Structural basis of the redox switch in the OxyR transcription factor

In vivo imaging of Ca2+, pH, and reactive oxygen species using fluorescent probes in plants

Changes in the levels of Ca(2+), pH, and reactive oxygen species (ROS) are recognized as key cellular regulators involved in diverse physiological and developmental processes in plants. Critical to understanding how they exert such widespread control is an appreciation of their spatial and temporal dynamics at levels from organ to organelle and from seconds to many hours. With appropriate controls, fluorescent sensors can provide a robust approach with which to quantify such changes in Ca(2+), pH, and ROS in real time, in vivo. The fluorescent cellular probes available for visualization split into two broad classes: (a) dyes and (b) an increasingly diverse set of genetically encoded sensors based around green fluorescent proteins (GFPs). The GFP probes in particular can be targeted to well-defined subcellular locales, offering the possibility of high-resolution mapping of these signals within the cell.

New insights into the genetic organization of the FK228 biosynthetic gene cluster in Chromobacterium violaceum no. 968

The biosynthetic gene cluster of FK228, an FDA-approved anticancer natural product, was identified and sequenced previously. The genetic organization of this gene cluster has now been delineated through systematic gene deletion and transcriptional analysis. As a result, the gene cluster is redefined to contain 12 genes: depA through depJ, depM, and a newly identified pathway regulatory gene, depR.

Specificity of the E. coli LysR-type transcriptional regulators

Background

Families of paralogous oligomeric proteins are common in biology. How the specificity of assembly evolves is a fundamental question of biology. The LysR-Type Transcriptional Regulators (LTTR) form perhaps the largest family of transcriptional regulators in bacteria. Because genomes often encode many LTTR family members, it is assumed that many distinct homooligomers are formed simultaneously in the same cell without interfering with each other's activities, suggesting specificity in the interactions. However, this assumption has not been systematically tested.

Methodology/Principal Findings

A negative-dominant assay with λcI repressor fusions was used to evaluate the assembly of the LTTRs in E. coli K-12. Thioredoxin (Trx)-LTTR fusions were used to challenge the homooligomeric interactions of λcI-LTTR fusions. Eight cI-LTTR fusions were challenged with twenty-eight Trx fusions. LTTRs could be divided into three classes based on their interactions with other LTTRs.

Conclusions/Significance

Multimerization of LTTRs in E. coli K-12 is mostly specific. However, under the conditions of the assay, many LTTRs interact with more than one noncognate partner. The physiological significance and physical basis for these interactions are not known.

Identification of gene products involved in the oxidative stress response of Moraxella catarrhalis

Moraxella catarrhalis is subjected to oxidative stress from both internal and environmental sources. A previous study (C. D. Pericone, K. Overweg, P. W. Hermans, and J. N. Weiser, Infect. Immun. 68:3990-3997, 2000) indicated that a wild-type strain of M. catarrhalis was very resistant to killing by exogenous hydrogen peroxide (H₂O₂). The gene encoding OxyR, a LysR family transcriptional regulator, was identified and inactivated in M. catarrhalis strain O35E, resulting in an increase in sensitivity to killing by H₂O₂ in disk diffusion assays and a concomitant aerobic serial dilution effect. Genes encoding a predicted catalase (KatA) and an alkyl hydroperoxidase (AhpCF) showed dose-dependent upregulation in wild-type cells exposed to H₂O₂. DNA microarray and real-time reverse transcription-PCR (RT-PCR) analyses identified M. catarrhalis genes whose expression was affected by oxidative stress in an OxyR-dependent manner. Testing of M. catarrhalis O35E katA and ahpC mutants for their abilities to scavenge exogenous H₂O₂ showed that the KatA catalase was responsible for most of this activity in the wild-type parent strain. The introduction of the same mutations into M. catarrhalis strain ETSU-4 showed that the growth of a ETSU-4 katA mutant was markedly inhibited by the addition of 50 mM H₂O₂ but that this mutant could still form a biofilm equivalent to that produced by its wild-type parent strain.

Reversal of aging-associated hippocampal synaptic plasticity deficits by reductants via regulation of thiol redox and NMDA receptor function

Deficits in learning and memory accompanied by age-related neurodegenerative diseases are closely related to the impairment of synaptic plasticity. In this study, we investigated the role of thiol redox status in the modulation of the N-methyl-d-aspartate receptor (NMDAR)-dependent long-term potentiation (LTP) in CA1 areas of hippocampal slices. Our results demonstrated that the impaired LTP induced by aging could be reversed by acute administration of reductants that can regulate thiol redox status directly, such as dithiothreitol or β-mercaptoethanol, but not by classical anti-oxidants such as vitamin C or trolox. This repair was mediated by the recruitment of aging-related deficits in NMDAR function induced by these reductants and was mimicked by glutathione, which can restore the age-associated alterations in endogenous thiol redox status. Moreover, antioxidant prevented but failed to reverse H(2)O(2) -induced impairment of NMDAR-mediated synaptic plasticity. These results indicate that the restoring of thiol redox status may be a more effective strategy than the scavenging of oxidants in the treatment of pre-existing oxidative injury in learning and memory.

Redox state of the endoplasmic reticulum is controlled by Ero1L-alpha and intraluminal calcium

Formation of intra- and intermolecular disulfide bonds is an essential step in the synthesis of secretory proteins. In eukaryotic cells, this process occurs in the endoplasmic reticulum (ER) and requires an oxidative environment with the action of several chaperones and folding catalysts. During protein folding, Ero1p oxidizes protein disulfide isomerase (PDI), which then directly catalyzes the formation of disulfide bonds in folding proteins. Recent cell-free studies suggest that the terminal electron acceptor in the pathway is molecular oxygen, with the resulting formation of hydrogen peroxide (H(2)O(2)). We report for the first time the measurement of ER H(2)O(2) level in live cells. By targeting a fluorescent protein-based H(2)O(2) sensor to various intracellular compartments, we show that the ER has the highest level of H(2)O(2), and this high concentration is well confined to the lumen of the organelle. Manipulation of the Ero1-Lalpha level--either by overexpression or by siRNA-mediated inhibition--caused parallel changes in luminal H(2)O(2), proving that the activity of Ero1-Lalpha results in H(2)O(2) formation in the ER. We also found that calcium mobilization from intracellular stores induces a decrease in ER H(2)O(2) level, suggesting a complex interplay between redox and calcium signaling in the mammalian ER.

SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch

We present structural and biochemical evidence for a redox switch in the archaeal transcriptional regulator SurR of Pyrococcus furiosus, a hyperthermophilic anaerobe. P. furiosus produces H(2) during fermentation, but undergoes a metabolic shift to produce H(2) S when elemental sulfur (S(0) ) becomes available. Changes in gene expression occur within minutes of S(0) addition, and the majority of these S(0) -responsive genes are regulatory targets of SurR, a key regulator involved in primary S(0) response. SurR was shown in vitro to have dual functionality, activating transcription of some of these genes, notably the hydrogenase operons, and repressing others, including a gene-encoding sulfur reductase. This work demonstrates via biochemical and structural evidence that the activity of SurR is modulated by cysteine residues in a CxxC motif that constitutes a redox switch. Oxidation of the switch with S(0) inhibits sequence-specific DNA binding by SurR, leading to deactivation of genes related to H(2) production and derepression of genes involved in S(0) metabolism.

Fluorescent protein-based redox probes

Redox biochemistry is increasingly recognized as an integral component of cellular signal processing and cell fate decision making. Unfortunately, our capabilities to observe and measure clearly defined redox processes in the natural context of living cells, tissues, or organisms are woefully limited. The most advanced and promising tools for specific, quantitative, dynamic and compartment-specific observations are genetically encoded redox probes derived from green fluorescent protein (GFP). Within only few years from their initial introduction, redox-sensitive yellow FP (rxYFP), redox-sensitive GFPs (roGFPs), and HyPer have generated enormous interest in applying these novel tools to monitor dynamic redox changes in vivo. As genetically encoded probes, these biosensors can be specifically targeted to different subcellular locations. A critical advantage of roGFPs and HyPer is their ratiometric fluorogenic behavior. Moreover, the probe scaffold of redox-sensitive fluorescent proteins (rxYFP and roGFPs) is amenable to molecular engineering, offering fascinating prospects for further developments. In particular, the engineering of redox relays between roGFPs and redox enzymes allows control of probe specificity and enhancement of sensitivity. Genetically encoded redox probes enable the functional analysis of individual proteins in cellular redox homeostasis. In addition, redox biosensor transgenic model organisms offer extended opportunities for dynamic in vivo imaging of redox processes.

Genetic analysis of the nitrogen assimilation control protein from Klebsiella pneumoniae

The nitrogen assimilation control protein (NAC) from Klebsiella pneumoniae is a typical LysR-type transcriptional regulator (LTTR) in many ways. However, the lack of a physiologically relevant coeffector for NAC and the fact that NAC can carry out many of its functions as a dimer make NAC unusual among the LTTRs. In the absence of a crystal structure for NAC, we analyzed the effects of amino acid substitutions with a variety of phenotypes in an attempt to identify functionally important features of NAC. A substitution that changed the glutamine at amino acid 29 to alanine (Q29A) resulted in a NAC that was seriously defective in binding to DNA. The H26D substitution resulted in a NAC that could bind and repress transcription but not activate transcription. The I71A substitution resulted in a NAC polypeptide that remained monomeric. NAC tetramers can bind to both long and shorter binding sites (like other LTTRs). However, the absence of a coeffector to induce the conformational change needed for the switch from the former to the latter raised a question. Are there two conformations of NAC, analogous to the other LTTRs? The G217R substitution resulted in a NAC that could bind to the longer sites but had difficulty in binding to the shorter sites, and the I222R and A230R substitutions resulted in a NAC that could bind to the shorter sites but had difficulty in binding properly to the longer sites. Thus, there appear to be two conformations of NAC that can freely interconvert in the absence of a coeffector.

A genetically encoded sensor for H2O2 with expanded dynamic range

Hydrogen peroxide is an important second messenger controlling intracellular signaling cascades by selective oxidation of redox active thiolates in proteins. Changes in intracellular [H(2)O(2)] can be tracked in real time using HyPer, a ratiometric genetically encoded fluorescent probe. Although HyPer is sensitive and selective for H(2)O(2) due to the properties of its sensing domain derived from the Escherichia coli OxyR protein, many applications may benefit from an improvement of the indicator's dynamic range. We here report HyPer-2, a probe that fills this demand. Upon saturating [H(2)O(2)] exposure, HyPer-2 undergoes an up to sixfold increase of the ratio F500/F420 versus a threefold change in HyPer. HyPer-2 was generated by a single point mutation A406V from HyPer corresponding to A233V in wtOxyR. This mutation was previously shown to destabilize interface between monomers in OxyR dimers. However, in HyPer-2, the A233V mutation stabilizes the dimer and expands the dynamic range of the probe.

Structural insight into the oxidation-sensing mechanism of the antibiotic resistance of regulator MexR

MexR functions as the primary regulator of the mexAB-oprM multidrug efflux expression in Pseudomonas aeruginosa. It has been shown that MexR senses oxidative stress by interprotomer disulphide bond formation between redox-active cysteines. This oxidation induces MexR to dissociate from the promoter DNA, thus activating the transcriptional expression of efflux pump genes. In this study, we present the crystal structure of MexR in its oxidized form at a resolution of 2.1 A. This crystal structure reveals the mechanism by which oxidative signal allosterically derepresses the MexR-controlled transcription activation.

Structural basis for NADH/NAD+ redox sensing by a Rex family repressor

Nicotinamide adenine dinucleotides have emerged as key signals of the cellular redox state. Yet the structural basis for allosteric gene regulation by the ratio of reduced NADH to oxidized NAD(+) is poorly understood. A key sensor among Gram-positive bacteria, Rex represses alternative respiratory gene expression until a limited oxygen supply elevates the intracellular NADH:NAD(+) ratio. Here we investigate the molecular mechanism for NADH/NAD(+) sensing among Rex family members by determining structures of Thermus aquaticus Rex bound to (1) NAD(+), (2) DNA operator, and (3) without ligand. Comparison with the Rex/NADH complex reveals that NADH releases Rex from the DNA site following a 40 degrees closure between the dimeric subunits. Complementary site-directed mutagenesis experiments implicate highly conserved residues in NAD-responsive DNA-binding activity. These rare views of a redox sensor in action establish a means for slight differences in the nicotinamide charge, pucker, and orientation to signal the redox state of the cell.

The structure of a reduced form of OxyR from Neisseria meningitidis

BACKGROUND

Survival of the human pathogen, Neisseria meningitidis, requires an effective response to oxidative stress resulting from the release of hydrogen peroxide by cells of the human immune system. In N. meningitidis, expression of catalase, which is responsible for detoxifying hydrogen peroxide, is controlled by OxyR, a redox responsive LysR-type regulator. OxyR responds directly to intracellular hydrogen peroxide through the reversible formation of a disulphide bond between C199 and C208 in the regulatory domain of the protein.

RESULTS

We report the first crystal structure of the regulatory domain of an OxyR protein (NMB0173 from N. meningitidis) in the reduced state i.e. with cysteines at positions 199 and 208. The protein was crystallized under reducing conditions and the structure determined to a resolution of 2.4 A. The overall fold of the Neisseria OxyR shows a high degree of similarity to the structure of a C199S mutant OxyR from E. coli, which cannot form the redox sensitive disulphide. In the neisserial structure, C199 is located at the start of helix alpha3, separated by 18 A from C208, which is positioned between helices alpha3 and alpha4. In common with other LysR-type regulators, full length OxyR proteins are known to assemble into tetramers. Modelling of the full length neisserial OxyR as a tetramer indicated that C199 and C208 are located close to the dimer-dimer interface in the assembled tetramer. The formation of the C199-C208 disulphide may thus affect the quaternary structure of the protein.

CONCLUSION

Given the high level of structural similarity between OxyR from N. meningitidis and E. coli, we conclude that the redox response mechanism is likely to be similar in both species, involving the reversible formation of a disulphide between C199-C208. Modelling suggests that disulphide formation would directly affect the interface between regulatory domains in an OxyR tetramer which in turn may lead to an alteration in the spacing/orientation of the DNA-binding domains and hence the interaction of OxyR with its DNA binding sites.

Snapshot of the interaction between HIV envelope glycoprotein 120 and protein disulfide isomerase

The human immunodeficiency virus-1 (HIV-1) envelope glycoprotein 120 (gp120) binds to cell surface receptors and mediates HIV entry. Previous studies suggest the cell surface protein disulfide isomerase (PDI) might interact with disulfide bond(s) of gp120 and thus facilitate HIV-1 entry. In the present study, a kinetic trapping approach was used to capture the disulfide cross-linking intermediate between gp120 and PDI. Active site mutant PDIs were prepared in which the C-terminal cysteine at the active site was replaced by a serine. The active site mutant PDIs were able to covalently cross-link with gp120 through a mixed disulfide bond in vitro. The cross-linking efficiency was enhanced by CD4 protein (primary receptor of HIV-1) and was inhibited both by bacitracin (a PDI inhibitor) and by catalytically inactive PDI. The present results suggested the cell surface PDI might play a role in HIV entry in vivo.

Susceptibility of isolated myofibrils to in vitro glutathionylation: Potential relevance to muscle functions

In this study we investigated the molecular mechanism of glutathionylation on isolated human cardiac myofibrils using several pro-glutathionylating agents. Total glutathionylated proteins appeared significantly enhanced with all the pro-oxidants used. The increase was completely reversed by the addition of a reducing agent, demonstrating that glutathione binding occurs by a disulfide and that the process is reversible. A sensitive target of glutathionylation was alpha-actin, showing a different reactivity to the several pro-glutathionylating agents by ELISA. Noteworthy, myosin although highly sensitive to the in vitro glutathionylation does not represent the primary glutathionylation target in isolated myofibrils. Light scattering measurements of the glutathionylated alpha-actin showed a slower polymerisation compared to the non-glutathionylated protein and force development was depressed after glutathionylation, when the myofibrils were mounted in a force recording apparatus. Interestingly, confocal laser scanning microscopy of cardiac cryosections indicated, for the first time, the constitutive glutathionylation of alpha-cardiac actin in human heart. Due to the critical location of alpha-actin in the contractile machinery and to its susceptibility to the oxidative modifications, glutathionylation may represent a mechanism for modulating sarcomere assembly and muscle functionality under patho-physiological conditions in vivo.

The LysR-type nitrogen assimilation control protein forms complexes with both long and short DNA binding sites in the absence of coeffectors

Most LysR-type transcriptional regulators (LTTRs) function as tetramers when regulating gene expression. The nitrogen assimilation control protein (NAC) generally functions as a dimer when binding to DNA and activating transcription. However, at some sites, NAC binds as a tetramer. Like many LTTRs, NAC tetramers can recognize sites with long footprints (74 bp for the site at nac) with a substantial DNA bend or short footprints (56 bp for the site at cod) with less DNA bending. However, unlike other LTTRs, NAC can recognize both types of sites in the absence of physiologically relevant coeffectors, suggesting that the two conformers of the NAC tetramer (extended and compact) are interchangeable without the need for any modification to induce or stabilize the change. In order for NAC to bind as a tetramer, three interactions must exist: an interaction between the two NAC dimers and an interaction between each NAC dimer and its corresponding binding site. The interaction between one dimer and its DNA site can be weak (recognizing a half-site rather than a full dimer-binding site), but the other two interactions must be strong. Since the conformation of the NAC tetramer (extended or compact) is determined by the nature of the DNA site without the intervention of a small molecule, we argue that the coeffector that determines the conformation of the NAC tetramer is the DNA site to which it binds.

Signaling functions of reactive oxygen species

We review signaling by reactive oxygen species, which is emerging as a major physiological process. However, among the reactive oxygen species, H(2)O(2) best fulfills the requirements of being a second messenger. Its enzymatic production and degradation, along with the requirements for the oxidation of thiols by H(2)O(2), provide the specificity for time and place that are required in signaling. Both thermodynamic and kinetic considerations suggest that among possible oxidation states of cysteine, formation of sulfenic acid derivatives or disulfides can be relevant as thiol redox switches in signaling. In this work, the general constraints that are required for protein thiol oxidation by H(2)O(2) to be fast enough to be relevant for signaling are discussed in light of the mechanism of oxidation of the catalytic cysteine or selenocysteine in thiol peroxidases. While the nonenzymatic reaction between thiol and H(2)O(2) is, in most cases, too slow to be relevant in signaling, the enzymatic catalysis of thiol oxidation by these peroxidases provides a potential mechanism for redox signaling.

Signaling functions of reactive oxygen species

We review signaling by reactive oxygen species, which is emerging as a major physiological process. However, among the reactive oxygen species, H(2)O(2) best fulfills the requirements of being a second messenger. Its enzymatic production and degradation, along with the requirements for the oxidation of thiols by H(2)O(2), provide the specificity for time and place that are required in signaling. Both thermodynamic and kinetic considerations suggest that among possible oxidation states of cysteine, formation of sulfenic acid derivatives or disulfides can be relevant as thiol redox switches in signaling. In this work, the general constraints that are required for protein thiol oxidation by H(2)O(2) to be fast enough to be relevant for signaling are discussed in light of the mechanism of oxidation of the catalytic cysteine or selenocysteine in thiol peroxidases. While the nonenzymatic reaction between thiol and H(2)O(2) is, in most cases, too slow to be relevant in signaling, the enzymatic catalysis of thiol oxidation by these peroxidases provides a potential mechanism for redox signaling.

The oligomerization of CynR in Escherichia coli

Deletion analysis and alanine-scanning based on a homology-based interaction model were used to identify determinants of oligomerization in the transcriptional regulator CynR, a member of the LysR-type transcriptional regulator (LTTR) family. Deletion analysis confirmed that the putative regulatory domain of CynR was essential for driving the oligomerization of lambda repressor-CynR fusion proteins. The interaction surface of a different LTTR and OxyR was mapped onto a multiple sequence alignment of the LTTR family. This mapping identified putative contacts in the CynR regulatory domain dimer interface, which were targeted for alanine-scanning mutagenesis. Oligomerization was assayed by the ability of mutant lambda repressor-CynR fusions to assemble in E. coli revealing interesting similarities and differences between OxyR and CynR.

Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold

LysR-type transcriptional regulators (LTTRs) constitute the largest family of regulators in prokaryotes. The full-length structures of the LTTR TsaR from Comamonas testosteroni T-2 and its complex with the natural inducer para-toluensulfonate have been characterized by X-ray diffraction. Both ligand-free and complexed forms reveal a dramatically different quaternary structure from that of CbnR from Ralstonia eutropha, or a putative LysR-type regulator from Pseudomonas aeruginosa, the only other determined full-length structures of tetrameric LTTRs. Although all three show a head-to-head tetrameric ring, TsaR displays an open conformation, whereas CbnR and PA01-PR present additional contacts in opposing C-terminal domains that close the ring. Such large differences may be due to a broader structural versatility than previously assumed or either, reflect the intrinsic flexibility of tetrameric LTTRs. On the grounds of the sliding dimer hypothesis of LTTR activation, we propose a structural model in which the closed structures could reflect the conformation of a ligand-free LTTR, whereas inducer binding would bring about local changes to disrupt the interface linking the two compact C-terminal domains. This could lead to a TsaR-like, open structure, where the pairs of recognition helices are closer to each other by more than 10 A.

Use of dimedone-based chemical probes for sulfenic acid detection evaluation of conditions affecting probe incorporation into redox-sensitive proteins

Sulfenic acids, formed as transient intermediates during the reaction of cysteine residues with peroxides, play significant roles in enzyme catalysis and regulation, and are also involved in the redox regulation of transcription factors and other signaling proteins. Therefore, interest in the identification of protein sulfenic acids has grown substantially in the past few years. Dimedone, which specifically traps sulfenic acids, has provided the basis for the synthesis of a novel group of compounds that derivatize 1,3-cyclohexadione, a dimedone analogue, with reporter tags such as biotin for affinity capture and fluorescent labels for visual detection. These reagents allow identification of the cysteine sites and proteins that are sensitive to oxidation and permit identification of the cellular conditions under which such oxidations occur. We have shown that these compounds are reactive and specific toward sulfenic acids and that the labeled proteins can be detected at high sensitivity using gel analysis or mass spectrometry. Here, we further characterize these reagents, showing that the DCP-Bio1 incorporation rates into three sulfenic acid containing proteins, papaya papain, Escherichia coli fRMsr, and the Salmonella typhimurium peroxiredoxin AhpC, are significantly different and, in the case of fRMsr, are unaffected by changes in buffer pH from 5.5 and 8.0. We also provide protocols to label protein sulfenic acids in cellular proteins, either by in situ labeling of intact cells or by labeling at the time of lysis. We show that the addition of alkylating reagents and catalase to the lysis buffer is critical in preventing the formation of sulfenic acid subsequent to cell lysis. Data presented herein also indicate that the need to standardize, as much as possible, the protein and reagent concentrations during labeling. Finally, we introduce several new test or control proteins that can be used to evaluate labeling procedures and efficiencies.

Disulfides as redox switches: from molecular mechanisms to functional significance

The molecular mechanisms underlying thiol-based redox control are poorly defined. Disulfide bonds between Cys residues are commonly thought to confer extra rigidity and stability to their resident protein, forming a type of proteinaceous spot weld. Redox biologists have been redefining the role of disulfides over the last 30-40 years. Disulfides are now known to form in the cytosol under conditions of oxidative stress. Isomerization of extracellular disulfides is also emerging as an important regulator of protein function. The current paradigm is that the disulfide proteome consists of two subproteomes: a structural group and a redox-sensitive group. The redox-sensitive group is less stable and often associated with regions of stress in protein structures. Some characterized redox-active disulfides are the helical CXXC motif, often associated with thioredoxin-fold proteins; and forbidden disulfides, a group of metastable disulfides that disobey elucidated rules of protein stereochemistry. Here we discuss the role of redox-active disulfides as switches in proteins.

Identification by MS/MS of disulfides produced by a functional redox transition

Among posttranslational modifications of proteins entailed with signal transduction, the redox transition is today brought to the focus as a major biochemical event accounting for the signaling functions of reactive oxygen species. Thermodynamic and kinetic criteria highlight hydroperoxides and protein disulfides as signaling and transducer elements, respectively, and growing biochemical evidence supports this notion. The protein Cys residue involved in this function must react fast and specifically with the oxidant and then with a second accessible Cys yielding the disulfide. These kinetic and structural constraints are shared with peroxidases and peroxiredoxins, which are competitors for the signaling hydroperoxide. In this chapter, a procedure based on MS/MS analysis for inter- and intrachain disulfide assignment in proteins undergoing redox-switch is presented. While the sensitivity of the modern MS/MS instruments permits the sequencing of double peptides linked by a disulfide bond, the major pitfall of the proteomic procedure is the thiol-disulfide scrambling taking place at the alkaline pH needed for the proteolytic reaction of trypsin. Instead, the use of pepsin at acidic pH prevents the disulfide scrambling, but the specificity of the proteolytic reaction is low and thus the complexity of fragmentation increases. We succeeded to limit this problem by heuristically assuming a conserved pepsin cleavage pattern of the protein both in the oxidized and the reduced form. Asymmetric cleavage of the disulfide by collisional fragmentation further corroborated the identification. In conclusion, the use of pepsin, integrated by a minimal computation, appears suitable for positively assigning inter- and intrachain disulfides generated by a functional redox-switch.

Conformational changes in redox pairs of protein structures

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.

Reactive electrophilic oxylipins: pattern recognition and signalling

Oxidized lipids in plants comprise a variety of reactive electrophiles that contain an alpha,beta-unsaturated carbonyl group. While some of these compounds are formed enzymatically, many of them are formed by non-enzymatic pathways. In addition to their chemical reactivity/toxicity low levels of these compounds are also biologically active. Despite their structural diversity and biosynthetic origin, common biological activities such as induction of defense genes, activation of detoxification responses and growth inhibition have been documented. However, reactive electrophilic oxylipins are poorly defined as a class of compounds but have at least two properties in common, i.e., lipophilicity and thiol-reactivity. Thiol-reactivity is a property of reactive oxylipins (RES) shared by reactive oxygen and nitrogen species (ROS and RNS) and enables these agents to modify proteins in vivo. Thiol-modification is assumed to represent a key mechanism involved in signal transduction. A metaanalysis of proteomic studies reveals that RES oxylipins, ROS and RNS apparently chemically modify a similar set of highly sensitive proteins, virtually all of which are targets for thioredoxins. Moreover, most of these proteins are redox-regulated, i.e., posttranslational thiol-modification alters the activity or function of these proteins. On the transcriptome level, effects of RES oxylipins and ROS on gene induction substantially overlap but are clearly different. Besides electrophilicity other structural properties such as target affinity apparently determine target selectivity and biological activity. In this context, different signalling mechanisms and signal transduction components identified in plants and non-plant organisms as well as putative functions of RES oxylipins are discussed.

The oligomerization of OxyR in Escherichia coli

We examine the contribution of residues at the dimer interface of the transcriptional regulator OxyR to oligomerization. Residues in contact across the dimer interface of OxyR were identified using the program Quaternary Contacts (QContacts). Site-directed mutagenesis was performed on the non-alanine or glycine residues identified in the resultant contact profile and the oligomerization ability of the mutant proteins was tested using the lambdacI repressor system to identify residues that are hot spots in OxyR. We compared the properties of these hot spots to those described in the literature from other systems. The hot spots identified in this study are not especially conserved amongst a set of OxyR orthologs.

The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators

LysR-type transcriptional regulators (LTTRs) form the largest family of bacterial regulators acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes. The LTTR, CrgA, from the human pathogen Neisseria meningitidis, is upregulated during bacterial-host cell contact. Here, we report the crystal structures of both regulatory domain and full-length CrgA, the first of a novel subclass of LTTRs that form octameric rings. Non-denaturing mass spectrometry analysis and analytical ultracentrifugation established that the octameric form of CrgA is the predominant species in solution in both the presence and absence of an oligonucleotide encompassing the CrgA-binding sequence. Furthermore, analysis of the isolated CrgA-DNA complex by mass spectrometry showed stabilization of a double octamer species upon DNA binding. Based on the observed structure and the mass spectrometry findings, a model is proposed in which a hexadecameric array of two CrgA oligomers binds to its DNA target site.

SUMO proteases: redox regulation and biological consequences

Small-ubiquitin modifier (SUMO) has emerged as a novel modification system that governs the activities of a wide spectrum of protein substrates. SUMO-specific proteases (SENP) are of particular interest, as they are responsible for both the maturation of SUMO precursors and for their deconjugation. The interruption of SENPs has been implicated in embryonic defects and carcinoma cells, indicating that a proper balance of SUMO conjugation and deconjugation is crucial. Recent advances in molecular and cellular biology have highlighted the distinct subcellular localization, and endopeptidase and isopeptidase activities of SENPs, suggesting that they are nonredundant. A better understanding of the molecular basis of SUMO recognition and hydrolytic cleavage has been obtained from the crystal structures of SENP-substrate complexes. While a number of proteomic studies have shown an upregulation of sumoylation, attention is now increasingly being directed towards the regulatory mechanism of sumoylation, in particular the oxidative effect. Findings on the oxidation-induced intermolecular disulfide of E1-E2 ligases and SENP1/2 have improved our understanding of the mechanism by which modification is switched up or down. More intriguingly, a growing body of evidence suggests that sumoylation cross-talks with other modifications, and that the upstream and downstream signaling pathway is co-regulated by more than one modifier.

Kinetic and thermodynamic aspects of cellular thiol-disulfide redox regulation

Regulation of intracellular thiol-disulfide redox status is an essential part of cellular homeostasis. This involves the regulation of both oxidative and reductive pathways, production of oxidant scavengers and, importantly, the ability of cells to respond to changes in the redox environment. In the cytosol, regulatory disulfide bonds are typically formed in spite of the prevailing reducing conditions and may thereby function as redox switches. Such disulfide bonds are protected from enzymatic reduction by kinetic barriers and are thus allowed to exist long enough to elicit the signal. Factors that affect the rate of thiol-disulfide exchange and stability of disulfide bonds are discussed within the framework of the underlying chemical foundations. This includes the effect of thiol acidity (pK(a)), the local electrostatic environment, molecular strain, and entropy. Even though a thiol-disulfide exchange reaction is thermodynamically favorable, it will only take place if the activation energy to form the transition state complex can be overcome. This is accomplished by enzymes, such as the oxidoreductases, that direct reactions in thermodynamically favorable directions by decreasing the activation energy barrier.

Redox-switch modulation of human SSADH by dynamic catalytic loop

Succinic semialdehyde dehydrogenase (SSADH) is involved in the final degradation step of the inhibitory neurotransmitter gamma-aminobutyric acid by converting succinic semialdehyde to succinic acid in the mitochondrial matrix. SSADH deficiency, a rare autosomal recessive disease, exhibits variable clinical phenotypes, including psychomotor retardation, language delay, behaviour disturbance and convulsions. Here, we present crystal structures of both the oxidized and reduced forms of human SSADH. Interestingly, the structures show that the catalytic loop of the enzyme undergoes large structural changes depending on the redox status of the environment, which is mediated by a reversible disulphide bond formation between a catalytic Cys340 and an adjacent Cys342 residues located on the loop. Subsequent in vivo and in vitro studies reveal that the 'dynamic catalytic loop' confers a response to reactive oxygen species and changes in redox status, indicating that the redox-switch modulation could be a physiological control mechanism of human SSADH. Structural basis for the substrate specificity of the enzyme and the impact of known missense point mutations associated with the disease pathogenesis are presented as well.

Influence of polyphenols on Escherichia coli resistance to oxidative stress

Among all polyphenols tested (tannic acid and flavonoids belonging to different subclasses) only tannin and quercetin significantly enhanced resistance of Escherichia coli to peroxide stress. Pretreatment of the cells with quercetin and tannin resulted in a decrease in the growth arrest duration under moderate H(2)O(2) concentration (2 mM) and an increase in survival under high (10 mM) doses. The shorter growth recovery period in pretreated cells was connected with more rapid H(2)O(2) elimination because of induced activity of scavenging enzymes. This effect was absent in the Delta oxyR mutant, which was unable to induce genes responding to peroxide stress. The data obtained suggest that the observed protection was a result of two overlapping effects: induction of OxyR regulon by low concentrations of H(2)O(2), accumulated during extracellular autoxidation of quercetin and tannin, and protection of synthesis of OxyR-regulated antioxidant enzymes during H(2)O(2) stress because of intracellular binding of iron by quercetin and tannin and suppressing Fenton chemistry.

OxyR is involved in the expression of thioredoxin reductase TrxB in Pseudomonas putida

OxyR regulates the expression of a peroxiredoxin (AhpC) and two catalases (KatA and KatB), which play roles in peroxide protection, at the transcription level in Pseudomonas putida KT2442. Proteome analysis indicated significantly increased amounts of the enzymes AhpC, KatA, KatB, and a peroxiredoxin reductase (AhpF) in the oxyR1 mutant cells; these increases reflected the upregulation of the expression of the genes encoding these enzymes. Additionally, although the effect of oxyR1 mutation on the trxB transcript level was not clearly evident, it increased the amount of thioredoxin reductase (TrxB) by fivefold. Primer extension analysis revealed that trxB was constitutively transcribed from the P1 site; however, hydrogen peroxide treatment lowered the transcription of trxB from P1 but induced its transcription from P2. Adjacent to the -35 base of the P2 initiation site, sequences similar to those involved in the proposed OxyR binding in Escherichia coli were found in a region to which OxyR was shown to bind. These observations suggest that in P. putida, OxyR regulates TrxB expression by promoting trxB transcription from the P2 site when oxidative stresses lowered the transcription from the constitutive P1 site.

OxyR tightly regulates catalase expression in Neisseria meningitidis through both repression and activation mechanisms

Mechanisms for coping with oxidative stress (OS) are crucial for the survival of pathogenic Neisseria spp. in the human host. In this study we investigate the mechanism by which OxyR finely regulates the catalase gene (kat) in Neisseria meningitidis. Detailed transcriptional analyses show that catalase is transcribed from a single promoter that is induced by H(2)O(2) in an OxyR-dependent manner and two key cysteine residues are essential for this. OxyR also represses the kat promoter: kat expression in the null mutant is at a constitutive intermediary level higher than uninduced, but lower than H(2)O(2)-induced levels in the wild type. Our data are consistent with a model in which OxyR binds to the kat promoter and exerts: (i) repression of transcription in the absence of OS signal and (ii) activation of the promoter in response to OS signal. This direct double-edged mechanism may ensure tight regulatory control of kat expression ensuring catalase is synthesized only when needed. In addition, our results provide an explanation for the altered OS resistance phenotypes seen in Neisseria mutant strains where, paradoxically, the oxyR mutants are more resistant than the wild type in oxidative killing assays.

Loss of the oxidative stress regulator OxyR in Pseudomonas aeruginosa PAO1 impairs growth under iron-limited conditions

Pyoverdine is the main siderophore secreted by fluorescent pseudomonads to scavenge iron in the extracellular environment. Iron uptake, however, needs to be tightly regulated, because free iron stimulates the formation of highly toxic oxygen derivatives. In the opportunistic pathogen Pseudomonas aeruginosa, the transcriptional regulator OxyR plays a key role in the upregulation of defense mechanisms against oxidative stress as it stimulates the expression of the antioxidant genes katB, ahpB and ahpCF after contact with oxidative stress-generating agents. Inactivation of the oxyR gene in Pseudomonas fluorescens ATCC 17400 and in P. aeruginosa PAO1 impairs pyoverdine-mediated iron uptake. The pyoverdine utilization defect can be restored by complementation with the oxyR gene of P. aeruginosa, as well as by adding catalase. Growth of the oxyR mutant in low- or high-iron media is also impaired at a low, but not at a high inoculum density. Uptake of radioactive (59)Fe pyoverdine is, however, not affected by the oxyR mutation, nor is the transcription of the fpvA gene encoding the ferripyoverdine receptor, suggesting that the defect lies in the inability to remove iron from the ferrisiderophore.

A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus

Oxidative stress serves as an important host/environmental signal that triggers a wide range of responses from the human pathogen Staphylococcus aureus. Among these, a thiol-based oxidation sensing pathway through a global regulator MgrA controls the virulence and antibiotic resistance of the bacterium. Herein, we report a new thiol-based oxidation sensing and regulation system that is mediated through a parallel global regulator SarZ. SarZ is a functional homologue of MgrA and is shown to affect the expression of approximately 87 genes in S. aureus. It uses a key Cys residue, Cys-13, to sense oxidative stress and to co-ordinate the expression of genes involved in metabolic switching, antibiotic resistance, peroxide stress defence, virulence, and cell wall properties. The discovery of this SarZ-mediated regulation, mostly independent from the MgrA-based regulation, fills a missing gap of oxidation sensing and response in S. aureus.

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Background

Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue.

Results

Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues.

Conclusion

We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.

Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein

In Bacillus subtilis, PerR is a metal-dependent sensor of hydrogen peroxide. PerR is a dimeric zinc protein with a regulatory site that coordinates either Fe(2+) (PerR-Zn-Fe) or Mn(2+) (PerR-Zn-Mn). Though most of the peroxide sensors use cysteines to detect H(2)O(2), it has been shown that reaction of PerR-Zn-Fe with H(2)O(2) leads to the oxidation of one histidine residue. Oxidation of PerR leads to the incorporation of one oxygen atom into His37 or His91. This study presents the crystal structure of the oxidized PerR protein (PerR-Zn-ox), which clearly shows a 2-oxo-histidine residue in position 37. Formation of 2-oxo-histidine is demonstrated and quantified by HPLC-MS/MS. EPR experiments indicate that PerR-Zn-H37ox retains a significant affinity for the regulatory metal, whereas PerR-Zn-H91ox shows a considerably reduced affinity for the metal ion. In spite of these major differences in terms of metal binding affinity, oxidation of His37 and/or His91 in PerR prevents DNA binding.

Transcriptional activation in yeast in response to copper deficiency involves copper-zinc superoxide dismutase

Copper is an essential trace element, yet excess copper can lead to membrane damage, protein oxidation, and DNA cleavage. To balance the need for copper with the necessity to prevent accumulation to toxic levels, cells have evolved sophisticated mechanisms to regulate copper acquisition, distribution, and storage. In Saccharomyces cerevisiae, transcriptional responses to copper deficiency are mediated by the copper-responsive transcription factor Mac1. Although Mac1 activates the transcription of genes involved in high affinity copper uptake during periods of deficiency, little is known about the mechanisms by which Mac1 senses or responds to reduced copper availability. Here we show that the copper-dependent enzyme Sod1 (Cu,Zn-superoxide dismutase) and its intracellular copper chaperone Ccs1 function in the activation of Mac1 in response to an external copper deficiency. Genetic ablation of either CCS1 or SOD1 results in a severe defect in the ability of yeast cells to activate the transcription of Mac1 target genes. The catalytic activity of Sod1 is essential for Mac1 activation and promotes a regulated increase in binding of Mac1 to copper response elements in the promoter regions of genomic Mac1 target genes. Although there is precedent for additional roles of Sod1 beyond protection of the cell from oxygen radicals, the involvement of this protein in copper-responsive transcriptional regulation has not previously been observed. Given the presence of both Sod1 and copper-responsive transcription factors in higher eukaryotes, these studies may yield important insights into how copper deficiency is sensed and appropriate cellular responses are coordinated.

Myosin as a potential redox-sensor: an in vitro study

A balanced redox status is necessary to optimize force production in contractile apparatus, where free radicals generated by skeletal muscle are involved in some basic physiological processes like excitation-contraction coupling. Protein glutathionylation has a key role in redox regulation of proteins and signal transduction. Here we show that myosin is sensitive to in vitro glutathionylation and MALDI-TOF analysis identified three potential sites of glutathione binding, two of them locating on the myosin head. Glutathionylation of myosin has an important impact on the protein structure, as documented by the lower fluorescence quantum yield of glutathionylated myosin and its increased susceptibility to the proteolytic cleavage. Myosin function is also sensitive to glutathionylation, which modulates its ATPase activity depending on GSSG redox balance. Thus, like the phosphorylation/dephosphorylation cycle, glutathionylation may represent a mechanism by which glutathione modulates sarcomere functions depending on the tissue redox state, and myosin may constitute a muscle redox-sensor.

Cellular defenses against superoxide and hydrogen peroxide

Life evolved in an anaerobic world; therefore, fundamental enzymatic mechanisms and biochemical pathways were refined and integrated into metabolism in the absence of any selective pressure to avoid reactivity with oxygen. After photosystem II appeared, environmental oxygen levels rose very slowly. During this time, microorganisms acquired oxygen tolerance by jettisoning enzymes that use glycyl radicals and exposed low-potential iron-sulfur clusters, which can be directly poisoned by oxygen. They also developed mechanisms to defend themselves against superoxide (O(2)()) and hydrogen peroxide, partially reduced oxygen species that are generated as inadvertent by-products of aerobic metabolism. Contemporary organisms have inherited both the vulnerabilities and the defenses of these ancestral microbes. Current research seeks to identify these, and bacteria comprise an exceptionally accessible experimental system that has provided many of the answers. This manuscript reviews recent developments and identifies remaining puzzles.

Thiol chemistry and specificity in redox signaling

Exposure of cells to sublethal oxidative stress results in the modulation of various signaling pathways. Oxidants can activate and inactivate transcription factors, membrane channels, and metabolic enzymes, and regulate calcium-dependent and phosphorylation signaling pathways. Oxidation and reduction of thiol proteins are thought to be the major mechanisms by which reactive oxidants integrate into cellular signal transduction pathways. This review focuses on mechanisms for sensing and transmitting redox signals, from the perspective of their chemical reactivity with specific oxidants. We discuss substrate preferences for different oxidants and how the kinetics of these reactions determines how each oxidant will react in a cell. This kinetic approach helps to identify initial oxidant-sensitive targets and elucidate mechanisms involved in transmission of redox signals. It indicates that only those proteins with very high reactivity, such as peroxiredoxins, are likely to be direct targets for hydrogen peroxide. Other more modestly reactive thiol proteins such as protein tyrosine phosphatases are more likely to become oxidized by an indirect mechanism. The review also examines oxidative changes observed during receptor-mediated signaling, the strengths and limitations of detection methods for reactive oxidant production, and the evidence for hydrogen peroxide acting as the second messenger. We discuss areas where observations in cell systems can be rationalized with the reactivity of specific oxidants and where further work is needed to understand the mechanisms involved.