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

Protein Kinase D Plays a Crucial Role in Maintaining Cardiac Homeostasis by Regulating Post-Translational Modifications of Myofilament Proteins

Protein kinase D (PKD) enzymes play important roles in regulating myocardial contraction, hypertrophy, and remodeling. One of the proteins phosphorylated by PKD is titin, which is involved in myofilament function. In this study, we aimed to investigate the role of PKD in cardiomyocyte function under conditions of oxidative stress. To do this, we used mice with a cardiomyocyte-specific knock-out of Prkd1, which encodes PKD1 (Prkd1loxP/loxP; αMHC-Cre; PKD1 cKO), as well as wild type littermate controls (Prkd1loxP/loxP; WT). We isolated permeabilized cardiomyocytes from PKD1 cKO mice and found that they exhibited increased passive stiffness (Fpassive), which was associated with increased oxidation of titin, but showed no change in titin ubiquitination. Additionally, the PKD1 cKO mice showed increased myofilament calcium (Ca2+) sensitivity (pCa50) and reduced maximum Ca2+-activated tension. These changes were accompanied by increased oxidation and reduced phosphorylation of the small myofilament protein cardiac myosin binding protein C (cMyBPC), as well as altered phosphorylation levels at different phosphosites in troponin I (TnI). The increased Fpassive and pCa50, and the reduced maximum Ca2+-activated tension were reversed when we treated the isolated permeabilized cardiomyocytes with reduced glutathione (GSH). This indicated that myofilament protein oxidation contributes to cardiomyocyte dysfunction. Furthermore, the PKD1 cKO mice exhibited increased oxidative stress and increased expression of pro-inflammatory markers interleukin (IL)-6, IL-18, and tumor necrosis factor alpha (TNF-α). Both oxidative stress and inflammation contributed to an increase in microtubule-associated protein 1 light chain 3 (LC3)-II levels and heat shock response by inhibiting the mammalian target of rapamycin (mTOR) in the PKD1 cKO mouse myocytes. These findings revealed a previously unknown role for PKD1 in regulating diastolic passive properties, myofilament Ca2+ sensitivity, and maximum Ca2+-activated tension under conditions of oxidative stress. Finally, we emphasized the importance of PKD1 in maintaining the balance of oxidative stress and inflammation in the context of autophagy, as well as cardiomyocyte function.

Exogenous priming of chitosan induces resistance in Chinese prickly ash against stem canker caused by Fusarium zanthoxyli

Stem canker is a highly destructive disease that threatens prickly ash plantations in China. This study demonstrated the effective control of stem canker in prickly ash using chitosan priming, reducing lesion areas by 46.77 % to 75.13 % across all chitosan treatments. The mechanisms underlying chitosan-induced systemic acquired resistance (SAR) in prickly ash were further investigated. Chitosan increased H2O2 levels and enhanced peroxidase and catalase enzyme activities. A well-constructed regulatory network depicting the genes involved in the SAR and their corresponding expression levels in prickly ash plants primed with chitosan was established based on transcriptomic analysis. Additionally, 224 ZbWRKYs were identified based on the whole genome of prickly ash, and their phylogenetic evolution, conserved motifs, domains and expression patterns of ZbWRKYs were comprehensively illustrated. The expression of 12 key genes related to the SAR was significantly increased by chitosan, as determined using reverse transcription-quantitative polymerase chain reaction. Furthermore, the activities of defensive enzymes and the accumulation of lignin and flavonoids in prickly ash were significantly enhanced by chitosan treatment. Taken together, this study provides valuable insights into the chitosan-mediated activation of the immune system in prickly ash, offering a promising eco-friendly approach for forest stem canker control.

Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.

Cyclophilin D in Mitochondrial Dysfunction: A Key Player in Neurodegeneration?

Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the "powerhouse of the cell" turns into the "factory of death" is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein CyPD is a peptidylprolyl cis-trans isomerase involved in the regulation of the permeability transition pore (mPTP). The mPTP is a multi-conductance channel in the inner mitochondrial membrane whose dysregulated opening can ultimately lead to cell death and whose involvement in pathology has been extensively documented over the past few decades. Moreover, several mPTP-independent CyPD interactions have been identified, indicating that CyPD could be involved in the fine regulation of several biochemical pathways. To further enrich the picture, CyPD undergoes several post-translational modifications that regulate both its activity and interaction with its clients. Here, we will dissect what is currently known about CyPD and critically review the most recent literature about its involvement in neurodegenerative disorders, focusing on Alzheimer's Disease and Parkinson's Disease, supporting the notion that CyPD could serve as a promising therapeutic target for the treatment of such conditions. Notably, significant efforts have been made to develop CyPD-specific inhibitors, which hold promise for the treatment of such complex disorders.

Exogenous melatonin enhances tomato heat resistance by regulating photosynthetic electron flux and maintaining ROS homeostasis

Heat stress reduces plant growth and reproduction and increases agricultural risks. As a natural compound, melatonin modulates broad aspects of the responses of plants to various biotic and abiotic stresses. However, regulation of the photosynthetic electron transfer, reactive oxygen species (ROS) homeostasis and the redox state of redox-sensitive proteins in the tolerance to heat stress induced by melatonin remain largely unknown. The oxygen evolution complex activity on the electron-donating side of photosystem II (PSII) is inhibited, and the electron transfer process from QA to QB on the electron-accepting side of PSII is inhibited. In this case, heat stress decreased the chlorophyll content, carbon assimilation rate, PSII activity, and the proportion of light absorbed by tomato seedlings during electron transfer. The ROS burst led to the breakdown of the PSII core protein. However, exogenous melatonin increased the net photosynthetic rate by 11.3% compared with heat stress, substantially reducing the restriction of photosynthetic systems induced by heat stress. Additionally, melatonin reduces the oxidative damage to PSII by balancing electron transfer on the donor, reactive center, and acceptor sides. Melatonin was used under heat stress to increase the activity of the antioxidant enzyme and preserve ROS equilibrium. In addition, redox proteomics also showed that melatonin controls the redox levels of proteins involved in photosynthesis, and stress and defense processes, which enhances the expression of oxidative genes. In conclusion, melatonin via controlling the photosynthetic electron transport and antioxidant, melatonin increased tomato heat stress tolerance and aided plant growth.

A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques

Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.

Base Dependent Rearrangement of Dithiane and Dithiolane under Visible-light Photoredox catalysis

The rearrangement of dithiolanes and dithianes to access disulfide-linked-dithioesters under visible-light photoredox catalysis via controlled C-S bond cleavage has been disclosed. Unlike, the usual deprotection of dithioacetals to corresponding aldehydes under the oxidative conditions, we observed unique regioselective oxidative reactivity of five and six membered cyclic dithioacetals to form disulfide-linked-dithioesters by exchanging DMAP and imidazole bases. The generality of the protocol has been demonstrated by exploring a wide range of substrates. As an application, in situ generated thiyl radical has been trapped with disulfides to prepare hetero-disulfides of potential utility. The protocol proved to be practical on gram scale quantity and relied on clean energy source for the transformation. Based on the series of control experiments, cyclic voltammetry and Stern-Volmer studies the plausible mechanism has been proposed.

Wheat genotypes with higher yield sensitivity to drought overproduced proline and lost minor biomass under severer water stress

To clarify the differences in growth and yield responses to drought stress among genotypes contrasting in environmental background, dryland and irrigated genotypes, as well as the underlying biochemical mechanism would provide valuable information for developing superior dryland cultivars. Pot experiments for the whole life cycle in fifteen genotypes and comparative metabolomics analysis for seedlings between two drought tolerant (DT) dryland genotypes and two drought sensitive (DS) irrigated ones were carried out. The DT dryland genotypes suffered heavy biomass loss during severer drought but showed minor yield loss ultimately, while the DS irrigated ones showed minor biomass loss but greater yield loss. Additionally, the superior DT dryland genotypes showed better yield performance under both drought stress and well-watered conditions, indicating their possessing both drought tolerance and high yield potential traits. Suffering severer drought stress, seedling leaves of the DS irrigated genotypes increased some amino acids and organic acids to maintain cell metabolism and accumulate more biomass. Proline in particular was overproduced, which might cause toxicity to cell systems and lead to enormous yield loss ultimately. In contrast, DT dryland genotypes increased the beneficial amino acid and phenolic acids to enhance cell self-protection for alleviating drought damage and efficiently minimized yield loss ultimately.

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.

Determination of Reactive Oxygen or Nitrogen Species and Novel Volatile Organic Compounds in the Defense Responses of Tomato Plants against Botrytis cinerea Induced by Trichoderma virens TRS 106

In the present study, Trichoderma virens TRS 106 decreased grey mould disease caused by Botrytis cinerea in tomato plants (S. lycopersicum L.) by enhancing their defense responses. Generally, plants belonging to the ‘Remiz’ variety, which were infected more effectively by B. cinerea than ‘Perkoz’ plants, generated more reactive molecules such as superoxide (O₂⁻) and peroxynitrite (ONOO⁻), and less hydrogen peroxide (H₂O₂), S-nitrosothiols (SNO), and green leaf volatiles (GLV). Among the new findings, histochemical analyses revealed that B. cinerea infection caused nitric oxide (NO) accumulation in chloroplasts, which was not detected in plants treated with TRS 106, while treatment of plants with TRS 106 caused systemic spreading of H₂O₂ and NO accumulation in apoplast and nuclei. SPME-GCxGC TOF-MS analysis revealed 24 volatile organic compounds (VOC) released by tomato plants treated with TRS 106. Some of the hexanol derivatives, e.g., 4-ethyl-2-hexynal and 1,5-hexadien-3-ol, and salicylic acid derivatives, e.g., 4-hepten-2-yl and isoamyl salicylates, are considered in the protection of tomato plants against B. cinerea for the first time. The results are valuable for further studies aiming to further determine the location and function of NO in plants treated with Trichoderma and check the contribution of detected VOC in plant protection against B. cinerea.

Direct Access to Thiocyano-Thioesters from Cyclic Thioacetals via Photoredox Catalysis: An Introduction of Two Functional Groups in One Pot

The cyanation of organic compounds is an important synthetic transformation and mainly relies on a toxic CN source. Undeniably, thiocyanate salt has emerged as a very mild and environmentally benign CN source, yet its synthetic utility for cyanation is highly limited to very few types of organic compounds. Herein, we report the direct cyanation of cyclic thioacetals for accessing compounds with two different functional groups (thiocyano-thioesters) in one pot using sodium thiocyanate via photoredox catalysis. The protocol has been further extended for the direct cyanation of disulfides and diselenide to access aryl thiocyanates and aryl selenocyanate. A plausible mechanism has been proposed based on a series of control experiments, cyclic voltammetry and Stern-Volmer studies.

Bacterial Mitigation of Drought Stress in Plants: Current Perspectives and Future Challenges

Climate change is emerging as a crucial issue with global attention and leading to abiotic stress conditions. There are different abiotic stress which affects the crop production among which drought is known to be most destructive stress affecting crop productivity and world's food security. Different approaches are under consideration to increase adaptability of the plants under drought stress with plant-microbe interactions being a greater area of focus. Stress-adaptive microbes either from the rhizosphere, internal tissue, or aerial parts of plants have been reported which through different mechanisms help the plants to cope up with drought and also promote their growth. These mechanisms include the accumulation of osmolytes, decrease in the inhibitory levels of ethylene by aminocyclopropane-1-carboxylate (ACC) deaminase enzyme, and furnishing the unavailable nutrients to plants. Microbial genera including Azotobacter, Bacillus, Ochrobactrum, Pseudomonas, and Serratia are known to be self-adaptive and growth promoters under drought stressed conditions. Stress-adaptive plant growth promoting (PGP) microbes thus are excellent candidates for stress alleviation in drought environment to provide maximum benefits to the plants. The present review deals with the effect of the drought stress on plants, biodiversity of the drought-adaptive microbes, mechanisms of the drought stress alleviation through enhancement of stress alleviators, reduction of the stress aggravators, and modification of the molecular pathways as well as the multiple PGP attributes of the drought-adaptive microbes.

Impacts of Mn, Fe, and Oxidative Stressors on MnSOD Activation by AtMTM1 and AtMTM2 in Arabidopsis

It has been reported that the mitochondrial carrier family proteins of AtMTM1 and AtMTM2 are necessary for manganese superoxide dismutase (MnSOD) activation in Arabidopsis, and are responsive to methyl viologen (MV)-induced oxidative stress. In this study, we showed that MnSOD activity was enhanced specifically by Mn treatments. By using AtMnSOD-overexpressing and AtMnSOD-knockdown mutant plants treated with the widely used oxidative stressors including MV, NaCl, H₂O₂, and tert-butyl hydroperoxide (t-BH), we revealed that Arabidopsis MnSOD was crucial for root-growth control and superoxide scavenging ability. In addition, it has been reported that E. coli MnSOD activity is inhibited by Fe and that MTM1-mutated yeast cells exhibit elevated Fe content and decreased MnSOD activity, which can be restored by the Fe²⁺-specific chelator, bathophenanthroline disulfonate (BPS). However, we showed that BPS inhibited MnSOD activity in AtMTM1 and AtMTM2 single- and double-mutant protoplasts, implying that altered Fe homeostasis affected MnSOD activation through AtMTM1 and AtMTM2. Notably, we used inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis to reveal an abnormal Fe/Mn ratio in the roots and shoots of AtMTM1 and AtMTM2 mutants under MV stress, indicating the importance of AtMTM1 in roots and AtMTM2 in shoots for maintaining Fe/Mn balance.

Are Methionine Sulfoxide-Containing Proteins Related to Seed Longevity? A Case Study of Arabidopsisthaliana Dry Mature Seeds Using Cyanogen Bromide Attack and Two-Dimensional-Diagonal Electrophoresis

In recent years, several reports pointed out the role of protein oxidation in seed longevity, notably regarding the oxidation of methionine (Met) residues to methionine sulfoxide (MetO) in proteins. To further consider this question, we present a handy proteomic method based on the use of two-dimensional diagonal electrophoresis (2Dd) and cyanogen bromide (CNBr) cleavage, which we refer to as 2Dd-CNBr. CNBr treatment of proteins causes the non-enzymatic hydrolysis of peptide bonds on the carboxyl side of reduced Met residues. However, Met oxidation causes a lack of cleavage, thus modifying the electrophoretic mobility of CNBr-induced peptides. This approach was first validated using bovine serum albumin as a model protein, which confirmed the possibility of distinguishing between oxidized and non-oxidized forms of Met-containing peptides in gels. Then, the 2Dd-CNBr method was applied to the Arabidopsis thaliana seed protein extract in a control (non-oxidized) condition and in an oxidized one (as obtained following hypochlorous acid treatment). Twenty-four oxidized Met residues in 19 proteins identified by mass spectrometry were found to be surface exposed in these proteins. In the three-dimensional environment of the oxidized Met, we detected amino acid residues that could be converted by oxidation (carbonylation) or by phosphorylation, suggesting a possible interplay between Met oxidation and the other protein modifications. The identification of the proteins oxidatively modified in Met residues revealed the finding that MetO-containing proteins are related to seed longevity. Based on these results, we suggest that the method presently described also has the potential for wider applications.

(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants

The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.

Phytoremediation of Heavy Metals in Tropical Soils an Overview

The geomorphological characteristics of the materials inherent in tropical soils, in addition to the excessive use of fertilizers and pesticides, industrial waste and residues, and novel pollutants derived from emerging new technologies such as nanomaterials, affect the functionality and resilience of the soil-microorganism-plant ecosystem; impacting phytoremediation processes and increasing the risk of heavy metal transfer into the food chain. The aim of this review is to provide a general overview of phytoremediation in tropical soils, placing special emphasis on the factors that affect this process, such as nanoagrochemicals, and highlighting the value of biodiversity among plant species that have the potential to grow and develop in soils impacted by heavy metals, as a useful resource upon which to base further research.

Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops

Drought stress is one of the most adverse abiotic stresses that hinder plants' growth and productivity, threatening sustainable crop production. It impairs normal growth, disturbs water relations and reduces water-use efficiency in plants. However, plants have evolved many physiological and biochemical responses at the cellular and organism levels, in order to cope with drought stress. Photosynthesis, which is considered one of the most crucial biological processes for survival of plants, is greatly affected by drought stress. A gradual decrease in CO₂ assimilation rates, reduced leaf size, stem extension and root proliferation under drought stress, disturbs plant water relations, reducing water-use efficiency, disrupts photosynthetic pigments and reduces the gas exchange affecting the plants adversely. In such conditions, the chloroplast, organelle responsible for photosynthesis, is found to counteract the ill effects of drought stress by its critical involvement as a sensor of changes occurring in the environment, as the first process that drought stress affects is photosynthesis. Beside photosynthesis, chloroplasts carry out primary metabolic functions such as the biosynthesis of starch, amino acids, lipids, and tetrapyroles, and play a central role in the assimilation of nitrogen and sulfur. Because the chloroplasts are central organelles where the photosynthetic reactions take place, modifications in their physiology and protein pools are expected in response to the drought stress-induced variations in leaf gas exchanges and the accumulation of ROS. Higher expression levels of various transcription factors and other proteins including heat shock-related protein, LEA proteins seem to be regulating the heat tolerance mechanisms. However, several aspects of plastid alterations, following a water deficit environment are still poorly characterized. Since plants adapt to various stress tolerance mechanisms to respond to drought stress, understanding mechanisms of drought stress tolerance in plants will lead toward the development of drought tolerance in crop plants. This review throws light on major droughts stress-induced molecular/physiological mechanisms in response to severe and prolonged drought stress and addresses the molecular response of chloroplasts in common vegetable crops. It further highlights research gaps, identifying unexplored domains and suggesting recommendations for future investigations.

Proteomics and Metabolomics Reveal the Regulatory Pathways of Ripening and Quality in Post-Harvest Kiwifruits

Understanding the metabolic modulation of major quality traits during ripening is critical for fruit quality improvement in kiwifruits. Here, integrated proteomic and metabolomic profiling was undertaken to comprehensively examine the dynamics of kiwifruit ripening. This data set presents a global view of the critical pathways involved in fruit ripening, and the contributions of key events to the regulation of kiwifruit ripening and softening, amino acid metabolism, balance in sugar accumulation and organic acid metabolism, glycolysis, and tricarboxylic acid (TCA) pathways were discussed. We suggested key enzymes for starch synthesis and degradation, including AGPase, SS, and SBE, especially for BMY, which was considered a key enzyme for starch degradation. In addition, our analysis implicated the key enzymes ACO4 and ACS9 in ethylene synthesis and the aspartate aminotransferase ASP3 in the conversion of amino acids. These results provide new insights into the modulation of fruit ripening, metabolism, and quality in post-harvest kiwifruits.

Mechanistic insight for DBP induced growth inhibition in Vigna radiata via oxidative stress and DNA damage

Chlorination is important to the safeness of recouped water; though it shows concern about disinfection by-products (DBPs) formation and its toxic effects. DBPs generation mostly specified by category of disinfectant utilized and naturally occurring organic matter present in the water pre and post disinfection. Plants are exposed to diverse stresses of environment across their lifespan. Reactive oxygen species (ROS) perform significant roles in preserving ordinary plant growth and enhancing their tolerance towards stress. This study is focused on the generation and elimination of ROS in apical meristematic growth and responses in Vigna radiata towards DBPs exposure. Phytotoxic and genotoxic effect of selected DBPs, TCAA (trichloroacetic acid), TCM (trichloromethane), TBM (tribromomethane) revealed concentration-dependent root length inhibition, germination index, vigour index, tolerance index, root/shoot ratio with higher EC₅₀ value for TCM (6000 mg/L, 50.26 mM) over TCAA and TBM (1850 mg/L, 11.32 mM; 4000 mg/L, 15.83 mM). DNA laddering assay demonstrated DBP induced DNA damage to be concentration-dependent too. The concentration-dependent increase in the lipid peroxidation, H₂O₂ generation for each DBPs examined with highest oxidative stress for TCAA over TBM and TCM at fixed concentration illustrates that possible mechanism behind observed toxicity may be via ROS. Its regulation by antioxidative defense enzymes activities can be attributed to observed decline in these enzymes (catalase, ascorbate peroxidase, guaiacol peroxidase) activities with increasing concentration again where TCAA found more significantly affected than TBM and TCM over control. Results thus provide a useful understanding of the mechanism of DBP induced phytotoxicity and genotoxicity in V.radiata.

Droplet-vitrification of Aranda Broga Blue orchid: Role of ascorbic acid on the antioxidant system and genetic fidelity assessments via RAPD and SCoT markers

A droplet-vitrification cryopreservation protocol has been successfully developed for Aranda Broga Blue orchid hybrid using protocorm-like bodies (PLBs). However, maximum growth regeneration percentage was recorded at 5% only based on previous report. Thus, to improve growth recovery of cryopreserved PLBs, cryopreservation stages were supplemented with ascorbic acid, tested at 50, 100 and 150 mg/L. However, results demonstrated that exogenous ascorbic acid was not favorable in regeneration of cryopreserved explants (maximum value of 1.67 % with 50 mg/L ascorbic acid supplementation). Total soluble protein and various antioxidant enzyme activities such as catalase (CAT), superoxide dismutase (SOD) and ascorbate peroxidase (APX) were evaluated after each cryopreservation stages in conjunction with the application of exogenous ascorbic acid. Addition of antioxidant must be carefully evaluated and its application may not guarantee successful growth recovery. RAPD and SCoT molecular analysis confirmed the genetic stability of regenerated cryopreserved PLBs as no polymorphism was detected compared to control PLBs culture.

Redox-Mediated Post-Translational Modifications of Proteolytic Enzymes and Their Role in Protease Functioning

Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to maintain cellular and extracellular homeostasis. The redox regulation of proteolysis provides a flexible dose-dependent mechanism for proteolytic activity control. The excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) in living organisms indicate pathological conditions, so redox-sensitive proteases can swiftly induce pro-survival responses or regulated cell death (RCD). At the same time, severe protein oxidation can lead to the dysregulation of proteolysis, which induces either protein aggregation or superfluous protein hydrolysis. Therefore, oxidative stress contributes to the onset of age-related dysfunction. In the present review, we consider the post-translational modifications (PTMs) of proteolytic enzymes and their impact on homeostasis.

Aphid-Triggered Changes in Oxidative Damage Markers of Nucleic Acids, Proteins, and Lipids in Maize (Zea mays L.) Seedlings

Prior experiments illustrated reactive oxygen species (ROS) overproduction in maize plants infested with bird-cherry-oat (Rhopalosiphum padi L.) aphids. However, there is no available data unveiling the impact of aphids feeding on oxidative damages of crucial macromolecules in maize tissues. Therefore, the purpose of the current study was to evaluate the scale of oxidative damages of genomic DNA, total RNA and mRNA, proteins, and lipids in seedling leaves of two maize genotypes (Złota Karłowa and Waza cvs—susceptible and relatively resistant to the aphids, respectively). The content of oxidized guanosine residues (8-hydroxy-2′-deoxyguanosine; 8-OHdG) in genomic DNA, 8-hydroxyguanosine (8-OHG) in RNA molecules, protein carbonyl groups, total thiols (T-SH), protein-bound thiols (PB-SH), non-protein thiols (NP-SH), malondialdehyde (MDA) and electrolyte leakage (EL) levels in maze plants were determined. In addition, the electrical penetration graphs (EPG) technique was used to monitor and the aphid stylet positioning and feeding modes in the hosts. Maize seedlings were infested with 0 (control), 30 or 60 R. padi adult apterae per plant. Substantial increases in the levels of RNA, protein and lipid oxidation markers in response to aphid herbivory, but no significant oxidative damages of genomic DNA, were found. Alterations in the studied parameters were dependent on maize genotype, insect abundance and infestation time.

Growth, accumulation, and antioxidative responses of two Salix genotypes exposed to cadmium and lead in hydroponic culture

Cd and Pb are a toxic environmental pollutant, and their elevated concentrations in the waters and soils could exert detriment effects on human health by food chain. In order to evaluate the capacity to heavy metal accumulation and the physiochemical responses of two Salix genotypes, a 35-day hydroponic seedling experiment was implemented with Salix matsudana Koidz. 'Shidi1' (A42) and Salix psammophila C. 'Huangpi1' (A94) under different concentrations of Cd (15 and 30 μM) or Pb (250 and 300 μM). The results showed that the biomass of A94 severely reduced more than that of A42. The accumulation ability of Cd in different plant organs followed the sequence of leaves > roots > stems. Pb primarily accumulated in the roots for both Salix genotypes (54.27 mg g^-1 for A42 and 54.52 mg g^-1 for A94). Translocation factors based on accumulation (TF') for Cd were more than 8.0, while TF's for Pb were less than 1.0 in both A42 and A94, implying they could be applied in the phytoremediation of Cd-contaminated sites due to their stronger ability to Cd phytoextraction. The stress of Cd or Pb significantly increased malondialdehyde (MDA) contents and increased photosynthetic rates in leaves of two Salix genotypes. Transpiration rates of willow were positively correlated with its Cd translocation. Both catalase (CAT) and peroxidase (POD) activities were suppressed, while the superoxide dismutase (SOD) was boosted with increasing Cd and Pb levels in the leaves and roots of the two willow genotypes, suggesting SOD plays an important role in the removal of ROS. The inconsistency of the changes in enzyme activity suggests that the integrated antioxidative mechanisms regulate the tolerance to Cd and Pb stress.

Nitric Oxide as a Beneficial Signaling Molecule in Trichoderma atroviride TRS25-Induced Systemic Defense Responses of Cucumber Plants Against Rhizoctonia solani

In the present study, Trichoderma atroviride TRS25 is presented as a biological control agent, which significantly limits the development of infection and reduces the disease caused by the pathogenic fungus Rhizoctonia solani in cucumber plants (Cucumis sativus L.). The systemic disease suppression is related to oxidative, signaling, and biochemical changes, that are triggered in response to a pathogen. Induction of systemic defense in cucumber by TRS25 greatly depends on the accumulation of signaling molecules including hydrogen peroxide (H2O2) and nitric oxide (NO) as well as salicylic acid (SA) and its derivatives including methyl salicylate (MeSA) and octyl salicylate (OSA). The study established that NO was accumulated in leaves and shoots of the cucumber plants, especially those pretreated with Trichoderma and inoculated with R. solani, where the compound was accumulated mainly in the cells localized in the vascular bundles and in epidermal tissues. We suggest, for the first time, that in the plants pretreated with TRS25, the accumulation of H2O2 and NO may be related to catalase (CAT) and S-nitrosoglutathione reductase (GSNOR) activity decrease. On the other hand, excessive accumulation of NO and SA may be controlled by forming their inactive forms, S-nitrosothiols (SNO) and salicylic acid glucosylated conjugates (SAGC), respectively. The obtained results suggest that the mentioned molecules may be an important component of the complex signaling network activated by TRS25, which is positively involved in systemic defense responses of cucumber plants against R. solani.

Directions for research and training in plant omics: Big Questions and Big Data

A key remit of the NSF-funded "Arabidopsis Research and Training for the 21st Century" (ART-21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART-21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post-doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.

Unveiling Kiwifruit Metabolite and Protein Changes in the Course of Postharvest Cold Storage

Actinidia deliciosa cv. Hayward fruit is renowned for its micro- and macronutrients, which vary in their levels during berry physiological development and postharvest processing. In this context, we have recently described metabolic pathways/molecular effectors in fruit outer endocarp characterizing the different stages of berry physiological maturation. Here, we report on the kiwifruit postharvest phase through an integrated approach consisting of pomological analysis combined with NMR/LC-UV/ESI-IT-MSⁿ- and 2D-DIGE/nanoLC-ESI-LIT-MS/MS-based proteometabolomic measurements. Kiwifruit samples stored under conventional, cold-based postharvest conditions not involving the use of dedicated chemicals were sampled at four stages (from fruit harvest to pre-commercialization) and analyzed in comparison for pomological features, and outer endocarp metabolite and protein content. About 42 metabolites were quantified, together with corresponding proteomic changes. Proteomics showed that proteins associated with disease/defense, energy, protein destination/storage, cell structure and metabolism functions were affected at precise fruit postharvest times, providing a justification to corresponding pomological/metabolite content characteristics. Bioinformatic analysis of variably represented proteins revealed a central network of interacting species, modulating metabolite level variations during postharvest fruit storage. Kiwifruit allergens were also quantified, demonstrating in some cases their highest levels at the fruit pre-commercialization stage. By lining up kiwifruit postharvest processing to a proteometabolomic depiction, this study integrates previous observations on metabolite and protein content in postharvest berries treated with specific chemical additives, and provides a reference framework for further studies on the optimization of fruit storage before its commercialization.

Plant-lead interactions: Transport, toxicity, tolerance, and detoxification mechanisms

Natural and human activities introduced an excess level of toxic lead (Pb) to the environment. Pb has no known biological significance and its interactions with plants lead to the production of reactive oxygen species (ROS). Pb and/or ROS have the potential to cause phytotoxicity by damaging the tissue ultrastructure, cellular components, and biomolecules. These damaging effects may possibly result in the inhibition of normal cellular functioning, physiological reactions, and overall plant performances. ROS play a dual role and act as a signaling molecule in plant defense system. This system encircles enzymatic and non-enzymatic antioxidative mechanisms. Catalase, superoxide dismutase, peroxidase, and enzymes from the ascorbate-glutathione cycle are the major enzymatic antioxidants, while non-enzymatic antioxidants include phenols, flavonoids, ascorbic acid, and glutathione. Pb removal from contaminated sites using plants depend on the plant's Pb accumulation capacity, Pb-induced phytotoxicity, and tolerance and detoxification mechanisms plants adopted to combat against this phytotoxicity. However, the consolidated information discussing Pb-plant interaction including Pb uptake and its translocation within tissues, Pb-mediated phytotoxic symptoms, antioxidative mechanisms, cellular, and protein metabolisms are rather limited. Thus, we aimed to present a consolidated information and critical discussions focusing on the recent studies related to the Pb-induced toxicity and oxidative stress situations in different plants. The important functions of different antioxidants in plants during Pb stress have been reviewed. Additionally, tolerance responses and detoxification mechanisms in the plant through the regulation of gene expression, and glutathione and protein metabolisms to compete against Pb-induced phytotoxicity are also briefly discussed herein.

Crosstalk between reactive oxygen species and nitric oxide in plants: Key role of S-nitrosoglutathione reductase

Nitric oxide (.NO) acts as signaling molecule in plants being involved in diverse physiological processes such as germination, root growth, stomata closing and response to biotic and abiotic stress. S-Nitrosoglutathione (GSNO) is the storage and transport form of.NO and has a very important function in.NO signaling since it can transfer its.NO moiety to other proteins (trans-nitrosylation). The level of GSNO and thus the level of S-nitrosylated proteins are regulated by GSNO-reductase (GSNOR). In this way, this enzyme regulates the S-nitrosothiol levels and plays a balancing role in fine-tuning.NO signaling. Interestingly, oxidative post-translationally modification of GSNOR inhibited the activity of this enzyme suggesting a direct crosstalk between ROS- and RNS-signaling. In this review article the regulatory effects of ROS on GSNOR are highlighted and their physiological function in context of crosstalk between ROS and.NO and species in plants are discussed.

HIV-1 tat expression and sulphamethoxazole hydroxylamine mediated oxidative stress alter the disulfide proteome in Jurkat T cells

Background

Adverse drug reactions (ADRs) are a significant problem for HIV patients, with the risk of developing ADRs increasing as the infection progresses to AIDS. However, the pathophysiology underlying ADRs remains unknown. Sulphamethoxazole (SMX) via its active metabolite SMX-hydroxlyamine, when used prophylactically for pneumocystis pneumonia in HIV-positive individuals, is responsible for a high incidence of ADRs. We previously demonstrated that the HIV infection and, more specifically, that the HIV-1 Tat protein can exacerbate SMX-HA-mediated ADRs. In the current study, Jurkat T cell lines expressing Tat and its deletion mutants were used to determine the effect of Tat on the thiol proteome in the presence and absence of SMX-HA revealing drug-dependent changes in the disulfide proteome in HIV infected cells.

Protein lysates from HIV infected Jurkat T cells and Jurkat T cells stably transfected with HIV Tat and Tat deletion mutants were subjected to quantitative slot blot analysis, western blot analysis and redox 2 dimensional (2D) gel electrophoresis to analyze the effects of SMX-HA on the thiol proteome.

Results

Redox 2D gel electrophoresis demonstrated that untreated, Tat-expressing cells contain a number of proteins with oxidized thiols. The most prominent of these protein thiols was identified as peroxiredoxin. The untreated, Tat-expressing cell lines had lower levels of peroxiredoxin compared to the parental Jurkat E6.1 T cell line. Conversely, incubation with SMX-HA led to a 2- to 3-fold increase in thiol protein oxidation as well as a significant reduction in the level of peroxiredoxin in all the cell lines, particularly in the Tat-expressing cell lines.

Conclusion

SMX-HA is an oxidant capable of inducing the oxidation of reactive protein cysteine thiols, the majority of which formed intermolecular protein bonds. The HIV Tat-expressing cell lines showed greater levels of oxidative stress than the Jurkat E6.1 cell line when treated with SMX-HA. Therefore, the combination of HIV Tat and SMX-HA appears to alter the activity of cellular proteins required for redox homeostasis and thereby accentuate the cytopathic effects associated with HIV infection of T cells that sets the stage for the initiation of an ADR.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-0991-x) contains supplementary material, which is available to authorized users.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.

Soluble expression of biologically active methionine sulfoxide reductase B1 (PaMsrB1) from Carica papaya in Escherichia coli and isolation of its protein targets

Plant methionine sulfoxide reductase B1 (MsrB1) protects the photosynthetic apparatus from oxidative damage by scavenging reactive oxygen species to repair Met-oxidized proteins in response to abiotic stresses and biotic attack. Papaya MsrB1 (PaMsrB1) was identified previously to interact with papaya ringspot virus NIa-Pro, and this interaction inhibits the import of PaMsrB1 into the chloroplast. Further functional characterization of PaMsrB1 requires the production of a biologically active purified recombinant protein. In this report, PaMsrB1 as a fusion protein containing an N-terminal maltose-binding protein (MBP) was expressed in Escherichia coli Rosetta (DE3) cells and purified. Production of soluble fusion protein was greater when the cells were cultured at 16 °C than at 37 °C. The Factor Xa protease digested MBP-PaMsrB1 fusion protein and subsequently purified recombinant PaMsrB1 specifically reduced the R-diastereomer of methionine sulfoxide (MetSO) and Dabsyl-MetSO to Met in the presence of dithiothreitol. Eight chloroplast-localized and five non-chloroplast-localized candidate proteins that interact with PaMsrB1 were isolated by affinity chromatography and liquid chromatography coupled to tandem mass spectrometry. The results provide a platform to further understand the anti-oxidative defense mechanism of PaMsrB1.

Hydrogen Peroxide Response in Leaves of Poplar (Populus simonii × Populus nigra) Revealed from Physiological and Proteomic Analyses

Hydrogen peroxide (H₂O₂) is one of the most abundant reactive oxygen species (ROS), which plays dual roles as a toxic byproduct of cell metabolism and a regulatory signal molecule in plant development and stress response. Populus simonii × Populus nigra is an important cultivated forest species with resistance to cold, drought, insect and disease, and also a key model plant for forest genetic engineering. In this study, H₂O₂ response in P. simonii × P. nigra leaves was investigated using physiological and proteomics approaches. The seedlings of 50-day-old P. simonii × P. nigra under H₂O₂ stress exhibited stressful phenotypes, such as increase of in vivo H₂O₂ content, decrease of photosynthetic rate, elevated osmolytes, antioxidant accumulation, as well as increased activities of several ROS scavenging enzymes. Besides, 81 H₂O₂-responsive proteins were identified in the poplar leaves. The diverse abundant patterns of these proteins highlight the H₂O₂-responsive pathways in leaves, including 14-3-3 protein and nucleoside diphosphate kinase (NDPK)-mediated signaling, modulation of thylakoid membrane structure, enhancement of various ROS scavenging pathways, decrease of photosynthesis, dynamics of proteins conformation, and changes in carbohydrate and other metabolisms. This study provides valuable information for understanding H₂O₂-responsive mechanisms in leaves of P. simonii × P. nigra.

An integrative overview of the molecular and physiological responses of sugarcane under drought conditions

Drought is the main abiotic stress constraining sugarcane production. However, our limited understanding of the molecular mechanisms involved in the drought stress responses of sugarcane impairs the development of new technologies to increase sugarcane drought tolerance. Here, an integrated approach was performed to reveal the molecular and physiological changes in two closely related sugarcane cultivars, including the most extensively planted cultivar in Brazil (cv. RB867515), in response to moderate (-0.5 MPa) and severe (-1 MPa) drought stress at the transcriptional, translational, and posttranslational levels. The results show common and cultivar exclusive changes in specific genes related to photosynthesis, carbohydrate, amino acid, and phytohormone metabolism. The novel phosphoproteomics and redox proteomic analysis revealed the importance of posttranslational regulation mechanisms during sugarcane drought stress. The shift to soluble sugar, secondary metabolite production, and activation of ROS eliminating processes in response to drought tolerance were mechanisms exclusive to cv. RB867515, helping to explain the better performance and higher production of this cultivar under these stress conditions.

Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs

Contents 937 I. 937 II. 938 III. 939 IV. 943 V. 947 VI. 948 948 References 949 SUMMARY: The orange carotenoid protein (OCP) is a water-soluble, photoactive protein involved in thermal dissipation of excess energy absorbed by the light-harvesting phycobilisomes (PBS) in cyanobacteria. The OCP is structurally and functionally modular, consisting of a sensor domain, an effector domain and a keto-carotenoid. On photoactivation, the OCP converts from a stable orange form, OCP^O , to a red form, OCP^R . Activation is accompanied by a translocation of the carotenoid deeper into the effector domain. The increasing availability of cyanobacterial genomes has enabled the identification of new OCP families (OCP1, OCP2, OCPX). The fluorescence recovery protein (FRP) detaches OCP1 from the PBS core, accelerating its back-conversion to OCP^O ; by contrast, other OCP families are not regulated by FRP. N-terminal domain homologs, the helical carotenoid proteins (HCPs), have been found among diverse cyanobacteria, occurring as multiple paralogous groups, with two representatives exhibiting strong singlet oxygen (¹ O₂ ) quenching (HCP2, HCP3) and another capable of dissipating PBS excitation (HCP4). Crystal structures are presently available for OCP1 and HCP1, and models of other HCP subtypes can be readily produced as a result of strong sequence conservation, providing new insights into the determinants of carotenoid binding and ¹ O₂ quenching.

Protein-Tannin Interactions of Tryptic Digests of α-Lactalbumin and Procyanidins

Protein-tannin interactions on a molecular level were investigated by using a model system containing peptides of α-lactalbumin and berry tannins (procyanidins). Oxidation of isolated tryptic peptide LDQWLCEK (m/z 1034) with procyanidin B2 or procyanidin fraction (PF) isolated from aronia juice was monitored by LC-ESI-MS. Procyanidin B2 and PF showed radical scavenging activities toward oxidation of the peptide with the peptide also preventing procyanidin B2 from degradation. Oxidation enhanced the cleavage of peptide between tryptophan and glutamine. Interaction products arising from WLCEK or WLCE residue and degradation product of procyanidin B2 were also identified using both size exclusion chromatography and LC-MS. Tryptophan and lysine were the amino acids most prone to interact with procyanidin B2. The study shows that protein-tannin interaction takes place during oxidation leading to both degradation of the parent compounds and formation of interaction products. This may in turn affect the quality of protein and tannin containing food.

Cadmium Bioavailability, Uptake, Toxicity and Detoxification in Soil-Plant System

This review summarizes the findings of the most recent studies, published from 2000 to 2016, which focus on the biogeochemical behavior of Cd in soil-plant systems and its impact on the ecosystem. For animals and people not subjected to a Cd-contaminated environment, consumption of Cd contaminated food (vegetables, cereals, pulses and legumes) is the main source of Cd exposure. As Cd does not have any known biological function, and can further cause serious deleterious effects both in plants and mammalian consumers, cycling of Cd within the soil-plant system is of high global relevance.The main source of Cd in soil is that which originates as emissions from various industrial processes. Within soil, Cd occurs in various chemical forms which differ greatly with respect to their lability and phytoavailability. Cadmium has a high phytoaccumulation index because of its low adsorption coefficient and high soil-plant mobility and thereby may enter the food chain. Plant uptake of Cd is believed to occur mainly via roots by specific and non-specific transporters of essential nutrients, as no Cd-specific transporter has yet been identified. Within plants, Cd causes phytotoxicity by decreasing nutrient uptake, inhibiting photosynthesis, plant growth and respiration, inducing lipid peroxidation and altering the antioxidant system and functioning of membranes. Plants tackle Cd toxicity via different defense strategies such as decreased Cd uptake or sequestration into vacuoles. In addition, various antioxidants combat Cd-induced overproduction of ROS. Other mechanisms involve the induction of phytochelatins, glutathione and salicylic acid.

Narrow-Leafed Lupin (Lupinus angustifolius) β1- and β6-Conglutin Proteins Exhibit Antifungal Activity, Protecting Plants against Necrotrophic Pathogen Induced Damage from Sclerotinia sclerotiorum and Phytophthora nicotianae

Vicilins (7S globulins) are seed storage proteins and constitute the main protein family in legume seeds, particularly in narrow-leafed lupin (Lupinus angustifolius L.; NLL), where seven vicilin genes, called β1- to β7-conglutin have been identified. Vicilins are involved in germination processes supplying amino acids for seedling growth and plant development, as well as in some cases roles in plant defense and protection against pathogens. The roles of NLL β-conglutins in plant defense are unknown. Here the potential role of five NLL β-conglutin family members in protection against necrotrophic fungal pathogens was investigated and it was demonstrated that recombinant purified 6xHis-tagged β1- and β6-conglutin proteins exhibited the strongest in vitro growth inhibitory activity against a range of necrotrophic fungal pathogens compared to β2, β3, and β4 conglutins. To examine activity in vivo, two representative necrotrophic pathogens, the fungus Sclerotinia sclerotiorum and oomycete Phytophthora nicotianae were used. Transient expression of β1- and β6-conglutin proteins in Nicotiana benthamiana leaves demonstrated in vivo growth suppression of both of these pathogens, resulting in low percentages of hyphal growth and elongation in comparison to control treated leaves. Cellular studies using β1- and β6-GFP fusion proteins showed these conglutins localized to the cell surface including plasmodesmata. Analysis of cellular death following S. sclerotiorum or P. nicotianae revealed both β1- and β6-conglutins suppressed pathogen induced cell death in planta and prevented pathogen induced suppression of the plant oxidative burst as determined by protein oxidation in infected compared to mock-inoculated leaves.

Proteomic analysis of S-nitrosylated and S-glutathionylated proteins in wheat seedlings with different dehydration tolerances

A loss of dehydration tolerance in wheat seedlings on the fifth day following imbibition is associated with a disturbance in cellular redox homeostasis, as documented by a shift of the reduced/oxidized glutathione ratio to a more oxidized state and a significant increase in the ratio of protein thiols to the total thiol group content. Therefore, the identification and characterization of redox-sensitive proteins are important steps toward understanding the molecular mechanisms of the loss of dehydration tolerance. In the present study, proteins that were differentially expressed between fully turgid (control), dehydrated tolerant (four-day-old) and dehydrated sensitive (six-day-old) wheat seedlings were analysed. Protein spots having at least a significant (p < 0.05) two-fold change in protein abundance were selected by Delta2D as differentially expressed, identified by MALDI-TOF and LC-MS/MS, and classified according to their function. The observed changes in the proteomic patterns of the differentially S-nitrosylated and S-glutathionylated proteins were highly specific in dehydration-tolerant and -sensitive wheat seedlings. The metabolic function of these proteins indicates that dehydration tolerance is mainly related to nucleic acids, protein metabolism, and energy metabolism. It has been proven that leaf-specific thionins BTH6 and DB4, chloroplastic 50S ribosomal protein L16, phospholipase A1-II delta, and chloroplastic thioredoxin M2 are both S-nitrosylated and S-glutathionylated upon water deficiency. Our results revealed the existence of interplay between S-nitrosylation and S-glutathionylation, two redox-regulated protein posttranslational modifications that could enhance plant defence mechanisms and/or facilitate the acclimation of plants to unfavourable environmental conditions.

Exogenously applied nitrate improves the photosynthetic performance and nitrogen metabolism in tomato (Solanumlycopersicum L. cv Pusa Rohini) under arsenic (V) toxicity

Tomato (Solanum lycopersicum L.) being a widespread and most commonly consumed vegetable all over the world has an important economic value for its producers and related food industries. It is a serious matter of concern as its production is affected by arsenic present in soil. So, the present study, investigated the toxicity of As(V) on photosynthetic performance along with nitrogen metabolism and its alleviation by exogenous application of nitrate. Plants were grown under natural conditions using soil spiked with 25 mg and 20 mM, As(V) and nitrate, respectively. Our results revealed that plant growth indices, photosynthetic pigments, and other major photosynthetic parameters like net photosynthetic rate and maximum quantum efficiency (F_v/F_m ) of photosystem II (PSII) were significantly (P ≤ 0.05) reduced under As(V) stress. However, nitrate application significantly (P ≤ 0.05) alleviated As(V) toxicity by improving the aforesaid plant responses and also restored the abnormal shape of guard cells. Nitrogen metabolism was assessed by studying the key nitrogen-metabolic enzymes. Exogenous nitrate revamped nitrogen metabolism through a major impact on activities of NR, NiR, GS and GOGAT enzymes and also enhanced the total nitrogen and NO content while malondialdehyde content, and membrane electrolytic leakage were remarkably reduced. Our study suggested that exogenous nitrate application could be considered as a cost effective approach in ameliorating As(V) toxicity.

Plant subcellular proteomics: Application for exploring optimal cell function in soybean

Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions.

BIOLOGICAL SIGNIFICANCE

Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.

Antioxidant enzymes as redox-based biomarkers: a brief review

The field of redox proteomics focuses to a large extent on analyzing cysteine oxidation in proteins under different experimental conditions and states of diseases. The identification and localization of oxidized cysteines within the cellular milieu is critical for understanding the redox regulation of proteins under physiological and pathophysiological conditions, and it will in turn provide important information that are potentially useful for the development of novel strategies in the treatment and prevention of diseases associated with oxidative stress. Antioxidant enzymes that catalyze oxidation/reduction processes are able to serve as redox biomarkers in various human diseases, and they are key regulators controlling the redox state of functional proteins. Redox regulators with antioxidant properties related to active mediators, cellular organelles, and the surrounding environments are all connected within a network and are involved in diseases related to redox imbalance including cancer, ischemia/reperfusion injury, neurodegenerative diseases, as well as normal aging. In this review, we will briefly look at the selected aspects of oxidative thiol modification in antioxidant enzymes and thiol oxidation in proteins affected by redox control of antioxidant enzymes and their relation to disease. [BMB Reports 2015; 48(4): 200-208]

Accumulation of Flavonols over Hydroxycinnamic Acids Favors Oxidative Damage Protection under Abiotic Stress

Efficient detoxification of reactive oxygen species (ROS) is thought to play a key role in enhancing the tolerance of plants to abiotic stresses. Although multiple pathways, enzymes, and antioxidants are present in plants, their exact roles during different stress responses remain unclear. Here, we report on the characterization of the different antioxidant mechanisms of tomato plants subjected to heat stress, salinity stress, or a combination of both stresses. All the treatments applied induced an increase of oxidative stress, with the salinity treatment being the most aggressive, resulting in plants with the lowest biomass, and the highest levels of H2O2 accumulation, lipid peroxidation, and protein oxidation. However, the results obtained from the transcript expression study and enzymatic activities related to the ascorbate-glutathione pathway did not fully explain the differences in the oxidative damage observed between salinity and the combination of salinity and heat. An exhaustive metabolomics study revealed the differential accumulation of phenolic compounds depending on the type of abiotic stress applied. An analysis at gene and enzyme levels of the phenylpropanoid metabolism concluded that under conditions where flavonols accumulated to a greater degree as compared to hydroxycinnamic acids, the oxidative damage was lower, highlighting the importance of flavonols as powerful antioxidants, and their role in abiotic stress tolerance.

ROS-Mediated Inhibition of S-nitrosoglutathione Reductase Contributes to the Activation of Anti-oxidative Mechanisms

Nitric oxide (NO) has emerged as a signaling molecule in plants being involved in diverse physiological processes like germination, root growth, stomata closing and response to biotic and abiotic stress. S-nitrosoglutathione (GSNO) as a biological NO donor has a very important function in NO signaling since it can transfer its NO moiety to other proteins (trans-nitrosylation). Such trans-nitrosylation reactions are equilibrium reactions and depend on GSNO level. The breakdown of GSNO and thus the level of S-nitrosylated proteins are regulated by GSNO-reductase (GSNOR). In this way, this enzyme controls S-nitrosothiol levels and regulates NO signaling. Here we report that Arabidopsis thaliana GSNOR activity is reversibly inhibited by H₂O₂in vitro and by paraquat-induced oxidative stress in vivo. Light scattering analyses of reduced and oxidized recombinant GSNOR demonstrated that GSNOR proteins form dimers under both reducing and oxidizing conditions. Moreover, mass spectrometric analyses revealed that H₂O₂-treatment increased the amount of oxidative modifications on Zn²⁺-coordinating Cys47 and Cys177. Inhibition of GSNOR results in enhanced levels of S-nitrosothiols followed by accumulation of glutathione. Moreover, transcript levels of redox-regulated genes and activities of glutathione-dependent enzymes are increased in gsnor-ko plants, which may contribute to the enhanced resistance against oxidative stress. In sum, our results demonstrate that reactive oxygen species (ROS)-dependent inhibition of GSNOR is playing an important role in activation of anti-oxidative mechanisms to damping oxidative damage and imply a direct crosstalk between ROS- and NO-signaling.

Structural and functional insight into the different oxidation states of SAV1875 from Staphylococcus aureus

Crystal structures of the wild-type and various mutants of SAV1875 with different cysteine oxidation states were elucidated. SAV1875 functions as a chaperone and the redox state of Cys105 may play an important role.