Recent developments in the application of proteomics to the analysis of plant responses to heavy metals

Evaluation of silicon influence on the mitigation of cadmium-stress in the development of Arabidopsis thaliana through total metal content, proteomic and enzymatic approaches

The mitigation of Cd-stress through Si addition to Arabidopsis thaliana cultivation is evaluated in terms of total metal content, proteomic and enzymatic approaches. Four different treatment are evaluated: TC (control, without Si or Cd addition), T1 (with Si addition), T2 (with Cd addition), and T3 (with Si and Cd addition). Through the total determination of Cd and Si in Arabidopsis leaves, the Cd concentration decreased by half when T2 is compared with T3 treatment. In terms of proteomic approach, some differential protein species are achieved by comparative proteomics through 2-D DIGE of all treatments evaluated. Fifty six differential abundant proteins spots (abundance factor ≥1.5) are detected, and 32 of them accurately characterized and identified through nESI-LC-MS/MS. These proteins are differentially produced due to Cd and/or Si treatments, which mainly include proteins associated with disease/defense, energy and metabolism. The most difference in the abundance of proteins is found due to the presence or absence of Si in plants treated with Cd. Regarding the enzymatic approaches, a major increase is found on APX, CAT and GR activities (5.0, 3.5, and 1.5-fold, respectively). The same is observed for the MDA concentration because an increase of 3-fold is found when TC are compared to those treated with T2. However, when T3 plants are evaluated, the enzymes activities are similar to TC plants. Differences ranging from 6.5 to 21% are detected considering the activity of SOD in the treatments (T1-T3 x TC). The decreased activities of CAT, APX and GR and lower MDA concentration indicate a lower reactive oxygen species production in plants treated with Cd and Si. Based on a proteomics point of view it is possible to conclude that Si-Cd interactions occur at protein level and allow plants to respond effectively to the Cd toxicity, revealing the active involvement of Si on mechanisms involved in Si-induced Cd tolerance in Arabidopsis plants. Additionally, from an enzymatic point of view, it is possible to conclude that Si positively interferes diminishing the negative effects of Cd in Arabidopsis by decreasing the reactive oxygen species generation and increasing the antioxidative enzyme activity.

Redox biology response in germinating Phaseolus vulgaris seeds exposed to copper: Evidence for differential redox buffering in seedlings and cotyledon

In agriculture, heavy metal contamination of soil interferes with processes associated with plant growth, development and productivity. Here, we describe oxidative and redox changes, and deleterious injury within cotyledons and seedlings caused by exposure of germinating (Phaseolus vulgaris L. var. soisson nain hâtif) seeds to copper (Cu). Cu induced a marked delay in seedling growth, and was associated with biochemical disturbances in terms of intracellular oxidative status, redox regulation and energy metabolism. In response to these alterations, modulation of activities of antioxidant proteins (thioredoxin and glutathione reductase, peroxiredoxin) occurred, thus preventing oxidative damage. In addition, oxidative modification of proteins was detected in both cotyledons and seedlings by one- and two-dimensional electrophoresis. These modified proteins may play roles in redox buffering. The changes in activities of redox proteins underline their fundamental roles in controlling redox homeostasis. However, observed differential redox responses in cotyledon and seedling tissues showed a major capacity of the seedlings' redox systems to protect the reduced status of protein thiols, thus suggesting quantitatively greater antioxidant protection of proteins in seedlings compared to cotyledon. To our knowledge, this is the first comprehensive redox biology investigation of the effect of Cu on seed germination.

Integrated physiological and proteomic analysis reveals underlying response and defense mechanisms of Brachypodium distachyon seedling leaves under osmotic stress, cadmium and their combined stresses

Drought stress, a major abiotic stress, commonly occurs in metal-contaminated environments and affects crop growth and yield. In this study, we performed the first integrated phenotypic, physiological, and proteomic analysis of Brachypodium distachyon L. seedling leaves under polyethylene glycol (PEG) mock osmotic stress, cadmium (Cd²⁺), and their combined stresses. Combined osmotic and Cd²⁺ stress had more significant effects than each individual stress on seedling growth, and the physiological traits and ultrastructures of leaves. Totally 117 differentially accumulated protein (DAP) spots detected by two-dimensional difference gel electrophoresis (2D-DIGE) were identified, and representing 89 unique proteins under individual and combined stresses. These DAPs were involved in photosynthesis/respiration (34%), energy and carbon metabolism (21%), stress/defense/detoxification (13%), protein folding and degradation (12%), and amino acid metabolism (7%). Principal component analysis (PCA) revealed that DAPs from the Cd²⁺ and combined stresses grouped much closer than those from osmotic stress, indicating Cd²⁺ and combined stresses resulted in more changes to the leaf proteome than osmotic stress alone. Protein-protein interaction analyses showed that a 14-3-3 centered sub-network could play important roles in responses to abiotic stresses. An overview pathway of proteome metabolic changes in Bd21 seedling leaves under combined stresses is proposed, representing a synergistic responsive network and underlying response and defense mechanisms.

SIGNIFICANCE

Drought stress is one of the major abiotic stresses, which commonly occurs in metal-contaminated environments, and affects crop growth and yield performance. We performed the first integrated phenotypic, physiological and proteomic analysis of Brachypodium distachyon L. seedling leaves under drought (PEG), cadmium (Cd²⁺) and their combined stresses.

Proteome characterization of copper stress responses in the roots of sorghum

Copper (Cu) is a important micronutrient for plants, but it is extremely toxic to plants at high concentration and can inactivate and disturb protein structures. To explore the Cu stress-induced tolerance mechanism, the present study was conducted on the roots of sorghum seedlings exposed to 50 and 100 µM CuSO₄ for 5 days. Accumulation of Cu increased in roots when the seedlings were treated with the highest concentration of Cu²⁺ ions (100 μM). Elevated Cu concentration provoked notable reduction of Fe, Zn, Ca, and Mn uptake in the roots of sorghum seedlings. In the proteome analysis, high-throughput two-dimensional polyacrylamide gel electrophoresis combined with MALDI-TOF-TOF MS was performed to explore the molecular responses of Cu-induced sorghum seedling roots. In two-dimensional silver-stained gels, 422 protein spots were identified in the 2-D gel whereas twenty-one protein spots (≥1.5-fold) were used to analyze mass spectrometry from Cu-induced sorghum roots. Among the 21 differentially expressed proteins, 10 proteins were increased, while 11 proteins were decreased due to the intake of Cu ions by roots of sorghum. Abundance of most of the identified proteins from the roots that function in stress response and metabolism was remarkably enhanced, while proteins involved in transcription and regulation were severely reduced. Taken together, these results imply insights into a potential molecular mechanism towards Cu stress in C₄ plant, sorghum.

Proteomic analysis on roots of Oenothera glazioviana under copper-stress conditions

Proteomic studies were performed to identify proteins involved in the response of Oenothera glazioviana seedlings under Cu stress. Exposure of 28-d-old seedlings to 50 μM CuSO4 for 3 d led to inhibition of shoot and root growth as well as a considerable increase in the level of lipid peroxidation in the roots. Cu absorbed by O. glazioviana accumulated more easily in the root than in the shoot. Label-free proteomic analysis indicated 58 differentially abundant proteins (DAPs) of the total 3,149 proteins in the roots of O. glazioviana seedlings, of which 36 were upregulated and 22 were downregulated under Cu stress conditions. Gene Ontology analysis showed that most of the identified proteins could be annotated to signal transduction, detoxification, stress defence, carbohydrate, energy, and protein metabolism, development, and oxidoreduction. We also retrieved 13 proteins from the enriched Kyoto Encyclopaedia of Genes and Genomes and the protein-protein interaction databases related to various pathways, including the citric acid (CA) cycle. Application of exogenous CA to O. glazioviana seedlings exposed to Cu alleviated the stress symptoms. Overall, this study provided new insights into the molecular mechanisms of plant response to Cu at the protein level in relation to soil properties.

Responses of Plant Proteins to Heavy Metal Stress-A Review

Plants respond to environmental pollutants such as heavy metal(s) by triggering the expression of genes that encode proteins involved in stress response. Toxic metal ions profoundly affect the cellular protein homeostasis by interfering with the folding process and aggregation of nascent or non-native proteins leading to decreased cell viability. However, plants possess a range of ubiquitous cellular surveillance systems that enable them to efficiently detoxify heavy metals toward enhanced tolerance to metal stress. As proteins constitute the major workhorses of living cells, the chelation of metal ions in cytosol with phytochelatins and metallothioneins followed by compartmentalization of metals in the vacuoles as well as the repair of stress-damaged proteins or removal and degradation of proteins that fail to achieve their native conformations are critical for plant tolerance to heavy metal stress. In this review, we provide a broad overview of recent advances in cellular protein research with regards to heavy metal tolerance in plants. We also discuss how plants maintain functional and healthy proteomes for survival under such capricious surroundings.

iTRAQ and virus-induced gene silencing revealed three proteins involved in cold response in bread wheat

By comparing the differentially accumulated proteins from the derivatives (UC 1110 × PI 610750) in the F₁₀ recombinant inbred line population which differed in cold-tolerance, altogether 223 proteins with significantly altered abundance were identified. The comparison of 10 cold-sensitive descendant lines with 10 cold-tolerant descendant lines identified 140 proteins that showed decreased protein abundance, such as the components of the photosynthesis apparatus and cell-wall metabolism. The identified proteins were classified into the following main groups: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, sulfur metabolism, nitrogen metabolism, RNA metabolism, energy production, cell-wall metabolism, membrane and transportation, and signal transduction. Results of quantitative real-time PCR of 20 differentially accumulated proteins indicated that the transcriptional expression patterns of 10 genes were consistent with their protein expression models. Virus-induced gene silencing of Hsp90, BBI, and REP14 genes indicated that virus-silenced plants subjected to cold stress had more severe drooping and wilting, an increased rate of relative electrolyte leakage, and reduced relative water content compared to viral control plants. Furthermore, ultrastructural changes of virus-silenced plants were destroyed more severely than those of viral control plants. These results indicate that Hsp90, BBI, and REP14 potentially play vital roles in conferring cold tolerance in bread wheat.

Modifications of the soluble proteome of a mediterranean strain of the invasive neurotoxic dinoflagellate Alexandrium catenella under metal stress conditions

The soluble proteome of the mediterranean strain ACT03 of the invasive neurotoxic dinoflagellate Alexandrium catenella exposed to lead or zinc at 6, 12 or 18μM (total concentrations), or under control conditions, was characterized by two-dimensional gel electrophoresis (2-DE). Zinc reduced (P<0.05) the total number of protein spots (-41%, -52% and -60%, at 6, 12 or 18μM, respectively). Besides, most of the proteins constituting the soluble proteome were down-regulated in response to lead or zinc stresses. These proteins were involved mainly in photosynthesis (20-37% for lead; 36-50% for zinc) (ribulose-1,5-bisphosphate carboxylase/oxygenase: RUBISCO; ferredoxin-NADP⁺ reductase: FNR; peridinin-chlorophyll a-protein: PCP), and in the oxidative stress response (29-34% for lead; 17-36% for zinc) (superoxide dismutase: SOD; proteasome α/β subunits). These negative effects could be partly compensated by the up-regulation of specific proteins such as ATP-synthase β subunit (+16.3 fold after exposure to lead at 12μM). Indeed, an increase in the abundance of ATP-synthase could enrich the ATP pool and provide more energy available for the cells to survive under metal stress, and make the ATP-synthase transport of metal cations out of the cells more efficient. Finally, this study shows that exposure to lead or zinc have a harmful effect on the soluble proteome of A. catenella ACT03, but also suggests the existence of an adaptative proteomic response to metal stresses, which could contribute to maintaining the development of this dinoflagellate in trace metal-contaminated ecosystems.

Proteomic profiling of vetiver grass (Chrysopogon zizanioides) under 2,4,6-trinitrotoluene (TNT) stress

Vetiver grass is an ideal plant for 2,4,6-trinitrotoluene (TNT) phytoremediation, due to its ability to tolerate and metabolize TNT as previously reported. The current study is the first attempt to investigate the changes in the proteomic profile of a plant under TNT stress. Vetiver plants were grown in nutrient media with varying concentrations of TNT (0, 25, 50, and 100 mg L^-1) for 10 days. Although the plants appeared healthy, significant biomass reductions (p = 0.0008) were observed in treated plants. Total proteins in the root decreased significantly (p = 0.0003). Proteomic analysis of root proteins revealed the downregulation of functional proteins involved in key cellular mechanisms such as transcription, ribosome biogenesis, nucleo-cytoplasmic transport of proteins, protein glycosylation, and translation. Growth-related proteins were downregulated; plant defense proteins were upregulated at lower TNT concentrations but downregulated at higher concentrations. Comprehensive understanding of changes in the proteomic profile provides important clues to the mechanism of TNT stress response and tolerance in vetiver.

Enhanced bioremediation of lead-contaminated soil by Solanum nigrum L. with Mucor circinelloides

Strain selected from mine tailings in Anshan for Pb bioremediation was characterized at the genetic level by internal transcribed spacer (ITS) sequencing. Results revealed that the strain belongs to Mucor circinelloides. Bioremediation of lead-contaminated soil was conducted using Solanum nigrum L. combined with M. circinelloides. The removal efficacy was in the order microbial/phytoremediation > phytoremediation > microbial remediation > control. The bioremediation rates were 58.6, 47.2, and 40.2% in microbial/phytoremediation, microbial remediation, and phytoremediation groups, respectively. Inoculating soil with M. circinelloides enhanced Pb removal and S. nigrum L. growth. The bioaccumulation factor (BF, 1.43), enrichment factor (EF, 1.56), and translocation factor (TF, 1.35) were higher than unit, suggesting an efficient ability of S. nigrum L. in Pb bioremediation. Soil fertility was increased after bioremediation according to change in enzyme activities. The results indicated that inoculating S. nigrum L. with M. circinelloides enhanced its efficiency for phytoremediation of soil contaminated with Pb.

Bioprospecting of Endophytes for Agricultural and Environmental Sustainability

The term endophytes refers to a group of endosymbionts usually bacterium, fungus or interactive bacterium-fungal species residing asymptomatically and grows within plants for at least a part of their life cycle intra- and intercelullarly in the tissues of higher plants without causing any visible manifestation of disease. The endophytes represent a potential source of novel natural and ecofriendly products for medicinal, agricultural and industrial uses with least adverse effect on the environment.

The enormous biological diversity coupled with their capability to biosynthesize bioactive secondary metabolites has provided the momentum for the researchers working on endophytes. The present review was undertaken to highlight the biotechnological processes and bioprospection of endophytes as potential antimicrobial agents, secondary metabolites, antibiotics, antagonists against disease causing phytopathogens, cytotoxic, anticancer, insecticidal, antioxidant antiviral compounds andisolation and production of bioactive compounds with potent enzymatic activities.

Endophyte enhances biodegradation and hydrolysis processes significantly important against pathogenic infection, biotransformation studies and production of compounds with immense industrial applications. The interaction of the endophytic microbiota with the plants are more protected and can withstand the adverse environmental conditions and contribute to plant growth, productivity, carbon sequestration, enhanced phytoremediation efficiencies and amelioration of metal induced toxicity. The strategies governed by the endophytes for efficient production of novel bioactive phytocompounds was comprehensively discussed.

The review envisaged the biodiversity, transmission of endophytes, plant endophyte interactions for the production of bioactive compounds for therapeutic, environmental and agricultural sustainability.

Physiological and proteomic analysis of selenium-mediated tolerance to Cd stress in cucumber (Cucumis sativus L.)

Selenium can mitigate cadmium toxicity in plants. However, the mechanism of this alleviation has not been fully understood. In the present study, the role of Se in inducing tolerance to Cd stress in cucumber was elucidated. Results showed that Se significantly alleviated Cd-induced growth inhibition, reduced Cd concentration, increased SPAD value and improved photosynthetic performance. Through proteomic analysis by two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry, 26 protein spots were identified, which were significantly influenced by Cd stress and/or Se application. Among these proteins, the abundance of 21 spots (10 in leaves and 11 in roots) were repressed in Cd-treated and up-accumulated or no-changed in Cd+Se-treated cucumber. These altered proteins were involved in the response to stress, metabolism, photosynthesis and storage, they were including glutathione S-transferase F8, heat shock protein STI-like, peroxidase, ascorbate oxidase, fructose-bisphosphate aldolase 2, NiR, Rieske type ion sulfur subunit and PsbP domain-containing protein 6. Furthermore, we identified five proteins with an increase in relative abundance after Cd treatment, they were involved in the functional groups active in response to stress and transport. The present study provided novel insights into Se-mediated tolerance of cucumber seedlings against Cd toxicity at the proteome level.

Proteomic Profiling of the Interactions of Cd/Zn in the Roots of Dwarf Polish Wheat (Triticum polonicum L.)

Cd and Zn have been shown to interact antagonistically or synergistically in various plants. In the present study of dwarf polish wheat (DPW)roots, Cd uptake was inhibited by Zn, and Zn uptake was inhibited by Cd, suggesting that Cd and Zn interact antagonistically in this plant. A study of proteomic changes showed that Cd, Zn, and Cd+Zn stresses altered the expression of 206, 303, and 190 proteins respectively. Among these, 53 proteins were altered significantly in response to all these stresses (Cd, Zn, and Cd+Zn), whereas 58, 131, and 47 proteins were altered in response to individual stresses (Cd, Zn, and Cd+Zn, respectively). Sixty-one differentially expressed proteins (DEPs) were induced in response to both Cd and Zn stresses; 33 proteins were induced in response to both Cd and Cd+Zn stresses; and 57 proteins were induced in response to both Zn and Cd+Zn stresses. These results indicate that Cd and Zn induce differential molecular responses, which result in differing interactions of Cd/Zn. A number of proteins that mainly participate in oxidation-reduction and GSH, SAM, and sucrose metabolisms were induced in response to Cd stress, but not Cd+Zn stress. This result indicates that these proteins participate in Zn inhibition of Cd uptake and ultimately cause Zn detoxification of Cd. Meanwhile, a number of proteins that mainly participate in sucrose and organic acid metabolisms and oxidation-reduction were induced in response to Zn stress but not Cd+Zn stress. This result indicates that these proteins participate in Cd inhibition of Zn uptake and ultimately cause the Cd detoxification of Zn. Other proteins induced in response to Cd, Zn, or Cd+Zn stress, participate in ribosome biogenesis, DNA metabolism, and protein folding/modification and may also participate in the differential defense mechanisms.

Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages

Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages.

Leaf-based physiological, metabolic, and ultrastructural changes in cultivated cotton cultivars under cadmium stress mediated by glutathione

Cadmium (Cd) pollution is present in the world over especially in the industrialized parts of the world. To reduce Cd accumulation in various crops especially food crops, alleviating agents such as reduced glutathione (GSH) can be applied, which are capable either to exclude or to sequester Cd contamination. This study investigated the leaf-based spatial distribution of physiological, metabolic, and microstructural changes in two cotton cultivars (Coker 312 and TM-1) under GSH-mediated Cd stress using single levels of Cd (50 μM) and GSH (50 μM) both separately and in mix along with control. Results showed that GSH revived the morphology and physiology of both cotton cultivars alone or in mix with Cd. Cd uptake was enhanced in all segments of leaf and whole leaf upon the addition of GSH. GSH alleviated Cd-induced reduction in the photosynthetic pigment compositions and chlorophyll a fluorescence parameters. Mean data of biomarkers (2,3,5-triphenyltetrazolium (TTC), total soluble protein (TSP), malondialdehyde (MDA), hydrogen peroxide (H2O2)) revealed the adverse effects of Cd stress on leaf segments of both cultivars, which were revived by GSH. The oxidative metabolism induced by Cd stress was profoundly influenced by exogenous GSH application. The microstructural alterations were mainly confined to chloroplastic regions of leaves under Cd-stressed conditions, which were greatly revived upon the GSH addition. As a whole, Cd stress greatly affected TM-1 as compared to Coker 312. These results suggest a positive role of GSH in alleviating Cd-mediated changes in different leaf sections of cotton cultivars.

Identification of Winter-Responsive Proteins in Bread Wheat Using Proteomics Analysis and Virus-Induced Gene Silencing (VIGS)

Proteomic approaches were applied to identify protein spots involved in cold responses in wheat. By comparing the differentially accumulated proteins from two cultivars (UC1110 and PI 610750) and their derivatives, as well as the F10 recombinant inbred line population differing in cold-tolerance, a total of 20 common protein spots representing 16 unique proteins were successfully identified using 2-DE method. Of these, 14 spots had significantly enhanced abundance in the cold-sensitive parental cultivar UC1110 and its 20 descendant lines when compared with the cold-tolerant parental cultivar PI 610750 and its 20 descendant lines. Six protein spots with reduced abundance were also detected. The identified protein spots are involved in stress/defense, carbohydrate metabolism, protein metabolism, nitrogen metabolism, energy metabolism, and photosynthesis. The 20 differentially expressed protein spots were chosen for quantitative real-time polymerase chain reaction (qRT-PCR) to investigate expression changes at the RNA level. The results indicated that the transcriptional expression patterns of 11 genes were consistent with their protein expression models. Among the three unknown proteins, Spot 20 (PAP6-like) showed high sequence similarities with PAP6. qRT-PCR results implied that cold and salt stresses increased the expression of PAP6-like in wheat leaves. Furthermore, VIGS (virus-induced gene silencing)-treated plants generated for PAP6-like were subjected to freezing stress, these plants had more serious droop and wilt, an increased rate of relative electrolyte leakage, reduced relative water content (RWC) and decreased tocopherol levels when compared with viral control plants. However, the plants that were silenced for the other two unknown proteins had no significant differences in comparison to the BSMV0-inoculated plants under freezing conditions. These results indicate that PAP6-like possibly plays an important role in conferring cold tolerance in wheat.

Proteomic and metabolomic analysis on the toxicological effects of Benzo[a]pyrene in pearl oyster Pinctada martensii

Benzo[a]pyrene (BaP) is one of the typical toxic polycyclic aromatic hydrocarbons (PAHs) that are widely present in marine environment. BaP has diverse toxic effects, including teratogenic, carcinogenic, mutagenic effects and so on, in various organisms. In this work, we focused on the differential proteomic and metabolomic responses in the digestive gland of pearl oyster Pinctada martensii exposed to two doses of BaP (1 and 10μg/L). Metabolic responses revealed that the high dose of BaP (10μg/L) mainly caused disturbances in osmotic regulation and energy metabolism in the digestive gland. Proteomic responses indicated that both doses of BaP induced disturbances in energy metabolism, cytoskeleton, cell injury, oxidative stress and signal transduction based on the differential proteomic biomarkers. Overall, these results demonstrated a number of potential biomarkers that were characterized by an integrated proteomic and metabolomic approach and provided a useful insight into the toxicological effects on pearl oyster P. martensii.

Local adaptation is associated with zinc tolerance in Pseudomonas endophytes of the metal-hyperaccumulator plant Noccaea caerulescens

Metal-hyperaccumulating plants, which are hypothesized to use metals for defence against pests and pathogens, provide a unique context in which to study plant-pathogen coevolution. Previously, we demonstrated that the high concentrations of zinc found in leaves of the hyperaccumulator Noccaea caerulescens provide protection against bacterial pathogens, with a potential trade-off between metal-based and pathogen-induced defences. We speculated that an evolutionary arms race between zinc-based defences in N. caerulescens and zinc tolerance in pathogens might have driven the development of the hyperaccumulation phenotype. Here, we investigate the possibility of local adaptation by bacteria to the zinc-rich environment of N. caerulescens leaves and show that leaves sampled from the contaminated surroundings of a former mine site harboured endophytes with greater zinc tolerance than those within plants of an artificially created hyperaccumulating population. Experimental manipulation of zinc concentrations in plants of this artificial population influenced the zinc tolerance of recovered endophytes. In laboratory experiments, only endophytic bacteria isolated from plants of the natural population were able to grow to high population densities in any N. caerulescens plants. These findings suggest that long-term coexistence with zinc-hyperaccumulating plants leads to local adaptation by endophytic bacteria to the environment within their leaves.

Leaf proteome characterization in the context of physiological and morphological changes in response to copper stress in sorghum

Copper (Cu) is an essential micronutrient required for normal growth and development of plants; however, at elevated concentrations in soil, copper is also generally considered to be one of the most toxic metals to plant cells due to its inhibitory effects against many physiological and biochemical processes. In spite of its potential physiological and economical significance, molecular mechanisms under Cu stress has so far been grossly overlooked in sorghum. To explore the molecular alterations that occur in response to copper stress, the present study was performed in ten-day-old Cu-exposed leaves of sorghum seedlings. The growth characteristics were markedly inhibited, and ionic alterations were prominently observed in the leaves when the seedlings were exposed to different concentrations (0, 100, and 150 µM) of CuSO4. Using two-dimensional gels with silver staining, 643 differentially expressed protein spots (≥1.5-fold) were identified as either significantly increased or reduced in abundance. Of these spots, a total of 24 protein spots (≥1.5-fold) from Cu-exposed sorghum leaves were successfully analyzed by MALDI-TOF-TOF mass spectrometry. Of the 24 differentially expressed proteins from Cu-exposed sorghum leaves, 13 proteins were up-regulated, and 11 proteins were down-regulated. The abundance of most identified protein species, which function in carbohydrate metabolism, stress defense and protein translation, was significantly enhanced, while that of another protein species involved in energy metabolism, photosynthesis and growth and development were severely reduced. The resulting differences in protein expression patterns together with related morpho-physiological processes suggested that these results could help to elucidate plant adaptation to Cu stress and provide insights into the molecular mechanisms of Cu responses in C4 plants.

Toxicity of heavy metals and metal-containing nanoparticles on plants

Plants are under the continual threat of changing climatic conditions that are associated with various types of abiotic stresses. In particular, heavy metal contamination is a major environmental concern that restricts plant growth. Plants absorb heavy metals along with essential elements from the soil and have evolved different strategies to cope with the accumulation of heavy metals. The use of proteomic techniques is an effective approach to investigate and identify the biological mechanisms and pathways affected by heavy metals and metal-containing nanoparticles. The present review focuses on recent advances and summarizes the results from proteomic studies aimed at understanding the response mechanisms of plants under heavy metal and metal-containing nanoparticle stress. Transport of heavy metal ions is regulated through the cell wall and plasma membrane and then sequestered in the vacuole. In addition, the role of different metal chelators involved in the detoxification and sequestration of heavy metals is critically reviewed, and changes in protein profiles of plants exposed to metal-containing nanoparticles are discussed in detail. Finally, strategies for gaining new insights into plant tolerance mechanisms to heavy metal and metal-containing nanoparticle stress are presented. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Heavy Metal Tolerance in Plants: Role of Transcriptomics, Proteomics, Metabolomics, and Ionomics

Heavy metal contamination of soil and water causing toxicity/stress has become one important constraint to crop productivity and quality. This situation has further worsened by the increasing population growth and inherent food demand. It has been reported in several studies that counterbalancing toxicity due to heavy metal requires complex mechanisms at molecular, biochemical, physiological, cellular, tissue, and whole plant level, which might manifest in terms of improved crop productivity. Recent advances in various disciplines of biological sciences such as metabolomics, transcriptomics, proteomics, etc., have assisted in the characterization of metabolites, transcription factors, and stress-inducible proteins involved in heavy metal tolerance, which in turn can be utilized for generating heavy metal-tolerant crops. This review summarizes various tolerance strategies of plants under heavy metal toxicity covering the role of metabolites (metabolomics), trace elements (ionomics), transcription factors (transcriptomics), various stress-inducible proteins (proteomics) as well as the role of plant hormones. We also provide a glance of some strategies adopted by metal-accumulating plants, also known as "metallophytes."

Proteomic analysis of chromium stress and sulfur deficiency responses in leaves of two canola (Brassica napus L.) cultivars differing in Cr(VI) tolerance

Sulfur (S) is an essential macronutrient for plant growth and development, and it plays an essential role in response to environmental stresses. Plants suffer with combined stress of S deficiency and hexavalent chromium [Cr(VI)] in the rhizosphere. Little is known about the impact of S deficiency on leaf metabolism of canola (Brassica napus L.) under Cr(VI) stress. Therefore, this study is the first to examine the effects of Cr(VI) stress and S deficiency in canola at a molecular level. A comparative proteomic approach was used to investigate the differences in protein abundance between Cr-tolerant NK Petrol and Cr-sensitive Sary cultivars. The germinated seeds were grown hydroponically in S-sufficient (+S) nutrient solution for 7 days and then subjected to S-deficiency (-S) for 7 days. S-deficient and +S seedlings were then exposed to 100μM Cr(VI) for 3 days. Protein patterns analyzed by two-dimensional electrophoresis (2-DE) revealed that 58 protein spots were differentially regulated by Cr(VI) stress (+S/+Cr), S-deficiency (-S/-Cr) and combined stress (-S/+Cr). Of these, 39 protein spots were identified by MALDI-TOF/TOF mass spectrometry. Differentially regulated proteins predominantly had functions not only in photosynthesis, but also in energy metabolism, stress defense, protein folding and stabilization, signal transduction, redox regulation and sulfur metabolism. Six stress defense related proteins including 2-Cys peroxiredoxin BAS1, glutathione S-transferase, ferritin-1, l-ascorbate peroxidase, thiazole biosynthetic enzyme and myrosinase-binding protein-like At3g16470 exhibited a greater increase in NK Petrol. The stress-related proteins play an important role in the detoxification of Cr(VI) and maintaining cellular homeostasis under variable S nutrition.

An integrated proteomic and metabolomic study on the gender-specific responses of mussels Mytilus galloprovincialis to tetrabromobisphenol A (TBBPA)

Tetrabromobisphenol A (TBBPA), accounting for the largest production of brominated flame-retardants (BFRs) along the Laizhou Bay in China, is of great concern due to its diverse toxicities. In this study, we focused on the gender-specific responses of TBBPA in mussel Mytilus galloprovincialis using an integrated proteomic and metabolomic approach. After exposure of TBBPA (10 µg L(-1)) for one month, a total of 9 metabolites and 67 proteins were altered in mussel gills from exposed group. The significant changes of metabolites in female mussel gills from exposed group exhibited the disturbances in energy metabolism and osmotic regulation, while in male samples only be found the variation of metabolites related to osmotic regulation. iTRAQ-based proteomic analysis showed biological differences between male and female mussel gills from solvent control group. The higher levels of proteins related to primary and energy metabolism and defense mechanisms in male mussel gills meant a greater anti-stress capability of male mussels. Further analysis revealed that TBBPA exposure affected multiple biological processes consisting of production and development, material and energy metabolism, signal transduction, gene expression, defense mechanisms and apoptosis in both male and female mussels with different mechanisms. Specially, the responsive proteins of TBBPA in male mussels signified higher tolerance limits than those in female individuals, which was consistent with the biological differences between male and female mussel gills from solvent control group. This work suggested that the gender differences should be considered in ecotoxicology.

Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO₃)₂ at 500 mg L^-1(Pb500) and 1000 mg L^-1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included "cell wall," "apoplast," "response to metal ion," "vacuole," and "peroxidase activity," and the critical enriched pathways were involved in "citric acid (TCA) cycle and respiratory electron transport," "pyruvate metabolism," "phenylalanine metabolism," "phenylpropanoid biosynthesis," and "carbon metabolism." Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)-glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.

Transcriptome Analysis of Cadmium-Treated Roots in Maize (Zea mays L.)

Cadmium (Cd) is a heavy metal and is highly toxic to all plant species. However, the underlying molecular mechanism controlling the effects of auxin on the Cd stress response in maize is largely unknown. In this study, the transcriptome produced by maize 'Zheng 58' root responses to Cd stress was sequenced using Illumina sequencing technology. In our study, six RNA-seq libraries yielded a total of 244 million clean short reads and 30.37 Gb of sequence data. A total of 6342 differentially expressed genes (DEGs) were grouped into 908 Gene Ontology (GO) categories and 198 Kyoto Encyclopedia of Genes and Genomes terms. GO term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Comparison of the transcript abundances for auxin biosynthesis, transport, and downstream response genes revealed a universal expression response under Cd treatment. Furthermore, our data showed that free indole-3-acetic acid (IAA) levels were significantly reduced; but IAA oxidase activity was up-regulated after Cd treatment in maize roots. The analysis of Cd activity in maize roots under different Cd and auxin conditions confirmed that auxin affected Cd accumulation in maize seedlings. These results will improve our understanding of the complex molecular mechanisms underlying the response to Cd stress in maize roots.

RNA-Seq Analysis of Rice Roots Reveals the Involvement of Post-Transcriptional Regulation in Response to Cadmium Stress

Widely-spread cadmium (Cd) pollution in the soil threatens both crop production and human health. How plants deal with the excess Cd are largely unknown. To evaluate the molecular mechanism by which plants respond to Cd stress, rice seedlings were treated with two concentrations of Cd and subjected to deep RNA sequencing. Comprehensive RNA-Seq analysis of rice roots under two gradients of Cd treatment revealed 1169 Cd toxicity-responsive genes. These genes were involved in the reactive oxygen species scavenging system, stress response, cell wall formation, ion transport, and signal transduction. Nine out of 93 predicted long non-coding RNAs (lncRNAs) were detected as Cd-responsive lncRNAs due to their high correlation with the Cd stress response. In addition, we analyzed alternative splicing (AS) events under different Cd concentrations. Four hundred and seventy-six differential alternatively spliced genes with 542 aberrant splicing events were identified. GO analysis indicated that these genes were highly enriched in oxidation reduction and cellular response to chemical stimulus. Real-time qRT-PCR validation analysis strengthened the reliability of our RNA-Seq results. The results suggest that post-transcriptional AS regulation may also be involved in plant responses to high Cd stress.

Transcriptome-wide analysis of chromium-stress responsive microRNAs to explore miRNA-mediated regulatory networks in radish (Raphanus sativus L.)

MicroRNAs (miRNAs) are small noncoding RNAs that play pivotal roles in plant growth, development and stress response. Chromium (Cr) is one of common environmental contaminants possessing potential health hazards to living organisms. To date, little is known about the regulatory roles of miRNAs in response to Cr stress in radish. To systematically identify Cr-responsive miRNAs and their targets in radish, two sRNA libraries derived from Cr-free (CK) and Cr-treated (Cr200) roots were constructed. With Solexa sequencing, 81 known and 72 novel miRNAs were identified, from which 54 known and 16 novel miRNAs were significantly differentially expressed under Cr stress. Several target genes for Cr-responsive miRNAs encode different transcription factor (TF) families, including SPLs, MYBs, ERFs and bZIPs, might regulate corresponding HM-related transcriptional processes in plants. Notably, a few key responsive enzymes or proteins, including HMA, YSL1 and ABC transporter protein were involved in Cr uptake and homeostasis process. Furthermore, the expression patterns of some Cr-responsive miRNAs and their targets were validated by RT-qPCR. This study represents the first characterization of Cr-responsive miRNAs and their targets in radish. The outcomes of this study could provide novel insights into miRNA-mediated regulatory mechanisms underlying plant response to Cr stress in root vegetable crops.

Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective

Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

Effect of short-term cadmium stress on Populus nigra L. detached leaves

Pollution by toxic metals, accumulating into soils as result of human activities, is a worldwide major concern in industrial countries. Plants exhibit different degrees of tolerance to heavy metals, as a consequence of their ability to exclude or accumulate them in particular tissues, organs or sub-cellular compartments. Molecular information about cellular processes affected by heavy metals is still largely incomplete. As a fast-growing, highly tolerant perennial plant species, poplar has become a model for environmental stress response investigations. To study the short-term effects of cadmium accumulation in leaves, we analyzed photosystem II (PSII) quantum yield, hydrogen peroxide (H2O2) generation, hormone levels variation, as well as proteome profile alteration of 50μM CdSO4 vacuum-infiltrated poplar (Populus nigra L.) detached leaves. Cadmium management brought about an early and sustained production of hydrogen peroxide, an increase of abscisic acid, ethylene and gibberellins content, as well as a decrease in cytokinins and auxin levels, whereas photosynthetic electron transport was unaffected. Proteomic analysis revealed that twenty-one proteins were differentially induced in cadmium-treated leaves. Identification of fifteen polypeptides allowed to ascertain that most of them were involved in stress response while the remaining ones were involved in photosynthetic carbon metabolism and energy production.

Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress

To explore the molecular basis of Sb tolerance mechanism in plant, a comparative proteomic analysis of both roots and leaves in Miscanthus sinensis has been conducted in combination with physiological and biochemical analyses. M. sinensis seedlings were exposed to different doses of Sb, and both roots and leaves were collected after 3 days of treatment. Two-dimensional gel electrophoresis (2-DE) and image analyses found that 29 protein spots showed 1.5-fold change in abundance in leaves and 19 spots in roots, of which 31 were identified by MALDI-TOF-MS and MALDI-TOF-TOF-MS. Proteins involved in antioxidant defense and stress response generally increased their expression all over the Sb treatments. In addition, proteins relative to transcription, signal transduction, energy metabolism and cell division and cell structure showed a variable expression pattern over Sb concentrations. Overall these findings provide new insights into the probable survival mechanisms by which M. sinensis could be adapting to Sb phytotoxicity.

Regulation of Cadmium-Induced Proteomic and Metabolic Changes by 5-Aminolevulinic Acid in Leaves of Brassica napus L

It is evident from previous reports that 5-aminolevulinic acid (ALA), like other known plant growth regulators, is effective in countering the injurious effects of heavy metal-stress in oilseed rape (Brassica napus L.). The present study was carried out to explore the capability of ALA to improve cadmium (Cd²⁺) tolerance in B. napus through physiological, molecular, and proteomic analytical approaches. Results showed that application of ALA helped the plants to adjust Cd²⁺-induced metabolic and photosynthetic fluorescence changes in the leaves of B. napus under Cd²⁺ stress. The data revealed that ALA treatment enhanced the gene expressions of antioxidant enzyme activities substantially and could increase the expression to a certain degree under Cd²⁺ stress conditions. In the present study, 34 protein spots were identified that differentially regulated due to Cd²⁺ and/or ALA treatments. Among them, 18 proteins were significantly regulated by ALA, including the proteins associated with stress related, carbohydrate metabolism, catalysis, dehydration of damaged protein, CO2 assimilation/photosynthesis and protein synthesis/regulation. From these 18 ALA-regulated proteins, 12 proteins were significantly down-regulated and 6 proteins were up-regulated. Interestingly, it was observed that ALA-induced the up-regulation of dihydrolipoyl dehydrogenase, light harvesting complex photo-system II subunit 6 and 30S ribosomal proteins in the presence of Cd²⁺ stress. In addition, it was also observed that ALA-induced the down-regulation in thioredoxin-like protein, 2, 3-bisphosphoglycerate, proteasome and thiamine thiazole synthase proteins under Cd²⁺ stress. Taken together, the present study sheds light on molecular mechanisms involved in ALA-induced Cd²⁺ tolerance in B. napus leaves and suggests a more active involvement of ALA in plant physiological processes than previously proposed.

Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms

In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.

Ultrastructural, metabolic and proteomic changes in leaves of upland cotton in response to cadmium stress

Present study explores physiological, biochemical and proteomic changes in leaves of upland cotton (ZMS-49) using 500 μM cadmium (Cd) along with control. Leaves' biomass and chlorophyll pigments decreased at 500 μM Cd. Cd contents in roots were higher than leaves. Levels of ROS ( [Formula: see text] and H2O2) both in vivo and in vitro and MDA contents were significantly increased. Chlorophyll parameters (F0, Fm, Fm(') and Fv/Fm), total soluble protein contents and APX showed a decline at 500 μM Cd. SOD, CAT and POD and GR activities significantly enhanced. Less ultrastructural alterations in leaves under Cd stress could be observed. Scanning micrographs at 500 μM Cd possessed less number of stomata as well as near absence of closed stomata. Cd could be located in cell wall, vacuoles and intracellular spaces. Important upregulated proteins were methionine synthase, ribulose 1,5-bisphosphate carboxylase, apoplastic anionic guaiacol peroxidase, glyceraldehydes-3-phosphate dehydrogenase (chloroplastic isoform) and ATP synthase D chain, (mitochondrial). Important downregulated proteins were seed storage proteins (vicilin and legumin), molecular chaperones (hsp70, chaperonin-60 alpha subunit; putative protein disulfide isomerase), ATP-dependent Clp protease, ribulose-1,5-bisphophate carboxylase/oxygenase large subunit. Increase in the activities of ROS-scavenging enzymes, less ultrastructural modification, Cd-deposition in dead parts of cells as well as active regulation of different proteins showed Cd-resistant nature of ZMS-49.

iTRAQ-based quantitative proteomic analyses on the gender-specific responses in mussel Mytilus galloprovincialis to tetrabromobisphenol A

Tetrabromobisphenol A (TBBPA) accounts for the largest production of brominated flame-retardants (BFRs) along the Laizhou Bay in China and is the most widely used BFR in industrial products. It can induce diverse toxicities including hepatotoxicity, nephrotoxicity, neurotoxicity and endocrine disrupting effects in mammalian and fish models. In this work, we applied iTRAQ-based proteomics to investigate the gender-specific responses in mussel Mytilus galloprovincialis to TBBPA. Thirty-one proteins were differentially expressed in hepatopancreas between male and female mussels, which clearly indicated the biological differences between male and female mussels at the protein level. After exposure of TBBPA (18.4 nmol/L) for one month, a total of 60 proteins were differentially expressed in response to the TBBPA treatment in mussel hepatopancreas, among which 33 and 29 proteins were significantly altered in TBBPA-treated male and female mussel samples, respectively. Only two of the 60 proteins were commonly altered in both male and female mussel samples exposed to TBBPA. Based on KEGG analysis, these differentially expressed proteins of TBBPA-induced effects were assigned to several groups, including cytoskeleton, reproduction and development, metabolism, signal transduction, gene expression, stress response and apoptosis. Overall, results indicated that TBBPA exposure could induce apoptosis, oxidative and immune stresses and disruption in energy, protein and lipid metabolisms in both male and female mussels with different mechanisms. This work suggested that the gender differences should be considered in ecotoxicoproteomics.

Comparative proteomic analysis of two tobacco (Nicotiana tabacum) genotypes differing in Cd tolerance

Tobacco can easily accumulate cadmium (Cd) in leaves and thus poses a potential threat to human health. Cd-stress-hydroponic-experiments were performed, and the proteomic and transcriptional features of two contrasting tobacco genotypes Yun-yan2 (Cd-tolerant) and Guiyan1 (Cd-sensitive) were compared. We identified 18 Cd-tolerance-associated proteins in leaves, using 2-dimensional gel electrophoresis coupled with mass spectrometry, whose expression were significantly induced in Yunyan2 leaves but down-regulated/unchanged in Guiyan1, or unchanged in Yunyan2 but down-regulated in Guiyan1 under 50 µM Cd stress. They are including epoxide hydrolase, enoyl-acyl-carrier-protein reductase, NPALDP1, chlorophyll a-b binding protein 25, heat shock protein 70 and 14-3-3 proteins. They categorized as 8 groups of their functions: metabolism, photosynthesis, stress response, signal transduction, protein synthesis, protein processing, transport and cell structure. Furthermore, the expression patterns of three Cd-responsive proteins were validated by quantitative real-time PCR. Our findings provide an insight into proteomic basis for Cd-detoxification in tobacco which offers molecular resource for Cd-tolerance.

Proteomic analysis of eucalyptus leaves unveils putative mechanisms involved in the plant response to a real condition of soil contamination by multiple heavy metals in the presence or absence of mycorrhizal/rhizobacterial additives

Here we report on the growth, accumulation performances of, and leaf proteomic changes in Eucalyptus camaldulensis plants harvested for different periods of time in an industrial, heavy metals (HMs)-contaminated site in the presence or absence of soil microorganism (AMs/PGPRs) additives. Data were compared to those of control counterparts grown in a neighboring nonpolluted district. Plants harvested in the contaminated areas grew well and accumulated HMs in their leaves. The addition of AMs/PGPRs to the polluted soil determined plant growth and metal accumulation performances that surpassed those observed in the control. Comparative proteomics suggested molecular mechanisms underlying plant adaptation to the HMs challenge. Similarly to what was observed in laboratory-scale investigations on other metal hyperaccumulators but not on HMs-sensitive plants, eucalyptus grown in the contaminated areas showed an over-representation of enzymes involved in photosynthesis and the Calvin cycle. AMs/PGPRs addition to the soil increased the activation of these energetic pathways, suggesting the existence of signaling mechanisms that address the energy/reductive power requirement associated with augmented growth performances. HMs-exposed plants presented an over-representation of antioxidant enzymes, chaperones, and proteins involved in glutathione metabolism. While some antioxidant enzymes/chaperones returned to almost normal expression values in the presence of AMs/PGPRs or in plants exposed to HMs for prolonged periods, proteins guaranteeing elevated glutathione levels were constantly over-represented. These data suggest that glutathione (and related phytochelatins) could act as key molecules for ensuring the effective formation of HMs-chelating complexes that are possibly responsible for the observed plant tolerance to metal stresses. Overall, these results suggest potential genetic traits for further selection of phytoremediating plants based on dedicated cloning or breeding programs.

Physiological and proteomic alterations in rice (Oryza sativa L.) seedlings under hexavalent chromium stress

Rice plants employ two strategies to cope with Cr toxicity: immobilizing Cr ions into cell walls to reduce its translocation and activating antioxidant defense to mitigate Cr-induced oxidative stress. The investigation aimed at understanding the physiological and proteomic responses of rice seedlings to hexavalent chromium (Cr(6+)) stress was conducted using two rice genotypes, which differ in Cr tolerance and accumulation. Cr toxicity (200 µM) heavily increased the accumulation of H2O2 and [Formula: see text], enhanced lipid peroxidation, decreased cell viability and consequently inhibited rice plant growth. Proteomic analyses suggest that the response of rice proteome to Cr stress is genotype- and Cr dosage-dependent and tissue specific. Sixty-four proteins, which show more than fourfold difference under either two Cr levels, have been successfully identified. They are involved in a range of cellular processes, including cell wall synthesis, energy production, primary metabolism, electron transport and detoxification. Two proteins related to cell wall structure, NAD-dependent epimerase/dehydratase and reversibly glycosylated polypeptide were greatly up-regulated by Cr stress. Their enhancements coupled with callose accumulation by Cr suggest that cell wall is an important barrier for rice plants to resist Cr stress. Some enzymes involved in antioxidant defense, such as ferredoxin-NADP reductase, NADP-isocitrate dehydrogenase, glyoxalase I (Gly I) and glutamine synthetase 1 (GS1) have also been identified in response to Cr stress. However, they were only detected in Cr-tolerant genotype, indicating the genotypic difference in the capacity of activating the defense system to fight against Cr-induced oxidative stress. Overall, two strategies in coping with Cr stress in rice plants can be hypothesized: (i) immobilizing Cr ions into cell walls to reduce its translocation and (ii) activating antioxidant defense to mitigate Cr-induced oxidative stress.

Differential cadmium and zinc distribution in relation to their physiological impact in the leaves of the accumulating Zygophyllum fabago L

Cadmium and zinc share many similar physiochemical properties, but their compartmentation, complexation and impact on other mineral element distribution in plant tissues may drastically differ. In this study, we address the impact of 10 μm Cd or 50 μm Zn treatments on ion distribution in leaves of a metallicolous population of the non-hyperaccumulating species Zygophyllum fabago at tissue and cell level, and the consequences on the plant response through a combined physiological, proteomic and metabolite approach. Micro-proton-induced X-ray emission and laser ablation inductively coupled mass spectrometry analyses indicated hot spots of Cd concentrations in the vicinity of vascular bundles in response to Cd treatment, essentially bound to S-containing compounds as revealed by extended X-ray absorption fine structure and non-protein thiol compounds analyses. A preferential accumulation of Zn occurred in vascular bundle and spongy mesophyll in response to Zn treatment, and was mainly bound to O/N-ligands. Leaf proteomics and physiological status evidenced a protection of photosynthetically active tissues and the maintenance of cell turgor through specific distribution and complexation of toxic ions, reallocation of some essential elements, synthesis of proteins involved in photosynthetic apparatus or C-metabolism, and metabolite synthesis with some specificities regarding the considered heavy metal treatment.

Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions

This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed.

BIOLOGICAL SIGNIFICANCE

This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.

Physiological and proteomic responses of different willow clones (Salix fragilis x alba) exposed to dredged sediment contaminated by heavy metals

High biomass producing species are considered as tools for remediation of contaminated soils. Willows (Salix spp.) are prominent study subjects in this regard. In this study, different willow clones (Salix fragilis x alba) were planted on heavy-metal polluted dredging sludge. A first objective was assessment of the biomass production for these clones. Using a Gupta statistic, four clones were identified as high biomass producers (HBP). For comparison, a group of four clones with lowest biomass production were selected (LBP). A second objective was to compare metal uptake as well as the physiological and proteomic responses of these two groups. All these complementary data's allow us to have a better picture of the health of the clones that would be used in phytoremediation programs. Cd, Zn, and Ni total uptake was higher in the HBPs but Pb total uptake was higher in LBPs. Our proteomic and physiological results showed that the LBPs were able to maintain cellular activity as much as the HBPs although the oxidative stress response was more pronounced in the LBPs. This could be due to the high Pb content found in this group although a combined effect of the other metals cannot be excluded.

Effect of salinity and calcium on tomato fruit proteome

Salinity is a major abiotic stress that adversely affects plant growth and productivity. The physiology of the tomato in salty and nonsalty conditions has been extensively studied, providing an invaluable base to understand the responses of the plants to cultural practices. However few data are yet available at the proteomic level looking for the physiological basis of fruit development, under salt stress. Here, we report the effects of salinity and calcium on fruit proteome variations of two tomato genotypes (Cervil and Levovil). Tomato plants were irrigated with a control solution (3 dSm(-1)) or with saline solutions (Na or Ca+Na at 7.6 dSm(-1)). Tomato fruits were harvested at two ripening stages: green (14 days post-anthesis) and red ripe. Total proteins were extracted from pericarp tissue and separated by two-dimensional gel electrophoresis. Among the 600 protein spots reproducibly detected, 53 spots exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. Most of the identified proteins were involved in carbon and energy metabolism, salt stress, oxidative stress, and proteins associated with ripening process. Overall, there was a large variation on proteins abundance between the two genotypes that can be correlated to salt treatment or/and fruit ripening stage. The results showed a protective effect of calcium that limited the impact of salinization on metabolism, ripening process, and induced plant salt tolerance. Collectively, this work has improved our knowledge about salt and calcium effect on tomato fruit proteome.

Managing heavy metal toxicity stress in plants: biological and biotechnological tools

The maintenance of ion homeostasis in plant cells is a fundamental physiological requirement for sustainable plant growth, development and production. Plants exposed to high concentrations of heavy metals must respond in order to avoid the deleterious effects of heavy metal toxicity at the structural, physiological and molecular levels. Plant strategies for coping with heavy metal toxicity are genotype-specific and, at least to some extent, modulated by environmental conditions. There is considerable interest in the mechanisms underpinning plant metal tolerance, a complex process that enables plants to survive metal ion stress and adapt to maintain growth and development without exhibiting symptoms of toxicity. This review briefly summarizes some recent cell biological, molecular and proteomic findings concerning the responses of plant roots to heavy metal ions in the rhizosphere, metal ion-induced reactions at the cell wall-plasma membrane interface, and various aspects of heavy metal ion uptake and transport in plants via membrane transporters. The molecular and genetic approaches that are discussed are analyzed in the context of their potential practical applications in biotechnological approaches for engineering increased heavy metal tolerance in crops and other useful plants.

Differential physiological, ultramorphological and metabolic responses of cotton cultivars under cadmium stress

Cadmium (Cd) stress may cause serious physiological, ultramorphological and biochemical anomalies in plants. Cd-induced physiological, subcellular and metabolic alterations in two transgenic cotton cultivars (BR001, GK30) and their parent line (Coker 312) were evaluated using 10, 100 and 1000 µM Cd. Germination, fresh biomass of roots, stems and leaves were significantly inhibited at 1000 µM Cd. Root volume tolerance index significantly increased (124.16%) in Coker 312 at 1000 µM Cd. In non-Cd stressed conditions, electron micrographs showed well-configured root meristem and leaf mesophyll cells. At 1000 µM Cd, greater ultramorphological alterations were observed in BR001 followed by GK30 and Coker 312. These changes were observed in nucleus, vacuoles, mitochondria and chloroplast. Dense precipitates, probably Cd, were seen in vacuoles, which were also attached to the cell walls. A considerable increase in number of nuclei, vacuoles, starch granules and plastoglobuli was observed in the electron micrographs of both roots and leaves at 1000 µM Cd. MDA contents were higher in roots of BR001 at 1000 µM Cd. Mean values of SOD activity in leaves of both BR001 and GK30 at 1000 µM Cd significantly increased as compared to the controls. POD activity in roots of BR001 and Coker 312 was greater at all Cd (10, 100, 1000 µM) levels over the control. Regarding APX, highest percent increase (71.64%) in roots of GK30 at 1000 µM Cd was found. Non-significant differences in CAT activity were observed at all levels of Cd stress in leaves of BR001 and GK30. Both transgenic cotton cultivars and their parental line invariably responded towards Cd stress. However, Coker 312 showed Cd-resistant behavior as compared to its progeny lines (BR001 and GK30).

Proteomic analysis of leaves and roots of common wheat (Triticum aestivum L.) under copper-stress conditions

Proteomic studies were performed to identify the protein species involved in copper (Cu) stress responses in common wheat. Two-week-old wheat seedlings were exposed to 100 μM CuSO4 treatment for 3 days. Growth of shoots and roots was markedly inhibited and lipid peroxidation was greatly increased. Cu was readily absorbed by wheat seedlings, with greater Cu contents in roots than in leaves. Using 2-DE method, 98 protein spots showed significantly enhanced or reduced abundance, of which 93 were successfully identified. Of these identified protein species, 49 and 44 were found in roots and leaves, respectively. Abundance of most of identified protein species, which function in signal transduction, stress defense, and energy production, was significantly enhanced, while that of many protein species involved in carbohydrate metabolism, protein metabolism, and photosynthesis was severely reduced. The Cu-responsive protein interaction network revealed 36 key proteins, most of which may be regulated by abscisic acid (ABA), ethylene, jasmonic acid (JA), and so on. Exogenous JA application showed a protective effect against Cu stress and significantly increased transcripts of the glutathione S-transferase (GST) gene. This study provides insight into the molecular mechanisms of Cu responses in higher plants.

Comparative proteomic analysis of rice shoots exposed to high arsenate

Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice (Oryza sativa "Nipponbare"), as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 µM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.