Protein S-nitrosylation: Role for nitric oxide signaling in neuronal death

Background

One of the signaling mechanisms mediated by nitric oxide (NO) is through S-nitrosylation, the reversible redox-based modification of cysteine residues, on target proteins that regulate a myriad of physiological and pathophysiological processes. In particular, an increasing number of studies have identified important roles for S-nitrosylation in regulating cell death.

Scope of review

The present review focuses on different targets and functional consequences associated with nitric oxide and protein S-nitrosylation during neuronal cell death.

Major conclusions

S-Nitrosylation exhibits double-edged effects dependent on the levels, spatiotemporal distribution, and origins of NO in the brain: in general Snitrosylation resulting from the basal low level of NO in cells exerts anti-cell death effects, whereas S-nitrosylation elicited by induced NO upon stressed conditions is implicated in pro-cell death effects.

General Significance

Dysregulated protein S-nitrosylation is implicated in the pathogenesis of several diseases including degenerative diseases of the central nervous system (CNS). Elucidating specific targets of S-nitrosylation as well as their regulatory mechanisms may aid in the development of therapeutic intervention in a wide range of brain diseases.     

S-nitrosylation of surfactant protein D as a modulator of pulmonary inflammation

Background

Surfactant protein D (SP-D) is a member of the family of proteins termed collagen-like lectins or “collectins” that play a role in non-antibody-mediated innate immune responses [1]. The primary function of SP-D is the modulation of host defense and inflammation [2].

Scope of review

This review will discuss recent findings on the physiological importance of SP-D S-nitrosylation in biological systems and potential mechanisms that govern SP-D mediated signaling.

Major conclusions

SP-D appears to have both pro- and anti-inflammatory signaling functions.SP-D multimerization is a critical feature of its function and plays an important role in efficient innate host defense. Under baseline conditions, SP-D forms a multimer in which the N-termini are hidden in the center and the C-termini are on the surface. This multimeric form of SP-D is limited in its ability to activate inflammation. However, NO can modify key cysteine residues in the hydrophobic tail domain of SP-D resulting in a dissociation of SP-D multimers into trimers, exposing the S-nitrosylated N-termini. The exposed S-nitrosylated tail domain binds to the calreticulin/CD91 receptor complex and initiates a pro-inflammatory response through phosphorylation of p38 and NF-κB activation [3,4]. In addition, the disassembled SP-D loses its ability to block TLR4, which also results in activation of NF-κB.

General significance

Recent studies have highlighted the capability of NO to modify SP-D through S-nitrosylation, causing the activation of a pro-inflammatory role for SP-D [3]. This represents a novel mechanism both for the regulation of SP-D function and NO's role in innate immunity, but also demonstrates that the S-nitrosylation can control protein function by regulating quaternary structure. This article is part of a Special Issue entitled Regulation of Cellular Processes by S-nitrosylation.     

Protein Microarray Characterization of the S-Nitrosoproteome

Nitric oxide (NO) mediates a substantial part of its physiologic functions via S-nitrosylation, however the cellular substrates for NO-mediated S-nitrosylation are largely unknown. Here we describe the S-nitrosoproteome using a high-density protein microarray chip containing 16,368 unique human proteins. We identified 834 potentially S-nitrosylated human proteins. Using a unique and highly specific labeling and affinity capture of S-nitrosylated proteins, 138 cysteine residues on 131 peptides in 95 proteins were determined, defining critical sites of NO''s actions. Of these cysteine residues 113 are novel sites of S-nitrosylation. A consensus sequence motif from these 834 proteins for S-nitrosylation was identified, suggesting that the residues flanking the S-nitrosylated cysteine are likely to be the critical determinant of whether the cysteine is S-nitrosylated. We identify eight ubiquitin E3 ligases, RNF10, RNF11, RNF41, RNF141, RNF181, RNF208, WWP2, and UBE3A, whose activities are modulated by S-nitrosylation, providing a unique regulatory mechanism of the ubiquitin proteasome system. These results define a new and extensive set of proteins that are susceptible to NO regulation via S-nitrosylation. Similar approaches could be used to identify other post-translational modification proteomes.It is known that NO regulates the majority of its physiologic function through S-nitrosylation (1). Protein-assisted or small molecule, S-nitrosoglutathione (GSNO)¹ trans-nitrosylation, oxidative S-nitrosation, and metalloprotein-catalyzed S-nitrosylation are the prominent cellular mechanisms that are utilized to S-nitrosylate proteins (2). A number of proteins are known to be S-nitrosylated and this post-translational modification can either activate or inactivate a protein''s biologic activity (1, 3). A number of attempts at probing tissue-specific S-nitrosoproteomes have been made, but the results of these are limited to proteins that are S-nitrosylated to a great degree and which are present at high concentrations (2, 4–6). Recently, to investigate determinants of S-nitrosylation, yeast and human target protein microarrays have been studied. However, these assay were limited because of the small number of proteins present on the chip (7). In addition, many proteins that are known to be S-nitrosylated have been studied through a targeted and biased approach (8). To overcome these shortcomings, we report the use of a 16,368 human protein microarray chip to better define the human S-nitrosoproteome.Ubiquitin is a 76-amino-acid long polypeptide that can be covalently added to lysine residues on targeted proteins either as single monomers or in chains. Ubiquitination of proteins can dramatically alter their function or localization depending on the number of ubiquitin attached and the nature of their linkages. The most well characterized ubiquitin-mediated process is targeting of the protein for degradation by the 26S proteasome, which occurs via poly-ubiquitination linked together through lysine 48 on the ubiquitin monomers. Ubiquitination occurs in a three-step enzymatic process in which the third enzyme, the ubiquitin protein ligase (E3) determines protein target specificity (9). NO S-nitrosylates the RING finger E3 ligases, parkin and XIAP, modifying their function (10, 11). In the case of parkin, S-nitrosylation transiently activates its E3 ligase activity, but ultimately inhibits its activity (12). In contrast, XIAP''s E3 ligase activity is unaffected by S-nitrosylation, but its anti-apoptotic function is compromised (11). Using the 16,368 human protein microarray, we identify a number of NO-regulated E3 ligases, the majority of which are activated by NO-dependent S-nitrosylation.     

Sinapinic acid can replace ascorbate in the biotin switch assay

Background

Protein S-nitrosation is an important post-translational modification altering protein function. Interaction of nitric oxide with thiols is an active area of research, and is one of the mechanisms by which NO exerts its biological effects. Biotin switch assay is the method, which has been developed to identify S-nitrosated proteins. The major concern with biotin switch assay includes reducing disulfide which may lead to false positives. We report a modification of the biotin switch assay where sinapinic acid is utilized instead of ascorbate to eliminate potential artifacts in the detection of S-nitrosated proteins.

Methods

The denitrosation ability of sinapinic acid was assessed by monitoring either the NO or NO₂^- released by chemiluminescent NO detection or by the griess assay, respectively. DTNB assay was used to compare disulfide reduction by ascorbate and sinapinic acid. Sinapinic acid and ascorbate were compared in the biotin switch detection of S-nitrosoproteins in RAW 264.7 cells ± S-nitrosocysteine (CysNO) exposure.

Results

We show that sinapinic acid has the ability to denitrosate S-nitrosothiols at pH 7.0 and denitrate plus denitrosate at pHs 8 and 8.5. Unlike ascorbate, sinapinic acid degrades S-nitrosothiols, but it does not reduce disulfide bridges.

Conclusions

Sinapinic acid denitrosate RSNO and does not reduce disulfides. Thus can readily replace ascorbate in detection of S-nitrosated proteins in biotin switch assay.

General significance

The work described is important in view of protein S-nitrosation. In this study we provide an important modification that eliminates artifacts in widely used technique for detecting the S-nitrosoproteome, the biotin switch assay.     

Redox atlas of the mouse : Immunohistochemical detection of glutaredoxin-, peroxiredoxin-, and thioredoxin-family proteins in various tissues of the laboratory mouse

Background

Oxidoreductases of the thioredoxin family of proteins have been thoroughly studied in numerous cellular and animal models mimicking human diseases. Despite of their well documented role in various disease conditions, no systematic information on the presence of these proteins is available.

Methods

Here, we have systematically analyzed the presence of some of the major constituents of the glutaredoxin (Grx)-, peroxiredoxin (Prx)-, and thioredoxin (Trx)-systems, i.e. Grx1, Grx2, Grx3 (TXNL-2/PICOT), Grx5, nucleoredoxin (Nrx), Prx1, Prx2, Prx3, Prx4, Prx5, Prx6, Trx1, thioredoxin reductase 1 (TrxR1), Trx2, TrxR2, and γ-glutamyl cysteine synthetase (γ-GCS) in various tissues of the mouse using immunohistochemistry.

Results

The identification of the Trx family proteins in the central nervous system, sensory organs, digestive system, lymphatic system, reproductive system, urinary system, respiratory system, endocrine system, skin, heart, and muscle revealed a number of significant differences between these proteins with respect to their distribution in these tissues.

Conclusion

Our results imply more specific functions and interactions between the proteins of this family than previously assumed.

General significance

Crucial functions of Trx family proteins have been demonstrated in various disease conditions. A detailed overview on their distribution in various tissues will be helpful to fully comprehend their potential role and the interactions of these proteins in the most thoroughly studied model for human diseases—the laboratory mouse.This article is part of a Special Issue entitled Human and Murine Redox Protein Atlases.     

Thioredoxin and glutaredoxin system proteins—immunolocalization in the rat central nervous system

Background

The oxidoreductases of the thioredoxin (Trx) family of proteins play a major role in the cellular response to oxidative stress. Redox imbalance is a major feature of brain damage. For instance, neuronal damage and glial reaction induced by a hypoxic–ischemic episode is highly related to glutamate excitotoxicity, oxidative stress and mitochondrial dysfunction. Most animal models of hypoxia–ischemia in the central nervous system (CNS) use rats to study the mechanisms involved in neuronal cell death, however, no comprehensive study on the localization of the redox proteins in the rat CNS was available.

Methods

The aim of this work was to study the distribution of the following proteins of the thioredoxin and glutathione/glutaredoxin (Grx) systems in the rat CNS by immunohistochemistry: Trx1, Trx2, TrxR1, TrxR2, Txnip, Grx1, Grx2, Grx3, Grx5, and γ-GCS, peroxiredoxin 1 (Prx1), Prx2, Prx3, Prx4, Prx5, and Prx6. We have focused on areas most sensitive to a hypoxia–ischemic insult: Cerebellum, striatum, hippocampus, spinal cord, substantia nigra, cortex and retina.

Results and conclusions

Previous studies implied that these redox proteins may be distributed in most cell types and regions of the CNS. Here, we have observed several remarkable differences in both abundance and regional distribution that point to a complex interplay and crosstalk between the proteins of this family.

General significance

We think that these data might be helpful to reveal new insights into the role of thiol redox pathways in the pathogenesis of hypoxia–ischemia insults and other disorders of the CNS.This article is part of a Special Issue entitled Human and Murine Redox Protein Atlases.     

Central bombesin possibly induces S-nitrosylation of cyclooxygenase-1 in pre-sympathetic neurons of rat hypothalamic paraventricular nucleus

Aims

Cyclooxygenase (COX) can be activated by nitric oxide-induced (NO-induced) conversion of cysteine thiol group of COX into S-nitrosothiol. We previously reported the involvement of brain COX/NO synthase (NOS) in centrally administered bombesin-, a stress-related neuropeptide, induced secretion of rat adrenal noradrenaline and adrenaline. To examine a possible involvement of the NO-induced modification of COX in bombesin-induced response, we investigated whether bombesin induces close proximity of COX-1 and neuronal NOS (nNOS) or S-nitroso-cysteine in pre-sympathetic spinally projecting neurons in the rat hypothalamic paraventricular nucleus (PVN), a regulatory center of adrenomedullary outflow.

Main methods

In twelve-week-old male Wistar rats, pre-sympathetic spinally projecting neurons in the PVN were labeled with a retrograde tracer Fluoro-Gold (FG). After intracerebroventricular administration of bombesin, we performed double immunohistochemical analysis for Fos and COX-1 or nNOS in FG-labeled PVN neurons. We also performed a fluorescent in situ proximity ligation assay (PLA) for visualizing of close proximity (< 40 nm) of COX-1 with nNOS or S-nitroso-cysteine.

Key. findings

Bombesin significantly increased the number of Fos-immunoreactive cells in FG-labeled PVN neurons with COX-1 or nNOS immunoreactivity. 7-Nitroindazole, a selective nNOS inhibitor, abolished Fos-immunoreactivity induced by bombesin in COX-1-immunoreactive FG-labeled PVN neurons. Bombesin also induced PLA-positive signals indicating close proximity of COX-1/nNOS and COX-1/S-nitroso-cysteine in FG-labeled PVN neurons.

Significance

Centrally administered bombesin possibly induces S-nitrosylation of COX-1 through close proximity of COX-1 and nNOS in pre-sympathetic spinally projecting PVN neurons, thereby activating COX-1 during the bombesin-induced activation of central adrenomedullary outflow in the rat.     

Redox Regulatory Mechanism of Transnitrosylation by Thioredoxin

Transnitrosylation and denitrosylation are emerging as key post-translational modification events in regulating both normal physiology and a wide spectrum of human diseases. Thioredoxin 1 (Trx1) is a conserved antioxidant that functions as a classic disulfide reductase. It also catalyzes the transnitrosylation or denitrosylation of caspase 3 (Casp3), underscoring its central role in determining Casp3 nitrosylation specificity. However, the mechanisms that regulate Trx1 transnitrosylation and denitrosylation of specific targets are unresolved. Here we used an optimized mass spectrometric method to demonstrate that Trx1 is itself nitrosylated by S-nitrosoglutathione at Cys⁷³ only after the formation of a Cys³²-Cys³⁵ disulfide bond upon which the disulfide reductase and denitrosylase activities of Trx1 are attenuated. Following nitrosylation, Trx1 subsequently transnitrosylates Casp3. Overexpression of Trx1^C32S/C35S (a mutant Trx1 with both Cys³² and Cys³⁵ replaced by serine to mimic the disulfide reductase-inactive Trx1) in HeLa cells promoted the nitrosylation of specific target proteins. Using a global proteomics approach, we identified 47 novel Trx1 transnitrosylation target protein candidates. From further bioinformatics analysis of this set of nitrosylated peptides, we identified consensus motifs that are likely to be the determinants of Trx1-mediated transnitrosylation specificity. Among these proteins, we confirmed that Trx1 directly transnitrosylates peroxiredoxin 1 at Cys¹⁷³ and Cys⁸³ and protects it from H₂O₂-induced overoxidation. Functionally, we found that Cys⁷³-mediated Trx1 transnitrosylation of target proteins is important for protecting HeLa cells from apoptosis. These data demonstrate that the ability of Trx1 to transnitrosylate target proteins is regulated by a crucial stepwise oxidative and nitrosative modification of specific cysteines, suggesting that Trx1, as a master regulator of redox signaling, can modulate target proteins via alternating modalities of reduction and nitrosylation.Nitric oxide (NO) is an important second messenger for signal transduction in cells. The production of cGMP by guanylyl cyclase, enabled by the binding of NO onto heme, is considered the primary mechanism responsible for the plethora of functions exerted by NO (1). However, S-nitrosylation, the covalent addition of the NO moiety onto cysteine thiols, is increasingly recognized as an important post-translational modification for regulating protein functions (for reviews, see Refs. 2 and 3). S-Nitrosylation is dynamic, reversible, site-specific, and modulated by selected cellular stimuli (4–7). With improved detection sensitivity, an increasing number of S-nitrosylated proteins have been identified by proteomics technologies (5, 8–13). Among the known modified proteins, nitrosylation occurs only on selected cysteines (4, 6, 14–17). Non-enzymatic mechanisms proposed to determine S-nitrosylation specificity include the availability of specific NO donors and protein microenvironments that stabilize the pK_a of acidic target cysteines (18). Furthermore, several enzymes, including hemoglobin (19, 20), superoxide dismutase 1 (21, 22), S-nitrosoglutathione reductase (23–25), and protein-disulfide isomerase (26), have been shown to possess either transnitrosylase or denitrosylase activities. However, an enzymatic system that governs site-specific transnitrosylation and denitrosylation, analogous to the kinase/phosphatase paradigm for regulating protein phosphorylation, has remained largely uncharacterized.Trx1¹ is an important antioxidant protein with protein reductase activity (27, 28). It has been characterized as an antiapoptotic protein because of its ability to suppress proapoptotic proteins, including apoptosis signal-regulating kinase 1 via disulfide reduction and Casp3 via transnitrosylation of Cys¹⁶³ (14, 29). Conversely, Trx1 can denitrosylate Casp3 at Cys¹⁶³, resulting in Casp3 activation (7). Trx1 appears to govern site-specific reversible nitrosylation of selected protein targets (14, 15), but what are the underlying mechanisms that regulate Trx1 transnitrosylation and denitrosylation activities? Are there additional Trx1-mediated transnitrosylation or denitrosylation targets that have not yet been identified? In this study, we used ESI-Q-TOF mass spectrometry (MS) to analyze the nitrosylation of Trx1 and a Casp3 peptide (Casp3p) under different redox conditions. Because of the labile nature of the S–NO bond, direct identification of S-nitrosylated proteins and their specific nitrosylation sites by MS remains challenging (8). A biotin switch method that is based on the derivatization of protein S–NO with a biotinylating agent is typically used for such analyses (8). However, like any indirect method, both false positive and negative identifications have been reported (30). Recently, we developed a method for direct analysis of protein S-nitrosylation by ESI-Q-TOF MS without prior chemical derivatization (31). Here we applied the same technique to determine the regulation of Trx1 by stepwise oxidative and nitrosative modifications of distinct cysteines and its subsequent ability to transnitrosylate target proteins. Nitrosative modification at Cys⁷³ of Trx1 cannot occur without prior attenuation of the Trx1 disulfide reductase and denitrosylase activities via either disulfide bond formation between Cys³² and Cys³⁵ or their mutation to serines. This is a key observation that has never been previously reported. Consequently, we designed a proteomics approach and discovered over 40 putative Trx1 transnitrosylation target proteins. We further characterized the Trx1 transnitrosylation proteome and identified three consensus motifs surrounding the putative Trx1 transnitrosylation sites, suggesting a protein-protein interaction mechanism for determining transnitrosylation specificity.     

Site-Specific Nitrosoproteomic Identification of Endogenously S-Nitrosylated Proteins in Arabidopsis

Nitric oxide (NO) regulates multiple developmental events and stress responses in plants. A major biologically active species of NO is S-nitrosoglutathione (GSNO), which is irreversibly degraded by GSNO reductase (GSNOR). The major physiological effect of NO is protein S-nitrosylation, a redox-based posttranslational modification mechanism by covalently linking an NO molecule to a cysteine thiol. However, little is known about the mechanisms of S-nitrosylation-regulated signaling, partly due to limited S-nitrosylated proteins being identified. In this study, we identified 1,195 endogenously S-nitrosylated peptides in 926 proteins from the Arabidopsis (Arabidopsis thaliana) by a site-specific nitrosoproteomic approach, which, to date, is the largest data set of S-nitrosylated proteins among all organisms. Consensus sequence analysis of these peptides identified several motifs that contain acidic, but not basic, amino acid residues flanking the S-nitrosylated cysteine residues. These S-nitrosylated proteins are involved in a wide range of biological processes and are significantly enriched in chlorophyll metabolism, photosynthesis, carbohydrate metabolism, and stress responses. Consistently, the gsnor1-3 mutant shows the decreased chlorophyll content and altered photosynthetic properties, suggesting that S-nitrosylation is an important regulatory mechanism in these processes. These results have provided valuable resources and new clues to the studies on S-nitrosylation-regulated signaling in plants.Nitric oxide (NO), a gaseous signaling molecule, plays important regulatory roles in higher plants, including seed dormancy and germination, root development and hypocotyl elongation, floral transition, senescence and cell death, phytohormone signaling, and responses to abiotic and biotic stresses (He et al., 2004; Besson-Bard et al., 2008; Hong et al., 2008; Neill et al., 2008; Leitner et al., 2009; Feng et al., 2013). S-Nitrosoglutathione (GSNO) is a major biologically active form of reactive nitrogen species (RNS) and functions as a primary NO donor. The endogenous GSNO homeostasis is highly dynamic, and the GSNO level is negatively regulated by GSNO reductase (GSNOR), an evolutionally conserved enzyme catalyzing irreversibly degrading GSNO (Liu et al., 2001). Mutations in the GSNOR gene cause the elevated GSNO level and consequently severe abnormalities under physiological and pathological conditions in various species (Liu et al., 2004; Feechan et al., 2005; Que et al., 2005; Lee et al., 2008; Chen et al., 2009; Moore et al., 2009; Kwon et al., 2012).In Arabidopsis (Arabidopsis thaliana), GSNOR1 is a single-copy gene, and the enzymatic activity of the encoded protein has been biochemically characterized (Sakamoto et al., 2002). Genetic studies revealed that the gsnor1-1 and gsnor1-2 mutants are gain-of-function mutations with increased GSNOR activity and a decreased cellular S-nitrosothiol level. Conversely, gsnor1-3 is a loss-of-function mutant with a significantly increased S-nitrosothiol level (Feechan et al., 2005). The defense responses mediated by distinct resistance (R) genes are significantly impaired in the gsnor1-3 mutant, and GSNOR1 functions as a positive regulator of the salicylic acid-regulated signaling network in the defense response (Feechan et al., 2005). In a genetic screen for thermotolerance-defective mutants, the sensitive to hot temperatures5 (hot5) mutant was characterized as having decreased heat acclimation and was shown to be allelic to gsnor1, indicating the importance of GSNOR1-regulated NO homeostasis in the regulation of the abiotic stress response (Lee et al., 2008). In an independent genetic screen for the oxidative stress-related mutants, the paraquat resistant2 (par2) mutant was also identified to be allelic to gsnor1, which showed an anti-cell death phenotype and multiple developmental defects, revealing the critical role of GSNOR1/HOT5/PAR2 in the regulation of oxidative stress-induced cell death (Chen et al., 2009). Similar to gsnor1-3, the hot5 and par2 allelic mutants also accumulate the significantly increased level of NO. As a result of this defect, these gsnor1/hot5/par2 mutants show a pleiotropic phenotype, with severe developmental abnormalities in both reproductive and vegetative stages (Lee et al., 2008; Chen et al., 2009; Kwon et al., 2012). These studies highlight the critical role of GSNOR1/HOT5/PAR2-modulated NO homeostasis in diverse physiological processes, including plant growth and development as well as in responses to both biotic and abiotic stresses. However, little is known about the underpinning molecular mechanisms of the NO-modulated signaling in various physiological processes.A major physiological effect of NO is executed by protein S-nitrosylation, a reversible posttranslational modification by covalent addition of an NO molecule onto a Cys thiol to form S-nitrosothiol (Jaffrey et al., 2001; Stamler et al., 2001). S-Nitrosothiols are dynamically labile in response to the intracellular redox status, allowing protein S-nitrosylation as a highly sensitive mechanism in the regulation of cellular signaling (Stamler et al., 2001; Hess et al., 2005). Emerging evidence indicates that S-nitrosylation regulates the function of the modified proteins by various mechanisms, including enzymatic activity, stability, subcellular localization, three-dimensional conformation changes, protein-protein interaction, and ligand binding (Hess et al., 2005; Wang et al., 2006; Astier et al., 2011; Gupta, 2011; Hess and Stamler, 2012). In Arabidopsis, S-nitrosylation has been shown as an important mechanism in regulating the stress responses. The activity of Met adenosyltransferase1 (MAT1), which catalyzes S-adenosyl-Met synthesis, was shown to be inhibited by S-nitrosylation (Lindermayr et al., 2006). S-nitrosylation negatively regulates the activity of a peroxynitrite detoxification enzyme, peroxiredoxin II E (PrxII E), and an NADPH oxidase, thereby modulating the oxidative stress in the defense response (Romero-Puertas et al., 2007; Yun et al., 2011). Moreover, S-nitrosylation has also been shown to regulate the conformational changes of NONEXPRESSOR OF PATHOGEN-RELATED1 (NPR1), a master regulator of the defense response, and the activity of SALICYLIC ACID-BINDING PROTEIN3 (SABP3), a key enzyme for salicylic acid biosynthesis (Tada et al., 2008; Wang et al., 2009). In addition, S-nitrosylation of TRANSPORT INHIBITOR RESPONSE1 (TIR1) and Arabidopsis Histidine Phosphotransfer Protein1 (AHP1), two key signaling components of the auxin and cytokinin pathways, respectively, plays an important role in regulating respective phytohormone signaling (Terrile et al., 2012; Feng et al., 2013). These studies illustrate the importance of S-nitrosylation in the regulation of diverse physiological processes in plants.S-Nitrosylation has been considered as one of the most important posttranslational modification mechanisms (Lane et al., 2001; Stamler et al., 2001; Hess et al., 2005). A growing number of S-nitrosylated proteins have been identified using the proteomic approach. To date, the S-nitrosoproteomic studies have identified more than 2,200 S-nitrosylated proteins, covering more than 4,100 S-nitrosylated Cys residues. Of those S-nitrosylated proteins, more than 95% were identified from mammals (Lee et al., 2012). Several proteomic studies in Arabidopsis identified a number of S-nitrosylated proteins (Lindermayr et al., 2005; Romero-Puertas et al., 2008; Palmieri et al., 2010; Fares et al., 2011; Puyaubert et al., 2014). In GSNO-treated cell suspension cultures and NO-treated leaves derived from Arabidopsis, 63 and 52 S-nitrosylated proteins were identified, which are involved in stress response, redox homeostasis, cytoskeleton organization, metabolic processes, and cellular signaling (Lindermayr et al., 2005). In an independent study, 16 S-nitrosylated proteins were identified from Arabidopsis seedlings undergoing the hypersensitive response (Romero-Puertas et al., 2008). In another independent analysis, 46 S-nitrosylated proteins were identified from cultured Arabidopsis suspension cells (Fares et al., 2011). In a more specific analysis, 11 mitochondria proteins were identified to be S-nitrosylated and/or glutathionylated (Palmieri et al., 2010). More recently, 62 endogenously S-nitrosylated proteins were identified from Arabidopsis seedlings (Puyaubert et al., 2014). Notably, a large number of the S-nitrosylated proteins are repeatedly identified in these analyses, thus confirming the validation of each study. Because of the labile nature of S-nitrosylation, most of the S-nitrosoproteomic studies used the protein samples treated with NO donors or the protein extracts prepared from NO donor-treated cells or tissues. The Arabidopsis gsnor1-3 mutants accumulate an excessive amount of NO (Feechan et al., 2005; Lee et al., 2008; Chen et al., 2009), and the identification of S-nitrosylated proteins in gsnor1-3 should depict a more comprehensive map of S-nitrosoproteome in Arabidopsis, and provide important clues on the molecular basis of the pleiotropic phenotype of the mutant.Because of the labile and dynamic nature of protein S-nitrosylation, large-scale identification of endogenously S-nitrosylated proteins remains technically challenging. At present, two major methods for identification of S-nitrosoproteome are shotgun and site-specific nitrosoproteomic analysis, both of which are based on the biotin-switch method and mass spectrometry (Jaffrey et al., 2001; Hao et al., 2006; Torta et al., 2008). In the shotgun analysis, S-nitrosylated proteins were first biotinylated, enriched by affinity-chromatography, and then identified by mass spectrometry. Although the method is relatively simple, the number of S-nitrosylated proteins identified by shotgun proteomics is often few due to various technical limitations (Torta et al., 2008). The identification capacity of nitrosoproteomics was greatly improved by the site-specific strategy, in which biotinylated proteins were first digested by trypsin and the enriched peptides were then characterized by mass spectrometry (Hao et al., 2006; Chen et al., 2010). Moreover, S-nitrosylated Cys residues can also be identified from site-specific nitrosoproteomic analysis.In this study, we performed a large-scale, site-specific proteomic analysis of endogenously S-nitrosylated proteins in Arabidopsis wild-type and gsnor1-3 seedlings, and identified 1,195 endogenously S-nitrosylated peptides in 926 proteins from the model plant species, representing the largest data set thus far reported in any organisms and providing important resources for future studies on S-nitrosylation-regulated signaling in plants.     

Albumin fusion renders thioredoxin an effective anti-oxidative and anti-inflammatory agent for preventing cisplatin-induced nephrotoxicity

Background

A strategy for preventing cisplatin nephrotoxicity due to enhanced oxidative stress and inflammatory response is highly desirable. Thioredoxin-1 (Trx), an endogenous redox-active protein, has a short retention time in the blood. A long acting form of Trx, human serum albumin-Trx (HSA-Trx), was produced by recombinant HSA fusion and its effectiveness in preventing cisplatin nephrotoxicity was examined.

Methods

HSA-Trx was prepared in Pichia expression system. Cisplatin-induced nephropathy mouse model was established by a single administration of cisplatin.

Results

Compared to saline, Trx or N-acetylcysteine, an intravenous administration of HSA-Trx attenuated the cisplatin-induced elevation in serum creatinine, blood urea nitrogen and urinary N-acetyl-β-d-glucosaminidase along with the decrease in creatinine clearance. HSA-Trx caused a substantial reduction in the histological features of renal tubular injuries and the apoptosis-positive tubular cells. Changes in superoxide, 8-OHdG, glutathione and nitrotyrosine levels indicated that HSA-Trx significantly suppressed renal oxidative stress. HSA-Trx also suppressed the elevation of TNF-α, IL-1β and IL-6. Administered fluorescein isothiocyanate-labeled HSA-Trx was found partially localized in the proximal tubular cells whereas majority remained in the blood circulation. Specific cellular uptake and the scavenging of intracellular reactive oxygen species by HSA-Trx were observed in HK-2 cells.

Conclusion

HSA-Trx could be a novel and effective approach for preventing cisplatin nephrotoxicity due to its prolonged anti-oxidative and anti-inflammatory action not only in extracellular compartment but also inside the proximal tubular cell.

General significance

We report the renoprotective effect of HSA-Trx against cisplatin nephrotoxicity. This work would enhance developing therapeutics against acute kidney injuries including cisplatin nephrotoxicity.     

DNA-maleimide: An improved maleimide compound for electrophoresis-based titration of reactive thiols in a specific protein

Background

Thiol-mediated redox regulation of proteins plays a key role in many cellular processes.

Methods

To understand the redox status of cysteinyl thiol groups of the desired proteins, we developed a new maleimide reagent: a maleimide-conjugated single strand DNA, DNA-maleimide (DNA-Mal).

Results

DNA-Mal labelled proteins run as a distinct band on SDS-PAGE, with a discrete 9.32 kDa mobility shift per label regardless of the protein species or electrophoretic conditions.

Conclusions

DNA-Mal labels free thiols like standard maleimide reagents, but possesses practical advantages in titration of the number and relative content of free thiols in a protein.

General significance

The versatility of DNA molecule enhances the application of DNA-Mal in a broader range of cysteine containing proteins.     

GPS-SNO: Computational Prediction of Protein S-Nitrosylation Sites with a Modified GPS Algorithm

As one of the most important and ubiquitous post-translational modifications (PTMs) of proteins, S-nitrosylation plays important roles in a variety of biological processes, including the regulation of cellular dynamics and plasticity. Identification of S-nitrosylated substrates with their exact sites is crucial for understanding the molecular mechanisms of S-nitrosylation. In contrast with labor-intensive and time-consuming experimental approaches, prediction of S-nitrosylation sites using computational methods could provide convenience and increased speed. In this work, we developed a novel software of GPS-SNO 1.0 for the prediction of S-nitrosylation sites. We greatly improved our previously developed algorithm and released the GPS 3.0 algorithm for GPS-SNO. By comparison, the prediction performance of GPS 3.0 algorithm was better than other methods, with an accuracy of 75.80%, a sensitivity of 53.57% and a specificity of 80.14%. As an application of GPS-SNO 1.0, we predicted putative S-nitrosylation sites for hundreds of potentially S-nitrosylated substrates for which the exact S-nitrosylation sites had not been experimentally determined. In this regard, GPS-SNO 1.0 should prove to be a useful tool for experimentalists. The online service and local packages of GPS-SNO were implemented in JAVA and are freely available at: http://sno.biocuckoo.org/.     

Powerful tumor cell growth-inhibiting activity of a synthetic derivative of atractyligenin: Involvement of PI3K/Akt pathway and thioredoxin system

Background

The semi-synthetic ent-kaurane 15-ketoatractyligenin methyl ester (SC2017) has been previously reported to possess high antiproliferative activity against several solid tumor-derived cell lines. Our study was aimed at investigating SC2017 tumor growth-inhibiting activity and the underlying mechanisms in Jurkat cells (T-cell leukemia) and xenograft tumor models.

Methods

Cell viability was evaluated by MTT assay. Cell cycle progression, reactive oxygen species (ROS) elevation and apoptotic hallmarks were monitored by flow cytometry. Inhibition of thioredoxin reductase (TrxR) by biochemical assays. Levels and/or activation status of signaling proteins were assessed by western blotting. Xenograft tumors were generated with HCT 116 colon carcinoma cells.

Results

SC2017 displayed cell growth-inhibiting activity against Jurkat cells (half maximal inhibitory concentration values (IC50) < 2 μM), but low cell-killing potential in human peripheral blood mononuclear cells (PBMC). The primary response of Jurkat cells to SC2017 was an arrest in G₂ phase followed by caspase-dependent apoptosis. Inhibition of PI3K/Akt pathway and TrxR activity by SC2017 was demonstrated by biochemical and pharmacological approaches. At least, SC2017 was found to inhibit xenograft tumor growth.

Conclusions

Our results demonstrate that SC2017 inhibits tumor cell growth in in vitro and in vivo models, but displays moderate toxicity against PBMC. We also demonstrate that SC2017 promotes caspase-dependent apoptosis in Jurkat cells by affecting Akt activation status and TrxR functionality.

General significance

Our observations suggest the semi-synthetic ent-kaurane SC2017 as a promising chemotherapeutic compound. SC2017 has, indeed, shown to possess tumor growth inhibiting activity and be able to counteract PI3K/Akt and Trx system survival signaling.     

Regulatory role of nitric oxide in the reduced survival of erythrocytes in visceral leishmaniasis

Background

Nitric oxide (NO) plays a vital role in maintaining the survivability of circulating erythrocytes. Here we have investigated whether NO depletion associated with visceral leishmaniasis (VL) is responsible for the reduced survival of erythrocytes observed during the disease.

Methods

Infected hamsters were treated with standard anti-leishmanial sodium stibogluconate (SAG) and NO donor isosorbide dinitrate (ISD). Erythrophagocytosis by macrophages was determined by labelling the cells with FITC followed by flow cytometry. Aggregation of band3 was estimated from band3 associated EMA fluorescence. Caspase 3 activity was measured using immunosorbent assay kit. Phosphatidylserine (PS) externalization and cell shrinkage were determined using annexin V. Aminophspholipid translocase and scramblase activities were measured following NBD-PS and NBD-PC internalization, respectively.

Results

Impairment of both synthesis and uptake of NO resulted in decreased bioavailability of this signaling molecule in erythrocytes in VL. NO level was replenished after simultaneous treatment with ISD and SAG. Combination treatment decreased red cell apoptosis in infected animals by deactivating caspase 3 through s-nitrosylation. Drug treatment prevented infection-mediated ATP depletion and altered calcium homeostasis in erythrocytes. Improved metabolic environment effectively amended dysregulation of aminophospholipid translocase and scramblase, which in turn reduced cell shrinkage, and exposure of phosphatidylserine on the cell surface under the diseased condition.

Conclusion and general significance

In this study, we have identified NO depletion to be an important factor in promoting premature hemolysis with the progress of leishmanial infection. The study implicates NO to be a possible target for future drug development towards the promotion of erythrocyte survival in VL.     

Transnitrosylating Nitric Oxide Species Directly Activate Type I Protein Kinase A, Providing a Novel Adenylate Cyclase-independent Cross-talk to ��-Adrenergic-like Signaling

The transnitrosylating nitric oxide (NO) donor nitrocysteine (CysNO) induced a disulfide bond between the two regulatory RI subunits of protein kinase A (PKA). The conventional NO donor S-nitroso-N-acetylpenicillamine failed to do this, consistent with our observation that it also did not promote protein S-nitrosylation. This disulfide oxidation event activated PKA and induced vasorelaxation independently of the classical β-adrenergic or NO signaling pathway. Activation of PKA had also been anticipated to exert a positive inotropic effect on the myocardium but did not. The lack of positive inotropy was explained by CysNO concomitantly activating protein kinase G (PKG) Iα. PKG was found to exert a partial negative inotropic influence regardless of whether PKA was activated by classical β-receptor stimulation or by disulfide bond formation. This work demonstrates that NO molecules that can induce S-nitrosylation directly activate type I PKA, providing a novel cross-talk to β-adrenergic-like signaling without receptor or adenylate cyclase stimulation. However, the expected positive inotropic consequences of PKA activation by this novel mechanism are countermanded by the simultaneous dual activation of PKGIα, which is also activated by CysNO.Nitric oxide (NO) initiates cell signaling by binding and activating soluble guanylate cyclase (sGC)² to produce the second messenger cGMP. cGMP primarily allosterically activates protein kinase G (PKG) but can also regulate other proteins. Although this NO-sGC-cGMP-PKG pathway is well defined (1), a second major mechanism of NO-dependent regulation has subsequently emerged. This involves NO covalently adducting to protein thiols, a process known as S-nitrosylation or S-nitrosation (2).Significant evidence continues to accumulate supporting protein S-nitrosylation as a fundamental regulator of protein and thus cell function (3). NO is produced in a regulated way (4), with a defined structural basis for selectivity in the proteins it covalently modifies (5, 6). Additional regulatory control can be achieved by the localization of NO synthase enzymes proximal to target proteins (6) and by reverse denitrosylation being enzymatically controlled (7). Indeed, many proteins appear to be basally S-nitrosylated, offering the potential for attenuation (8) as well as potentiation of signaling.Although stable regulatory S-nitrosylation occurs in some proteins, in others, it serves as an intermediate prior to transition to other redox states, especially disulfides (9). Previously, we searched for proteins that form interprotein disulfides in response to hydrogen peroxide (H₂O₂), identifying the regulatory RI subunit of protein kinase A (PKA) as such a protein (10, 11). This appears to activate the kinase (11), although the mechanism is not yet precisely defined. There is a rational structural basis for interprotein disulfide formation in PKA RI in response to H₂O₂. The RI dimer is held together by an N-terminal amphipathic leucine zipper in which the monomers are aligned antiparallel to each other with both Cys¹⁷ residues directly facing the corresponding Cys³⁸ residues on the opposite chains (12). H₂O₂-mediated RI disulfide formation is likely via protein sulfenic acid formation by one thiol in the Cys¹⁷ and Cys³⁸ disulfide-forming pair, prior to reduction by the other cysteine to yield the covalently conjugated dimer. Intriguingly, this pair of thiol-disulfide switches in RI is located directly on either side of the protein kinase A anchor protein-binding domain (13). This provides a rational structural basis for the PKA RI-protein kinase A anchor protein interaction being redox-modulated, as the interaction is strongly anticipated to change depending on the oxidation state of the cysteine switches, which flank the interaction locus (11).We hypothesized that NO may also be able to drive RI disulfide formation via an S-nitrosylated catalytic redox intermediate in a mechanism analogous to transient sulfenation formation during H₂O₂-induced covalent conjugation. This conceptual link between NO and PKA was investigated by comparing the biochemical and functional responses of cardiovascular tissue to the NO donors S-nitroso-N-acetylpenicillamine (SNAP) and nitrocysteine (CysNO). The authentic NO donor SNAP did not promote RI disulfide formation, whereas CysNO did so efficiently, consistent with its established thiol-oxidizing transnitrosylating ability. We show that disulfide-mediated activation of PKA significantly contributes to vasorelaxation induced by CysNO. However, disulfide activation of PKA failed to exert a positive inotropic influence in isolated hearts exposed to CysNO, which was difficult to reconcile with the kinase being truly activated by oxidation. Further investigations showed that this lack of positive inotropy following CysNO-induced oxidation is explained by the co-activation of PKGIα, which we demonstrated previously can be disulfide-activated (15). PKGIα serves as a master regulator of cardiac inotropy, dominating the system to prevent increases in cardiac contractility. Thus, thiol-oxidizing derivatives of NO can activate PKA and so exert β-adrenergic-like signaling, although dual activation of PKG prevents the anticipated positive inotropy.     

Regulation of Plant Glycine Decarboxylase by S-Nitrosylation and Glutathionylation

Mitochondria play an essential role in nitric oxide (NO) signal transduction in plants. Using the biotin-switch method in conjunction with nano-liquid chromatography and mass spectrometry, we identified 11 candidate proteins that were S-nitrosylated and/or glutathionylated in mitochondria of Arabidopsis (Arabidopsis thaliana) leaves. These included glycine decarboxylase complex (GDC), a key enzyme of the photorespiratory C₂ cycle in C3 plants. GDC activity was inhibited by S-nitrosoglutathione due to S-nitrosylation/S-glutathionylation of several cysteine residues. Gas-exchange measurements demonstrated that the bacterial elicitor harpin, a strong inducer of reactive oxygen species and NO, inhibits GDC activity. Furthermore, an inhibitor of GDC, aminoacetonitrile, was able to mimic mitochondrial depolarization, hydrogen peroxide production, and cell death in response to stress or harpin treatment of cultured Arabidopsis cells. These findings indicate that the mitochondrial photorespiratory system is involved in the regulation of NO signal transduction in Arabidopsis.Nitric oxide (NO) has emerged as a new chemical messenger in plant biology. It can interact with a variety of intracellular and extracellular targets, acting as either a cytotoxic or a cytoprotective agent. NO stimulates seed germination in different species, and a decrease in NO levels has been associated with fruit maturation and senescence of flowers (Beligni and Lamattina, 2001). NO production has been observed in response to several biotic and abiotic stimuli, such as pathogen infection, bacterial elicitors, high temperature, osmotic stress, and UV-B light (Durner et al., 1998; Barroso et al., 1999; Krause and Durner, 2004; Zeidler et al., 2004; Shapiro, 2005; Corpas et al., 2008; Kolbert et al., 2008; Zhao et al., 2009).Despite the proven importance of NO, little is known about signaling pathways downstream from it. During both programmed cell death and defense responses, NO requires cGMP and cADP Rib as secondary messengers (Wendehenne et al., 2001). Furthermore, NO activates mitogen-activated protein kinases in different plant species during stress signaling (Nakagami et al., 2005). However, direct biological activity of NO arises from chemical reactions between proteins and NO itself (Foster and Stamler, 2004; Dahm et al., 2006). S-Nitrosylation is a labile posttranslational modification with a half-life of seconds to a few minutes and represents a very sensitive mechanism for regulating cellular processes (Hess et al., 2005). More than 100 candidate S-nitrosylated proteins were identified from extracts of Arabidopsis (Arabidopsis thaliana) cultured cells treated with the NO donor S-nitrosoglutathione (GSNO) and from Arabidopsis leaves treated with gaseous NO (Lindermayr et al., 2005). Using the same proteomic approach, changes were characterized in S-nitrosylated proteins in Arabidopsis leaves undergoing a hypersensitive response (Romero-Puertas et al., 2008).In animals, mitochondria play a crucial role in S-nitrosylation-dependent NO signaling (Foster and Stamler, 2004). The mitochondrion is an essential organelle for normal cellular function, being an important site of ATP synthesis and an integrator for apoptotic signaling (Skulachev, 1999). Mitochondria interact with NO at several levels. One particularly well-characterized example is the inhibition of complex IV (cytochrome c oxidase) via binding of NO to its binuclear CuB/heme a₃ site (Cleeter et al., 1994). There are several reasons why S-nitrosylation may be an important mitochondrial regulatory mechanism. For example, mitochondria contain sizeable pools of thiols and transition metals, all of which are known to modulate nitrosothiol (SNO) biochemistry (Foster and Stamler, 2004). In addition, mitochondria are highly membranous and accumulate lipophilic molecules such as NO. Interesting in this respect is the fact that the formation of the S-nitrosylating intermediate N₂O₃ is enhanced within membranes (Burwell et al., 2006).The role of mitochondria in stress-related responses has been investigated in both animals and plants. Endogenous nitrosylation of the catalytic Cys site of a subset of mitochondrial caspases serves as an on/off switch regulating caspase activity during apoptosis (Mannick et al., 2001). Moreover, cytochrome c, which is modified by NO at its heme iron during apoptosis, is released from mitochondria into the cytoplasm, which plays a critical role in many forms of apoptosis by stimulating apoptosome formation and subsequent caspase activation (Schonhoff et al., 2003). We previously showed that a prime target of NO in plants is the mitochondrial apparatus, causing an inhibition of KCN-sensitive respiration and an activation of alternative respiration via alternative oxidase (AOX; Huang et al., 2002; Krause and Durner, 2004; Livaja et al., 2008).The aim of this study was to identify possible targets for S-nitrosylation in mitochondria of Arabidopsis leaves in order to gain more insight into the regulatory function of NO at the protein level. Using a proteomic approach involving the highly specific biotin-switch method for detection and purification of S-nitrosylated proteins (Jaffrey and Snyder, 2001) in conjunction with liquid chromatography and tandem mass spectrometry (nanoLC/MS/MS), we could identify 11 mitochondrial proteins as targets for S-nitrosylation. Among these identified proteins, we focused our attention on the P-subunit of the Gly decarboxylase complex (GDC), which is an integral part of the photorespiratory system. Since the release of apoptotic factors from mitochondria may be a result of inhibition of respiration, transition of mitochondrial permeability, and formation of reactive oxygen species (ROS; Saviani et al., 2002; Taylor et al., 2004; Chen and Gibson, 2008), we investigated the molecular mechanism and the function of GDC-Cys modification in Arabidopsis.     

<Emphasis Type="Italic">S</Emphasis>-Nitrosylation Regulates Cell Survival and Death in the Central Nervous System

Nitric oxide (NO), which is produced from nitric oxide synthase, is an important cell signaling molecule that is crucial for many physiological functions such as neuronal death, neuronal survival, synaptic plasticity, and vascular homeostasis. This diffusible gaseous compound functions as an effector or second messenger in many intercellular communications and/or cell signaling pathways. Protein S-nitrosylation is a posttranslational modification that involves the covalent attachment of an NO group to the thiol side chain of select cysteine residues on target proteins. This process is thought to be very important for the regulation of cell death, cell survival, and gene expression in the central nervous system (CNS). However, there have been few reports on the role of protein S-nitrosylation in CNS disorders. Here, we briefly review specific examples of S-nitrosylation, with particular emphasis on its functions in neuronal cell death and survival. An understanding of the role and mechanisms underlying the effects of protein S-nitrosylation on neurodegenerative/neuroprotective events may reveal a novel therapeutic strategy for rescuing neurons in neurodegenerative diseases.     

Nitric oxide is required for the auxin-induced activation of NADPH-dependent thioredoxin reductase and protein denitrosylation during root growth responses in arabidopsis

Background and Aims Auxin is the main phytohormone controlling root development in plants. This study uses pharmacological and genetic approaches to examine the role of auxin and nitric oxide (NO) in the activation of NADPH-dependent thioredoxin reductase (NTR), and the effect that this activity has on root growth responses in Arabidopsis thaliana.Methods Arabidopsis seedlings were treated with auxin with or without the NTR inhibitors auranofin (ANF) and 1-chloro-2, 4-dinitrobenzene (DNCB). NTR activity, lateral root (LR) formation and S-nitrosothiol content were measured in roots. Protein S-nitrosylation was analysed by the biotin switch method in wild-type arabidopsis and in the double mutant ntra ntrb.Key Results The auxin-mediated induction of NTR activity is inhibited by the NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (CPTIO), suggesting that NO is downstream of auxin in this regulatory pathway. The NTR inhibitors ANF and DNCB prevent auxin-mediated activation of NTR and LR formation. Moreover, ANF and DNCB also inhibit auxin-induced DR5 : : GUS and BA3 : : GUS gene expression, suggesting that the auxin signalling pathway is compromised without full NTR activity. Treatment of roots with ANF and DNCB increases total nitrosothiols (SNO) content and protein S-nitrosylation, suggesting a role of the NTR-thioredoxin (Trx)-redox system in protein denitrosylation. In agreement with these results, the level of S-nitrosylated proteins is increased in the arabidopsis double mutant ntra ntrb as compared with the wild-type.Conclusions The results support for the idea that NTR is involved in protein denitrosylation during auxin-mediated root development. The fact that a high NO concentration induces NTR activity suggests that a feedback mechanism to control massive and unregulated protein S-nitrosylation could be operating in plant cells.