Protein tyrosine nitration in plants: Present knowledge, computational prediction and future perspectives

Atmospheric nitrogen dioxide suppresses the activity of phytochrome interacting factor 4 to suppress hypocotyl elongation

MAIN CONCLUSION

Ambient concentrations of atmospheric nitrogen dioxide (NO2) inhibit the binding of PIF4 to promoter regions of auxin pathway genes to suppress hypocotyl elongation in Arabidopsis. Ambient concentrations (10-50 ppb) of atmospheric nitrogen dioxide (NO2) positively regulate plant growth to the extent that organ size and shoot biomass can nearly double in various species, including Arabidopsis thaliana (Arabidopsis). However, the precise molecular mechanism underlying NO2-mediated processes in plants, and the involvement of specific molecules in these processes, remain unknown. We measured hypocotyl elongation and the transcript levels of PIF4, encoding a bHLH transcription factor, and its target genes in wild-type (WT) and various pif mutants grown in the presence or absence of 50 ppb NO2. Chromatin immunoprecipitation assays were performed to quantify binding of PIF4 to the promoter regions of its target genes. NO2 suppressed hypocotyl elongation in WT plants, but not in the pifq or pif4 mutants. NO2 suppressed the expression of target genes of PIF4, but did not affect the transcript level of the PIF4 gene itself or the level of PIF4 protein. NO2 inhibited the binding of PIF4 to the promoter regions of two of its target genes, SAUR46 and SAUR67. In conclusion, NO2 inhibits the binding of PIF4 to the promoter regions of genes involved in the auxin pathway to suppress hypocotyl elongation in Arabidopsis. Consequently, PIF4 emerges as a pivotal participant in this regulatory process. This study has further clarified the intricate regulatory mechanisms governing plant responses to environmental pollutants, thereby advancing our understanding of how plants adapt to changing atmospheric conditions.

Emerging concern of nano-pollution in agro-ecosystem: Flip side of nanotechnology

Nanomaterials (NMs) have proven to be a game-changer in agriculture, showcasing their potential to boost plant growth and safeguarding crops. The agricultural sector has widely adopted NMs, benefiting from their small size, high surface area, and optical properties to augment crop productivity and provide protection against various stressors. This is attributed to their unique characteristics, contributing to their widespread use in agriculture. Human exposure from various components of agro-environmental sectors (soil, crops) NMs residues are likely to upsurge with exposure paths may stimulates bioaccumulation in food chain. With the aim to achieve sustainability, nanotechnology (NTs) do exhibit its potentials in various domains of agriculture also have its flip side too. In this review article we have opted a fusion approach using bibliometric based analysis of global research trend followed by a holistic assessment of pros and cons i.e. toxicological aspect too. Moreover, we have also tried to analyse the current scenario of policy associated with the application of NMs in agro-environment.

Persulfidation of plant and bacteroid proteins is involved in legume nodule development and senescence

Legumes establish symbiosis with rhizobia, forming nitrogen-fixing nodules. The central role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in nodule biology has been clearly established. Recently, hydrogen sulfide (H2S) and other reactive sulfur species (RSS) have emerged as novel signaling molecules in animals and plants. A major mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification of proteins. To identify possible functions of H2S in nodule development and senescence, we used the tag-switch method to quantify changes in the persulfidation profile of common bean (Phaseolus vulgaris) nodules at different developmental stages. Proteomic analyses indicate that persulfidation plays a regulatory role in plant and bacteroid metabolism and senescence. The effect of a H2S donor on nodule functioning and on several proteins involved in ROS and RNS homeostasis was also investigated. Our results using recombinant proteins and nodulated plants support a crosstalk among H2S, ROS, and RNS, a protective function of persulfidation on redox-sensitive enzymes, and a beneficial effect of H2S on symbiotic nitrogen fixation. We conclude that the general decrease of persulfidation levels observed in plant proteins of aging nodules is one of the mechanisms that disrupt redox homeostasis leading to senescence.

Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation

Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.

Nickel oxide nanoparticles induce cell wall modifications, root anatomical changes, and nitrosative signaling in ecotypes of Ni hyperaccumulator Odontarrhena lesbiaca

The industrial application and environmental release of nickel oxide NPs (NiO NPs) is increasing, but the details of their relationship with plants are largely unknown. In this work, the cellular, tissue, organ, and molecular level responses of three ecotypes of Ni hyperaccumulator Odontarrhena lesbiaca grown in the presence of high doses of NiO NP (250 mg/L and 500 mg/L) were studied. All three ecotypes showed a similar accumulation of Ni in the presence of nano Ni, and in the case of NiO NPs, the root-to-shoot Ni translocation was slighter compared to the bulk Ni. In all three ecotypes, the walls of the root cells effectively prevented internalization of NiO NPs, providing cellular defense against Ni overload. Exposure to NiO NP led to an increase in cortex thickness and the deposition of lignin-suberin and pectin in roots, serving as a tissue-level defense mechanism against excessive Ni. Exposure to NiO NP did not modify or cause a reduction in some biomass parameters of the Ampeliko and Loutra ecotypes, while it increased all parameters in Olympos. The free salt form of Ni exerted more negative effects on biomass production than the nanoform, and the observed effects of NiO NPs can be attributed to the release of Ni ions. Nitric oxide and peroxynitrite levels were modified by NiO NPs in an ecotype-dependent manner. The changes in the abundance and activity of S-nitrosoglutathione reductase protein triggered by NiO NPs suggest that the enzyme is regulated by NiO NPs at the post-translational level. The NiO NPs slightly intensified protein tyrosine nitration, and the slight differences between the ecotypes were correlated with their biomass production in the presence of NiO NPs. Overall, the Odontarrhena lesbiaca ecotypes exhibited tolerance to NiO NPs at the cellular, tissue, organ/organism and molecular levels, demonstrating various defense mechanisms and changes in the metabolism of reactive nitrogen species metabolism and nitrosative protein modification.

Measurement of Reactive Oxygen Species and Nitric Oxide from Tomato Plants in Response to Abiotic and Biotic Stresses

Nitric oxide (NO) is a free radical molecule that has been known to influence several cellular processes such as plant growth, development, and stress responses. NO together with reactive oxygen species (ROS) play a role in signaling process. Due to extremely low half-life of these radicals in cellular environment, it is often difficult to precisely monitor them. Each method has some advantages and disadvantages; hence, it is important to measure using multiple methods. To interpret the role of each signaling molecule in numerous biological processes, sensitive and focused methods must be used. In addition to this complexity, these Reactive Oxygen Species (ROS) and NO react with each other leads to nitro-oxidative stress in plants. Using tomato as a model system here, we demonstrate stepwise protocols for measurement of NO by chemiluminescence, DAF fluorescence, nitrosative stress by western blot, and ROS measurement by NBT and DAB under stress conditions such as osmotic stress and Botrytis infection. While describing methods, we also emphasized on benefits, drawbacks, and broader applications of these methods.

Nitro-oxidative response to internalized multi-walled carbon nanotubes in Brassica napus and Solanum lycopersicum

In addition to their beneficial effects on plant physiology, multi-walled carbon nanotubes (MWCNTs) are harmful to plants in elevated concentrations. This study compared the effects of two doses of MWCNT (10 and 80 mg/L) in Brassica napus and Solanum lycopersicum seedlings focusing on nitro-oxidative processes. The presence of MWCNTs was detectable in the root and hypocotyl of both species. Additionally, transmission electron microscopy analysis revealed that MWCNTs are heavily transformed within the root cells forming large aggregates. The uptake of MWCNTs negatively affected root viability and root cell proliferation of both species, but more intense toxicity was observed in S. lycopersicum compared to B. napus. The presence of MWCNT triggered more intense protein carbonylation in the relative sensitive S. lycopersicum, where increased hydrogen peroxide levels were observed. Moreover, MWCNT exposure increased the level of physiological protein tyrosine nitration which was more intense in S. lycopersicum where notable peroxynitrite accumulation occurred. These suggest for the first time that MWCNT triggers secondary nitro-oxidative stress which contributes to its toxicity. Moreover, the results indicate that the extent of the nitro-oxidative processes is associated with the extent of MWCNT toxicity.

Antioxidative Defense, Suppressed Nitric Oxide Accumulation, and Synthesis of Protective Proteins in Roots and Leaves Contribute to the Desiccation Tolerance of the Resurrection Plant Haberlea rhodopensis

The desiccation tolerance of plants relies on defense mechanisms that enable the protection of macromolecules, biological structures, and metabolism. Although the defense of leaf tissues exposed to solar irradiation is challenging, mechanisms that protect the viability of the roots, yet largely unexplored, are equally important for survival. Although the photosynthetic apparatus in leaves contributes to the generation of oxidative stress under drought stress, we hypothesized that oxidative stress and thus antioxidative defense is also predominant in the roots. Thus, we aimed for a comparative analysis of the protective mechanisms in leaves and roots during the desiccation of Haberlea rhodopensis. Consequently, a high content of non-enzymatic antioxidants and high activity of antioxidant enzymes together with the activation of specific isoenzymes were found in both leaves and roots during the final stages of desiccation of H. rhodopensis. Among others, catalase and glutathione reductase activity showed a similar tendency of changes in roots and leaves, whereas, unlike that in the leaves, superoxide dismutase activity was enhanced under severe but not under medium desiccation in roots. Nitric oxide accumulation in the root tips was found to be sensitive to water restriction but suppressed under severe desiccation. In addition to the antioxidative defense, desiccation induced an enhanced abundance of dehydrins, ELIPs, and sHSP 17.7 in leaves, but this was significantly better in roots. In contrast to leaf cells, starch remained in the cells of the central cylinder of desiccated roots. Taken together, protective compounds and antioxidative defense mechanisms are equally important in protecting the roots to survive desiccation. Since drought-induced damage to the root system fundamentally affects the survival of plants, a better understanding of root desiccation tolerance mechanisms is essential to compensate for the challenges of prolonged dry periods.

Nitric Oxide in Plant Functioning: Metabolism, Signaling, and Responses to Infestation with Ecdysozoa Parasites

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological processes in plants, including responses to biotic and abiotic stresses. Changes in endogenous NO concentration lead to activation/deactivation of NO signaling and NO-related processes. This paper presents the current state of knowledge on NO biosynthesis and scavenging pathways in plant cells and highlights the role of NO in post-translational modifications of proteins (S-nitrosylation, nitration, and phosphorylation) in plants under optimal and stressful environmental conditions. Particular attention was paid to the interactions of NO with other signaling molecules: reactive oxygen species, abscisic acid, auxins (e.g., indole-3-acetic acid), salicylic acid, and jasmonic acid. In addition, potential common patterns of NO-dependent defense responses against attack and feeding by parasitic and molting Ecdysozoa species such as nematodes, insects, and arachnids were characterized. Our review definitely highlights the need for further research on the involvement of NO in interactions between host plants and Ecdysozoa parasites, especially arachnids.

Molecular mechanisms underlying the toxicity and detoxification of trace metals and metalloids in plants

Plants take up a wide range of trace metals/metalloids (hereinafter referred to as trace metals) from the soil, some of which are essential but become toxic at high concentrations (e.g., Cu, Zn, Ni, Co), while others are non-essential and toxic even at relatively low concentrations (e.g., As, Cd, Cr, Pb, and Hg). Soil contamination of trace metals is an increasing problem worldwide due to intensifying human activities. Trace metal contamination can cause toxicity and growth inhibition in plants, as well as accumulation in the edible parts to levels that threatens food safety and human health. Understanding the mechanisms of trace metal toxicity and how plants respond to trace metal stress is important for improving plant growth and food safety in contaminated soils. The accumulation of excess trace metals in plants can cause oxidative stress, genotoxicity, programmed cell death, and disturbance in multiple physiological processes. Plants have evolved various strategies to detoxify trace metals through cell-wall binding, complexation, vacuolar sequestration, efflux, and translocation. Multiple signal transduction pathways and regulatory responses are involved in plants challenged with trace metal stresses. In this review, we discuss the recent progress in understanding the molecular mechanisms involved in trace metal toxicity, detoxification, and regulation, as well as strategies to enhance plant resistance to trace metal stresses and reduce toxic metal accumulation in food crops.

Dynamics of nitration during dark-induced leaf senescence in Arabidopsis reveals proteins modified by tryptophan nitration

Nitric oxide (NO) is a critical molecule that links plant development with stress responses. Herein, new insights into the role of NO metabolism during leaf senescence in Arabidopsis are presented. A gradual decrease in NO emission accompanied dark-induced leaf senescence (DILS), and a transient wave of peroxynitrite (ONOO-) formation was detected by day 3 of DILS. The boosted ONOO- did not promote tryptophan (Trp) nitration, while the pool of 6-nitroTrp-containing proteins was depleted as senescence progressed. Immunoprecipitation combined with mass spectrometry was used to identify 63 and 4 characteristic 6-nitroTrp-containing proteins in control and individually darkened leaves, respectively. The potential in vivo targets of Trp nitration were mainly related to protein biosynthesis and carbohydrate metabolism. In contrast, nitration of tyrosine-containing proteins was intensified 2-fold on day 3 of DILS. Also, nitrative modification of RNA and DNA increased significantly on days 3 and 7 of DILS, respectively. Taken together, ONOO- can be considered a novel pro-senescence regulator that fine-tunes the redox environment for selective bio-target nitration. Thus, DILS-triggered nitrative changes at RNA and protein levels promote developmental shifts during the plant's lifespan and temporal adjustment in plant metabolism under suboptimal environmental conditions.

Redox post-translational modifications and their interplay in plant abiotic stress tolerance

The impact of climate change entails a progressive and inexorable modification of the Earth's climate and events such as salinity, drought, extreme temperatures, high luminous intensity and ultraviolet radiation tend to be more numerous and prolonged in time. Plants face their exposure to these abiotic stresses or their combination through multiple physiological, metabolic and molecular mechanisms, to achieve the long-awaited acclimatization to these extreme conditions, and to thereby increase their survival rate. In recent decades, the increase in the intensity and duration of these climatological events have intensified research into the mechanisms behind plant tolerance to them, with great advances in this field. Among these mechanisms, the overproduction of molecular reactive species stands out, mainly reactive oxygen, nitrogen and sulfur species. These molecules have a dual activity, as they participate in signaling processes under physiological conditions, but, under stress conditions, their production increases, interacting with each other and modifying and-or damaging the main cellular components: lipids, carbohydrates, nucleic acids and proteins. The latter have amino acids in their sequence that are susceptible to post-translational modifications, both reversible and irreversible, through the different reactive species generated by abiotic stresses (redox-based PTMs). Some research suggests that this process does not occur randomly, but that the modification of critical residues in enzymes modulates their biological activity, being able to enhance or inhibit complete metabolic pathways in the process of acclimatization and tolerance to the exposure to the different abiotic stresses. Given the importance of these PTMs-based regulation mechanisms in the acclimatization processes of plants, the present review gathers the knowledge generated in recent years on this subject, delving into the PTMs of the redox-regulated enzymes of plant metabolism, and those that participate in the main stress-related pathways, such as oxidative metabolism, primary metabolism, cell signaling events, and photosynthetic metabolism. The aim is to unify the existing information thus far obtained to shed light on possible fields of future research in the search for the resilience of plants to climate change.

Nitrate–Nitrite–Nitric Oxide Pathway: A Mechanism of Hypoxia and Anoxia Tolerance in Plants

Oxygen (O₂) is the most crucial substrate for numerous biochemical processes in plants. Its deprivation is a critical factor that affects plant growth and may lead to death if it lasts for a long time. However, various biotic and abiotic factors cause O₂ deprivation, leading to hypoxia and anoxia in plant tissues. To survive under hypoxia and/or anoxia, plants deploy various mechanisms such as fermentation paths, reactive oxygen species (ROS), reactive nitrogen species (RNS), antioxidant enzymes, aerenchyma, and adventitious root formation, while nitrate (NO₃⁻), nitrite (NO₂⁻), and nitric oxide (NO) have shown numerous beneficial roles through modulating these mechanisms. Therefore, in this review, we highlight the role of reductive pathways of NO formation which lessen the deleterious effects of oxidative damages and increase the adaptation capacity of plants during hypoxia and anoxia. Meanwhile, the overproduction of NO through reductive pathways during hypoxia and anoxia leads to cellular dysfunction and cell death. Thus, its scavenging or inhibition is equally important for plant survival. As plants are also reported to produce a potent greenhouse gas nitrous oxide (N₂O) when supplied with NO₃⁻ and NO₂⁻, resembling bacterial denitrification, its role during hypoxia and anoxia tolerance is discussed here. We point out that NO reduction to N₂O along with the phytoglobin-NO cycle could be the most important NO-scavenging mechanism that would reduce nitro-oxidative stress, thus enhancing plants’ survival during O₂-limited conditions. Hence, understanding the molecular mechanisms involved in reducing NO toxicity would not only provide insight into its role in plant physiology, but also address the uncertainties seen in the global N₂O budget.

Nitric oxide mediated alleviation of abiotic challenges in plants

Agriculture and ecosystem are negatively influenced by the abiotic stresses which create solemn pressures on plants as they are sessile in nature leading to excessive losses in economy. For maintenance of sustainable agriculture and to fulfil the cumulative call of food for rapidly growing population worldwide, it becomes crucial to protects the crop plants from climate fluctuations. Plants fight back against these challenges by generation of redox molecules comprising reactive oxygen species (ROS) and reactive nitrogen species (RNS) and cause modulation at cellular, physiological and molecular levels. Nitric oxide (NO) deliver tolerance to several biotic and abiotic stresses in plants by acting as signalling molecule or free radicals. It is also intricated in several developmental processes in plants using different mechanisms. Supplementation of exogenous NO reduce toxicity of abiotic stresses and provide resistance. In this review article, we summarize the recent research studies (five years) depicting the functional role of NO in alleviation of abiotic stresses such as drought, cold, heat, heavy metals and flooding. Moreover, by investigating studies found that among heavy metals works associated with Hg, Pb, and Cr is limited comparatively. Additionally, role of NO in abiotic stress resistance such as cold, freezing and heat stress less/poorly investigated. Consequently, further emphasis should be diverted towards how NO can facilitate protection against these stresses. In recent studies mostly beneficial role of NO against abiotic challenges have been elucidated by observing physiological/biochemical parameters but relatively inadequate research done at the transcripts level or gene regulation subsequently researchers should include it in future. Lastly, brief outline and an evaluative discussion on the present information and future prospective provided. Altogether, these inclusive experimental agendas could facilitate in future to produce climate tolerant plants. This will help to confront the constant fluctuations in the environment and to reduce the challenges in way of agriculture productivity and global food demands.

The Role of Nitric Oxide Signaling in Plant Responses to Cadmium Stress

Nitric oxide (NO) is a widely distributed gaseous signaling molecule in plants that can be synthesized through enzymatic and non-enzymatic pathways and plays an important role in plant growth and development, signal transduction, and response to biotic and abiotic stresses. Cadmium (Cd) is a heavy metal pollutant widely found in the environment, which not only inhibits plant growth but also enters humans through the food chain and endangers human health. To reduce or avoid the adverse effects of Cd stress, plants have evolved a range of coping mechanisms. Many studies have shown that NO is also involved in the plant response to Cd stress and plays an important role in regulating the resistance of plants to Cd stress. However, until now, the mechanisms by which Cd stress regulates the level of endogenous NO accumulation in plant cells remained unclear, and the role of exogenous NO in plant responses to Cd stress is controversial. This review describes the pathways of NO production in plants, the changes in endogenous NO levels in plants under Cd stress, and the effects of exogenous NO on regulating plant resistance to Cd stress.

Interaction between Melatonin and NO: Action Mechanisms, Main Targets, and Putative Roles of the Emerging Molecule NOmela

Melatonin (MEL), a ubiquitous indolamine molecule, has gained interest in the last few decades due to its regulatory role in plant metabolism. Likewise, nitric oxide (NO), a gasotransmitter, can also affect plant molecular pathways due to its function as a signaling molecule. Both MEL and NO can interact at multiple levels under abiotic stress, starting with their own biosynthetic pathways and inducing a particular signaling response in plants. Moreover, their interaction can result in the formation of NOmela, a very recently discovered nitrosated form of MEL with promising roles in plant physiology. This review summarizes the role of NO and MEL molecules during plant development and fruit ripening, as well as their interactions. Due to the impact of climate-change-related abiotic stresses on agriculture, this review also focuses on the role of these molecules in mediating abiotic stress tolerance and the main mechanisms by which they operate, from the upregulation of the entire antioxidant defense system to the post-translational modifications (PTMs) of important molecules. Their individual interaction and crosstalk with phytohormones and H₂S are also discussed. Finally, we introduce and summarize the little information available about NOmela, an emerging and still very unknown molecule, but that seems to have a stronger potential than MEL and NO separately in mediating plant stress response.

Protein tyrosine nitration in atherosclerotic endothelial dysfunction

Accumulation of reactive oxygen species (ROS) can induce both protein tyrosine nitration and endothelial dysfunction in atherosclerosis. Endothelial dysfunction refers to impaired endothelium-dependent vasorelaxation that can be triggered by an imbalance in nitric oxide (NO) production and consumption. ROS reacts with NO to generate peroxynitrite, decreasing NO bioavailability. Peroxynitrite also promotes protein tyrosine nitration in vivo that can affect protein structure and function and further damage endothelial function. In this review, we discuss the process of protein tyrosine nitration, increased expression of nitrated proteins in cardiovascular disease and their association with endothelial dysfunction, and the interference of tyrosine nitration with antioxidants and the protective role in endothelial dysfunction. These may lead us to the conception that protein tyrosine nitration may be one of the causes of endothelial dysfunction, and help us gain information about the mechanism of endothelial dysfunction underlying atherosclerosis.

Protein Tyrosine Nitration in Plant Nitric Oxide Signaling

Nitric oxide (NO), which is ubiquitously present in living organisms, regulates many developmental and stress-activated processes in plants. Regulatory effects exerted by NO lies mostly in its chemical reactivity as a free radical. Proteins are main targets of NO action as several amino acids can undergo NO-related post-translational modifications (PTMs) that include mainly S-nitrosylation of cysteine, and nitration of tyrosine and tryptophan. This review is focused on the role of protein tyrosine nitration on NO signaling, making emphasis on the production of NO and peroxynitrite, which is the main physiological nitrating agent; the main metabolic and signaling pathways targeted by protein nitration; and the past, present, and future of methodological and strategic approaches to study this PTM. Available information on identification of nitrated plant proteins, the corresponding nitration sites, and the functional effects on the modified proteins will be summarized. However, due to the low proportion of in vivo nitrated peptides and their inherent instability, the identification of nitration sites by proteomic analyses is a difficult task. Artificial nitration procedures are likely not the best strategy for nitration site identification due to the lack of specificity. An alternative to get artificial site-specific nitration comes from the application of genetic code expansion technologies based on the use of orthogonal aminoacyl-tRNA synthetase/tRNA pairs engineered for specific noncanonical amino acids. This strategy permits the programmable site-specific installation of genetically encoded 3-nitrotyrosine sites in proteins expressed in Escherichia coli, thus allowing the study of the effects of specific site nitration on protein structure and function.

ROS Metabolism Perturbation as an Element of Mode of Action of Allelochemicals

The allelopathic interaction between plants is one of the elements that influences plant communities. It has been commonly studied by applying tissue extracts onto the acceptors or by treating them with isolated allelotoxins. Despite descriptive observations useful for agricultural practice, data describing the molecular mode of action of allelotoxins cannot be found. Due to the development of -omic techniques, we have an opportunity to investigate specific reactive oxygen species (ROS)-dependent changes in proteome or transcriptome that are induced by allelochemicals. The aim of our review is to summarize data on the ROS-induced modification in acceptor plants in response to allelopathic plants or isolated allelochemicals. We present the idea of how ROS are involved in the hormesis and plant autotoxicity phenomena. As an example of an -omic approach in studies of the mode of action of allelopatic compounds, we describe the influence of meta-tyrosine, an allelochemical exudated from roots of fescues, on nitration-one of nitro-oxidative posttranslational protein modification in the roots of tomato plants. We conclude that ROS overproduction and an induction of oxidative stress are general plants' responses to various allelochemicals, thus modification in ROS metabolisms is regarded as an indirect mode of action of allelochemicals.

Involvement of nitric oxide (NO) in plant responses to metalloids

Plants respond to the limited or excess supply of metalloids, boron (B), silicon (Si), selenium (Se), arsenic (As), and antimony (Sb) via complex signaling pathways that are mainly regulated by nitric oxide (NO). The absorption of metalloids from the soil is facilitated by pathways that involve aquaporins, aquaglyceroporins, phosphate, and sulfate transporters; however, their regulation by NO is poorly understood. Using in silico software, we predicted the S-nitrosation of known metalloid transporters, proposing NO-dependent regulation of metalloid transport systems at the posttranslational level. NO intensifies the stress-mitigating effect of Si, whereas in the case of Se, As, and Sb, the accumulation of NO or reactive nitrogen species contributes to toxicity. NO promotes the beneficial effect of low Se concentrations and mitigates the damage caused by B deficiency. In addition, the exogenous application of NO donor, sodium nitroprusside, reduces B, Se, and As toxicity. The primary role of NO in metalloid stress response is to mitigate oxidative stress by activating antioxidant defense at the level of protein activity and gene expression. This review discusses the role of NO in plant responses to metalloids and suggests future research directions.

Computational prediction of NO-dependent posttranslational modifications in plants: Current status and perspectives

The perception and transduction of nitric oxide (NO) signal is achieved by NO-dependent posttranslational modifications (PTMs) among which S-nitrosation and tyrosine nitration has biological significance. In plants, 100-1000 S-nitrosated and tyrosine nitrated proteins have been identified so far by mass spectrometry. The determination of NO-modified protein targets/amino acid residues is often methodologically challenging. In the past decade, the growing demand for the knowledge of S-nitrosated or tyrosine nitrated sites has motivated the introduction of bioinformatics tools. For predicting S-nitrosation seven computational tools have been developed (GPS-SNO, SNOSite, iSNO-PseACC, iSNO-AAPAir, PSNO, PreSNO, RecSNO). Four predictors have been developed for indicating tyrosine nitration sites (GPS-YNO2, iNitro-Tyr, PredNTS, iNitroY-Deep), and one tool (DeepNitro) predicts both NO-dependent PTMs. The advantage of these computational tools is the fast provision of large amount of information. In this review, the available software tools have been tested on plant proteins in which S-nitrosated or tyrosine nitrated sites have been experimentally identified. The predictors showed distinct performance and there were differences from the experimental results partly due to the fact that the three-dimensional protein structure is not taken into account by the computational tools. Nevertheless, the predictors excellently establish experiments, and it is suggested to apply all available tools on target proteins and compare their results. In the future, computational prediction must be developed further to improve the precision with which S-nitrosation/tyrosine nitration-sites are identified.

Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling

Legumes include several major crops that can fix atmospheric nitrogen in symbiotic root nodules, thus reducing the demand for nitrogen fertilizers and contributing to sustainable agriculture. Global change models predict increases in temperature and extreme weather conditions. This scenario might increase plant exposure to abiotic stresses and negatively affect crop production. Regulation of whole plant physiology and nitrogen fixation in legumes during abiotic stress is complex, and only a few mechanisms have been elucidated. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are key players in the acclimation and stress tolerance mechanisms of plants. However, the specific redox-dependent signaling pathways are far from understood. One mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification (PTM) of proteins. Redox-based PTMs occur in the cysteine thiol group (oxidation, S-nitrosylation, S-glutathionylation, persulfidation), and also in methionine (oxidation), tyrosine (nitration), and lysine and arginine (carbonylation/glycation) residues. Unraveling PTM patterns under different types of stress and establishing the functional implications may give insight into the underlying mechanisms by which the plant and nodule respond to adverse conditions. Here, we review current knowledge on redox-based PTMs and their possible consequences in legume and nodule biology.

GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes

In the past, reactive nitrogen species (RNS) were supposed to be stress-induced by-products of disturbed metabolism that cause oxidative damage to biomolecules. However, emerging evidence demonstrates a substantial role of RNS as endogenous signals in eukaryotes. In plants, S-nitrosoglutathione (GSNO) is the dominant RNS and serves as the ^•NO donor for S-nitrosation of diverse effector proteins. Remarkably, the endogenous GSNO level is tightly controlled by S-nitrosoglutathione reductase (GSNOR) that irreversibly inactivates the glutathione-bound NO to ammonium. Exogenous feeding of diverse RNS, including GSNO, affected chromatin accessibility and transcription of stress-related genes, but the triggering function of RNS on these regulatory processes remained elusive. Here, we show that GSNO reductase-deficient plants (gsnor1-3) accumulate S-adenosylmethionine (SAM), the principal methyl donor for methylation of DNA and histones. This SAM accumulation triggered a substantial increase in the methylation index (MI = [SAM]/[S-adenosylhomocysteine]), indicating the transmethylation activity and histone methylation status in higher eukaryotes. Indeed, a mass spectrometry-based global histone profiling approach demonstrated a significant global increase in H3K9me2, which was independently verified by immunological detection using a selective antibody. Since H3K9me2-modified regions tightly correlate with methylated DNA regions, we also determined the DNA methylation status of gsnor1-3 plants by whole-genome bisulfite sequencing. DNA methylation in the CG, CHG, and CHH contexts in gsnor1-3 was significantly enhanced compared to the wild type. We propose that GSNOR1 activity affects chromatin accessibility by controlling the transmethylation activity (MI) required for maintaining DNA methylation and the level of the repressive chromatin mark H3K9me2.

Regulation of ascorbate-glutathione cycle by exogenous nitric oxide and hydrogen peroxide in soybean roots under arsenate stress

The role of nitric oxide (NO) and hydrogen peroxide (H2O2) is well known for regulating plant abiotic stress responses. However, underlying mechanisms are still poorly understood. Therefore, the present study investigated the involvement of NO and H2O2 signalling in the regulation of arsenate toxicity (AsV) in soybean roots employing a pharmacological approach. Results show that AsV toxicity declined root length and biomass due to greater As accumulation in the cell wall and cellular organelles. Arsenate induced cell death due to enhanced levels of reactive oxygen species, lipid and protein oxidation and down-regulation in ascorbate-glutathione cycle and redox states of ascorbate and glutathione. These results correlate with lower endogenous level of NO. Interestingly, addition of L-NAME increased AsV toxicity. However, addition of SNP reverses effect of L-NAME, suggesting that endogenous NO has a role in mitigating AsV toxicity. Exogenous H2O2 also demonstrated capability of alleviating AsV stress, while NAC reversed the protective effect of H2O2. Furthermore, DPI application further increased AsV toxicity, suggesting that endogenous H2O2 is also implicated in mitigating AsV stress. SNP was not able to mitigate AsV toxicity in the presence of DPI, suggesting that H2O2 might have acted downstream of NO in accomplishing amelioration of AsV toxicity.

Advances in Understanding of Desiccation Tolerance of Lichens and Lichen-Forming Algae

Lichens are symbiotic associations (holobionts) established between fungi (mycobionts) and certain groups of cyanobacteria or unicellular green algae (photobionts). This symbiotic association has been essential in the colonization of terrestrial dry habitats. Lichens possess key mechanisms involved in desiccation tolerance (DT) that are constitutively present such as high amounts of polyols, LEA proteins, HSPs, a powerful antioxidant system, thylakoidal oligogalactolipids, etc. This strategy allows them to be always ready to survive drastic changes in their water content. However, several studies indicate that at least some protective mechanisms require a minimal time to be induced, such as the induction of the antioxidant system, the activation of non-photochemical quenching including the de-epoxidation of violaxanthin to zeaxanthin, lipid membrane remodeling, changes in the proportions of polyols, ultrastructural changes, marked polysaccharide remodeling of the cell wall, etc. Although DT in lichens is achieved mainly through constitutive mechanisms, the induction of protection mechanisms might allow them to face desiccation stress in a better condition. The proportion and relevance of constitutive and inducible DT mechanisms seem to be related to the ecology at which lichens are adapted to.

cROStalk for Life: Uncovering ROS Signaling in Plants and Animal Systems, from Gametogenesis to Early Embryonic Development

This review explores the role of reactive oxygen species (ROS)/Ca2+ in communication within reproductive structures in plants and animals. Many concepts have been described during the last years regarding how biosynthesis, generation products, antioxidant systems, and signal transduction involve ROS signaling, as well as its possible link with developmental processes and response to biotic and abiotic stresses. In this review, we first addressed classic key concepts in ROS and Ca2+ signaling in plants, both at the subcellular, cellular, and organ level. In the plant science field, during the last decades, new techniques have facilitated the in vivo monitoring of ROS signaling cascades. We will describe these powerful techniques in plants and compare them to those existing in animals. Development of new analytical techniques will facilitate the understanding of ROS signaling and their signal transduction pathways in plants and mammals. Many among those signaling pathways already have been studied in animals; therefore, a specific effort should be made to integrate this knowledge into plant biology. We here discuss examples of how changes in the ROS and Ca2+ signaling pathways can affect differentiation processes in plants, focusing specifically on reproductive processes where the ROS and Ca2+ signaling pathways influence the gametophyte functioning, sexual reproduction, and embryo formation in plants and animals. The study field regarding the role of ROS and Ca2+ in signal transduction is evolving continuously, which is why we reviewed the recent literature and propose here the potential targets affecting ROS in reproductive processes. We discuss the opportunities to integrate comparative developmental studies and experimental approaches into studies on the role of ROS/ Ca2+ in both plant and animal developmental biology studies, to further elucidate these crucial signaling pathways.

Downstream Signalling from Molecular Hydrogen

Molecular hydrogen (H2) is now considered part of the suite of small molecules that can control cellular activity. As such, H2 has been suggested to be used in the therapy of diseases in humans and in plant science to enhance the growth and productivity of plants. Treatments of plants may involve the creation of hydrogen-rich water (HRW), which can then be applied to the foliage or roots systems of the plants. However, the molecular action of H2 remains elusive. It has been suggested that the presence of H2 may act as an antioxidant or on the antioxidant capacity of cells, perhaps through the scavenging of hydroxyl radicals. H2 may act through influencing heme oxygenase activity or through the interaction with reactive nitrogen species. However, controversy exists around all the mechanisms suggested. Here, the downstream mechanisms in which H2 may be involved are critically reviewed, with a particular emphasis on the H2 mitigation of stress responses. Hopefully, this review will provide insight that may inform future research in this area.

Nitric oxide signaling in the plant nucleus: the function of nitric oxide in chromatin modulation and transcription

Nitric oxide (NO) is involved in a vast number of physiologically important processes in plants, such as organ development, stress resistance, and immunity. Transduction of NO bioactivity is generally achieved by post-translational modification of proteins, with S-nitrosation of cysteine residues as the predominant form. While traditionally the subcellular location of the factors involved was of lesser importance, recent studies identified the connection between NO and transcriptional activity and thereby raised the question about the route of NO into the nuclear sphere. Identification of NO-affected transcription factors and chromatin-modifying histone deacetylases implicated the important role of NO signaling in the plant nucleus as a regulator of epigenetic mechanisms and gene transcription. Here, we discuss the relationship between NO and its directly regulated protein targets in the nuclear environment, focusing on S-nitrosated chromatin modulators and transcription factors.

Nitric oxide signalling in plant nanobiology: current status and perspectives

Plant nanobiology as a novel research field provides a scientific basis for the agricultural use of nanoparticles (NPs). Plants respond to the presence of nanomaterials by synthesizing signal molecules, such as the multifunctional gaseous nitric oxide (NO). Several reports have described the effects of different nanomaterials (primarily chitosan NPs, metal oxide NPs, and carbon nanotubes) on endogenous NO synthesis and signalling in different plant species. Other works have demonstrated the ameliorating effect of exogenous NO donor (primarily sodium nitroprusside) treatments on NP-induced stress. NO-releasing NPs are preferred alternatives to chemical NO donors, and evaluating their effects on plants has recently begun. Previous studies clearly indicate that endogenous NO production in the presence of nanomaterials or NO levels increased by exogenous treatments (NO-releasing NPs or chemical NO donors) exerts growth-promoting and stress-ameliorating effects in plants. Furthermore, an NP-based nanosensor for NO detection in plants has been developed, providing a new and excellent perspective for basic research and also for the evaluation of plants' health status in agriculture.

Nitric oxide, other reactive signalling compounds, redox, and reductive stress

Nitric oxide (NO) and other reactive nitrogen species (RNS) are key signalling molecules in plants, but they do not work in isolation. NO is produced in cells, often increased in response to stress conditions, but many other reactive compounds used in signalling are generated and accumulate spatially and temporally together. This includes the reactive oxygen species (ROS), such as hydrogen peroxide (H2O2), and hydrogen sulfide (H2S). Here, the interactions with such other reactive molecules is briefly reviewed. Furthermore, along with ROS and H2S, NO will potentially contribute to the overall intracellular redox of the cell. However, RNS will exist in redox couples and therefore the influence of the cellular redox on such couples will be explored. In discussions of the aberrations in intracellular redox it is usually oxidation, so-called oxidative stress, which is discussed. Here, we consider the notion of reductive stress and how this may influence the signalling which may be mediated by NO. By getting a more holistic view of NO biology, the influence on cell activity of NO and other RNS can be more fully understood, and may lead to the elucidation of methods for NO-based manipulation of plant physiology, leading to better stress responses and improved crops in the future.

Regulation of glutamine synthetase activity by transcriptional and posttranslational modifications negatively influences ganoderic acid biosynthesis in Ganoderma lucidum

Glutamine synthetase (GS), a central nitrogen metabolic enzyme, plays important roles in the nitrogen regulation network and secondary metabolism in fungi. However, the mechanisms by which external nitrogen sources regulate fungal GS activity have not been determined. Here, we found that GS activity was inhibited under nitrate conditions in Ganoderma lucidum. By constructing gs-silenced strains and adding 1 mM GS inhibitor to inhibit GS activity, we found that a decrease in GS activity led to a decrease in ganoderic acid biosynthesis. The transcription of gs increased approximately five fold under nitrate conditions compared with that under ammonia. Electrophoretic mobility shift and yeast one-hybrid assay showed that gs was transcriptionally regulated by AreA. Although both gs expression and GS protein content increased under nitrate conditions, the GS activity still decreased. Treatment of recombinant GS with SIN-1 (protein nitration donor) resulted in a strengthened nitration accompanied by a 71% decrease in recombinant GS activity. Furthermore, intracellular GS could be nitrated from mycelia cultivated under nitrate conditions. These results indicated that GS activity could be inhibited by NO-mediated protein nitration. Our findings provide the first insight into the role of transcriptional and posttranslational regulation of GS activity in regulating secondary metabolism in fungi.

The Effect of Foliar Selenium (Se) Treatment on Growth, Photosynthesis, and Oxidative-Nitrosative Signalling of Stevia rebaudiana Leaves

Selenium (Se) enrichment of Stevia rebaudiana Bertoni can serve a dual purpose, on the one hand to increase plant biomass and stress tolerance and on the other hand to produce Se fortified plant-based food. Foliar Se spraying (0, 6, 8, 10 mg/L selenate, 14 days) of Stevia plantlets resulted in slightly decreased stevioside and rebaudioside A concentrations, and it also caused significant increment in stem elongation, leaf number, and Se content, suggesting that foliar Se supplementation can be used as a biofortifying approach. Furthermore, Se slightly limited photosynthetic CO₂ assimilation (A_N, g_sw, C_i/C_a), but exerted no significant effect on chlorophyll, carotenoid contents and on parameters associated with photosystem II (PSII) activity (F_V/F_M, F₀, Y(NO)), indicating that Se causes no photodamage in PSII. Further results indicate that Se is able to activate PSI-cyclic electron flow independent protection mechanisms of the photosynthetic apparatus of Stevia plants. The applied Se activated superoxide dismutase (SOD) isoenzymes (MnSOD1, FeSOD1, FeSOD2, Cu/ZnSOD1, Cu/ZnSOD2) and down-regulated NADPH oxidase suggesting the Se-induced limitation of superoxide anion levels and consequent oxidative signalling in Stevia leaves. Additionally, the decrease in S-nitrosoglutathione reductase protein abundance and the intensification of protein tyrosine nitration indicate Se-triggered nitrosative signalling. Collectively, these results suggest that Se supplementation alters Stevia shoot morphology without significantly affecting biomass yield and photosynthesis, but increasing Se content and performing antioxidant effects, which indicates that foliar application of Se may be a promising method in Stevia cultivation.

Regulation of Dual Activity of Ascorbate Peroxidase 1 From Arabidopsis thaliana by Conformational Changes and Posttranslational Modifications

Ascorbate peroxidase (APX) is an important reactive oxygen species (ROS)-scavenging enzyme, which catalyzes the removal of hydrogen peroxide (H₂O₂) to prevent oxidative damage. The peroxidase activity of APX is regulated by posttranslational modifications (PTMs), such as S-nitrosylation, tyrosine nitration, and S-sulfhydration. In addition, it has been recently reported that APX functions as a molecular chaperone, protecting rice against heat stress. In this study, we attempted to identify the various functions of APX in Arabidopsis and the effects of PTMs on these functions. Cytosol type APX1 from Arabidopsis thaliana (AtAPX1) exists in multimeric forms ranging from dimeric to high-molecular-weight (HMW) complexes. Similar to the rice APX2, AtAPX1 plays a dual role behaving both as a regular peroxidase and a chaperone molecule. The dual activity of AtAPX1 was strongly related to its structural status. The main dimeric form of the AtAPX1 protein showed the highest peroxidase activity, whereas the HMW form exhibited the highest chaperone activity. Moreover, in vivo studies indicated that the structure of AtAPX1 was regulated by heat and salt stresses, with both involved in the association and dissociation of complexes, respectively. Additionally, we investigated the effects of S-nitrosylation, S-sulfhydration, and tyrosine nitration on the protein structure and functions using gel analysis and enzymatic activity assays. S-nitrosylation and S-sulfhydration positively regulated the peroxidase activity, whereas tyrosine nitration had a negative impact. However, no effects were observed on the chaperone function and the oligomeric status of AtAPX1. Our results will facilitate the understanding of the role and regulation of APX under abiotic stress and posttranslational modifications.

Tyrosine Nitration of Flagellins: a Response of Sinorhizobium meliloti to Nitrosative Stress

Rhizobia are bacteria which can either live as free organisms in the soil or interact with plants of the legume family with, as a result, the formation of root organs called nodules in which differentiated endosymbiotic bacteria fix atmospheric nitrogen to the plant's benefit. In both lifestyles, rhizobia are exposed to nitric oxide (NO) which can be perceived as a signaling or toxic molecule. NO can act at the transcriptional level but can also modify proteins by S-nitrosylation of cysteine or nitration of tyrosine residues. However, only a few molecular targets of NO have been described in bacteria and none of them have been characterized in rhizobia. Here, we examined tyrosine nitration of Sinorhizobium meliloti proteins induced by NO. We found three tyrosine-nitrated proteins in S. meliloti grown under free-living conditions, in response to an NO donor. Two nitroproteins were identified by mass spectrometry and correspond to flagellins A and B. We showed that one of the nitratable tyrosines is essential to flagellin function in motility.IMPORTANCE Rhizobia are found as free-living bacteria in the soil or in interaction with plants and are exposed to nitric oxide (NO) in both environments. NO is known to have many effects on animals, plants, and bacteria where only a few molecular targets of NO have been described so far. We identified flagellin A and B by mass spectrometry as tyrosine-nitrated proteins in Sinorhizobium meliloti in vivo We also showed that one of the nitratable tyrosines is essential to flagellin function in motility. The results enhanced our understanding of NO effects on rhizobia. Identification of bacterial flagellin nitration opens a new possible role of NO in plant-microbe interactions.

Nitric Oxide Signaling in Plants

Nitric oxide (NO) is an integral part of cell signaling mechanisms in animals and plants. In plants, its enzymatic generation is still controversial. Evidence points to nitrate reductase being important, but the presence of a nitric oxide synthase-like enzyme is still contested. Regardless, NO has been shown to mediate many developmental stages in plants, and to be involved in a range of physiological responses, from stress management to stomatal aperture closure. Downstream from its generation are alterations of the actions of many cell signaling components, with post-translational modifications of proteins often being key. Here, a collection of papers embraces the differing aspects of NO metabolism in plants.

Differential modulation of S-nitrosoglutathione reductase and reactive nitrogen species in wild and cultivated tomato genotypes during development and powdery mildew infection

Nitric oxide plays an important role in the pathogenesis of Pseudoidium neolycopersici, the causative agent of tomato powdery mildew. S-nitrosoglutathione reductase, the key enzyme of S-nitrosothiol homeostasis, was investigated during plant development and following infection in three genotypes of Solanum spp. differing in their resistance to P. neolycopersici. Levels and localization of reactive nitrogen species (RNS) including NO, S-nitrosoglutathione (GSNO) and peroxynitrite were studied together with protein nitration and the activity of nitrate reductase (NR). GSNOR expression profiles and enzyme activities were modulated during plant development and important differences among Solanum spp. genotypes were observed, accompanied by modulation of NO, GSNO, peroxynitrite and nitrated proteins levels. GSNOR was down-regulated in infected plants, with exception of resistant S. habrochaites early after inoculation. Modulations of GSNOR activities in response to pathogen infection were found also on the systemic level in leaves above and below the inoculation site. Infection strongly increased NR activity and gene expression in resistant S. habrochaites in contrast to susceptible S. lycopersicum. Obtained data confirm the key role of GSNOR and modulations of RNS during plant development under normal conditions and point to their involvement in molecular mechanisms of tomato responses to biotrophic pathogens on local and systemic levels.

Hydrogenases and the Role of Molecular Hydrogen in Plants

Molecular hydrogen (H2) has been suggested to be a beneficial treatment for a range of species, from humans to plants. Hydrogenases catalyze the reversible oxidation of H2, and are found in many organisms, including plants. One of the cellular effects of H2 is the selective removal of reactive oxygen species (ROS) and reactive nitrogen species (RNS), specifically hydroxyl radicals and peroxynitrite. Therefore, the function of hydrogenases and the action of H2 needs to be reviewed in the context of the signalling roles of a range of redox active compounds. Enzymes can be controlled by the covalent modification of thiol groups, and although motifs targeted by nitric oxide (NO) can be predicted in hydrogenases sequences it is likely that the metal prosthetic groups are the target of inhibition. Here, a selection of hydrogenases, and the possibility of their control by molecules involved in redox signalling are investigated using a bioinformatics approach. Methods of treating plants with H2 along with the role of H2 in plants is also briefly reviewed. It is clear that studies report significant effects of H2 on plants, improving growth and stress responses, and therefore future work needs to focus on the molecular mechanisms involved.

ZnO nanoparticles induce cell wall remodeling and modify ROS/ RNS signalling in roots of Brassica seedlings

Cell wall-associated defence against zinc oxide nanoparticles (ZnO NPs) as well as nitro-oxidative signalling and its consequences in plants are poorly examined. Therefore, this study compares the effect of chemically synthetized ZnO NPs (~45 nm, 25 or 100 mg/L) on Brassica napus and Brassica juncea seedlings. The effects on root biomass and viability suggest that B. napus is more tolerant to ZnO NP exposure relative to B. juncea. This may be due to the lack of Zn ion accumulation in the roots, which is related to the increase in the amount of lignin, suberin, pectin and in peroxidase activity in the roots of B. napus. TEM results indicate that root cell walls of 25 mg/L ZnO NP-treated B. napus may bind Zn ions. Additionally, callose accumulation possibly contribute to root shortening in both Brassica species as the effect of 100 mg/L ZnO NPs. Further results suggest that in the roots of the relatively sensitive B. juncea the levels of superoxide radical, hydrogen peroxide, hydrogen sulfide, nitric oxide, peroxinitrite and S-nitrosoglutathione increased as the effect of high ZnO NP concentration meaning that ZnO NP intensifies nitro-oxidative signalling. In B. napus; however, reactive oxygen species signalling was intensified, but reactive nitrogen species signalling wasn't activated by ZnO NPs. Collectively, these results indicate that ZnO NPs induce cell wall remodeling which may be associated with ZnO NP tolerance. Furthermore, plant tolerance against ZnO NPs is associated rather with nitrosative signalling than oxidative modifications.

Reorganization of Protein Tyrosine Nitration Pattern Indicates the Relative Tolerance of Brassica napus (L.) over Helianthus annuus (L.) to Combined Heavy Metal Treatment

Metal-polluted areas, especially where municipal sewage is used as fertilizer, often have high concentrations of more than one metal. The development of the root system is regulated by a complex signaling network, which includes reactive oxygen and nitrogen species. The delicate balance of the endogenous signal system can be affected by various environmental stimuli including heavy metals (HMs) in excess. Our goal was to analyze the microelement homeostasis, root architecture, and to determine the underlying changes in the nitro-oxidative status in the root system of rapeseed (Brassica napus L.) and sunflower (Helianthus annuus L.) subjected to combined HM treatments. The effect of model-sewage in two different layouts was simulated in rhizotron system by only supplementing the highest HM concentrations (Cd, Cr, Cu, Hg, Ni, Pb, and Zn) legally allowed. The two species reacted differently to combined HM treatment; compared to the relatively sensitive sunflower, rapeseed showed better metal translocation capability and root growth even at the more severe treatment, where the pattern of protein tyrosine nitration was reorganized. The obtained results, especially the increased nitric oxide content and changed pattern of tyrosine nitration in rapeseed, can indicate acclimation and species-specific nitro-oxidative responses to combined HM stress.

Tyr-nitration in maize CDKA;1 results in lower affinity for ATP binding

Cyclin-dependent kinase A (CDKA) is a key component for cell cycle progression. The catalytic kinase activity depends on the protein's ability to form an active complex with cyclins and on phosphoregulatory mechanisms. Cell cycle arrest and plant growth impairment under abiotic stress have been linked to different molecular processes triggered by increased levels of reactive oxygen and nitrogen species (ROS and RNS). Among these, posttranslational modifications (PTMs) of key proteins such as CDKA;1 may be of significance. Herein, isolated maize embryo axes were subjected to sodium nitroprusside (SNP) as an inductor of nitrosative conditions to evaluate if CDKA;1 protein was a target for RNS. A high degree of protein nitration was detected; this included the specific Tyr-nitration of CDKA;1. Tyr15 and Tyr19, located at the ATP-binding site, were the selective targets for nitration according to both in silico analysis using the predictive software GPS-YNO₂, and in vitro mass spectrometry studies of recombinant nitrated ZmCDKA;1. Spectrofluorometric measurements demonstrated a reduction of ZmCDKA;1-NO₂ affinity for ATP. From these results, we conclude that Tyr nitration in CDKA;1 could act as an active modulator of cell cycle progression during redox stress.

Peroxynitrite induced signaling pathways in plant response to non-proteinogenic amino acids

Nitro/oxidative modifications of proteins and RNA nitration resulted from altered peroxynitrite generation are elements of the indirect mode of action of canavanine and meta-tyrosine in plants Environmental conditions and stresses, including supplementation with toxic compounds, are known to impair reactive oxygen (ROS) and reactive nitrogen species (RNS) homeostasis, leading to modification in production of oxidized and nitrated derivatives. The role of nitrated and/or oxidized biotargets differs depending on the stress factors and developmental stage of plants. Canavanine (CAN) and meta-tyrosine (m-Tyr) are non-proteinogenic amino acids (NPAAs). CAN, the structural analog of arginine, is found mostly in seeds of Fabaceae species, as a storage form of nitrogen. In mammalian cells, CAN is used as an anticancer agent due to its inhibitory action on nitric oxide synthesis. m-Tyr is a structural analogue of phenylalanine and an allelochemical found in root exudates of fescues. In animals, m-Tyr is recognized as a marker of oxidative stress. Supplementation of plants with CAN or m-Tyr modify ROS and RNS metabolism. Over the last few years of our research, we have collected the complex data on ROS and RNS metabolism in tomato (Solanum lycopersicum L.) plants exposed to CAN or m-Tyr. In addition, we have shown the level of nitrated RNA (8-Nitro-guanine) in roots of seedlings, stressed by the tested NPAAs. In this review, we describe the model of CAN and m-Tyr mode of action in plants based on modifications of signaling pathways induced by ROS/RNS with a special focus on peroxynitrite induced RNA and protein modifications.

Nitro-oxidative signalling induced by chemically synthetized zinc oxide nanoparticles (ZnO NPs) in Brassica species

Due to their release into the environment, zinc oxide nanoparticles (ZnO NPs) may come in contact with plants. In elevated concentrations, ZnO NPs induce reactive oxygen species (ROS) production, but the metabolism of reactive nitrogen species (RNS) and the consequent nitro-oxidative signalling has not been examined so far. In this work, Brassica napus and Brassica juncea seedlings were treated with chemically synthetized ZnO NPs (∼8 nm, 0, 25 or 100 mg/L). At low dose (25 mg/L) ZnO NP exerted a positive effect, while at elevated concentration (100 mg/L) it was toxic to both species. Additionally, B. juncea was more tolerant to ZnO NPs than B. napus. The ZnO NPs could enter the root cells due to their small (∼8 nm) size which resulted in the release of Zn²⁺ and subsequently increased Zn²⁺ content in the plant organs. ZnO NPs disturbed superoxide radical and hydrogen peroxide homeostasis and modulated ROS metabolic enzymes (NADPH oxidase, superoxide dismutase, ascorbate peroxidase) and non-enzymatic antioxidants (ascorbate and glutathione) inducing similar changes in oxidative signalling in both Brassica species. The homeostasis of RNS (nitric oxide, peroxynitrite and S-nitrosoglutathione) was also altered by ZnO NPs; however, changes in nitrosative signalling proved to be different in the examined species. Moreover, ZnO NPs triggered changes in protein carbonylation and nitration. These results suggest that ZnO NPs induce changes in nitro-oxidative signalling which may contribute to ZnO NP toxicity. Furthermore, difference in ZnO NP tolerance of Brassica species is more likely related to nitrosative than to oxidative signalling.

Interactions between metabolism and chromatin in plant models

BACKGROUND

One of the fascinating aspects of epigenetic regulation is that it provides means to rapidly adapt to environmental change. This is particularly relevant in the plant kingdom, where most species are sessile and exposed to increasing habitat fluctuations due to global warming. Although the inheritance of epigenetically controlled traits acquired through environmental impact is a matter of debate, it is well documented that environmental cues lead to epigenetic changes, including chromatin modifications, that affect cell differentiation or are associated with plant acclimation and defense priming. Still, in most cases, the mechanisms involved are poorly understood. An emerging topic that promises to reveal new insights is the interaction between epigenetics and metabolism.

SCOPE OF REVIEW

This study reviews the links between metabolism and chromatin modification, in particular histone acetylation, histone methylation, and DNA methylation, in plants and compares them to examples from the mammalian field, where the relationship to human diseases has already generated a larger body of literature. This study particularly focuses on the role of reactive oxygen species (ROS) and nitric oxide (NO) in modulating metabolic pathways and gene activities that are involved in these chromatin modifications. As ROS and NO are hallmarks of stress responses, we predict that they are also pivotal in mediating chromatin dynamics during environmental responses.

MAJOR CONCLUSIONS

Due to conservation of chromatin-modifying mechanisms, mammals and plants share a common dependence on metabolic intermediates that serve as cofactors for chromatin modifications. In addition, plant-specific non-CG methylation pathways are particularly sensitive to changes in folate-mediated one-carbon metabolism. Finally, reactive oxygen and nitrogen species may fine-tune epigenetic processes and include similar signaling mechanisms involved in environmental stress responses in plants as well as animals.

Distinct redox signalling and nickel tolerance in Brassica juncea and Arabidopsis thaliana

Despite of its essentiality, nickel (Ni) in excess is toxic for plants partly due to the overproduction of reactive oxygen species (ROS) and the consequent increase in oxidative stress signalling. However, in Ni-stressed plants little is known about the signal transduction of reactive nitrogen species (RNS) and protein tyrosine nitration as the protein-level consequence of increased RNS formation. Our experiments compared the nickel accumulation and tolerance, the redox signalling and the protein nitration in the agar-grown Arabidopsis thaliana and Brassica juncea exposed to Ni (50 μM nickel chloride). Studying GUS-tagged Arabidopsis lines (ARR5::GUS, ACS8::GUS and DR5::GUS) revealed that Ni-increased lateral root (LR) emergence, and concomitantly reduced LR initiation were accompanied by elevated levels of auxin, cytokinin, and ethylene in the LRs or in upper root parts, whereas Ni-induced primary root shortening is related to decreased auxin, and increased cytokinin and ethylene levels. These suggest the Ni-induced disturbance of hormonal balance in the root system. Results of the comparative study showed that weaker Ni tolerance of A. thaliana was coupled with a Ni-induced increase in RNS, ROS, and hydrogen sulfide levels, as well as with an increase in redox signalling and consequent increment of protein nitration. However, in relative Ni tolerant B. juncea, redox signalling (except for peroxynitrite) was not modified, and Ni-induced intensification of protein tyrosine nitration was less pronounced. Data collectively show that the better Ni tolerance of Brassica juncea may be related to the capability of preventing the induction of redox signalling and consequently to the slighter increase in protein nitration.

Melatonin-Nitric Oxide Crosstalk and Their Roles in the Redox Network in Plants

Melatonin, an amine hormone highly conserved during evolution, has a wide range of physiological functions in animals and plants. It is involved in plant growth, development, maturation, and aging, and also helps ameliorate various types of abiotic and biotic stresses, including salt, drought, heavy metals, and pathogens. Melatonin-related growth and defense responses of plants are complex, and involve many signaling molecules. Among these, the most important one is nitric oxide (NO), a freely diffusing amphiphilic biomolecule that can easily cross the cell membrane, produce rapid signal responses, and participate in a wide variety of physiological reactions. NO-induced S-nitrosylation is also involved in plant defense responses. NO interacts with melatonin as a long-range signaling molecule, and helps regulate plant growth and maintain oxidative homeostasis. Exposure of plants to abiotic stresses causes the increase of endogenous melatonin levels, with the consequent up-regulation of melatonin synthesis genes, and further increase of melatonin content. The application of exogenous melatonin causes an increase in endogenous NO and up-regulation of defense-related transcription factors, resulting in enhanced stress resistance. When plants are infected by pathogenic bacteria, NO acts as a downstream signal to lead to increased melatonin levels, which in turn induces the mitogen-activated protein kinase (MAPK) cascade and associated defense responses. The application of exogenous melatonin can also promote sugar and glycerol production, leading to increased levels of salicylic acid and NO. Melatonin and NO in plants can function cooperatively to promote lateral root growth, delay aging, and ameliorate iron deficiency. Further studies are needed to clarify certain aspects of the melatonin/NO relationship in plant physiology.

S-Nitrosothiol Signaling Is involved in Regulating Hydrogen Peroxide Metabolism of Zinc-Stressed Arabidopsis

Accumulation of heavy metals such as zinc (Zn) disturbs the metabolism of reactive oxygen (e.g. hydrogen peroxide, H2O2) and nitrogen species (e.g. nitric oxide, NO; S-nitrosoglutathione, GSNO) in plant cells; however, their signal interactions are not well understood. Therefore, this study examines the interplay between H2O2 metabolism and GSNO signaling in Arabidopsis. Comparing the Zn tolerance of the wild type (WT), GSNO reductase (GSNOR) overexpressor 35S::FLAG-GSNOR1 and GSNOR-deficient gsnor1-3, we observed relative Zn tolerance of gsnor1-3, which was not accompanied by altered Zn accumulation capacity. Moreover, in gsnor1-3 plants Zn did not induce NO/S-nitrosothiol (SNO) signaling, possibly due to the enhanced activity of NADPH-dependent thioredoxin reductase. In WT and 35S::FLAG-GSNOR1, GSNOR was inactivated by Zn, and Zn-induced H2O2 is directly involved in the GSNOR activity loss. In WT seedlings, Zn resulted in a slight intensification of protein nitration detected by Western blot and protein S-nitrosation observed by resin-assisted capture of SNO proteins (RSNO-RAC). LC-MS/MS analyses indicate that Zn induces the S-nitrosation of ascorbate peroxidase 1. Our data collectively show that Zn-induced H2O2 may influence its own level, which involves GSNOR inactivation-triggered SNO signaling. These data provide new evidence for the interplay between H2O2 and SNO signaling in Arabidopsis plants affected by metal stress.

Short-Term Low Temperature Induces Nitro-Oxidative Stress that Deregulates the NADP-Malic Enzyme Function by Tyrosine Nitration in Arabidopsis thaliana

Low temperature (LT) negatively affects plant growth and development via the alteration of the metabolism of reactive oxygen and nitrogen species (ROS and RNS). Among RNS, tyrosine nitration, the addition of an NO₂ group to a tyrosine residue, can modulate reduced nicotinamide-dinucleotide phosphate (NADPH)-generating systems and, therefore, can alter the levels of NADPH, a key cofactor in cellular redox homeostasis. NADPH also acts as an indispensable electron donor within a wide range of enzymatic reactions, biosynthetic pathways, and detoxification processes, which could affect plant viability. To extend our knowledge about the regulation of this key cofactor by this nitric oxide (NO)-related post-translational modification, we analyzed the effect of tyrosine nitration on another NADPH-generating enzyme, the NADP-malic enzyme (NADP-ME), under LT stress. In Arabidopsis thaliana seedlings exposed to short-term LT (4 °C for 48 h), a 50% growth reduction accompanied by an increase in the content of superoxide, nitric oxide, and peroxynitrite, in addition to diminished cytosolic NADP-ME activity, were found. In vitro assays confirmed that peroxynitrite inhibits cytosolic NADP-ME2 activity due to tyrosine nitration. The mass spectrometric analysis of nitrated NADP-ME2 enabled us to determine that Tyr-73 was exclusively nitrated to 3-nitrotyrosine by peroxynitrite. The in silico analysis of the Arabidopsis NADP-ME2 protein sequence suggests that Tyr73 nitration could disrupt the interactions between the specific amino acids responsible for protein structure stability. In conclusion, the present data show that short-term LT stress affects the metabolism of ROS and RNS, which appears to negatively modulate the activity of cytosolic NADP-ME through the tyrosine nitration process.

Zinc-induced root architectural changes of rhizotron-grown B. napus correlate with a differential nitro-oxidative response

Roots have a noteworthy plasticity: due to different stress conditions their architecture can change to favour seedling vigour and yield stability. The development of the root system is regulated by a complex and diverse signalling network, which besides hormonal factors, includes reactive oxygen (ROS) - and nitrogen species (RNS). The delicate balance of the endogenous signal system can be affected by various environmental stimuli, such as the excess of essential heavy metals, like zinc (Zn). Zn at low concentration, is able to induce the morphological and physiological adaptation of the root system, but in excess it exerts toxic effects on plants. In this study the effect of a low, growth-inducing, and a high, growth inhibiting Zn concentrations on the early development of Brassica napus (L.) root architecture and the underlying nitro-oxidative mechanisms were studied in a soil-filled rhizotron system. The growth-inhibiting Zn treatment resulted in elevated protein tyrosine nitration due to the imbalance in ROS and RNS homeostasis, however its pattern was not changed compared to the control. This nitro-oxidative stress was accompanied by serious changes in the cell wall composition and decrease in the cell proliferation and viability, due to the high Zn uptake and disturbed microelement homeostasis in the root tips. During the positive root growth response, a tyrosine nitration-pattern reorganisation was observed; there were no substantial changes in ROS and RNS balance and the viability and proliferation of the root tips' meristematic zone decreased to a lesser extent, as a result of a lower Zn uptake. The obtained results suggest that Zn in different amounts triggers different root growth responses accompanied by distinct changes in the pattern and strength of tyrosine nitration, proposing that nitrosative processes have an important role in the stress-induced root growth responses.

Current approaches to measure nitric oxide in plants

Nitric oxide (NO) is now established as an important signalling molecule in plants where it influences growth, development, and responses to stress. Despite extensive research, the most appropriate methods to measure and localize these signalling radicals are debated and still need investigation. Many confounding factors such as the presence of other reactive intermediates, scavenging enzymes, and compartmentation influence how accurately each can be measured. Further, these signalling radicals have short half-lives ranging from seconds to minutes based on the cellular redox condition. Hence, it is necessary to use sensitive and specific methods in order to understand the contribution of each signalling molecule to various biological processes. In this review, we summarize the current knowledge on NO measurement in plant samples, via various methods. We also discuss advantages, limitations, and wider applications of each method.

Alternative oxidase is an important player in the regulation of nitric oxide levels under normoxic and hypoxic conditions in plants

Plant mitochondria possess two different pathways for electron transport from ubiquinol: the cytochrome pathway and the alternative oxidase (AOX) pathway. The AOX pathway plays an important role in stress tolerance and is induced by various metabolites and signals. Previously, several lines of evidence indicated that the AOX pathway prevents overproduction of superoxide and other reactive oxygen species. More recent evidence suggests that AOX also plays a role in regulation of nitric oxide (NO) production and signalling. The AOX pathway is induced under low phosphate, hypoxia, pathogen infections, and elicitor treatments. The induction of AOX under aerobic conditions in response to various stresses can reduce electron transfer through complexes III and IV and thus prevents the leakage of electrons to nitrite and the subsequent accumulation of NO. Excess NO under various stresses can inhibit complex IV; thus, the AOX pathway minimizes nitrite-dependent NO synthesis that would arise from enhanced electron leakage in the cytochrome pathway. By preventing NO generation, AOX can reduce peroxynitrite formation and tyrosine nitration. In contrast to its function under normoxia, AOX has a specific role under hypoxia, where AOX can facilitate nitrite-dependent NO production. This reaction drives the phytoglobin-NO cycle to increase energy efficiency under hypoxia.