana

The crystal structure of the semireduced form of cyclic nucleotide phosphodiesterase (CPDase) from Arabidopsis thaliana has been solved by molecular replacement and refined at the resolution of 1.8 A. We have previously reported the crystal structure of the native form of this enzyme, whose main target is ADP-ribose 1",2"-cyclic phosphate, a product of the tRNA splicing reaction. CPDase possesses six cysteine residues, four of which are involved in forming two intra-molecular disulfide bridges. One of these bridges, between Cys-104 and Cys-110, is opened in the semireduced CPDase, whereas the other remains intact. This change of the redox state leads to a conformational rearrangement in the loop covering the active site of the protein. While the native structure shows this partially disordered loop in a coil conformation, in the semireduced enzyme the N-terminal lobe of this loop winds up and elongates the preceding alpha-helix. The semireduced state of CPDase also enabled co-crystallization with a putative inhibitor of its enzymatic activity, 2',3'-cyclic uridine vanadate. The ligand is bound within the active site, and the mode of binding is in agreement with the previously proposed enzymatic mechanism. Selected biophysical properties of the oxidized and the semireduced CPDase are also discussed.

Reactive oxygen species, antioxidants, and the mammalian thioredoxin system

Reactive oxygen species (ROS) are known mediators of intracellular signaling cascades. Excessive production of ROS may, however, lead to oxidative stress, loss of cell function, and ultimately apoptosis or necrosis. A balance between oxidant and antioxidant intracellular systems is hence vital for cell function, regulation, and adaptation to diverse growth conditions. Thioredoxin reductase (TrxR) in conjunction with thioredoxin (Trx) is a ubiquitous oxidoreductase system with antioxidant and redox regulatory roles. In mammals, extracellular forms of Trx also have cytokine-like effects. Mammalian TrxR has a highly reactive active site selenocysteine residue resulting in a profound reductive capacity, reducing several substrates in addition to Trx. Due to the reactivity of TrxR, the enzyme is inhibited by many clinically used electrophilic compounds including nitrosoureas, aurothioglucose, platinum compounds, and retinoic acid derivatives. The properties of TrxR in combination with the functions of Trx position this system at the core of cellular thiol redox control and antioxidant defense. In this review, we focus on the reactions of the Trx system with ROS molecules and different cellular antioxidant enzymes. We summarize the TrxR-catalyzed regeneration of several antioxidant compounds, including ascorbic acid (vitamin C), selenium-containing substances, lipoic acid, and ubiquinone (Q10). We also discuss the general cellular effects of TrxR inhibition. Dinitrohalobenzenes constitute a unique class of immunostimulatory TrxR inhibitors and we consider the immunomodulatory effects of dinitrohalobenzene compounds in view of their reactions with the Trx system.

A novel sugar-stimulated covalent switch in a sugar sensor

The bgl sensory system is composed of a membrane-bound sugar sensor, BglF, and a transcriptional regulator, BglG. The sensor BglF has several enzymatic activities: in its nonstimulated state, it acts as BglG phosphorylase; in the presence of beta-glucoside in the growth medium, it acts as BglG dephosphorylase and as the beta-glucoside phosphotransferase. The same active site on BglF, Cys-24, is responsible for the phosphorylation of both the stimulating sugar and the BglG protein. BglF is composed of three domains, two hydrophilic and one hydrophobic. Our previous results suggested that catalysis of the sugar-stimulated functions depends on specific interactions between the B domain, which contains the active site cysteine, and the integral membrane C domain. We report here that the stimulating sugar triggers the formation of a disulfide bond between the active site cysteine and another cysteine in the membrane-embedded domain of BglF. Inability of a mutant BglF protein to form the disulfide bridge between the B and C domains correlates with its inability to catalyze the sugar-stimulated functions. The ability of the cysteine residue in BglF to bind covalently either to a phosphoryl group or to another cysteine residue, depending on the protein stimulation state, suggests a novel way to control signaling by alternative bond formation.

Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase

Macrophage activation determines the outcome of infection by Mycobacterium tuberculosis (Mtb). Interferon-gamma (IFN-gamma) activates macrophages by driving Janus tyrosine kinase (JAK)/signal transducer and activator of transcription-dependent induction of transcription and PKR-dependent suppression of translation. Microarray-based experiments reported here enlarge this picture. Exposure to IFN-gamma and/or Mtb led to altered expression of 25% of the monitored genome in macrophages. The number of genes suppressed by IFN-gamma exceeded the number of genes induced, and much of the suppression was transcriptional. Five times as many genes related to immunity and inflammation were induced than suppressed. Mtb mimicked or synergized with IFN-gamma more than antagonized its actions. Phagocytosis of nonviable Mtb or polystyrene beads affected many genes, but the transcriptional signature of macrophages infected with viable Mtb was distinct. Studies involving macrophages deficient in inducible nitric oxide synthase and/or phagocyte oxidase revealed that these two antimicrobial enzymes help orchestrate the profound transcriptional remodeling that underlies macrophage activation.