Proteomic identification of S-nitrosylated proteins in Arabidopsis

Molecular mechanisms of generation for nitric oxide and reactive oxygen species, and role of the radical burst in plant immunity

Rapid production of nitric oxide (NO) and reactive oxygen species (ROS) has been implicated in the regulation of innate immunity in plants. A potato calcium-dependent protein kinase (StCDPK5) activates an NADPH oxidase StRBOHA to D by direct phosphorylation of N-terminal regions, and heterologous expression of StCDPK5 and StRBOHs in Nicotiana benthamiana results in oxidative burst. The transgenic potato plants that carry a constitutively active StCDPK5 driven by a pathogen-inducible promoter of the potato showed high resistance to late blight pathogen Phytophthora infestans accompanied by HR-like cell death and H(2)O(2) accumulation in the attacked cells. In contrast, these plants showed high susceptibility to early blight necrotrophic pathogen Alternaria solani, suggesting that oxidative burst confers high resistance to biotrophic pathogen, but high susceptibility to necrotrophic pathogen. NO and ROS synergistically function in defense responses. Two MAPK cascades, MEK2-SIPK and cytokinesis-related MEK1-NTF6, are involved in the induction of NbRBOHB gene in N. benthamiana. On the other hand, NO burst is regulated by the MEK2-SIPK cascade. Conditional activation of SIPK in potato plants induces oxidative and NO bursts, and confers resistance to both biotrophic and necrotrophic pathogens, indicating the plants may have obtained during evolution the signaling pathway which regulates both NO and ROS production to adapt to wide-spectrum pathogens.

Protein nitration during defense response in Arabidopsis thaliana

Nitric oxide and reactive oxygen species play a key role in the plant hypersensitive disease resistance response, and protein tyrosine nitration is emerging as an important mechanism of their co-operative interaction. Up to now, the proteins targeted by this post-translational modification in plants are still totally unknown. In this study, we analyzed for the first time proteins undergoing nitration during the hypersensitive response by analyzing via 1D- and 2D-western blot the protein extracts from Arabidopsis thaliana plants challenged with an avirulent bacterial pathogen (Pseudomonas syringae pv. Tomato). We show that the plant disease resistance response is correlated with a modulation of nitration of proteins involved in important cellular process, such as photosynthesis, glycolysis and nitrate assimilation. These findings shed new light on the signaling functions of nitric oxide and reactive oxygen species, paving the way on studies on the role of this post-translational modification in plants.

Protein tyrosine nitration: a new challenge in plants

Nitric oxide metabolism in plant cells has a relative short history. Nitration is a chemical process which consists of introducing a nitro group (-NO(2)) into a chemical compound. In biological systems, this process has been found in different molecules such as proteins, lipids and nucleic acids that can affect its function. This mini-review offers an overview of this process with special emphasis on protein tyrosine nitration in plants and its involvement in the process of nitrosative stress.

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.

Hsp90 is regulated by a switch point in the C-terminal domain

Heat shock protein 90 (Hsp90) is an abundant, dimeric ATP-dependent molecular chaperone, and ATPase activity is essential for its in vivo functions. S-nitrosylation of a residue located in the carboxy-terminal domain has been shown to affect Hsp90 activity in vivo. To understand how variation of a specific amino acid far away from the amino-terminal ATP-binding site regulates Hsp90 functions, we mutated the corresponding residue and analysed yeast and human Hsp90 variants both in vivo and in vitro. Here, we show that this residue is a conserved, strong regulator of Hsp90 functions, including ATP hydrolysis and chaperone activity. Unexpectedly, the variants alter both the C-terminal and N-terminal association properties of Hsp90, and shift its conformational equilibrium within the ATPase cycle. Thus, S-nitrosylation of this residue allows the fast and efficient fine regulation of Hsp90.

Unraveling the S-nitrosoproteome: tools and strategies

One of the major tasks to be accomplished in the postgenomic era is the characterization of PTMs in proteins. The S-nitrosation of protein thiols is a redox-based PTM that modulating enzymatic activity, subcellular localization, complex formation, and degradation of proteins, largely contributes to the complexity of cellular proteomes. Although the detection of S-nitrosated proteins is problematical due to the lability of S-nitrosothiols, with the improvement of molecular tools an increasing range of proteins has been shown to undergo S-nitrosation. We here review recent proteomic approaches for the systematic assessment of potential targets for protein S-nitrosation. The development of new analytical methods and strategies over the past several years now allows us to investigate the nitrosoproteome on a global scale.

Quantitative measurement of specific biomarkers for protein oxidation, nitration and glycation in Arabidopsis leaves

Higher plants are continually exposed to reactive oxygen and nitrogen species during their lives. Together with glucose and reactive dicarbonyls, these can modify proteins spontaneously, leading to protein oxidation, nitration and glycation. These reactions have the potential to damage proteins and have an impact on physiological processes. The levels of protein oxidation, nitration and glycation adducts were assayed, using liquid chromatography coupled with tandem mass spectrometry, in total leaf extracts over a diurnal cycle and when exposed to conditions that promote oxidative stress. Changes in the levels of oxidation, glycation and nitration adducts were found between the light and dark phases under non-stress conditions. A comparison between wild-type plants and a mutant lacking peptide methionine sulfoxide reductase (pmsr2-1) showed increased protein oxidation, nitration and glycation of specific amino acid residues during darkness in pmsr2-1. Short-term excess light exposure, which promoted oxidative stress, led to increased protein glycation, specifically by glyoxal. This suggested that any increased oxidative damage to proteins was within the repair capacity of the plant. The methods developed here provide the means to simultaneously detect a range of protein oxidation, nitration and glycation adducts within a single sample. Thus, these methods identify a range of biomarkers to monitor a number of distinct biochemical processes that have an impact on the proteome and therefore the physiological state of the plant.

The role of annexin 1 in drought stress in Arabidopsis

Annexins act as targets of calcium signals in eukaryotic cells, and recent results suggest that they play an important role in plant stress responses. We found that in Arabidopsis (Arabidopsis thaliana), AnnAt1 (for annexin 1) mRNA levels were up-regulated in leaves by most of the stress treatments applied. Plants overexpressing AnnAt1 protein were more drought tolerant and knockout plants were more drought sensitive than ecotype Columbia plants. We also observed that hydrogen peroxide accumulation in guard cells was reduced in overexpressing plants and increased in knockout plants both before and after treatment with abscisic acid. Oxidative protection resulting from AnnAt1 overexpression could be due to the low level of intrinsic peroxidase activity exhibited by this protein in vitro, previously linked to a conserved histidine residue found in a peroxidase-like motif. However, analyses of a mutant H40A AnnAt1 protein in a bacterial complementation test and in peroxidase activity assays indicate that this residue is not critical to the ability of AnnAt1 to confer oxidative protection. To further examine the mechanism(s) linking AnnAt1 expression to stress resistance, we analyzed the reactive S3 cluster to determine if it plays a role in AnnAt1 oligomerization and/or is the site for posttranslational modification. We found that the two cysteine residues in this cluster do not form intramolecular or intermolecular bonds but are highly susceptible to oxidation-driven S-glutathionylation, which decreases the Ca(2+) affinity of AnnAt1 in vitro. Moreover, S-glutathionylation of AnnAt1 occurs in planta after abscisic acid treatment, which suggests that this modification could be important in regulating the cellular function of AnnAt1 during stress responses.

Nitric oxide donor-mediated inhibition of phosphorylation shows that light-mediated degradation of photosystem II D1 protein and phosphorylation are not tightly linked

An outcome of the photochemistry during oxygenic photosynthesis is the rapid turn over of the D1 protein in the light compared to the other proteins of the photosystem II (PS II) reaction center. D1 is a major factor of PS II instability and its replacement a primary event of the PS II repair cycle. D1 also undergoes redox-dependent phosphorylation prior to its degradation. Although it has been suggested that phosphorylation modulates D1 metabolism, reversible D1 phosphorylation was reported not to be essential for PS II repair in Arabidopsis. Thus, the involvement of phosphorylation in D1 degradation is controversial. We show here that nitric oxide donors inhibit in vivo phosphorylation of the D1 protein in Spirodela without inhibiting degradation of the protein. Thus, D1 phosphorylation is not tightly linked to D1 degradation in the intact plant.

Nitric oxide modulates dynamic actin cytoskeleton and vesicle trafficking in a cell type-specific manner in root apices

NO is an important regulatory molecule in eukaryotes. Much of its effect is ascribed to the action of NO as a signalling molecule. However, NO can also directly modify proteins thus affecting their activities. Although the signalling functions of NO are relatively well recognized in plants, very little is known about its potential influence on the structural integrity of plant cells. In this study, the reorganization of the actin cytoskeleton, and the recycling of wall polysaccharides in plants via the endocytic pathway in the presence of NO or NO-modulating substances were analysed. The actin cytoskeleton and endocytosis in maize (Zea mays) root apices were visualized with fluorescence immunocytochemistry. The organization of the actin cytoskeleton is modulated via NO levels and the extent of such modulation is cell-type specific. In endodermis cells, actin cables change their orientation from longitudinal to oblique and cellular cross-wall domains become actin-depleted/depolymerized. The reaction is reversible and depends on the type of NO donor. Actin-dependent vesicle trafficking is also affected. This was demonstrated through the analysis of recycled wall material transported to newly-formed cell plates and BFA compartments. Therefore, it is concluded that, in plant cells, NO affects the functioning of the actin cytoskeleton and actin-dependent processes. Mechanisms for the reorganization of the actin cytoskeleton are cell-type specific, and such rearrangements might selectively impinge on the functioning of various cellular domains. Thus, the dynamic actin cytoskeleton could be considered as a downstream effector of NO signalling in cells of root apices.

Nitric oxide suppresses growth and development in the unicellular green alga Micrasterias denticulata

Nitric oxide (NO), a key molecule in inter- and intracellular signalling, is implicated in developmental processes, host defense, and apoptosis in higher plants. We investigated the effect of NO on development in the unicellular green alga, Micrasterias denticulata, using two different NO donors, S-nitroso-N-acetyl-dl-penicillamine (SNAP) and sodium nitroprusside (SNP). Investigations at the light microsopic level revealed that both NO donors suppressed cell growth. Ultrastructural analyses were performed with SNAP- as well as SNP-treated cells and, additionally, with the control compound N-acetyl-d-penicillamine (NAP). Cells incubated with NO donors lacked a secondary wall and dictyosomal function was impaired, whereas NAP-treated cells showed no difference in development and organelle structure compared to control cells. Moreover, cisternae of the Golgi stacks were slightly involute and no vesicles were pinched off after SNAP and SNP incubation. The NO scavenger cPTIO (2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide, potassium salt) abrogated the effect of SNP, thus confirming that inhibition of cell growth is due to nitric oxide. Addition of iodoacetic acid, an inhibitor of cysteine-containing enzymes, like glyceraldehyde-3-phosphate dehydrogenase (GAPDH), evoked similar effects on cell growth and secondary wall formation as obtained by treatment with NO donors. Therefore, we hypothesize that NO inhibits activity of enzymes involved in the secretory pathway, such as GAPDH, via S-nitrosylation of the cysteine residue and, consequently, modulates cell growth in M. denticulata.

NO release by nitric oxide donors in vitro and in planta

Artificial nitric oxide (NO) donors are widely used as tools to study the role of NO in plants. However, reliable and reproducible characterisation of metabolic responses induced by different NO donors is complicated by the variability of their NO release characteristics. The latter are affected by different physical and biological factors including temperature and light. Here we critically evaluate NO release characteristics of the donors sodium nitroprusside (SNP), S-nitrosoglutathione (GSNO) and nitric oxide synthase (NOS), both in vitro and in planta (Nicotiana tabacum L. cv. BelW3) and assess their effects on NO dependent processes such as the transcriptional regulation of the mitochondrial alternative oxidase gene (AOX1a), accumulation of H(2)O(2) and induction of cell death. We demonstrate that, contrary to NOS and SNP, GSNO is not an efficient NO generator in leaf tissue. Furthermore, spectrophotometric measurement of NO with a haemoglobin assay, rather than diaminofluorescein (DAF-FM) based detection, is best suited for the quantification of tissue NO. In spite of the different NO release signatures by SNP and NOS in tissue, the NO dependent responses examined were similar, suggesting that there is a critical threshold for the NO response.

Plant proteomics: concepts, applications, and novel strategies for data interpretation

Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.

Protein targets of tyrosine nitration in sunflower (Helianthus annuus L.) hypocotyls

Tyrosine nitration is recognized as an important post-translational protein modification in animal cells that can be used as an indicator of a nitrosative process. However, in plant systems, there is scant information on proteins that undergo this process. In sunflower hypocotyls, the content of tyrosine nitration (NO(2)-Tyr) and the identification of nitrated proteins were studied by high-performance liquid chromatography with tandem mass spectrometry (LC-MS/MS) and proteomic approaches, respectively. In addition, the cell localization of nitrotyrosine proteins and peroxynitrite were analysed by confocal laser-scanning microscopy (CLSM) using antibodies against 3-nitrotyrosine and 3'-(p-aminophenyl) fluorescein (APF) as the fluorescent probe, in that order. The concentration of Tyr and NO(2)-Tyr in hypocotyls was 0.56 micromol mg(-1) protein and 0.19 pmol mg(-1) protein, respectively. By proteomic analysis, a total of 21 nitrotyrosine-immunopositive proteins were identified. These targets include proteins involved in photosynthesis, and in antioxidant, ATP, carbohydrate, and nitrogen metabolism. Among the proteins identified, S-adenosyl homocysteine hydrolase (SAHH) was selected as a model to evaluate the effect of nitration on SAHH activity using SIN-1 (a peroxynitrite donor) as the nitrating agent. When the hypocotyl extracts were exposed to 0.5 mM, 1 mM, and 5 mM SIN-1, the SAHH activity was inhibited by some 49%, 89%, and 94%, respectively. In silico analysis of the barley SAHH sequence, characterized Tyr448 as the most likely potential target for nitration. In summary, the present data are the first in plants concerning the content of nitrotyrosine and the identification of candidates of protein nitration. Taken together, the results suggest that Tyr nitration occurs in plant tissues under physiological conditions that could constitute an important process of protein regulation in such a way that, when it is overproduced in adverse circumstances, it can be used as a marker of nitrosative stress.

Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana

The aspartate-derived amino acid pathway in plants leads to the biosynthesis of lysine, methionine, threonine, and isoleucine. These four amino acids are essential in the diets of humans and other animals, but are present in growth-limiting quantities in some of the world's major food crops. Genetic and biochemical approaches have been used for the functional analysis of almost all Arabidopsis thaliana enzymes involved in aspartate-derived amino acid biosynthesis. The branch-point enzymes aspartate kinase, dihydrodipicolinate synthase, homoserine dehydrogenase, cystathionine gamma synthase, threonine synthase, and threonine deaminase contain well-studied sites for allosteric regulation by pathway products and other plant metabolites. In contrast, relatively little is known about the transcriptional regulation of amino acid biosynthesis and the mechanisms that are used to balance aspartate-derived amino acid biosynthesis with other plant metabolic needs. The aspartate-derived amino acid pathway provides excellent examples of basic research conducted with A. thaliana that has been used to improve the nutritional quality of crop plants, in particular to increase the accumulation of lysine in maize and methionine in potatoes.

Proteomic analysis of protein S-nitrosylation

Nitric oxide (NO) produces covalent PTMs of specific cysteine residues, a process known as S-nitrosylation. This route is dynamically regulated and is one of the major NO signalling pathways known to have strong and dynamic interactions with redox signalling. In agreement with this scenario, binding of NO to key cysteine groups can be linked to a broad range of physiological and pathological cellular events, such as smooth muscle relaxation, neurotransmission and neurodegeneration. The characterization of S-nitrosylated residues and the functional relevance of this protein modification are both essential information needed to understand the action of NO in living organisms. In this review, we focus on recent advances in this field and on state-of-the-art proteomic approaches which are aimed at characterizing the S-nitrosylome in different biological backgrounds.

The role of radical burst via MAPK signaling in plant immunity

Plants rely on the innate immune system to defend themselves from pathogen attacks. Reactive oxygen species (ROS) and nitric oxide (NO) play key roles in the activation of disease resistance mechanisms in plants. The evolutionarily conserved mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules in eukaryotes and have been implicated in the plant innate immunity. There have been many disputations about the relationship between the radicals (ROS and NO) and MAPK cascades. Recently, we found that MAPK cascades participate in the regulation of the radical burst. Here, we discuss the regulatory mechanisms of the oxidative and NO bursts in response to pathogen attacks, and crosstalk between MAPK signaling and the radical burst.

Selective fluorescent labeling of S-nitrosothiols (S-FLOS): a novel method for studying S-nitrosation

Protein S-nitrosation is a reversible post-translation modification critical for redox-sensitive cell signaling that is typically studied using the Biotin Switch method. This method and subsequent modifications usually require avidin binding or Western blot analysis to detect biotin labeled proteins. We describe here a modification of the Biotin Switch assay that eliminates the need for Western blot or avidin enrichment protocols and allows direct comparison of the S-nitrosation state proteins from two different samples in the same gel lane or on the same 2D gel. This S-FLOS method offers detection, identification and quantification of S-nitrosated proteins, with the potential for site-specific identification of nitrosation events.

Plant immunity requires conformational changes [corrected] of NPR1 via S-nitrosylation and thioredoxins

Changes in redox status have been observed during immune responses in different organisms, but the associated signaling mechanisms are poorly understood. In plants, these redox changes regulate the conformation of NPR1, a master regulator of salicylic acid (SA)-mediated defense genes. NPR1 is sequestered in the cytoplasm as an oligomer through intermolecular disulfide bonds. We report that S-nitrosylation of NPR1 by S-nitrosoglutathione (GSNO) at cysteine-156 facilitates its oligomerization, which maintains protein homeostasis upon SA induction. Conversely, the SA-induced NPR1 oligomer-to-monomer reaction is catalyzed by thioredoxins (TRXs). Mutations in both NPR1 cysteine-156 and TRX compromised NPR1-mediated disease resistance. Thus, the regulation of NPR1 is through the opposing action of GSNO and TRX. These findings suggest a link between pathogen-triggered redox changes and gene regulation in plant immunity.

Plant immunity requires conformational changes [corrected] of NPR1 via S-nitrosylation and thioredoxins

Changes in redox status have been observed during immune responses in different organisms, but the associated signaling mechanisms are poorly understood. In plants, these redox changes regulate the conformation of NPR1, a master regulator of salicylic acid (SA)-mediated defense genes. NPR1 is sequestered in the cytoplasm as an oligomer through intermolecular disulfide bonds. We report that S-nitrosylation of NPR1 by S-nitrosoglutathione (GSNO) at cysteine-156 facilitates its oligomerization, which maintains protein homeostasis upon SA induction. Conversely, the SA-induced NPR1 oligomer-to-monomer reaction is catalyzed by thioredoxins (TRXs). Mutations in both NPR1 cysteine-156 and TRX compromised NPR1-mediated disease resistance. Thus, the regulation of NPR1 is through the opposing action of GSNO and TRX. These findings suggest a link between pathogen-triggered redox changes and gene regulation in plant immunity.

Microbial oligosaccharides differentially induce volatiles and signalling components in Medicago truncatula

Plants perceive biotic stimuli by recognising a multitude of different signalling compounds originating from the interacting organisms. Some of these substances represent pathogen-associated molecular patterns, which act as general elicitors of defence reactions. But also beneficial microorganisms like rhizobia take advantage of compounds structurally related to certain elicitors, i.e. Nod-factors, to communicate their presence to the host plant. In a bioassay-based study we aimed to determine to what extent distinct oligosaccharidic signals are able to elicit overlapping responses, including the emission of volatile organic compounds which is mainly considered a typical mode of inducible indirect defence against herbivores. The model legume Medicago truncatula Gaertn. was challenged with pathogen elicitors (beta-(1,3)-beta-(1,6)-glucans and N,N',N'',N'''-tetraacetylchitotetraose) and two Nod-factors, with one of them being able to induce a nodulation response in M. truncatula. Single oligosaccharidic elicitors caused the emission of volatile organic compounds, mainly sesquiterpenoids. The volatile blends detected were quite characteristic for the applied compounds, which could be pinpointed by multivariate statistical methods. As potential mediators of this response, the levels of jasmonic acid and salicylic acid were determined. Strikingly, neither of these phytohormones exhibited changing levels correlating with enhanced volatile emission. All stimuli tested caused an overproduction of reactive oxygen species, whereas nitric oxide accumulation was only effected by elicitors that were equally able to induce volatile emission. Thus, all signalling compounds tested elicited distinct reaction patterns. However, similarities between defence reactions induced by herbivory and pathogen-derived elicitors could be ascertained; but also Nod-factors were able to trigger defence-related reactions.

Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study

Hydroponic isotope labelling of entire plants (HILEP) is a cost-effective method enabling metabolic labelling of whole and mature plants with a stable isotope such as (15)N. By utilising hydroponic media that contain (15)N inorganic salts as the sole nitrogen source, near to 100% (15)N-labelling of proteins can be achieved. In this study, it is shown that HILEP, in combination with mass spectrometry, is suitable for relative protein quantitation of seven week-old Arabidopsis plants submitted to oxidative stress. Protein extracts from pooled (14)N- and (15)N-hydroponically grown plants were fractionated by SDS-PAGE, digested and analysed by liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS). Proteins were identified and the spectra of (14)N/(15)N peptide pairs were extracted using their m/z chromatographic retention time, isotopic distributions, and the m/z difference between the (14)N and (15)N peptides. Relative amounts were calculated as the ratio of the sum of the peak areas of the two distinct (14)N and (15)N peptide isotope envelopes. Using Mascot and the open source trans-proteomic pipeline (TPP), the data processing was automated for global proteome quantitation down to the isoform level by extracting isoform specific peptides. With this combination of metabolic labelling and mass spectrometry it was possible to show differential protein expression in the apoplast of plants submitted to oxidative stress. Moreover, it was possible to discriminate between differentially expressed isoforms belonging to the same protein family, such as isoforms of xylanases and pathogen-related glucanases (PR 2).

Post-translational modification of host proteins in pathogen-triggered defence signalling in plants

Microbial plant pathogens impose a continuous threat to global food production. Similar to animals, an innate immune system allows plants to recognize pathogens and swiftly activate defence. To activate a rapid response, receptor-mediated pathogen perception and subsequent downstream signalling depends on post-translational modification (PTM) of components essential for defence signalling. We discuss different types of PTMs that play a role in mounting plant immunity, which include phosphorylation, glycosylation, ubiquitination, sumoylation, nitrosylation, myristoylation, palmitoylation and glycosylphosphatidylinositol (GPI)-anchoring. PTMs are rapid, reversible, controlled and highly specific, and provide a tool to regulate protein stability, activity and localization. Here, we give an overview of PTMs that modify components essential for defence signalling at the site of signal perception, during secondary messenger production and during signalling in the cytoplasm. In addition, we discuss effectors from pathogens that suppress plant defence responses by interfering with host PTMs.

Redox signal integration: from stimulus to networks and genes

Recent research has established redox-dependent thiol modification of proteins as a major regulatory layer superimposed on most cell functional categories in plants. Modern proteomics and forward as well as reverse genetics approaches have enabled the identification of a high number of novel targets of redox regulation. Redox-controlled processes range from metabolism to transport, transcription and translation. Gene activity regulation by transcription factors such as TGA, Athb-9 and RAP2 directly or indirectly is controlled by the redox state. Knowledge on putative redox sensors such as the peroxiredoxins, on redox transmitters including thioredoxins and glutaredoxins and biochemical mechanisms of their linkage to the metabolic redox environment has emerged as the framework of a functional redox regulatory network. Its basic principle is similar in eukaryotic cells and particularly complex in the photosynthesizing chloroplast. Methods and knowledge are now at hand to develop a quantitative understanding of redox signalling and the redox regulatory network in the eukaryotic cell.

Regulation of plant cytosolic glyceraldehyde 3-phosphate dehydrogenase isoforms by thiol modifications

Cytosolic NAD-dependent glyceraldehyde 3-P dehydrogenase (GAPDH; GapC; EC 1.2.1.12) catalyzes the oxidation of triose phosphates during glycolysis in all organisms, but additional functions of the protein has been put forward. Because of its reactive cysteine residue in the active site, it is susceptible to protein modification and oxidation. The addition of GSSG, and much more efficiently of S-nitrosoglutathione, was shown to inactivate the enzymes from Arabidopsis thaliana (isoforms GapC1 and 2), spinach, yeast and rabbit muscle. Inactivation was fully or at least partially reversible upon addition of DTT. The incorporation of glutathione upon formation of a mixed disulfide could be shown using biotinylated glutathione ethyl ester. Furthermore, using the biotin-switch assay, nitrosylated thiol groups could be shown to occur after treatment with nitric oxide donors. Using mass spectrometry and mutant proteins with one cysteine lacking, both cysteines (Cys-155 and Cys-159) were found to occur as glutathionylated and as nitrosylated forms. In preliminary experiments, it was shown that both GapC1 and GapC2 can bind to a partial gene sequence of the NADP-dependent malate dehydrogenase (EC 1.2.1.37; At5g58330). Transiently expressed GapC-green fluorescent protein fusion proteins were localized to the nucleus in A. thaliana protoplasts. As nuclear localization and DNA binding of GAPDH had been shown in numerous systems to occur upon stress, we assume that such mechanism might be part of the signaling pathway to induce increased malate-valve capacity and possibly other protective systems upon overreduction and initial formation of reactive oxygen and nitrogen species as well as to decrease and protect metabolism at the same time by modification of essential cysteine residues.

Identification of the cysteine nitrosylation sites in human endothelial nitric oxide synthase

S-nitrosylation, or the replacement of the hydrogen atom in the thiol group of cysteine residues by a -NO moiety, is a physiologically important posttranslational modification. In our previous work we have shown that S-nitrosylation is involved in the disruption of the endothelial nitric oxide synthase (eNOS) dimer and that this involves the disruption of the zinc (Zn) tetrathiolate cluster due to the S-nitrosylation of Cysteine 98. However, human eNOS contains 28 other cysteine residues whose potential to undergo S-nitrosylation has not been determined. Thus, the goal of this study was to identify the cysteine residues within eNOS that are susceptible to S-nitrosylation in vitro. To accomplish this, we utilized a modified biotin switch assay. Our modification included the tryptic digestion of the S-nitrosylated eNOS protein to allow the isolation of S-nitrosylated peptides for further identification by mass spectrometry. Our data indicate that multiple cysteine residues are capable of undergoing S-nitrosylation in the presence of an excess of a nitrosylating agent. All these cysteine residues identified were found to be located on the surface of the protein according to the available X-ray structure of the oxygenase domain of eNOS. Among those identified were Cys 93 and 98, the residues involved in the formation of the eNOS dimer through a Zn tetrathiolate cluster. In addition, cysteine residues within the reductase domain were identified as undergoing S-nitrosylation. We identified cysteines 660, 801, and 1113 as capable of undergoing S-nitrosylation. These cysteines are located within regions known to bind flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and nicotinamide adenine dinucleotide (NADPH) although from our studies their functional significance is unclear. Finally we identified cysteines 852, 975/990, and 1047/1049 as being susceptible to S-nitrosylation. These cysteines are located in regions of eNOS that have not been implicated in any known biochemical functions and the significance of their S-nitrosylation is not clear from this study. Thus, our data indicate that the eNOS protein can be S-nitrosylated at multiple sites other than within the Zn tetrathiolate cluster, suggesting that S-nitrosylation may regulate eNOS function in ways other than simply by inducing dimer collapse.

Post-translational modifications mediated by reactive nitrogen species: Nitrosative stress responses or components of signal transduction pathways?

In animal cells, nitric oxide and NO-derived molecules have been shown to mediate post-translational modifications such as S-nitrosylation and protein tyrosine nitration which are associated with cell signalling and pathological processes, respectively. In plant cells, knowledge of the function of these post-translational modifications under physiological and stress conditions is still very rudimentary. In this addendum, we briefly examine how reactive nitrogen species (RNS) can exert important effects on proteins that could mediate signalling processes in plants.

Proteomic analysis of S-nitrosylated proteins in Arabidopsis thaliana undergoing hypersensitive response

Nitric oxide (NO) has a fundamental role in the plant hypersensitive disease resistance response (HR), and S-nitrosylation is emerging as an important mechanism for the transduction of its bioactivity. A key step toward elucidating the mechanisms by which NO functions during the HR is the identification of the proteins that are subjected to this PTM. By using a proteomic approach involving 2-DE and MS we characterized, for the first time, changes in S-nitrosylated proteins in Arabidopsis thaliana undergoing HR. The 16 S-nitrosylated proteins identified are mostly enzymes serving intermediary metabolism, signaling and antioxidant defense. The study of the effects of S-nitrosylation on the activity of the identified proteins and its role during the execution of the disease resistance response will help to understand S-nitrosylation function and significance in plants.

Nitric oxide synthesis and signalling in plants

As with all organisms, plants must respond to a plethora of external environmental cues. Individual plant cells must also perceive and respond to a wide range of internal signals. It is now well-accepted that nitric oxide (NO) is a component of the repertoire of signals that a plant uses to both thrive and survive. Recent experimental data have shown, or at least implicated, the involvement of NO in reproductive processes, control of development and in the regulation of physiological responses such as stomatal closure. However, although studies concerning NO synthesis and signalling in animals are well-advanced, in plants there are still fundamental questions concerning how NO is produced and used that need to be answered. For example, there is a range of potential NO-generating enzymes in plants, but no obvious plant nitric oxide synthase (NOS) homolog has yet been identified. Some studies have shown the importance of NOS-like enzymes in mediating NO responses in plants, while other studies suggest that the enzyme nitrate reductase (NR) is more important. Still, more published work suggests the involvement of completely different enzymes in plant NO synthesis. Similarly, it is not always clear how NO mediates its responses. Although it appears that in plants, as in animals, NO can lead to an increase in the signal cGMP which leads to altered ion channel activity and gene expression, it is not understood how this actually occurs. NO is a relatively reactive compound, and it is not always easy to study. Furthermore, its biological activity needs to be considered in conjunction with that of other compounds such as reactive oxygen species (ROS) which can have a profound effect on both its accumulation and function. In this paper, we will review the present understanding of how NO is produced in plants, how it is removed when its signal is no longer required and how it may be both perceived and acted upon.

MAPK signaling regulates nitric oxide and NADPH oxidase-dependent oxidative bursts in Nicotiana benthamiana

Nitric oxide (NO) and reactive oxygen species (ROS) act as signals in innate immunity in plants. The radical burst is induced by INF1 elicitin, produced by the oomycete pathogen Phytophthora infestans. NO ASSOCIATED1 (NOA1) and NADPH oxidase participate in the radical burst. Here, we show that mitogen-activated protein kinase (MAPK) cascades MEK2-SIPK/NTF4 and MEK1-NTF6 participate in the regulation of the radical burst. NO generation was induced by conditional activation of SIPK/NTF4, but not by NTF6, in Nicotiana benthamiana leaves. INF1- and SIPK/NTF4-mediated NO bursts were compromised by the knockdown of NOA1. However, ROS generation was induced by either SIPK/NTF4 or NTF6. INF1- and MAPK-mediated ROS generation was eliminated by silencing Respiratory Burst Oxidase Homolog B (RBOHB), an inducible form of the NADPH oxidase. INF1-induced expression of RBOHB was compromised in SIPK/NTF4/NTF6-silenced leaves. These results indicated that INF1 regulates NOA1-mediated NO and RBOHB-dependent ROS generation through MAPK cascades. NOA1 silencing induced high susceptibility to Colletotrichum orbiculare but not to P. infestans; conversely, RBOHB silencing decreased resistance to P. infestans but not to C. orbiculare. These results indicate that the effects of the radical burst on the defense response appear to be diverse in plant-pathogen interactions.

S-nitrosylated proteins of a medicinal CAM plant Kalanchoe pinnata- ribulose-1,5-bisphosphate carboxylase/oxygenase activity targeted for inhibition

Nitric oxide (NO) is a signaling molecule that affects a myriad of processes in plants. However, the mechanistic details are limited. NO post-translationally modifies proteins by S-nitrosylation of cysteines. The soluble S-nitrosoproteome of a medicinal, crassulacean acid metabolism (CAM) plant, Kalanchoe pinnata, was purified using the biotin switch technique. Nineteen targets were identified by MALDI-TOF mass spectrometry, including proteins associated with carbon, nitrogen and sulfur metabolism, the cytoskeleton, stress and photosynthesis. Some were similar to those previously identified in Arabidopsis thaliana, but kinesin-like protein, glycolate oxidase, putative UDP glucose 4-epimerase and putative DNA topoisomerase II had not been identified as targets previously for any organism. In vitro and in vivo nitrosylation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), one of the targets, was confirmed by immunoblotting. Rubisco plays a central role in photosynthesis, and the effect of S-nitrosylation on its enzymatic activity was determined using NaH14CO3. The NO-releasing compound S-nitrosoglutathione inhibited its activity in a dose-dependent manner suggesting Rubisco inactivation by nitrosylation for the first time.

On-gel fluorescent visualization and the site identification of S-nitrosylated proteins

Mounting evidence indicates that S-nitrosylation of critical cysteine residues in a protein represents a common feature of protein function regulation and cell signaling. However, the progress in studying the exact role of S-nitrosylation has been hampered by a lack of rapid and accurate methods for the detection of these S-nitrosylated proteins and the exact modification sites. In this article, we report a fluorescence-based method in which the S-nitrosylated cysteines are converted into 7-amino-4-methylcoumarin-3-acetic acid (AMCA) fluorophore-labeled cysteines-termed the AMCA switch method. The labeled proteins are then analyzed by nonreducing SDS-PAGE, and the S-nitrosylated proteins can be readily detected as brilliant blue bands after the activation of ultraviolet light. Furthermore, the sites of modification can be determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-gel tryptic digestion of the fluorescent band, and the recognizable AMCA tag in the MS spectra ensures the accurate site identification of the nitrosocysteines. Therefore, our method offers some apparent advantages by direct visualization of on-gel image of S-nitrosylated proteins, shorter experiment time by skipping the anti-biotin immunoblotting step, and elimination of the potential interference of endogenous biotinylated proteins. Based on this method, we detected the S-nitrosylation and the modified site in bovine serum albumin and gankyrin after in vitro S-nitrosylation. Overall, our results indicate that the AMCA switch method is a fast and accurate method to identify the S-nitrosylated protein and the modification sites.

Modulation of nitrosative stress by S-nitrosoglutathione reductase is critical for thermotolerance and plant growth in Arabidopsis

Nitric oxide (NO) is a key signaling molecule in plants. This analysis of Arabidopsis thaliana HOT5 (sensitive to hot temperatures), which is required for thermotolerance, uncovers a role of NO in thermotolerance and plant development. HOT5 encodes S-nitrosoglutathione reductase (GSNOR), which metabolizes the NO adduct S-nitrosoglutathione. Two hot5 missense alleles and two T-DNA insertion, protein null alleles were characterized. The missense alleles cannot acclimate to heat as dark-grown seedlings but grow normally and can heat-acclimate in the light. The null alleles cannot heat-acclimate as light-grown plants and have other phenotypes, including failure to grow on nutrient plates, increased reproductive shoots, and reduced fertility. The fertility defect of hot5 is due to both reduced stamen elongation and male and female fertilization defects. The hot5 null alleles show increased nitrate and nitroso species levels, and the heat sensitivity of both missense and null alleles is associated with increased NO species. Heat sensitivity is enhanced in wild-type and mutant plants by NO donors, and the heat sensitivity of hot5 mutants can be rescued by an NO scavenger. An NO-overproducing mutant is also defective in thermotolerance. Together, our results expand the importance of GSNOR-regulated NO homeostasis to abiotic stress and plant development.

Nitric oxide in plants: production and cross-talk with Ca2+ signaling

Nitric oxide (NO) is a diatomic gas that performs crucial functions in a wide array of physiological processes in animals. The past several years have revealed much about its roles in plants. It is well established that NO is synthesized from nitrite by nitrate reductase (NR) and via chemical pathways. There is increasing evidence for the occurrence of an alternative pathway in which NO production is catalysed from L-arginine by a so far non-identified enzyme. Contradictory results have been reported regarding the respective involvement of these enzymes in specific physiological conditions. Although much remains to be proved, we assume that these inconsistencies can be accounted for by the limited specificity of the pharmacological agents used to suppress NO synthesis but also by the reduced content of L-arginine as well as the inactivity of nitrate-permeable anion channels in nitrate reductase- and/or nitrate/nitrite-deficient plants. Another unresolved issue concerns the molecular mechanisms underlying NO effects in plants. Here, we provide evidence that the second messenger Ca2+, as well as protein kinases including MAPK and SnRK2, are very plausible mediators of the NO signals. These findings open new perspectives about NO-based signaling in plants.

Redox proteomics: basic principles and future perspectives for the detection of protein oxidation in plants

The production and scavenging of chemically reactive species, such as ROS/RNS, are central to a broad range of biotic and abiotic stress and physiological responses in plants. Among the techniques developed for the identification of oxidative stress-induced modifications on proteins, the so-called 'redox proteome', proteomics appears to be the best-suited approach. Oxidative or nitrosative stress leaves different footprints in the cell in the form of different oxidatively modified components and, using the redox proteome, it will be possible to decipher the potential roles played by ROS/RNS-induced modifications in stressed cells. The purpose of this review is to present an overview of the latest research endeavours in the field of plant redox proteomics to identify the role of post-translational modifications of proteins in developmental cell stress. All the strategies set up to analyse the different oxidized/nitrosated amino acids, as well as the different reactivities of ROS and RNS for different amino acids are revised and discussed. A growing body of evidence indicates that ROS/RNS-induced protein modifications may be of physiological significance, and that in some cellular stresses they may act causatively and not arise as a secondary consequence of cell damage. Thus, although previously the oxidative modification of proteins was thought to represent a detrimental process in which the modified proteins were irreversibly inactivated, it is now clear that, in plants, oxidatively/nitrosatively modified proteins can be specific and reversible, playing a key role in normal cell physiology. In this sense, redox proteomics will have a central role in the definition of redox molecular mechanisms associated with cellular stresses.

Zeatin-induced nitric oxide (NO) biosynthesis in Arabidopsis thaliana mutants of NO biosynthesis and of two-component signaling genes

* Here, cytokinin-induced nitric oxide (NO) biosynthesis and cytokinin responses were investigated in Arabidopsis thaliana wild type and mutants defective in NO biosynthesis or cytokinin signaling components. * NO release from seedlings was quantified by a fluorometric method and, by microscopy, observed NO biosynthesis as fluorescence increase of DAR-4M AM (diaminorhodamine 4M acetoxymethyl ester) in different tissues. * Atnoa1 seedlings were indistinguishable in NO tissue distribution pattern and morphological responses, induced by zeatin, from wild-type seedlings. Wild-type and nia1,2 seedlings, lacking nitrate reductase (NR), responded to zeatin with an increase within 3 min in NO biosynthesis so that NR does not seem relevant for rapid NO induction, which was mediated by an unknown 2-(2-aminoethyl)2-thiopseudourea (AET)-sensitive enzyme and was quenched by 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-1-oxy-3-oxide (PTIO). Long-term morphological responses to zeatin were severely altered and NO biosynthesis was increased in nia1,2 seedlings. As cytokinin signaling mutants we used the single-receptor knockout cre1/ahk4, three double-receptor knockouts (ahk2,3, ahk2,4, ahk3,4) and triple-knockout ahp1,2,3 plants. All cytokinin-signaling mutants showed aberrant tissue patterns of NO accumulation in response to zeatin and altered morphological responses to zeatin. * Because aberrant NO biosynthesis correlated with aberrant morphological responses to zeatin the hypothesis was put forward that NO is an intermediate in cytokinin signaling.