Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites

Exploring the puzzle of reactive oxygen species acting on root hair cells

Reactive oxygen species (ROS) are essential signaling molecules that enable cells to respond rapidly to a range of stimuli. The ability of plants to recognize various stressors, incorporate a variety of environmental inputs, and initiate stress-response networks depends on ROS. Plants develop resilience and defensive systems as a result of these processes. Root hairs are central components of root biology since they increase the surface area of the root, anchor it in the soil, increase its ability to absorb water and nutrients, and foster interactions between microorganisms. In this review, we specifically focused on root hair cells and we highlighted the identification of ROS receptors, important new regulatory hubs that connect ROS production, transport, and signaling in the context of two hormonal pathways (auxin and ethylene) and under low temperature environmental input related to nutrients. As ROS play a crucial role in regulating cell elongation rates, root hairs are rapidly gaining traction as a very valuable single plant cell model for investigating ROS homeostasis and signaling. These promising findings might soon facilitate the development of plants and roots that are more resilient to environmental stressors.

The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes

Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112 000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra 'Protein list analysis' tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.

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.

Functionality of Reactive Oxygen Species (ROS) in Plants: Toxicity and Control in Poaceae Crops Exposed to Abiotic Stress

Agriculture and changing environmental conditions are closely related, as weather changes could adversely affect living organisms or regions of crop cultivation. Changing environmental conditions trigger different abiotic stresses, which ultimately cause the accumulation of reactive oxygen species (ROS) in plants. Common ROS production sites are the chloroplast, endoplasmic reticulum, plasma membrane, mitochondria, peroxisomes, etc. The imbalance in ROS production and ROS detoxification in plant cells leads to oxidative damage to biomolecules such as lipids, nucleic acids, and proteins. At low concentrations, ROS initiates signaling events related to development and adaptations to abiotic stress in plants by inducing signal transduction pathways. In plants, a stress signal is perceived by various receptors that induce a signal transduction pathway that activates numerous signaling networks, which disrupt gene expression, impair the diversity of kinase/phosphatase signaling cascades that manage the stress response in the plant, and result in changes in physiological responses under various stresses. ROS production also regulates ABA-dependent and ABA-independent pathways to mitigate drought stress. This review focuses on the common subcellular location of manufacturing, complex signaling mechanisms, and networks of ROS, with an emphasis on cellular effects and enzymatic and non-enzymatic antioxidant scavenging mechanisms of ROS in Poaceae crops against drought stress and how the manipulation of ROS regulates stress tolerance in plants. Understanding ROS systems in plants could help to create innovative strategies to evolve paths of cell protection against the negative effects of excessive ROS in attempts to improve crop productivity in adverse environments.

Dynamic interplay of reactive oxygen and nitrogen species (ROS and RNS) in plant resilience: unveiling the signaling pathways and metabolic responses to biotic and abiotic stresses

KEY MESSAGE

Plants respond to environmental challenges by producing reactive species such as ROS and RNS, which play critical roles in signaling pathways that lead to adaptation and survival strategies. Understanding these pathways, as well as their detection methods and effects on plant development and metabolism, provides insight into increasing crop tolerance to combined stresses. Plants encounter various environmental stresses (abiotic and biotic) that affect plant growth and development. Plants sense biotic and abiotic stresses by producing different molecules, including reactive species, that act as signaling molecules and stimulate secondary messengers and subsequent gene transcription. Reactive oxygen and nitrogen species (ROS and RNS) are produced in both physiological and pathological conditions in the plasma membranes, chloroplasts, mitochondria, and endoplasmic reticulum. Various techniques, including spectroscopy, chromatography, and fluorescence methods, are used to detect highly reactive, short-half-life ROS and RNS either directly or indirectly. In this review, we highlight the roles of ROS and RNS in seed germination, root development, senescence, mineral nutrition, and post-harvest control. In addition, we provide information on the specialized metabolism involved in plant growth and development. Secondary metabolites, including alkaloids, flavonoids, and terpenoids, are produced in low concentrations in plants for signaling and metabolism. Strategies for improving crop performance under combined drought and pathogen stress conditions are discussed in this review.

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.

Hydrogen peroxide sulfenylates and inhibits the photorespiratory enzyme PGLP1 to modulate plant thermotolerance

Climate change is resulting in more frequent and rapidly changing temperatures at both extremes that severely affect the growth and production of plants, particularly crops. Oxidative stress caused by high temperatures is one of the most damaging factors for plants. However, the role of hydrogen peroxide (H2O2) in modulating plant thermotolerance is largely unknown, and the regulation of photorespiration essential for C3 species remains to be fully clarified. Here, we report that heat stress promotes H2O2 accumulation in chloroplasts and that H2O2 stimulates sulfenylation of the chloroplast-localized photorespiratory enzyme 2-phosphoglycolate phosphatase 1 (PGLP1) at cysteine 86, inhibiting its activity and promoting the accumulation of the toxic metabolite 2-phosphoglycolate. We also demonstrate that PGLP1 has a positive function in plant thermotolerance, as PGLP1 antisense lines have greater heat sensitivity and PGLP1-overexpressing plants have higher heat-stress tolerance than the wild type. Together, our results demonstrate that heat-induced H2O2 in chloroplasts sulfenylates and inhibits PGLP1 to modulate plant thermotolerance. Furthermore, targeting CATALASE2 to chloroplasts can largely prevent the heat-induced overaccumulation of H2O2 and the sulfenylation of PGLP1, thus conferring thermotolerance without a plant growth penalty. These findings reveal that heat-induced H2O2 in chloroplasts is important for heat-caused plant damage.

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.

Cysteine oxidation as a regulatory mechanism of Arabidopsis plastidial NAD-dependent malate dehydrogenase

Malate dehydrogenases (MDHs) catalyze a reversible NAD(P)-dependent-oxidoreductase reaction that plays an important role in central metabolism and redox homeostasis of plant cells. Recent studies suggest a moonlighting function of plastidial NAD-dependent MDH (plNAD-MDH; EC 1.1.1.37) in plastid biogenesis, independent of its enzyme activity. In this study, redox effects on activity and conformation of recombinant plNAD-MDH from Arabidopsis thaliana were investigated. We show that reduced plNAD-MDH is active while it is inhibited upon oxidation. Interestingly, the presence of its cofactors NAD+ and NADH could prevent oxidative inhibition of plNAD-MDH. In addition, a conformational change upon oxidation could be observed via non-reducing SDS-PAGE. Both effects, its inhibition and conformational change, were reversible by re-reduction. Further investigation of single cysteine substitutions and mass spectrometry revealed that oxidation of plNAD-MDH leads to oxidation of all four cysteine residues. However, cysteine oxidation of C129 leads to inhibition of plNAD-MDH activity and oxidation of C147 induces its conformational change. In contrast, oxidation of C190 and C333 does not affect plNAD-MDH activity or structure. Our results demonstrate that plNAD-MDH activity can be reversibly inhibited, but not inactivated, by cysteine oxidation and might be co-regulated by the availability of its cofactors in vivo.

Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity

Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.

PbrWRKY62-PbrADC1 module involves in superficial scald development of Pyrus bretschneideri Rehd.fruit via regulating putrescine biosynthesis

Putrescine plays a role in superficial scald development during the cold storage of pear fruit. However, the molecular mechanism behind this phenomenon has not been un-fully clarified until recently. In this study, a conjoint analysis of metabolites and gene expression profiles in the putrescine-metabolic pathway of P. bretschneideri Rehd. fruit followed by experimental validation revealed that PbrADC1, forming a homodimer in the chloroplast, was involved in putrescine biosynthesis and thus fruit chilling resistance. Additionally, the substrate-binding residue Cys546 in PbrADC1, whose activity was modified by H2O2, played a crucial role in arginine decarboxylation into agmatine. Through a combined analysis of the distribution of cis-acting elements in the PbrADC1 promoter as well as the expression profiles of related transcription factors (TFs), several TFs were identified as upstream regulators of PbrADC1 gene. Further investigation revealed that the nuclear PbrWRKY62 could directly bind to the W-box elements in the PbrADC1 promoter, activate its expression, enhance putrescine accumulation, and thus increase fruit chilling tolerance. In conclusion, our results suggest that the PbrWRKY62-PbrADC1 module is involved in the development of superficial scald in P. bretschneideri Rehd. fruit via regulating putrescine biosynthesis. Consequently, these findings could serve as valuable genetic resources for breeding scald-resistant pear fruit.

Hydrogen Sulfide in the Oxidative Stress Response of Plants: Crosstalk with Reactive Oxygen Species

Growing evidence suggests that exposure of plants to unfavorable environments leads to the accumulation of hydrogen sulfide (H2S) and reactive oxygen species (ROS). H2S interacts with the ROS-mediated oxidative stress response network at multiple levels. Therefore, it is essential to elucidate the mechanisms by which H2S and ROS interact. The molecular mechanism of action by H2S relies on the post-translational modification of the cysteine sulfur group (-SH), known as persulfidation. H2S cannot react directly with -SH, but it can react with oxidized cysteine residues, and this oxidation process is induced by H2O2. Evidently, ROS is involved in the signaling pathway of H2S and plays a significant role. In this review, we summarize the role of H2S-mediated post-translational modification mechanisms in oxidative stress responses. Moreover, the mechanism of interaction between H2S and ROS in the regulation of redox reactions is focused upon, and the positive cooperative role of H2S and ROS is elucidated. Subsequently, based on the existing evidence and clues, we propose some potential problems and new clues to be explored, which are crucial for the development of the crosstalk mechanism of H2S and ROS in plants.

Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.

Proteome-wide identification of methylglyoxalated proteins in rapeseed (Brassica napus L.)

Methylglyoxal (MG), a highly reactive cellular metabolite, is crucial for plant growth and environmental responses. MG may function by modifying its target proteins, but little is known about MG-modified proteins in plants. Here, MG-modified proteins were pulled down by an antibody against methylglyoxalated proteins and detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. We identified 543 candidate proteins which are involved in multiple enzymatic activities and metabolic processes. A great number of candidate proteins were predicted to localize to cytoplasm, chloroplast, and nucleus, consistent with the known subcellular compartmentalization of MG. By further analyzing the raw LC-MS/MS data, we obtained 42 methylglyoxalated peptides in 35 proteins and identified 10 methylglyoxalated lysine residues in a myrosinase-binding protein (BnaC06G0061400ZS). In addition, we demonstrated that MG modifies the glycolate oxidase and β-glucosidase to enhance and inhibit the enzymatic activity, respectively. Together, our study contributes to the investigation of the MG-modified proteins and their potential roles in rapeseed.

H2O2-dependent oxidation of the transcription factor GmNTL1 promotes salt tolerance in soybean

Reactive oxygen species (ROS) play an essential role in plant growth and responses to environmental stresses. Plant cells sense and transduce ROS signaling directly via hydrogen peroxide (H2O2)-mediated posttranslational modifications (PTMs) on protein cysteine residues. Here, we show that the H2O2-mediated cysteine oxidation of NAC WITH TRANS-MEMBRANE MOTIF1-LIKE 1 (GmNTL1) in soybean (Glycine max) during salt stress promotes its release from the endoplasmic reticulum (ER) membrane and translocation to the nucleus. We further show that an oxidative posttranslational modification on GmNTL1 residue Cys-247 steers downstream amplification of ROS production by binding to and activating the promoters of RESPIRATORY BURST OXIDASE HOMOLOG B (GmRbohB) genes, thereby creating a feed-forward loop to fine-tune GmNTL1 activity. In addition, oxidation of GmNTL1 Cys-247 directly promotes the expression of CATION H+ EXCHANGER 1 (GmCHX1)/SALT TOLERANCE-ASSOCIATED GENE ON CHROMOSOME 3 (GmSALT3) and Na+/H+ Antiporter 1 (GmNHX1). Accordingly, transgenic overexpression of GmNTL1 in soybean increases the H2O2 levels and K+/Na+ ratio in the cell, promotes salt tolerance, and increases yield under salt stress, while an RNA interference-mediated knockdown of GmNTL1 elicits the opposite effects. Our results reveal that the salt-induced oxidation of GmNTL1 promotes its relocation and transcriptional activity through an H2O2-mediated posttranslational modification on cysteine that improves resilience of soybean against salt stress.

SmWRKY11 acts as a positive regulator in eggplant response to salt stress

Salt stress is one of the most threatening abiotic stresses to plants, which can seriously affect plant growth, development, reproduction, and yield. However, the mechanisms of plant against salt stress largely remain unclear. Herein, SmWRKY11, an assumed WRKY transcription factor, was functionally characterized in eggplant against salt stress. SmWRKY11 was significantly up-regulated by salt, dehydration stress, and ABA treatment. SmWRKY11 located in the nucleus, and the Plant_zn_clust conserved domain exhibited transcriptional activation activity. Silencing of SmWRKY11 enhanced the susceptibility of eggplant to salt stress, accompanied by significantly down-regulation of transcript expression levels of salt stress defense-related genes SmNCED1, SmGSTU10, and positive regulator of salt stress response SmERF1 as well as increase of hydrogen peroxide (H2O2) content and decrease of the enzyme activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). In addition, silencing of SmERF1 also could significantly down-regulate SmWRKY11 expression in eggplant response to salt stress. By luciferase reporter assay and chromatin immunoprecipitation PCR assay, SmERF1 expression was found to be indirectly activated by SmWRKY11. These data indicate that SmWRKY11 acts as a positive regulator by forming positive feedback loop with SmERF1 via an indirect regulatory manner in eggplant response to salt stress.

Exploring the potential role of hydrogen sulfide and jasmonic acid in plants during heavy metal stress

In plants, hydrogen sulfide (H2S) is mainly considered as a gaseous transmitter or signaling molecule that has long been recognized as an essential component of numerous plant cellular and physiological processes. Several subcellular compartments in plants use both enzymatic and non-enzymatic mechanisms to generate H2S. Under normal and stress full conditions exogenous administration of H2S supports a variety of plant developmental processes, including growth and germination, senescence, defense, maturation and antioxidant machinery in plants. Due to their gaseous nature, they are efficiently disseminated to various areas of the cell to balance antioxidant pools and supply sulphur to the cells. Numerous studies have also been reported regarding H2S ability to reduce heavy metal toxicity when combined with other signaling molecules like nitric oxide (NO), abscisic acid (ABA), calcium ion (Ca2+), hydrogen peroxide (H2O2), salicylic acid (SA), ethylene (ETH), jasmonic acid (JA), proline (Pro), and melatonin. The current study focuses on multiple pathways for JA and H2S production as well as their signaling functions in plant cells under varied circumstances, more specifically under heavy metal, which also covers role of H2S and Jasmonic acid during heavy metal stress and interaction of hydrogen sulfide with Jasmonic acid.

CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry

Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.

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.

ROS: Important factor in plant stem cell fate regulation

Reactive oxygen species (ROS) are initially considered to be toxic byproducts of aerobic metabolic reactions. However, increasing evidence has shown that they have emerged as signaling molecules involved in several basic biological processes. Recent studies highlight the pivotal role of ROS in the maintenance of shoot and root stem cell niche. In this review, we discuss the impact of ROS distribution and their gradients on the stability of the stem cell niches (SCN) in shoot apical meristem (SAM) and root apical meristem (RAM) by determining the balance between stemness and differentiation. We also summarize several important transcription factors that are involved in the regulation of ROS balance in SAM and RAM, regulating key enzymes in ROS metabolism, especially SOD and peroxidase. ROS are also tightly interconnected with phytohormones in the control of the stem cell fate. Besides, ROS are also important regulators of the cell cycle in controlling the size of the stem cells. Understanding the regulation mechanisms of ROS production, polarization gradient distribution, homeostasis, and downstream signal transduction in cells will open exciting new perspectives for plant developmental biology.

BiGRUD-SA: Protein S-sulfenylation sites prediction based on BiGRU and self-attention

S-sulfenylation is a vital post-translational modification (PTM) of proteins, which is an intermediate in other redox reactions and has implications for signal transduction and protein function regulation. However, there are many restrictions on the experimental identification of S-sulfenylation sites. Therefore, predicting S-sulfoylation sites by computational methods is fundamental to studying protein function and related biological mechanisms. In this paper, we propose a method named BiGRUD-SA based on bi-directional gated recurrent unit (BiGRU) and self-attention mechanism to predict protein S-sulfenylation sites. We first use AAC, BLOSUM62, AAindex, EAAC and GAAC to extract features, and do feature fusion to obtain original feature space. Next, we use SMOTE-Tomek method to handle data imbalance. Then, we input the processed data to the BiGRU and use self-attention mechanism to do further feature extraction. Finally, we input the data obtained to the deep neural networks (DNN) to identify S-sulfenylation sites. The accuracies of training set and independent test set are 96.66% and 95.91% respectively, which indicates that our method is conducive to identifying S-sulfenylation sites. Furthermore, we use a data set of S-sulfenylation sites in Arabidopsis thaliana to effectively verify the generalization ability of BiGRUD-SA method, and obtain better prediction results.

Exploring aquaporin functions during changes in leaf water potential

Maintenance of optimal leaf tissue humidity is important for plant productivity and food security. Leaf humidity is influenced by soil and atmospheric water availability, by transpiration and by the coordination of water flux across cell membranes throughout the plant. Flux of water and solutes across plant cell membranes is influenced by the function of aquaporin proteins. Plants have numerous aquaporin proteins required for a multitude of physiological roles in various plant tissues and the membrane flux contribution of each aquaporin can be regulated by changes in protein abundance, gating, localisation, post-translational modifications, protein:protein interactions and aquaporin stoichiometry. Resolving which aquaporins are candidates for influencing leaf humidity and determining how their regulation impacts changes in leaf cell solute flux and leaf cavity humidity is challenging. This challenge involves resolving the dynamics of the cell membrane aquaporin abundance, aquaporin sub-cellular localisation and location-specific post-translational regulation of aquaporins in membranes of leaf cells during plant responses to changes in water availability and determining the influence of cell signalling on aquaporin permeability to a range of relevant solutes, as well as determining aquaporin influence on cell signalling. Here we review recent developments, current challenges and suggest open opportunities for assessing the role of aquaporins in leaf substomatal cavity humidity regulation.

The self-association of cytoplasmic malate dehydrogenase 1 promotes malate biosynthesis and confers disease resistance in cassava

Malate dehydrogenase (MDH) as an essential metabolic enzyme is widely involved in plant developmental processes. However, the direct relationship between its structural basis and in vivo roles especially in plant immunity remains elusive. In this study, we found that cytoplasmic cassava (Manihot esculenta, Me) MDH1 was essential for plant disease resistance against cassava bacterial blight (CBB). Further investigation revealed that MeMDH1 positively modulated cassava disease resistance, accompanying the regulation of salicylic acid (SA) accumulation and pathogensis-related protein 1 (MePR1) expression. Notably, the metabolic product of MeMDH1 (malate) also improved disease resistance in cassava, and its application rescued the disease susceptibility and decreased immune responses of MeMDH1-silenced plants, indicating that malate was responsible for MeMDH1-mediated disease resistance. Interestingly, MeMDH1 relied on Cys330 residues to form homodimer, which was directly related with MeMDH1 enzyme activity and the corresponding malate biosynthesis. The crucial role of Cys330 residue in MeMDH1 was further confirmed by in vivo functional comparison between overexpression of MeMDH1 and MeMDH1C330A in cassava disease resistance. Taken together, this study highlights that MeMDH1 confers improved plant disease resistance through protein self-association to promote malate biosynthesis, extending the knowledge of the relationship between its structure and cassava disease resistance.

Essential role of the CD docking motif of MPK4 in plant immunity, growth, and development

MAPKs are universal eukaryotic signaling factors whose functioning is assumed to depend on the recognition of a common docking motif (CD) by its activators, substrates, and inactivators. We studied the role of the CD domain of Arabidopsis MPK4 by performing interaction studies and determining the ligand-bound MPK4 crystal structure. We revealed that the CD domain of MPK4 is essential for interaction and activation by its upstream MAPKKs MKK1, MKK2, and MKK6. Cys181 in the CD site of MPK4 was shown to become sulfenylated in response to reactive oxygen species in vitro. To test the function of C181 in vivo, we generated wild-type (WT) MPK4-C181, nonsulfenylatable MPK4-C181S, and potentially sulfenylation mimicking MPK4-C181D lines in the mpk4 knockout background. We analyzed the phenotypes in growth, development, and stress responses, revealing that MPK4-C181S has WT activity and complements the mpk4 phenotype. By contrast, MPK4-C181D cannot be activated by upstream MAPKK and cannot complement the phenotypes of mpk4. Our findings show that the CD motif is essential and is required for activation by upstream MAPKK for MPK4 function. Furthermore, growth, development, or immunity functions require upstream activation of the MPK4 protein kinase.

Salt stress-induced chloroplastic hydrogen peroxide stimulates pdTPI sulfenylation and methylglyoxal accumulation

High salinity, an adverse environmental factor affecting about 20% of irrigated arable land worldwide, inhibits plant growth and development by causing oxidative stress, damaging cellular components, and disturbing global metabolism. However, whether and how reactive oxygen species disturb the metabolism of salt-stressed plants remain elusive. Here, we report that salt-induced hydrogen peroxide (H2O2) inhibits the activity of plastid triose phosphate isomerase (pdTPI) to promote methylglyoxal (MG) accumulation and stimulates the sulfenylation of pdTPI at cysteine 74. We also show that MG is a key factor limiting the plant growth, as a decrease in MG levels completely rescued the stunted growth and repressed salt stress tolerance of the pdtpi mutant. Furthermore, targeting CATALASE 2 into chloroplasts to prevent salt-induced overaccumulation of H2O2 conferred salt stress tolerance, revealing a role for chloroplastic H2O2 in salt-caused plant damage. In addition, we demonstrate that the H2O2-mediated accumulation of MG in turn induces H2O2 production, thus forming a regulatory loop that further inhibits the pdTPI activity in salt-stressed plants. Our findings, therefore, illustrate how salt stress induces MG production to inhibit the plant growth.

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.

Hydrogen sulfide signaling in plants

SIGNIFICANCE

Hydrogen sulfide (H2S) is a multitasking potent regulator that facilitates plant growth, development, and responses to environmental stimuli.

RECENT ADVANCES

The important beneficial effects of H2S in various aspects of plant physiology aroused the interest of this chemical for agriculture. Protein cysteine persulfidation has been recognized as the main redox regulatory mechanism of H2S signaling. An increasing number of studies, including large-scale proteomic analyses and function characterizations, have revealed that H2S-mediated persulfidations directly regulate protein functions, altering downstream signaling in plants. To date, the importance of H2S-mediated persufidation in several abscisic acid signaling-controlling key proteins has been assessed as well as their role in stomatal movements, largely contributing to the understanding of the plant H2S-regulatory mechanism.

CRITICAL ISSUES

The molecular mechanisms of the H2S sensing and transduction in plants remain elusive. The correlation between H2S-mediated persulfidation with other oxidative posttranslational modifications of cysteines are still to be explored.

FUTURE DIRECTIONS

Implementation of advanced detection approaches for the spatiotemporal monitoring of H2S levels in cells and the current proteomic profiling strategies for the identification and quantification of the cysteine site-specific persulfidation will provide insight into the H2S signaling in plants.

Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience

Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H₂O₂-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of the mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, as for sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and in enhanced resilience to oxidative stress.

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.

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.

Proteome-wide analysis of hydrogen peroxide-induced protein carbonylation in Arabidopsis thaliana

INTRODUCTION

Protein carbonylation is a non-enzymatic and irreversible post-translational modification that occurs naturally in living organisms under the direct or indirect effect of reactive oxygen species (ROS). In animals, signaling pathways involving numerous carbonylated proteins have been identified, highlighting the dual role of these molecules in ROS signal transduction. In plants, studies on phytohormone signaling (auxin, methyl jasmonate, abscisic acid) have shown that reactive carbonyl species (RCS: acrolein, malondialdehyde, 4-hydroxynonenal, etc.), derived from the action of ROS on lipids, play important roles in secondary root formation and stomatal closure. However, the carbonylated proteins involved in these signaling pathways remain to be identified.

METHODS

In this study, we analyzed proteins responsive to carbonylation by exogenous hydrogen peroxide (H2O2) by profiling the carbonyl proteome extracted from Arabidopsis thaliana leaves after H2O2 treatment. Carbonylated proteins were enriched at the peptide level and analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS).

RESULTS AND DISCUSSION

We identified 35 and 39 uniquely carbonylated proteins in the untreated and the H2O2-treated plant samples, respectively. In comparison to the control treatment, gene ontology enrichment analysis revealed that most of the carbonylated proteins identified in the H2O2-treated plant samples are related to sulfate adenylyl transferases and amidophosphoribosyl transferases involved in the immune system response, defense response, and external stimulus-response. These results indicated that exogenous H2O2 caused a change in the pattern of protein carbonylation in A. thaliana leaves. Protein carbonylation may thus influence the plant transcriptome and metabolism in response to H2O2 and ROS-triggering external stimuli.

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.

Abscisic acid-controlled redox proteome of Arabidopsis and its regulation by heterotrimeric Gβ protein

The plant hormone abscisic acid (ABA) plays crucial roles in regulation of stress responses and growth modulation. Heterotrimeric G-proteins are key mediators of ABA responses. Both ABA and G-proteins have also been implicated in intracellular redox regulation; however, the extent to which reversible protein oxidation manipulates ABA and/or G-protein signaling remains uncharacterized. To probe the role of reversible protein oxidation in plant stress response and its dependence on G-proteins, we determined the ABA-dependent reversible redoxome of wild-type and Gβ-protein null mutant agb1 of Arabidopsis. We quantified 6891 uniquely oxidized cysteine-containing peptides, 923 of which show significant changes in oxidation following ABA treatment. The majority of these changes required the presence of G-proteins. Divergent pathways including primary metabolism, reactive oxygen species response, translation and photosynthesis exhibited both ABA- and G-protein-dependent redox changes, many of which occurred on proteins not previously linked to them. We report the most comprehensive ABA-dependent plant redoxome and uncover a complex network of reversible oxidations that allow ABA and G-proteins to rapidly adjust cellular signaling to adapt to changing environments. Physiological validation of a subset of these observations suggests that functional G-proteins are required to maintain intracellular redox homeostasis and fully execute plant stress responses.

Reactive oxygen species function as signaling molecules in controlling plant development and hormonal responses

Reactive oxygen species (ROS) serve as second messengers in plant signaling pathways to remodel plant growth and development. New insights into how enzymatic ROS-producing machinery is regulated by hormones or localized during development have provided a framework for understanding the mechanisms that control ROS accumulation patterns. Signaling-mediated increases in ROS can then modulate the activity of proteins through reversible oxidative modification of specific cysteine residues. Plants also control the synthesis of antioxidants, including plant-specialized metabolites, to further define when, where, and how much ROS accumulate. The availability of sophisticated imaging capabilities, combined with a growing tool kit of ROS detection technologies, particularly genetically encoded biosensors, sets the stage for improved understanding of ROS as signaling molecules.

The cytosolic thiol peroxidase PRXIIB is an intracellular sensor for H2O2 that regulates plant immunity through a redox relay

Rapid production of H₂O₂ is a hallmark of plant responses to diverse pathogens and plays a crucial role in signalling downstream of various receptors that perceive immunogenic patterns. However, mechanisms by which plants sense H₂O₂ to regulate immunity remain poorly understood. We show that endogenous H₂O₂ generated upon immune activation is sensed by the thiol peroxidase PRXIIB via oxidation at Cys51, and this is essential for stomatal immunity against Pseudomonas syringae. We further show that in immune-stimulated cells, PRXIIB conjugates via Cys51 with the type 2C protein phosphatase ABA insensitive 2 (ABI2), subsequently transducing H₂O₂ signal to ABI2. This oxidation dramatically sensitizes H₂O₂-mediated inhibition of the ABI2 phosphatase activity in vitro and is required for stomatal immunity in plants. Together, our results illustrate a redox relay, with PRXIIB as a sensor for H₂O₂ and ABI2 as a target protein, that mediates reactive oxygen species signalling during plant immunity.

Proteome-wide identification of S-sulfenylated cysteines reveals metabolic response to freezing stress after cold acclimation in Brassica napus

Redox regulation plays a wide role in plant growth, development, and adaptation to stresses. Sulfenylation is one of the reversible oxidative post-transcriptional modifications. Here we performed an iodoTMT-based proteomic analysis to identify the redox sensitive proteins in vivo under freezing stress after cold acclimation in Brassica napus. Totally, we obtained 1,372 sulfenylated sites in 714 proteins. The overall sulfenylation level displayed an increased trend under freezing stress after cold acclimation. We identified 171 differentially sulfenylated proteins (DSPs) under freezing stress, which were predicted to be mainly localized in chloroplast and cytoplasm. The up-regulated DSPs were mainly enriched in photosynthesis and glycolytic processes and function of catalytic activity. Enzymes involved in various pathways such as glycolysis and Calvin-Benson-Bassham (CBB) cycle were generally sulfenylated and the metabolite levels in these pathways was significantly reduced under freezing stress after cold acclimation. Furthermore, enzyme activity assay confirmed that the activity of cytosolic pyruvate kinase and malate dehydrogenase 2 was significantly reduced under H₂O₂ treatment. Our study provides a landscape of redox sensitive proteins in B. napus in response to freezing stress after cold acclimation, which proposes a basis for understanding the redox regulation in plant metabolic response to freezing stress after cold acclimation.

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.

A modification-centric assessment tool for the performance of chemoproteomic probes

Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.

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.

Genetic Manipulation of Reactive Oxygen Species (ROS) Homeostasis Utilizing CRISPR/Cas9-Based Gene Editing in Rice

Reactive oxygen species (ROS) are now recognized as key signals in plant stress responses. Adverse environmental conditions can either promote ROS production or downregulate antioxidative enzymes, leading to the alteration of redox homeostasis and activation of ROS-linked stress signaling. To uncover their signaling mechanisms and to characterize related components, genetic modification of ROS homeostasis is a central approach. CRISPR/Cas9-based genome editing system has become a powerful tool for gene mutation in a variety of organisms, including plants. Within this chapter, we describe a method that can be applied to manipulate ROS homeostasis in rice (Oryza sativa L.) utilizing CRISPR/Cas9 technology. Step-by-step protocols including the design and construction of Cas9/sgRNA, agrobacterium-mediated transformation, and mutation characterization are described. Application of this system in editing a rice catalase gene CatC, a key antioxidative enzyme in controlling ROS homeostasis, is also presented.

Rice GLUTATHIONE PEROXIDASE1-mediated oxidation of bZIP68 positively regulates ABA-independent osmotic stress signaling

Osmotic stress caused by drought and high salinity is a significant environmental threat that limits plant growth and agricultural yield. Redox regulation plays an important role in plant stress responses, but the mechanisms by which plants perceive and transduce redox signals are still underexplored. Here, we report a critical function for the thiol peroxidase GPX1 in osmotic stress response in rice, where it serves as a redox sensor and transducer. GPX1 is quickly oxidized upon exposure to osmotic stress and forms an intramolecular disulfide bond, which is required for the activation of bZIP68, a VRE-like basic leucine zipper (bZIP) transcription factor involved in the ABA-independent osmotic stress response pathway. The disulfide exchange between GPX1 and bZIP68 induces homo-tetramerization of bZIP68 and thus positively regulates osmotic stress response by regulating osmotic-responsive gene expression. Furthermore, we discovered that the nuclear translocation of GPX1 is regulated by its acetylation under osmotic stress. Taken together, our findings not only uncover the redox regulation of the GPX1-bZIP68 module during osmotic stress but also highlight the coordination of protein acetylation and redox signaling in plant osmotic stress responses.

Abiotic stress-triggered oxidative challenges: Where does H2S act?

Hydrogen sulfide (H₂S) was once principally considered the perpetrator of plant growth cessation and cell death. However, this has become an antiquated view, with cumulative evidence showing that the H₂S serves as a biological signaling molecule notably involved in abiotic stress response and adaptation, such as defense by phytohormone activation, stomatal movement, gene reprogramming, and plant growth modulation. Reactive oxygen species (ROS)-dependent oxidative stress is involved in these responses. Remarkably, an ever-growing body of evidence indicates that H₂S can directly interact with ROS processing systems in a redox-dependent manner, while it has been gradually recognized that H₂S-based posttranslational modifications of key protein cysteine residues determine stress responses. Furthermore, the reciprocal interplay between H₂S and nitric oxide (NO) in regulating oxidative stress has significant importance. The interaction of H₂S with NO and ROS during acclimation to abiotic stress may vary from synergism to antagonism. However, the molecular pathways and factors involved remain to be identified. This review not only aims to provide updated information on H₂S action in regulating ROS-dependent redox homeostasis and signaling, but also discusses the mechanisms of H₂S-dependent regulation in the context of oxidative stress elicited by environmental cues.

Hydrogen sulfide attenuates intracellular oxidative stress via repressing glycolate oxidase activities in Arabidopsis thaliana

BACKGROUND

Hydrogen sulfide (H₂S) has been proposed to exert anti-oxidative effect under many environmental stresses; however, how it influences oxidative stress remains largely unclear.

RESULTS

Here, we assessed the effects of H₂S on oxidative stress responses such as salicylic acid (SA)-dependent cell death, which triggered by increased H₂O₂ availability in Arabidopsis thaliana catalase-deficient mutants cat2 displaying around 20% wild-type catalase activity. H₂S generation and its producing enzyme _L-cysteine desulfhydrase (LCD/DES) were found to transient increase in response to intracellular oxidative stress. Although introducing the mutation of des1, an important LCD, into the cat2 background produced little effect, H₂S fumigation not only rescued the cell death phenotype of cat2 plant, but also attenuated SA accumulation and oxidation of the glutathione pool. Unexpectedly, the activities of major components of ascorbate-glutathione pathway were less affected by the presence of H₂S treatment, but decreased glycolate oxidase (GOX) in combination with accumulation of glycolate implied H₂S treatment impacts the cellular redox homeostasis by repressing the GOX-catalyzed reaction likely via altering the major GOX transcript levels.

CONCLUSIONS

Our findings reveal a link between H₂S and peroxisomal H₂O₂ production that has implications for the understanding of the multifaceted roles of H₂S in the regulation of oxidative stress responses.

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.

Exploring Posttranslational Modifications with the Plant PTM Viewer

An increasing numbed and diversity of protein posttranslational modifications are mapped by proteomics. Knowledge of modified protein sites can be of direct relevance to steer downstream functional studies, but such information can be difficult to distill from the numerous individual studies that often report modified sites in supplementary data files. In this chapter, we provide basic instructions and use cases to browse and collect plant protein modifications from over 100 studies in a user-friendly manner with the Plant PTM Viewer. The Plant PTM Viewer ( https://www.psb.ugent.be/PlantPTMViewer ) is a central resource compiling currently 24 modifications types for ten thousands of plant proteins. Next to viewing modifications for a protein of interest, we demonstrate how evolutionary conserved modifications can be retrieved using PTM Blast. In addition, modifications themselves located in a motif or sequence context of interest can be retrieved by PTM search. Altogether, these operations can be performed, are intuitive, and open for non-bioinformatic experts.

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.

Using DCP-Rho1 as a fluorescent probe to visualize sulfenic acid-containing proteins in living plant cells

Among the biologically relevant reactive oxygen species (ROS), hydrogen peroxide (H₂O₂) has special properties. H₂O₂ can diffuse across membranes, has a low reactivity, and is very stable. Deprotonated cysteine residues in proteins can be oxidized by H₂O₂ into a highly reactive sulfenic acid derivative (-SOH), which can react with another cysteine to form a disulfide. Under higher oxidative stress the sulfenic acid undergo further oxidation to sulfinic acid (Cys-SO₂H), which can subsequently be reduced. The sulfinic acid can be hyperoxidized to sulfonic acid (Cys-SO₃H), whose reduction is irreversible. Formation of sulfenic acids can have a role in sensing oxidative stress, signal transduction, modulating localization and activity to regulate protein functions. Therefore, there is an emerging interest in trying to understand the pool of proteins that result in these sorts of modification in response to oxidative stress. This is known as the sulfenome and several approaches have been developed in animal and plant cells to analyze the sulfenome under different stress responses. These approaches can be proteomic, molecular, immunological (i.e., antibodies), or expressing genetically encoded probes that specifically react to sulfenic modifications. In this chapter, we describe an additional approach that allows visualization of sulfenic modification in vivo. This is newly developed fluorescent probe DCP-Rho1 can be implemented in any plant cell to analyze the sulfenic modification.

Characterization of RBPome in Oxidative Stress Conditions

Cellular redox signaling is triggered by accumulation of various reactive oxygen species (ROS) that integrate with other signaling cascades to enable plants to ultimately respond to (a)biotic stresses. The identification of key regulators underlying redox signaling networks is therefore of high priority. This chapter describes an improved mRNA interactome capture method that allows to systematically detect oxidative stress responsive regulators in the post-transcriptional gene regulation (PTGR) pathway. The protocol includes PSB-D suspension cell culture preparation, setup of oxidative stress conditions, short-term exposure to UV irradiation, cell lysis, pull-down and purification of crosslinked messenger ribonucleoproteins, their mass spectrometric analyses, and identification of proteome by statistical analyses. As result, a comprehensive inventory of the functional oxidative stress responsive RBPome (OxRBPome) is generated, which paves the way toward new insights into PTGR processes in redox signaling.