Site-specific nitrosoproteomic identification of endogenously S-nitrosylated proteins in Arabidopsis

Redox regulation of gene expression: proteomics reveals multiple previously undescribed redox-sensitive cysteines in transcription complexes and chromatin modifiers

Redox signalling is crucial for regulating plant development and adaptation to environmental changes. Proteins with redox-sensitive cysteines can sense oxidative stress and modulate their functions. Recent proteomics efforts have comprehensively mapped the proteins targeted by oxidative modifications. The nucleus, the epicentre of transcriptional reprogramming, contains a large number of proteins that control gene expression. Specific redox-sensitive transcription factors have long been recognized as key players in decoding redox signals in the nucleus and thus in regulating transcriptional responses. Consequently, the redox regulation of the nuclear transcription machinery and its cofactors has received less attention. In this review, we screened proteomic datasets for redox-sensitive cysteines on proteins of the core transcription complexes and chromatin modifiers in Arabidopsis thaliana. Our analysis indicates that redox regulation affects every step of gene transcription, from initiation to elongation and termination. We report previously undescribed redox-sensitive subunits in transcription complexes and discuss the emerging challenges in unravelling the landscape of redox-regulated processes involved in nuclear gene transcription.

S-nitrosylation may inhibit the activity of COP1 in plant photomorphogenesis

Protein S-nitrosylation, which is defined by the covalent attachment of nitric oxide (NO) to the thiol group of cysteine residues, is known to play critical roles in plant development and stress responses. NO promotes seedling photomorphogenesis and NO emission is enhanced by light. However, the function of protein S-nitrosylation in plant photomorphogenesis is largely unknown. E3 ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and transcription factor ELONGATED HYPOCOTYL 5 (HY5) antagonistically regulate seedling photomorphogenesis. COP1 inhibits plant photomorphogenesis by targeting photomorphogenic promoters like HY5 for 26S proteasome degradation. Here, we report that COP1 is S-nitrosylated in vitro. Mass spectrometry analyses revealed that two evolutionarily well conserved residues, cysteine 425 and cysteine 607, in the WD40 domain of COP1 are S-nitrosylated. S-nitrosylated glutathione (GSNO) is an important physiological NO donor for protein S-nitrosylation. The Arabidopsis (Arabidopsis thaliana) gsnor1-3 mutant, which accumulates higher level of GSNO, accumulated higher HY5 levels than wildtype (WT), indicating that COP1 activity is inhibited. Protein S-nitrosylation can be reversed by Thioredoxin-h5 (TRXh5) in plants. Indeed, COP1 interacts directly with TRXh5 and its close homolog TRXh3. Moreover, catalase 3 (CAT3) acts as a transnitrosylase that transfers NO to its target proteins like GSNO reductase (GSNOR). We found that CAT3 interacts with COP1 in plants. Taken together, our data indicate that the activity of COP1 is likely inhibited by NO via S-nitrosylation to promote the accumulation of HY5 and photomorphogenesis.

Study on a Mechanism of Improving MaAPX1 Protein Activity by Mutating Methionine to Lysine

Ascorbate peroxidases (APXs) are key components of the ascorbate-glytathione cycle, which plays an important role in removing excess reactive oxygen species (ROS) in plants. Herein, MaAPX1 was verified as being involved in the ripening and senescence of banana fruit, exhibiting responsiveness to the accumulation of ROS and the oxidation of proteins. Site-directed mutation was applied to explore the mechanism of MaAPX1 activity changes. We found that the 32-site cysteine (Cys, C) served as a potential S-nitrosylation site. The mutant MaAPX1C32S activity was decreased significantly when Cys32 was mutated to serine (Ser, S). Intriguingly, the neighboring conserved 36-site methionine (Met, M), which is adjacent to Cys32, displayed an enzyme activity that was approximately five times higher than that of the wild-type MaAPX1 when mutated to lysine (Lys, K). Utilizing LC-MS/MS spectroscopy coupled with stopped-flow analysis showed that the enhanced MaAPX1M36K activity might be due to the increased S-nitrosylation level of Cys32 and the promotion of intermediate (compound I, the first intermediate product of the reaction of APX with H2O2) production. Molecular docking simulations showed that the S-N bond between Cys32 and Lys36 in MaAPX1M36K might have a function in protecting the thiol of Cys32 from oxidation. MaAPX1M36K, a promising mutant, possesses immense potential for improving the antioxidant capabilities of APX in the realm of bioengineering technology research.

De-nitrosylation Coordinates Appressorium Function for Infection of the Rice Blast Fungus

As a signaling molecule, nitric oxide (NO) regulates the development and stress response in different organisms. The major biological activity of NO is protein S-nitrosylation, whose function in fungi remains largely unclear. Here, it is found in the rice blast fungus Magnaporthe oryzae, de-nitrosylation process is essential for functional appressorium formation during infection. Nitrosative stress caused by excessive accumulation of NO is harmful for fungal infection. While the S-nitrosoglutathione reductase GSNOR-mediated de-nitrosylation removes excess NO toxicity during appressorium formation to promote infection. Through an indoTMT switch labeling proteomics technique, 741 S-nitrosylation sites in 483 proteins are identified. Key appressorial proteins, such as Mgb1, MagB, Sps1, Cdc42, and septins, are activated by GSNOR through de-nitrosylation. Removing S-nitrosylation sites of above proteins is essential for proper protein structure and appressorial function. Therefore, GSNOR-mediated de-nitrosylation is an essential regulator for appressorium formation. It is also shown that breaking NO homeostasis by NO donors, NO scavengers, as well as chemical inhibitor of GSNOR, shall be effective methods for fungal disease control.

The Molecular Frequency, Conservation and Role of Reactive Cysteines in Plant Lipid Metabolism

Cysteines (Cys) are chemically reactive amino acids containing sulfur that play diverse roles in plant biology. Recent proteomics investigations in Arabidopsis thaliana have revealed the presence of thiol post-translational modifications (PTMs) in several Cys residues. These PTMs are presumed to impact protein structure and function, yet mechanistic data regarding the specific Cys susceptible to modification and their biochemical relevance remain limited. To help address these limitations, we have conducted a wide-ranging analysis by integrating published datasets encompassing PTM proteomics (comparing S-sulfenylation, persulfidation, S-nitrosylation and S-acylation), genomics and protein structures, with a specific focus on proteins involved in plant lipid metabolism. The prevalence and distribution of modified Cys residues across all analyzed proteins is diverse and multifaceted. Nevertheless, by combining an evaluation of sequence conservation across 100+ plant genomes with AlphaFold-generated protein structures and physicochemical predictions, we have unveiled structural propensities associated with Cys modifications. Furthermore, we have identified discernible patterns in lipid biochemical pathways enriched with Cys PTMs, notably involving beta-oxidation, jasmonic acid biosynthesis, fatty acid biosynthesis and wax biosynthesis. These collective findings provide valuable insights for future investigations targeting the mechanistic foundations of Cys modifications and the regulation of modified proteins in lipid metabolism and other metabolic pathways.

Nitric oxide alleviates programmed cell death induced by cadmium in Solanum lycopersicum seedlings through protein S-nitrosylation

Cadmium (Cd), as a non-essential and toxic heavy metal in plants, has deleterious effects on plant physiological and biochemical processes. Nitric oxide (NO) is one of the most important signaling molecules for plants to response diverse stresses. Here, we found that Cd-induced programmed cell death (PCD) was accompanied by NO bursts, which exacerbated cell death when NO was removed and vice versa. Proteomic analysis of S-nitrosylated proteins showed that the differential proteins in Cd-induced PCD and in NO-alleviated PCD mainly exist together in carbohydrate metabolism and amino acid metabolism, while some of the differential proteins exist alone in metabolism of cofactors and vitamins and lipid metabolism. Meanwhile, S-nitrosylation of proteins in porphyrin and chlorophyll metabolism and starch and sucrose metabolism could explain the leaf chlorosis induced by PCD. Moreover, protein transport protein SEC23, ubiquitinyl hydrolase 1 and pathogenesis-related protein 1 were identified to be S-nitrosylated in vivo, and their expressions were increased in Cd-induced PCD while decreased in NO treatment. Similar results were obtained in tomato seedlings with higher S-nitrosylation. Taken together, our results indicate that NO might be involved in the regulation of Cd-induced PCD through protein S-nitrosylation, especially proteins involved in PCD response.

Arabidopsis Transcriptomics Reveals the Role of Lipoxygenase2 (AtLOX2) in Wound-Induced Responses

In wounded Arabidopsis thaliana leaves, four 13S-lipoxygenases (AtLOX2, AtLOX3, AtLOX4, AtLOX6) act in a hierarchical manner to contribute to the jasmonate burst. This leads to defense responses with LOX2 playing an important role in plant resistance against caterpillar herb-ivory. In this study, we sought to characterize the impact of AtLOX2 on wound-induced phytohormonal and transcriptional responses to foliar mechanical damage using wildtype (WT) and lox2 mutant plants. Compared with WT, the lox2 mutant had higher constitutive levels of the phytohormone salicylic acid (SA) and enhanced expression of SA-responsive genes. This suggests that AtLOX2 may be involved in the biosynthesis of jasmonates that are involved in the antagonism of SA biosynthesis. As expected, the jasmonate burst in response to wounding was dampened in lox2 plants. Generally, 1 h after wounding, genes linked to jasmonate biosynthesis, jasmonate signaling attenuation and abscisic acid-responsive genes, which are primarily involved in wound sealing and healing, were differentially regulated between WT and lox2 mutants. Twelve h after wounding, WT plants showed stronger expression of genes associated with plant protection against insect herbivory. This study highlights the dynamic nature of jasmonate-responsive gene expression and the contribution of AtLOX2 to this pathway and plant resistance against insects.

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.

Ascorbate peroxidase in fruits and modulation of its activity by reactive species

Ascorbate peroxidase (APX) is one of the enzymes of the ascorbate-glutathione cycle and is the key enzyme that breaks down H2O2 with the aid of ascorbate as an electron source. APX is present in all photosynthetic eukaryotes from algae to higher plants and, at the cellular level, it is localized in all subcellular compartments where H2O2 is generated, including the apoplast, cytosol, plastids, mitochondria, and peroxisomes, either in soluble form or attached to the organelle membranes. APX activity can be modulated by various post-translational modifications including tyrosine nitration, S-nitrosation, persulfidation, and S-sulfenylation. This allows the connection of H2O2 metabolism with other relevant signaling molecules such as NO and H2S, thus building a complex coordination system. In both climacteric and non-climacteric fruits, APX plays a key role during the ripening process and during post-harvest, since it participates in the regulation of both H2O2 and ascorbate levels affecting fruit quality. Currently, the exogenous application of molecules such as NO, H2S, H2O2, and, more recently, melatonin is seen as a new alternative to maintain and extend the shelf life and quality of fruits because they can modulate APX activity as well as other antioxidant systems. Therefore, these molecules are being considered as new biotechnological tools to improve crop quality in the horticultural industry.

Redox proteomics of PANC-1 cells reveals the significance of HIF-1 signaling protein oxidation in pancreatic ductal adenocarcinoma pathogenesis

BACKGROUND

Protein cysteine oxidation is substantially involved in various biological and pathogenic processes, but its implications in pancreatic cancer development remains poorly understood.

METHODS AND RESULTS

In this study, we performed a global characterization of protein oxidation targets in PDAC cells through iodoTMT-based quantitative proteomics, which identified over 4300 oxidized cysteine sites in more than 2100 proteins in HPDE6c7 and PANC-1 cells. Among them, 1715 cysteine residues were shown to be differentially oxidized between HPDE6c7 and PANC-1 cells. Also, charged amino acids including aspartate, glutamate and lysine were significantly overrepresented in flanking sequences of oxidized cysteines. Differentially oxidized proteins in PANC-1 cells were enriched in multiple cancer-related biological processes and signaling pathways. Specifically, the HIF-1 signaling proteins exhibited significant oxidation alterations in PANC-1 cells, and the reduced PHD2 oxidation in human PDAC tissues was correlated with lower survival time in pancreatic cancer patients.

CONCLUSION

These investigations provided new insights into protein oxidation-regulated signaling and biological processes during PDAC pathogenesis, which might be further explored for pancreatic cancer diagnosis and treatment.

Drought memory in Acanthostachys strobilacea, a CAM epiphytic bromeliad

Stress memory is the development of altered responses to stress due to previous exposure, which might result in increased tolerance. Biochemical and physiological parameters shown to be positively affected by stress memory include those of the antioxidant and nitrosative metabolism, photosynthetic pigments and osmolyte content. Epiphytic bromeliads likely present stress memory since they experience frequent droughts in the canopies. Thus, we aimed to evaluate if the epiphytic bromeliad Acanthostachys strobilacea (Schult. & Schult.f.) Klotzsch shows improved metabolic stress defence responses to a second drought and rewatering cycle compared to a single exposure. In a controlled environment chamber, 90-day-old plants were exposed to one or two drought-rewatering cycles of 14 days without irrigation and 5 days of rewatering each. Sampling occurred after the final drought and rewatering periods for one or two cycles treatments. The free amino acid, chlorophyll, and carotenoid levels and S-nitrosoglutathione reductase (GSNOR) activity were higher at the second drought than at the first exposure. The rise in nocturnal acidification (indicative of increased CAM activity) caused by the initial drought persisted through the second drought-rewatering cycle, implying a lasting memory effect on CAM activity. Furthermore, the second recovery did not induce glutathione accumulation, as in the first rewatering event, suggesting the pre-exposure to drought reduced this thiol's demand during a later recovery. Our results evidence metabolic changes related to drought stress memory in A. strobilacea, supporting this mechanism might be involved in the tolerance of epiphytic bromeliads to intermittent droughts.

Calcium Signaling and the Response to Heat Shock in Crop Plants

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).

Nitric oxide controls shoot meristem activity via regulation of DNA methylation

Despite the importance of Nitric Oxide (NO) as signaling molecule in both plant and animal development, the regulatory mechanisms downstream of NO remain largely unclear. Here, we show that NO is involved in Arabidopsis shoot stem cell control via modifying expression and activity of ARGONAUTE 4 (AGO4), a core component of the RNA-directed DNA Methylation (RdDM) pathway. Mutations in components of the RdDM pathway cause meristematic defects, and reduce responses of the stem cell system to NO signaling. Importantly, we find that the stem cell inducing WUSCHEL transcription factor directly interacts with AGO4 in a NO dependent manner, explaining how these two signaling systems may converge to modify DNA methylation patterns. Taken together, our results reveal that NO signaling plays an important role in controlling plant stem cell homeostasis via the regulation of de novo DNA methylation.

S-nitrosylation of RABG3E positively regulates vesicle trafficking to promote salt tolerance

Nitric oxide (NO) is a key signaling molecule affecting the response of plants to salt stress; however, the underlying molecular mechanism is poorly understood. In this study, we conducted a phenotype analysis and found that the small GTPase RABG3E (RAB7) promotes salt tolerance in Arabidopsis thaliana. NO promotes the S-nitrosylation of RAB7 at Cys-171, which in turn helps maintain the ion balance in salt-stressed plants. Furthermore, the S-nitrosylation of RAB7 at Cys-171 enhances the enzyme's GTPase activity, thereby promoting vesicle trafficking and increasing its interaction with phosphatidylinositol phosphates-especially phosphatidylinositol-4-phosphate (PI4P). Exogenously applied PI4P increases vesicle trafficking and promotes salt tolerance depending on the S-nitrosylation of RAB7 at Cys-171. These findings illustrate a unique mechanism in salt tolerance, by which NO regulates vesicle trafficking and ion homeostasis through the S-nitrosylation of RAB7 and its interaction with PI4P.

Reactive oxygen species- and nitric oxide-dependent regulation of ion and metal homeostasis in plants

Deterioration and impoverishment of soil, caused by environmental pollution and climate change, result in reduced crop productivity. To adapt to hostile soils, plants have developed a complex network of factors involved in stress sensing, signal transduction, and adaptive responses. The chemical properties of reactive oxygen species (ROS) and reactive nitrogen species (RNS) allow them to participate in integrating the perception of external signals by fine-tuning protein redox regulation and signal transduction, triggering specific gene expression. Here, we update and summarize progress in understanding the mechanistic basis of ROS and RNS production at the subcellular level in plants and their role in the regulation of ion channels/transporters at both transcriptional and post-translational levels. We have also carried out an in silico analysis of different redox-dependent modifications of ion channels/transporters and identified cysteine and tyrosine targets of nitric oxide in metal transporters. Further, we summarize possible ROS- and RNS-dependent sensors involved in metal stress sensing, such as kinases and phosphatases, as well as some ROS/RNS-regulated transcription factors that could be involved in metal homeostasis. Understanding ROS- and RNS-dependent signaling events is crucial to designing new strategies to fortify crops and improve plant tolerance of nutritional imbalance and metal toxicity.

Photorespiration: regulation and new insights on the potential role of persulfidation

Photorespiration has been considered a 'futile' cycle in C3 plants, necessary to detoxify and recycle the metabolites generated by the oxygenating activity of Rubisco. However, several reports indicate that this metabolic route plays a fundamental role in plant metabolism and constitutes a very interesting research topic. Many open questions still remain with regard to photorespiration. One of these questions is how the photorespiratory process is regulated in plants and what factors contribute to this regulation. In this review, we summarize recent advances in the regulation of the photorespiratory pathway with a special focus on the transcriptional and post-translational regulation of photorespiration and the interconnections of this process with nitrogen and sulfur metabolism. Recent findings on sulfide signaling and protein persulfidation are also described.

Regulation of V-ATPase by Jasmonic Acid: Possible Role of Persulfidation

Vacuolar H+-translocating ATPase (V-ATPase) is a proton pump crucial for plant growth and survival. For this reason, its activity is tightly regulated, and various factors, such as signaling molecules and phytohormones, may be involved in this process. The aim of this study was to explain the role of jasmonic acid (JA) in the signaling pathways responsible for the regulation of V-ATPase in cucumber roots and its relationship with other regulators of this pump, i.e., H2S and H2O2. We analyzed several aspects of the JA action on the enzyme, including transcriptional regulation, modulation of protein levels, and persulfidation of selected V-ATPase subunits as an oxidative posttranslational modification induced by H2S. Our results indicated that JA functions as a repressor of V-ATPase, and its action is related to a decrease in the protein amount of the A and B subunits, the induction of oxidative stress, and the downregulation of the E subunit persulfidation. We suggest that both H2S and H2O2 may be downstream components of JA-dependent negative proton pump regulation. The comparison of signaling pathways induced by two negative regulators of the pump, JA and cadmium, revealed that multiple pathways are involved in the V-ATPase downregulation in cucumber roots.

NO Is Not the Same as GSNO in the Regulation of Fe Deficiency Responses by Dicot Plants

Iron (Fe) is abundant in soils but with a poor availability for plants, especially in calcareous soils. To favor its acquisition, plants develop morphological and physiological responses, mainly in their roots, known as Fe deficiency responses. In dicot plants, the regulation of these responses is not totally known, but some hormones and signaling molecules, such as auxin, ethylene, glutathione (GSH), nitric oxide (NO) and S-nitrosoglutathione (GSNO), have been involved in their activation. Most of these substances, including auxin, ethylene, GSH and NO, increase their production in Fe-deficient roots while GSNO, derived from GSH and NO, decreases its content. This paradoxical result could be explained with the increased expression and activity in Fe-deficient roots of the GSNO reductase (GSNOR) enzyme, which decomposes GSNO to oxidized glutathione (GSSG) and NH3. The fact that NO content increases while GSNO decreases in Fe-deficient roots suggests that NO and GSNO do not play the same role in the regulation of Fe deficiency responses. This review is an update of the results supporting a role for NO, GSNO and GSNOR in the regulation of Fe deficiency responses. The possible roles of NO and GSNO are discussed by taking into account their mode of action through post-translational modifications, such as S-nitrosylation, and through their interactions with the hormones auxin and ethylene, directly related to the activation of morphological and physiological responses to Fe deficiency in dicot plants.

Involvement of NO in V-ATPase Regulation in Cucumber Roots under Control and Cadmium Stress Conditions

Nitric oxide (NO) is a signaling molecule that participates in plant adaptation to adverse environmental factors. This study aimed to clarify the role of NO in the regulation of vacuolar H+-ATPase (V-ATPase) in the roots of cucumber seedlings grown under control and Cd stress conditions. In addition, the relationship between NO and salicylic acid (SA), as well as their interrelations with hydrogen sulfide (H2S) and hydrogen peroxide (H2O2), have been verified. The effect of NO on V-ATPase was studied by analyzing two enzyme activities, the expression level of selected VHA genes and the protein level of selected VHA subunits in plants treated with a NO donor (sodium nitroprusside, SNP) and NO biosynthesis inhibitors (tungstate, WO42- and N-nitro-L-arginine methyl ester, L-NAME). Our results indicate that NO functions as a positive regulator of V-ATPase and that this regulation depends on NO generated by nitrate reductase and NOS-like activity. It was found that the mechanism of NO action is not related to changes in the gene expression or protein level of the V-ATPase subunits. The results suggest that in cucumber roots, NO signaling interacts with the SA pathway and, to a lesser extent, with two other known V-ATPase regulators, H2O2 and H2S.

NADP-Dependent Malic Enzyme Genes in Sweet Pepper Fruits: Involvement in Ripening and Modulation by Nitric Oxide (NO)

NADPH is an indispensable cofactor in a wide range of physiological processes that is generated by a family of NADPH dehydrogenases, of which the NADP-dependent malic enzyme (NADP-ME) is a member. Pepper (Capsicum annuum L.) fruit is a horticultural product consumed worldwide that has great nutritional and economic relevance. Besides the phenotypical changes that pepper fruit undergoes during ripening, there are many associated modifications at transcriptomic, proteome, biochemical and metabolic levels. Nitric oxide (NO) is a recognized signal molecule with regulatory functions in diverse plant processes. To our knowledge, there is very scarce information about the number of genes encoding for NADP-ME in pepper plants and their expression during the ripening of sweet pepper fruit. Using a data mining approach to evaluate the pepper plant genome and fruit transcriptome (RNA-seq), five NADP-ME genes were identified, and four of them, namely CaNADP-ME2 to CaNADP-ME5, were expressed in fruit. The time course expression analysis of these genes during different fruit ripening stages, including green immature (G), breaking point (BP) and red ripe (R), showed that they were differentially modulated. Thus, while CaNADP-ME3 and CaNADP-ME5 were upregulated, CaNADP-ME2 and CaNADP-ME4 were downregulated. Exogenous NO treatment of fruit triggered the downregulation of CaNADP-ME4. We obtained a 50-75% ammonium-sulfate-enriched protein fraction containing CaNADP-ME enzyme activity, and this was assayed via non-denaturing polyacrylamide gel electrophoresis (PAGE). The results allow us to identify four isozymes designated from CaNADP-ME I to CaNADP-ME IV. Taken together, the data provide new pieces of information on the CaNADP-ME system with the identification of five CaNADP-ME genes and how the four genes expressed in pepper fruits are modulated during ripening and exogenous NO gas treatment.

FAT-switch-based quantitative S-nitrosoproteomics reveals a key role of GSNOR1 in regulating ER functions

Reversible protein S-nitrosylation regulates a wide range of biological functions and physiological activities in plants. However, it is challenging to quantitively determine the S-nitrosylation targets and dynamics in vivo. In this study, we develop a highly sensitive and efficient fluorous affinity tag-switch (FAT-switch) chemical proteomics approach for S-nitrosylation peptide enrichment and detection. We quantitatively compare the global S-nitrosylation profiles in wild-type Arabidopsis and gsnor1/hot5/par2 mutant using this approach, and identify 2,121 S-nitrosylation peptides in 1,595 protein groups, including many previously unrevealed S-nitrosylated proteins. These are 408 S-nitrosylated sites in 360 protein groups showing an accumulation in hot5-4 mutant when compared to wild type. Biochemical and genetic validation reveal that S-nitrosylation at Cys337 in ER OXIDOREDUCTASE 1 (ERO1) causes the rearrangement of disulfide, resulting in enhanced ERO1 activity. This study offers a powerful and applicable tool for S-nitrosylation research, which provides valuable resources for studies on S-nitrosylation-regulated ER functions in plants.

S-nitrosylation of ACO homolog 4 improves ethylene synthesis and salt tolerance in tomato

Crop loss due to soil salinization is a global threat to agriculture. Nitric oxide (NO) and ethylene involve in multiple plant tolerance. However, their interaction in salt resistance remains largely elusive. We tested the mutual induction between NO and ethylene, and then identified an 1-aminocyclopropane-1-carboxylate oxidase homolog 4 (ACOh4) that influences ethylene synthesis and salt tolerance through NO-mediated S-nitrosylation. Both NO and ethylene positively responded to salt stress. Furthermore, NO participated in salt-induced ethylene production. Salt tolerance evaluation showed that function of NO was abolished by inhibiting ethylene production. Conversely, function of ethylene was little influenced by blocking NO generation. ACO was identified as the target of NO to control ethylene synthesis. In vitro and in vivo results suggested that ACOh4 was S-nitrosylated at Cys172, resulting in its enzymatic activation. Moreover, ACOh4 was induced by NO through transcriptional manner. Knockdown of ACOh4 abolished NO-induced ethylene production and salt tolerance. At physiological status, ACOh4 positively regulates the Na⁺ and H⁺ efflux, and keeps K⁺ /Na⁺ homeostasis by promoting salt-resistive genes' transcripts. Our findings validate a role of NO-ethylene module in salt tolerance and uncover a novel mechanism of how NO promoting ethylene synthesis against adversity.

Catalase: A critical node in the regulation of cell fate

Catalase (CAT) is an extensively studied if somewhat enigmatic enzyme that is at the heart of eukaryotic antioxidant systems with a canonical role in peroxisomal function. The CAT family of proteins exert control over a wide range of plant growth and defence processes. CAT proteins are subject to many types of post-translational modification (PTM), which modify activity, ligand binding, stability, compartmentation and function. The CAT interactome involves many cytosolic and nuclear proteins that appear to be essential for protein functions. Hence, the CAT network of roles extends far beyond those associated with peroxisomal metabolism. Some pathogen effector proteins are able to redirect CAT to the nucleus and recent evidence indicates CAT can traffic to the nucleus in the absence of exogenous proteins. While the mechanisms that target CAT to the nucleus are not understood, CAT activity in the cytosol and nucleus is promoted by interactions with nucleoredoxin. Here we discuss recent findings that have been pivotal in generating a step change in our understanding of CAT functions in plant cells.

Cysteine thiol-based post-translational modification: What do we know about transcription factors?

Reactive electrophilic species are ubiquitous in plant cells, where they contribute to specific redox-regulated signaling events. Redox signaling is known to modulate gene expression during diverse biological processes, including plant growth, development, and environmental stress responses. Emerging data demonstrates that transcription factors (TFs) are a main target of cysteine thiol-based oxidative post-translational modifications (OxiPTMs), which can alter their transcriptional activity and thereby convey redox information to the nucleus. Here, we review the significant progress that has been made in characterizing cysteine thiol-based OxiPTMs, their biochemical properties, and their functional effects on plant TFs. We discuss the underlying mechanism of redox regulation and its contribution to various physiological processes as well as still outstanding challenges in redox regulation of plant gene expression.

H2 O2 , NO, and H2 S networks during root development and signalling under physiological and challenging environments: Beneficial or toxic?

Hydrogen peroxide (H₂ O₂ ) is a reactive oxygen species (ROS) and a key modulator of the development and architecture of the root system under physiological and adverse environmental conditions. Nitric oxide (NO) and hydrogen sulphide (H₂ S) also exert myriad functions on plant development and signalling. Accumulating pieces of evidence show that depending upon the dose and mode of applications, NO and H₂ S can have synergistic or antagonistic actions in mediating H₂ O₂ signalling during root development. Thus, H₂ O₂ -NO-H₂ S crosstalk might essentially impart tolerance to elude oxidative stress in roots. Growth and proliferation of root apex involve crucial orchestration of NO and H₂ S-mediated ROS signalling which also comprise other components including mitogen-activated protein kinase, cyclins, cyclin-dependent kinases, respiratory burst oxidase homolog (RBOH), and Ca²⁺ flux. This assessment provides a comprehensive update on the cooperative roles of NO and H₂ S in modulating H₂ O₂ homoeostasis during root development, abiotic stress tolerance, and root-microbe interaction. Furthermore, it also analyses the scopes of some fascinating future investigations associated with strigolactone and karrikins concerning H₂ O₂ -NO-H₂ S crosstalk in plant roots.

The role of nitric oxide and hydrogen sulfide in regulation of redox homeostasis at extreme temperatures in plants

Nitric oxide and hydrogen sulfide, as important signaling molecules (gasotransmitters), are involved in many functions of plant organism, including adaptation to stress factors of various natures. As redox-active molecules, NO and H₂S are involved in redox regulation of functional activity of many proteins. They are also involved in maintaining cell redox homeostasis due to their ability to interact directly and indirectly (functionally) with ROS, thiols, and other molecules. The review considers the involvement of nitric oxide and hydrogen sulfide in plant responses to low and high temperatures. Particular attention is paid to the role of gasotransmitters interaction with other signaling mediators (in particular, with Ca²⁺ ions and ROS) in the formation of adaptive responses to extreme temperatures. Pathways of stress-induced enhancement of NO and H₂S synthesis in plants are considered. Mechanisms of the NO and H₂S effect on the activity of some proteins of the signaling system, as well as on the state of antioxidant and osmoprotective systems during adaptation to stress temperatures, were analyzed. Possibilities of practical use of nitric oxide and hydrogen sulfide donors as inductors of plant adaptive responses are discussed.

Free Radicals Mediated Redox Signaling in Plant Stress Tolerance

Abiotic and biotic stresses negatively affect plant cellular and biological processes, limiting their growth and productivity. Plants respond to these environmental cues and biotrophic attackers by activating intricate metabolic-molecular signaling networks precisely and coordinately. One of the initial signaling networks activated is involved in the generation of reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS). Recent research has exemplified that ROS below the threshold level can stimulate plant survival by modulating redox homeostasis and regulating various genes of the stress defense pathway. In contrast, RNS regulates the stress tolerance potential of crop plants by modulating post-translation modification processes, such as S-nitrosation and tyrosine nitration, improving the stability of protein and DNA and activating the expression of downstream stress-responsive genes. RSS has recently emerged as a new warrior in combating plant stress-induced oxidative damage by modulating various physiological and stress-related processes. Several recent findings have corroborated the existence of intertwined signaling of ROS/RNS/RSS, playing a substantial role in crop stress management. However, the molecular mechanisms underlying their remarkable effect are still unknown. This review comprehensively describes recent ROS/RNS/RSS biology advancements and how they can modulate cell signaling and gene regulation for abiotic stress management in crop plants. Further, the review summarizes the latest information on how these ROS/RNS/RSS signaling interacts with other plant growth regulators and modulates essential plant functions, particularly photosynthesis, cell growth, and apoptosis.

Expanding roles for S-nitrosylation in the regulation of plant immunity

Following pathogen recognition, plant cells produce a nitrosative burst resulting in a striking increase in nitric oxide (NO), altering the redox state of the cell, which subsequently helps orchestrate a plethora of immune responses. NO is a potent redox cue, efficiently relayed between proteins through its co-valent attachment to highly specific, powerfully reactive protein cysteine (Cys) thiols, resulting in formation of protein S-nitrosothiols (SNOs). This process, known as S-nitrosylation, can modulate the function of target proteins, enabling responsiveness to cellular redox changes. Key targets of S-nitrosylation control the production of reactive oxygen species (ROS), the transcription of immune-response genes, the triggering of the hypersensitive response (HR) and the establishment of systemic acquired resistance (SAR). Here, we bring together recent advances in the control of plant immunity by S-nitrosylation, furthering our appreciation of how changes in cellular redox status reprogramme plant immune function.

Protein-protein interactions in plant antioxidant defense

The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca²⁺, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.

Plant homocysteine, a methionine precursor and plant's hallmark of metabolic disorders

Homocysteine (Hcy) is a sulfur-containing non-proteinogenic amino acid, which arises from redox-sensitive methionine metabolism. In plants, Hcy synthesis involves both cystathionine β-lyase and S-adenosylhomocysteine hydrolase activities. Thus, Hcy itself is crucial for de novo methionine synthesis and S-adenosylmethionine recycling, influencing the formation of ethylene, polyamines, and nicotianamine. Research on mammalian cells has shown biotoxicity of this amino acid, as Hcy accumulation triggers oxidative stress and the associated lipid peroxidation process. In addition, the presence of highly reactive groups induces Hcy and Hcy derivatives to modify proteins by changing their structure and function. Currently, Hcy is recognized as a critical, independent hallmark of many degenerative metabolic diseases. Research results indicate that an enhanced Hcy level is also toxic to yeast and bacteria cells. In contrast, in the case of plants the metabolic status of Hcy remains poorly examined and understood. However, the presence of the toxic Hcy metabolites and Hcy over-accumulation during the development of an infectious disease seem to suggest harmful effects of this amino acid also in plant cells. The review highlights potential implications of Hcy metabolism in plant physiological disorders caused by environmental stresses. Moreover, recent research advances emphasize that recognizing the Hcy mode of action in various plant systems facilitates verification of the potential status of Hcy metabolites as bioindicators of metabolism disorders and thus may constitute an element of broadly understood biomonitoring.

Insights into the expression of DNA (de)methylation genes responsive to nitric oxide signaling in potato resistance to late blight disease

Our previous study concerning the pathogen-induced biphasic pattern of nitric oxide (NO) burst revealed that the decline phase and a low level of NO, due to S-nitrosoglutathione reductase (GSNOR) activity, might be decisive in the upregulation of stress-sensitive genes via histone H3/H4 methylation in potato leaves inoculated with avr P. infestans. The present study refers to the NO-related impact on genes regulating DNA (de)methylation, being in dialog with histone methylation. The excessive amounts of NO after the pathogen or GSNO treatment forced the transient upregulation of histone SUVH4 methylation and DNA hypermethylation. Then the diminished NO bioavailability reduced the SUVH4-mediated suppressive H3K9me2 mark on the R3a gene promoter and enhanced its transcription. However, we found that the R3a gene is likely to be controlled by the RdDM methylation pathway. The data revealed the time-dependent downregulation of the DCL3, AGO4, and miR482e genes, exerting upregulation of the targeted R3a gene correlated with ROS1 overexpression. Based on these results, we postulate that the biphasic waves of NO burst in response to the pathogen appear crucial in establishing potato resistance to late blight through the RdDM pathway controlling R gene expression.

Regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses

Selective autophagy functions as a regulatory mechanism by targeting native and functional proteins to ensure their proper levels and activities in plant adaptive responses. Autophagy is a cellular degradation and recycling pathway with a key role in cellular homeostasis and metabolism. Autophagy is initiated with the biogenesis of autophagosomes, which fuse with the lysosomes or vacuoles to release their contents for degradation. Under nutrient starvation or other adverse environmental conditions, autophagy usually targets unwanted or damaged proteins, organelles and other cellular components for degradation and recycling to promote cell survival. Over the past decade, however, a substantial number of studies have reported that autophagy in plants also functions as a regulatory mechanism by targeting enzymes, structural and regulatory proteins that are not necessarily damaged or dysfunctional to ensure their proper abundance and function to facilitate cellular changes required for response to endogenous and environmental conditions. During plant-pathogen interactions in particular, selective autophagy targets specific pathogen components as a defense mechanism and pathogens also utilize autophagy to target functional host factors to suppress defense mechanisms. Autophagy also targets native and functional protein regulators of plant heat stress memory, hormone signaling, and vesicle trafficking associated with plant responses to abiotic and other conditions. In this review, we discuss advances in the regulatory roles of selective autophagy through targeting of native proteins in plant adaptive responses, what questions remain and how further progress in the analysis of these special regulatory roles of autophagy can help understand biological processes important to plants.

Nitric oxide alleviates salt stress through protein S-nitrosylation and transcriptional regulation in tomato seedlings

NO enhances the resistance of tomato seedlings to salt stress through protein S-nitrosylation and transcriptional regulation, which involves the regulation of MAPK signaling and carbohydrate metabolism. Nitric oxide (NO) regulates various physiological and biochemical processes and stress responses in plants. We found that S-nitrosoglutathione (GSNO) treatment significantly promoted the growth of tomato seedling under NaCl stress, indicating that NO plays a positive role in salt stress resistance. Moreover, GSNO pretreatment resulted in an increase of endogenous NO level, S-nitrosothiol (SNO) content, S-nitrosoglutathione reductase (GSNOR) activity and GSNOR expression under salt stress, implicating that S-nitrosylation might be involved in NO-alleviating salt stress. To further explore whether S-nitrosylation is a key molecular mechanism of NO-alleviating salt stress, the biotin-switch technique and liquid chromatography/mass spectrometry/mass spectrometry (LC-MS/MS) were conducted. A total of 1054 putative S-nitrosylated proteins have been identified, which were mainly enriched in chloroplast, cytoplasm and mitochondrion. Among them, 15 and 22 S-nitrosylated proteins were involved in mitogen-activated protein kinase (MAPK) signal transduction and carbohydrate metabolism, respectively. In MAPK signaling, various S-nitrosylated proteins, SAM1, SAM3, SAM, PP2C and SnRK, were down-regulated and MAPK, MAPKK and MAPKK5 were up-regulated at the transcriptional level by GSNO treatment under salt stress compared to NaCl treatment alone. The GSNO pretreatment could reduce ethylene production and ABA content under NaCl stress. In addition, the activities of enzyme identified in carbohydrate metabolism, their expression at the transcriptional level and the metabolite content were up-regulated by GSNO supplication under salt stress, resulting in the activation of glycolysis and tricarboxylic acid cycle (TCA) cycles. Thus, these results demonstrated that NO might beneficially regulate MAPK signaling at transcriptional levels and activate carbohydrate metabolism at the post-translational and transcriptional level, protecting seedlings from energy deficiency and salinity, thereby alleviating salt stress-induced damage in tomato seedlings. It provides initial insights into the regulatory mechanisms of NO in response to salt stress.

Two chloroplast-localized MORF proteins act as chaperones to maintain tetrapyrrole biosynthesis

Tetrapyrroles have essential functions as pigments and cofactors during plant growth and development, and the tetrapyrrole biosynthesis pathway is tightly controlled. Multiple organellar RNA editing factors (MORFs) are required for editing of a wide variety of RNA sites in chloroplasts and mitochondria, but their biochemical properties remain elusive. Here, we uncovered the roles of chloroplast-localized MORF2 and MORF9 in modulating tetrapyrrole biosynthesis and embryogenesis in Arabidopsis thaliana. The lack or reduced transcripts of MORF2 or MORF9 significantly affected biosynthesis of the tetrapyrrole precursor 5-aminolevulinic acid and accumulation of Chl and other tetrapyrrole intermediates. MORF2 directly interacts with multiple tetrapyrrole biosynthesis enzymes and regulators, including NADPH:PROTOCHLOROPHYLLIDE OXIDOREDUCTASE B (PORB) and GENOMES UNCOUPLED4 (GUN4). Strikingly, MORF2 and MORF9 display holdase chaperone activity, alleviate the aggregation of PORB in vitro, and are essential for POR accumulation in vivo. Moreover, both MORF2 and MORF9 significantly stimulate magnesium chelatase activity. Our findings reveal a previously unknown biochemical property of MORF proteins as chaperones and point to a new layer of post-translational control of the tightly regulated tetrapyrrole biosynthesis in plants.

Redox regulation of enzymes involved in sulfate assimilation and in the synthesis of sulfur-containing amino acids and glutathione in plants

Sulfur is essential in plants because of its presence in numerous molecules including the two amino acids, cysteine, and methionine. Cysteine serves also for the synthesis of glutathione and provides sulfur to many other molecules including protein cofactors or vitamins. Plants absorb sulfate from their environment and assimilate it via a reductive pathway which involves, respectively, a series of transporters and enzymes belonging to multigenic families. A tight control is needed to adjust each enzymatic step to the cellular requirements because the whole pathway consumes energy and produces toxic/reactive compounds, notably sulfite and sulfide. Glutathione is known to regulate the activity of some intermediate enzymes. In particular, it provides electrons to adenosine 5'-phosphosulfate reductases but also regulates the activity of glutamate-cysteine ligase by reducing a regulatory disulfide. Recent proteomic data suggest a more extended post-translational redox control of the sulfate assimilation pathway enzymes and of some associated reactions, including the synthesis of both sulfur-containing amino acids, cysteine and methionine, and of glutathione. We have summarized in this review the known oxidative modifications affecting cysteine residues of the enzymes involved. In particular, a prominent regulatory role of protein persulfidation seems apparent, perhaps because sulfide produced by this pathway may react with oxidized thiol groups. However, the effect of persulfidation has almost not yet been explored.

Thiol-based Oxidative Posttranslational Modifications (OxiPTMs) of Plant Proteins

The thiol group of cysteine (Cys) residues, often present in the active center of the protein, is of particular importance to protein function, which is significantly determined by the redox state of a protein's environment. Our knowledge of different thiol-based oxidative posttranslational modifications (oxiPTMs), which compete for specific protein thiol groups, has increased over the last 10 years. The principal oxiPTMs include S-sulfenylation, S-glutathionylation, S-nitrosation, persulfidation, S-cyanylation and S-acylation. The role of each oxiPTM depends on the redox cellular state, which in turn depends on cellular homeostasis under either optimal or stressful conditions. Under such conditions, the metabolism of molecules such as glutathione, NADPH (reduced nicotinamide adenine dinucleotide phosphate), nitric oxide, hydrogen sulfide and hydrogen peroxide can be altered, exacerbated and, consequently, outside the cell's control. This review provides a broad overview of these oxiPTMs under physiological and unfavorable conditions, which can regulate the function of target proteins.

Proteomic Analysis of S-Nitrosation Sites During Somatic Embryogenesis in Brazilian Pine, Araucaria angustifolia (Bertol.) Kuntze

Cysteine S-nitrosation is a redox-based post-translational modification that mediates nitric oxide (NO) regulation of various aspects of plant growth, development and stress responses. Despite its importance, studies exploring protein signaling pathways that are regulated by S-nitrosation during somatic embryogenesis have not been performed. In the present study, endogenous cysteine S-nitrosation site and S-nitrosated proteins were identified by iodo-TMT labeling during somatic embryogenesis in Brazilian pine, an endangered native conifer of South America. In addition, endogenous -S-nitrosothiol (SNO) levels and S-nitrosoglutathione reductase (GSNOR) activity were determined in cell lines with contrasting embryogenic potential. Overall, we identified an array of proteins associated with a large variety of biological processes and molecular functions with some of them already described as important for somatic embryogenesis (Class IV chitinase, pyruvate dehydrogenase E1 and dehydroascorbate reductase). In total, our S-nitrosoproteome analyses identified 18 endogenously S-nitrosated proteins and 50 in vitro S-nitrosated proteins (after GSNO treatment) during cell culture proliferation and embryo development. Furthermore, SNO levels and GSNOR activity were increased during embryo formation. These findings expand our understanding of the Brazilian pine proteome and shed novel insights into the potential use of pharmacological manipulation of NO levels by using NO inhibitors and donors during somatic embryogenesis.

High Nitric Oxide Concentration Inhibits Photosynthetic Pigment Biosynthesis by Promoting the Degradation of Transcription Factor HY5 in Tomato

Photosynthetic pigments in higher plants, including chlorophyll and carotenoid, are crucial for photosynthesis and photoprotection. Previous studies have shown that nitric oxide (NO) plays a dual role in plant photosynthesis. However, how pigment biosynthesis is suppressed by NO remains unclear. In this study, we generated NO-accumulated gsnor mutants, applied exogenous NO donors, and used a series of methods, including reverse transcription quantitative PCR, immunoblotting, chromatin immunoprecipitation, electrophoretic mobility shift, dual-luciferase, and NO content assays, to explore the regulation of photosynthetic pigment biosynthesis by NO in tomato. We established that both endogenous and exogenous NO inhibited pigment accumulation and photosynthetic capacities. High levels of NO stimulated the degradation of LONG HYPOCOTYL 5 (HY5) protein and further inactivated the transcription of genes encoding protochlorophyllide oxidoreductase C (PORC) and phytoene synthase 2 (PSY2)—two enzymes that catalyze the rate-limiting steps in chlorophyll and carotenoid biosynthesis. Our findings provide a new insight into the mechanism of NO signaling in modulating HY5-mediated photosynthetic pigment biosynthesis at the transcriptional level in tomato plants.

Nitric oxide negatively regulates gibberellin signaling to coordinate growth and salt tolerance in Arabidopsis

In response to dynamically altered environments, plants must finely coordinate the balance between growth and stress responses for their survival. However, the underpinning regulatory mechanisms remain largely elusive. The phytohormone gibberellin promotes growth via a derepression mechanism by proteasomal degradation of the DELLA transcription repressors. Conversely, the stress-induced burst of nitric oxide (NO) enhances stress tolerance, largely relaying on NO-mediated S-nitrosylation, a redox-based posttranslational modification. Here, we show that S-nitrosylation of Cys-374 in the Arabidopsis RGA protein, a key member of DELLAs, inhibits its interaction with the F-box protein SLY1, thereby preventing its proteasomal degradation under salinity condition. The accumulation of RGA consequently retards growth but enhances salt tolerance. We propose that NO negatively regulates gibberellin signaling via S-nitrosylation of RGA to coordinate the balance of growth and stress responses when challenged by adverse environments.

Hsp70 in Redox Homeostasis

Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.

Nitric Oxide Signaling and Its Association with Ubiquitin-Mediated Proteasomal Degradation in Plants

Nitric oxide (NO) is a versatile signaling molecule with diverse roles in plant biology. The NO-mediated signaling mechanism includes post-translational modifications (PTMs) of target proteins. There exists a close link between NO-mediated PTMs and the proteasomal degradation of proteins via ubiquitylation. In some cases, ubiquitin-mediated proteasomal degradation of target proteins is followed by an NO-mediated post-translational modification on them, while in other cases NO-mediated PTMs can regulate the ubiquitylation of the components of ubiquitin-mediated proteasomal machinery for promoting their activity. Another pathway that links NO signaling with the ubiquitin-mediated degradation of proteins is the N-degron pathway. Overall, these mechanisms reflect an important mechanism of NO signal perception and transduction that reflect a close association of NO signaling with proteasomal degradation via ubiquitylation. Therefore, this review provides insight into those pathways that link NO-PTMs with ubiquitylation.

Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism

Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.

Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling

Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.

Nitric oxide, gravity response, and a unified schematic of plant signaling

Plant signaling components are often involved in numerous processes. Calcium, reactive oxygen species, and other signaling molecules are essential to normal biotic and abiotic responses. Yet, the summation of these components is integrated to produce a specific response despite their involvement in a myriad of response cascades. In the response to gravity, the role of many of these individual components has been studied, but a specific sequence of signals has not yet been assembled into a cohesive schematic of gravity response signaling. Herein, we provide a review of existing knowledge of gravity response and differential protein and gene regulation induced by the absence of gravity stimulus aboard the International Space Station and propose an integrated theoretical schematic of gravity response incorporating that information. Recent developments in the role of nitric oxide in gravity signaling provided some of the final contextual pillars for the assembly of the model, where nitric oxide and the role of cysteine S-nitrosation may be central to the gravity response. The proposed schematic accounts for the known responses to reorientation with respect to gravity in roots-the most well studied gravitropic plant tissue-and is supported by the extensive evolutionary conservation of regulatory amino acids within protein components of the signaling schematic. The identification of a role of nitric oxide in regulating the TIR1 auxin receptor is indicative of the broader relevance of the schematic in studying a multitude of environmental and stress responses. Finally, there are several experimental approaches that are highlighted as essential to the further study and validation of this schematic.

Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco

Photosynthetically produced electrons provide energy for various metabolic pathways, including carbon reduction. Four Calvin-Benson cycle enzymes and several other plastid proteins are activated in the light by reduction of specific cysteines via thioredoxins, a family of electron transporters operating in redox regulation networks. How does this network link the photosynthetic chain with cellular metabolism? Using a time-resolved redox proteomic method, we have investigated the redox network in vivo during the dark–to–low light transition. We show that redox states of some thioredoxins follow the photosynthetic linear electron transport rate. While some redox targets have kinetics compatible with an equilibrium with one thioredoxin (TRXf), reduction of other proteins shows specific kinetic limitations, allowing fine-tuning of each redox-regulated step of chloroplast metabolism. We identified five new redox-regulated proteins, including proteins involved in Mg²⁺ transport and ¹O₂ signaling. Our results provide a system-level functional view of the photosynthetic redox regulation network.

Quantitative Proteome Profiling of a S-Nitrosoglutathione Reductase (GSNOR) Null Mutant Reveals a New Class of Enzymes Involved in Nitric Oxide Homeostasis in Plants

Nitric oxide (NO) is a short-lived radical gas that acts as a signaling molecule in all higher organisms, and that is involved in multiple plant processes, including germination, root growth, and fertility. Regulation of NO-levels is predominantly achieved by reaction of oxidation products of NO with glutathione to form S-nitrosoglutathione (GSNO), the principal bioactive form of NO. The enzyme S-nitrosoglutathione reductase (GSNOR) is a major route of NADH-dependent GSNO catabolism and is critical to NO homeostasis. Here, we performed a proteomic analysis examining changes in the total leaf proteome of an Arabidopsis thaliana GSNOR null mutant (hot5-2/gsnor1-3). Significant increases or decreases in proteins associated with chlorophyll metabolism and with redox and stress metabolism provide insight into phenotypes observed in hot5-2/gsnor1-3 plants. Importantly, we identified a significant increase in proteins that belong to the aldo-keto reductase (AKR) protein superfamily, AKR4C8 and 9. Because specific AKRs have been linked to NO metabolism in mammals, we expressed and purified A. thaliana AKR4C8 and 9 and close homologs AKR4C10 and 11 and determined that they have NADPH-dependent activity in GSNO and S-nitroso-coenzyme A (SNO-CoA) reduction. Further, we found an increase of NADPH-dependent GSNO reduction activity in hot5-2/gsnor1-3 mutant plants. These data uncover a new, NADPH-dependent component of NO metabolism that may be integrated with NADH-dependent GSNOR activity to control NO homeostasis in plants.

Knockout of FER decreases cadmium concentration in roots of Arabidopsis thaliana by inhibiting the pathway related to iron uptake

Identifying the genes that affect cadmium (Cd) accumulation in plants is a prerequisite for minimizing dietary Cd uptake from contaminated edible parts of plants by genetic engineering. This study showed that Cd stress inhibited the expression of FERONIA (FER) gene in the roots of wild-type Arabidopsis. Knockout of FER in fer-4 mutants downregulated the Cd-induced expression of several genes related to iron (Fe) uptake, including IRT1, bHLH38, NRAMP1, NRAMP3, FRO2 andFIT. In addition, the Cd concentration in fer-4 mutant roots reduced to approximately half of that in the wild-type seedlings. As a result, the Cd tolerance of fer-4 was higher. Furthermore, increased Fe supplementation had little effect on the Cd tolerance of fer-4 mutants, but clearly improved the Cd tolerance of wild-type seedlings, showing that the alleviation of Cd toxicity by Fe depends on the action of FER. Taken together, the findings demonstrate that the knockout of FER might provide a strategy to reduce Cd contamination and improve the Cd tolerance in plants by regulating the pathways related to Fe uptake.

Characteristics and functions of glyceraldehyde 3-phosphate dehydrogenase S-nitrosylation during controlled aging of elm and Arabidopsis seeds

Seed aging is the gradual decline in seed vigor, during which programmed cell death (PCD) occurs. The functions of nitric oxide (NO) are exerted through protein S-nitrosylation, a reversible post-translational modification. During seed aging, more than 80 proteins are S-nitrosylated, but the particular role of individual proteins is unknown. Here, we showed that the S-nitrosylation level of glyceraldehyde 3-phosphate dehydrogenase (UpGAPDH) in elm (Ulmus pumila L.) seeds increased after controlled deterioration treatment. UpGAPDH was S-nitrosylated at Cys154 during S-nitrosoglutathione (GSNO) treatment, and its oligomerization was triggered both in vitro and in elm seeds. Interestingly, UpGAPDH interacted with the mitochondrial voltage-dependent anion channel in an S-nitrosylation-dependent way. Some UpGAPDH-green fluorescent protein in Arabidopsis protoplasts co-localized with mitochondria during the GSNO treatment, while the S-nitrosylation-defective UpGAPDH C154S-GFP protein did not. Seeds of oxUpGAPDH lines showed cell death and lost seed vigor rapidly during controlled deterioration treatment-triggered seed aging, while those overexpressing S-nitrosylation-defective UpGAPDH-Cys154 did not. Our results suggest that S-nitrosylation of UpGAPDH may accelerate cell death and seed deterioration during controlled deterioration treatment. These results provide new insights into the effects of UpGAPDH S-nitrosylation on protein interactions and seed aging.

The Modus Operandi of Hydrogen Sulfide(H2S)-Dependent Protein Persulfidation in Higher Plants

Protein persulfidation is a post-translational modification (PTM) mediated by hydrogen sulfide (H₂S), which affects the thiol group of cysteine residues from target proteins and can have a positive, negative or zero impact on protein function. Due to advances in proteomic techniques, the number of potential protein targets identified in higher plants, which are affected by this PTM, has increased considerably. However, its precise impact on biological function needs to be evaluated at the experimental level in purified proteins in order to identify the specific cysteine(s) residue(s) affected. It also needs to be evaluated at the cellular redox level given the potential interactions among different oxidative post-translational modifications (oxiPTMs), such as S-nitrosation, glutathionylation, sulfenylation, S-cyanylation and S-acylation, which also affect thiol groups. This review aims to provide an updated and comprehensive overview of the important physiological role exerted by persulfidation in higher plants, which acts as a cellular mechanism of protein protection against irreversible oxidation.

Protein Persulfidation in Plants: Function and Mechanism

As an endogenous gaseous transmitter, the function of hydrogen sulfide (H2S) has been extensively studied in plants. Once synthesized, H2S may be involved in almost all life processes of plants. Among them, a key route for H2S bioactivity occurs via protein persulfidation, in which process oxidizes cysteine thiol (R-SH) groups into persulfide (R-SSH) groups. This process is thought to underpin a myriad of cellular processes in plants linked to growth, development, stress responses, and phytohormone signaling. Multiple lines of emerging evidence suggest that this redox-based reversible post-translational modification can not only serve as a protective mechanism for H2S in oxidative stress, but also control a variety of biochemical processes through the allosteric effect of proteins. Here, we collate emerging evidence showing that H2S-mediated persulfidation modification involves some important biochemical processes such as growth and development, oxidative stress, phytohormone and autophagy. Additionally, the interaction between persulfidation and S-nitrosylation is also discussed. In this work, we provide beneficial clues for further exploration of the molecular mechanism and function of protein persulfidation in plants in the future.