The Phosphoproteomic Response of Rice Seedlings to Cadmium Stress

Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses

Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.

Heavy metal stress and mitogen activated kinase transcription factors in plants: Exploring heavy metal-ROS influences on plant signalling pathways

Due to their stationary nature, plants are exposed to a diverse range of biotic and abiotic stresses, of which heavy metal (HM) stress poses one of the most detrimental abiotic stresses, targeting diverse plant processes. HMs instigate the overproduction of reactive oxygen species (ROS), and to mitigate the adverse effects of ROS, plants induce multiple defence mechanisms. Besides the negative implications of overproduction of ROS, these molecules play a multitude of signalling roles in plants, acting as a central player in the complex signalling network of cells. One of the ROS-associated signalling mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signalling pathway which transduces extracellular stimuli into intracellular responses. Plant MAPKs have been implicated in signalling involved in stress response, phytohormone regulation, and cell cycle cues. However, the influence of various HMs on MAPK activation has not been well documented. In this review, we address and summarise several aspects related to various HM-induced ROS signalling. Additionally, we touch on how these signals activate the MAPK cascade and the downstream transcription factors that influence plant responses to HMs. Moreover, we propose a workflow that could characterise genes associated with MAPKs and their roles during plant HM stress responses.

Auxin is involved in cadmium accumulation in rice through controlling nitric oxide production and the ability of cell walls to bind cadmium

Although auxin has been linked to plants' responses to cadmium (Cd) stress, the exact mechanism is yet elusive. The objective of the current investigation was to determine the role and the mechanism of auxin in controlling rice's Cd accumulation. Rice roots with Cd stress have higher endogenous auxin levels, and exogenous auxin combined Cd treatment could reduce root cell wall's hemicellulose content when compared with Cd treatment alone, which in turn reduced its fixation of Cd, as well as decreased the expression of OsCd1 (a major facilitator superfamily gene), OsNRAMP1/5 (Natural Resistance-Associated Macrophage Protein 1/5), OsZIP5/9 (Zinc Transporter 5/9), and OsHMA2 (Heavy Metal ATPase 2) that participated in Cd uptake and root to shoot translocation. Furthermore, less Cd accumulated in the shoots as a result of auxin's impact in increasing the expression of OsCAL1 (Cadmium accumulation in Leaf 1), OsABCG36/OsPDR9 (G-type ATP-binding cassette transporter/Pleiotropic drug resistance 9), and OsHMA3, which were in charge of Cd efflux and sequestering into vacuoles, respectively. Additionally, auxin decreased endogenous nitric oxide (NO) levels and antioxidant enzyme activity, while treatment of a NO scavenger-cPTIO-reduced auxin's alleviatory effects. In conclusion, the rice's ability to tolerate Cd toxicity was likely increased by the auxin-accelerated cell wall Cd exclusion mechanism, a pathway that controlled by the buildup of NO.

Cadmium tolerance and hyperaccumulation in plants - A proteomic perspective of phytoremediation

Cadmium (Cd) is a major environmental pollutant and poses a risk of transfer into the food chain through contaminated plants. Mechanisms underlying Cd tolerance and hyperaccumulation in plants are not fully understood. Proteomics-based approaches facilitate an in-depth understanding of plant responses to Cd stress at the systemic level by identifying Cd-inducible differentially abundant proteins (DAPs). In this review, we summarize studies related to proteomic changes associated with Cd-tolerance mechanisms in Cd-tolerant crops and Cd-hyperaccumulating plants, especially the similarities and differences across plant species. The enhanced DAPs identified through proteomic studies can be potential targets for developing Cd-hyperaccumulators to remediate Cd-contaminated environments and Cd-tolerant crops with low Cd content in the edible organs. This is of great significance for ensuring the food security of an exponentially growing global population. Finally, we discuss the methodological drawbacks in current proteomic studies and propose that better protocols and advanced techniques should be utilized to further strengthen the reliability and applicability of future Cd-stress-related studies in plants. This review provides insights into the improvement of phytoremediation efficiency and an in-depth study of the molecular mechanisms of Cd enrichment in plants.

Proteome and phosphoproteome analysis of 2,4-epibrassinolide-mediated cold stress response in cucumber seedlings

The 2, 4-epibrassinolide (EBR) significantly increased plants cold tolerance. However, mechanisms of EBR in regulating cold tolerance in phosphoproteome and proteome levels have not been reported. The mechanism of EBR regulating cold response in cucumber was studied by multiple omics analysis. In this study, phosphoproteome analysis showed that cucumber responded to cold stress through multi-site serine phosphorylation, while EBR further upregulated single-site phosphorylation for most of cold-responsive phosphoproteins. Association analysis of the proteome and phosphoproteome revealed that EBR reprogrammed proteins in response to cold stress by negatively regulating protein phosphorylation and protein content, and phosphorylation negatively regulated protein content in cucumber. Further functional enrichment analysis of proteome and phosphoproteome showed that cucumber mainly upregulated phosphoproteins related to spliceosome, nucleotide binding and photosynthetic pathways in response to cold stress. However, different from the EBR regulation in omics level, hypergeometric analysis showed that EBR further upregulated 16 cold-up-responsive phosphoproteins participated photosynthetic and nucleotide binding pathways in response to cold stress, suggested their important function in cold tolerance. Analysis of cold-responsive transcription factors (TFs) by correlation between proteome and phosphoproteome showed that cucumber regulated eight class TFs may through protein phosphorylation under cold stress. Further combined with cold-related transcriptome found that cucumber phosphorylated eight class TFs, and mainly through targeting major hormone signal genes by bZIP TFs in response to cold stress, while EBR further increased these bZIP TFs (CsABI5.2 and CsABI5.5) phosphorylation level. In conclusion, the EBR mediated schematic of molecule response mechanisms in cucumber under cold stress was proposed.

New insights into cadmium tolerance and accumulation in tomato: Dissecting root and shoot responses using cross-genotype grafting

Cadmium (Cd) is one of the most threatening soil and water contaminants in agricultural settings. In previous studies, we observed that Cd affects the metabolism and physiology of tomato (Solanum lycopersicum) plants even after short-term exposure. The objective of this research was to use cross-genotype grafting to distinguish between root- and shoot-mediated responses of tomato genotypes with contrasting Cd tolerance at the early stages of Cd exposure. This study provides the first report of organ-specific contributions in two tomato genotypes with contrasting Cd tolerance: Solanum lycopersicum cv. Calabash Rouge and Solanum lycopersicum cv. Pusa Ruby (which have been classified and further characterized as sensitive (S) and tolerant (T) to Cd, respectively). Scion S was grafted onto rootstock S (S/S) and rootstock T (S/T), and scion T was grafted onto rootstock T (T/T) and rootstock S (T/S). A 35 μM cadmium chloride (CdCl₂) treatment was used for stress induction in a hydroponic system. Both shoot and root contributions to Cd responses were observed, and they varied in a genotype- and/or organ-dependent manner for nutrient concentrations, oxidative stress parameters, antioxidant enzymes, and transporters gene expression. The findings overall provide evidence for the dominant role of the tolerant rootstock system in conferring reduced Cd uptake and accumulation. The lowest leaf Cd concentrations were observed in T/T (215.11 μg g^-1 DW) and S/T (235.61 μg g^-1 DW). Cadmium-induced decreases in leaf dry weight were observed only in T/S (-8.20%) and S/S (-13.89%), which also were the only graft combinations that showed decreases in chlorophyll content (-3.93% in T/S and -4.05% in S/S). Furthermore, the results show that reciprocal grafting is a fruitful approach for gaining insights into the organ-specific modulation of Cd tolerance and accumulation during the early stages of Cd exposure.

Proteomic Changes in Paspalum fasciculatum Leaves Exposed to Cd Stress

(1) Background: Cadmium is a toxic heavy metal that is widely distributed in water, soil, and air. It is present in agrochemicals, wastewater, battery waste, and volcanic eruptions. Thus, it can be absorbed by plants and enter the trophic chain. P. fasciculatum is a plant with phytoremediation capacity that can tolerate Cd stress, but changes in its proteome related to this tolerance have not yet been identified. (2) Methods: We conducted a quantitative analysis of the proteins present in P. fasciculatum leaves cultivated under greenhouse conditions in mining soils doped with 0 mg kg−1 (control), 30 mg kg−1, or 50 mg kg−1. This was carried out using the label-free shotgun proteomics technique. In this way, we determined the changes in the proteomes of the leaves of these plants, which allowed us to propose some tolerance mechanisms involved in the response to Cd stress. (3) Results: In total, 329 variable proteins were identified between treatments, which were classified into those associated with carbohydrate and energy metabolism; photosynthesis; structure, transport, and metabolism of proteins; antioxidant stress and defense; RNA and DNA processing; and signal transduction. (4) Conclusions: Based on changes in the differences in the leaf protein profiles between treatments, we hypothesize that some proteins associated with signal transduction (Ras-related protein RABA1e), HSPs (heat shock cognate 70 kDa protein 2), growth (actin-7), and cellular development (actin-1) are part of the tolerance response to Cd stress.

Proteomic and physiological analyses to elucidate nitric oxide-mediated adaptive responses of barley under cadmium stress

Nitric oxide (NO) is known to induce plant resistance for several environmental stresses. The protective roles of NO in cadmium (Cd) toxicity have been well documented for various plant species; nevertheless, little information is available about its molecular regulation in improving Cd tolerance of barley plants. Therefore, we combined a comparative proteomics with physiological analyses to evaluate the potential roles of NO in alleviating Cd stress (50 μM) in barley (Hordeum vulgare L.) seedlings. Exogenous application of NO donor sodium nitroprusside (SNP, 100 μM) decreased the Cd-mediated seedling growth inhibition. This observation was supported by the reduction of lipid peroxidation as well as the improvement of chlorophyll content and inhibition of hydrogen peroxide accumulation. Activities of the superoxide dismutase and guaiacol peroxidase were reduced following the application of SNP, while ascorbate peroxidase activity was enhanced. In this study, a total of 34 proteins were significantly regulated by NO in the leaves under Cd stress using a gel-based proteomic approach. The proteomic analysis showed that several pathways were noticeably influenced by NO including photosynthesis and carbohydrate metabolism, protein metabolism, energy metabolism, stress defense, and signal transduction. These results provide new evidence that NO induce photosynthesis and energy metabolism which may enhance Cd tolerance in barley seedlings.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01214-3.

Phytochemical analysis reveals an antioxidant defense response in Lonicera japonica to cadmium-induced oxidative stress

Cadmium (Cd), though potentially beneficial at lower levels to some plant species, at higher levels is a toxic metal that is detrimental to plant growth and development. Cd is also a carcinogen to humans and other contaminated plant consumers, affecting the kidneys and reducing bone strength. In this study we investigated responses of growth, chlorophyll content, reactive oxygen species levels, and antioxidant responses to Cd in honeysuckle leaves (Lonicera japonica Thunb.), a potential Cd hyperaccumulator. Results indicated that plant height, dry weight, leaf area, and chlorophyll content increased when honeysuckle was exposed to 10 mg kg^-1 or 30 mg kg^-1 Cd (low concentration). However, in response to 150 mg kg^-1 or 200 mg kg^-1 Cd (high concentration) these growth parameters and chlorophyll content significantly decreased relative to untreated control plant groups. Higher levels of superoxide radical (O₂^·-) and hydrogen peroxide (H₂O₂) were observed in high concentration Cd groups. The activities of ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase were enhanced with exposure to increasing levels of Cd. Additionally, the Ascorbate-Glutathione (AsA-GSH) cycle was activated for the removal of H₂O₂ in honeysuckle in response to elevated Cd. The Pearson correlation analysis, a redundancy analysis, and a permutation test indicated that proline and APX were dominant antioxidants for removing O₂^·- and H₂O₂. The antioxidants GSH and non-protein thiols (NPTs) also increased as the concentration of Cd increased.

(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.

Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

Comparative phosphoproteomic analysis of tomato genotypes with contrasting cadmium tolerance

A first insight into the effects of cadmium exposure on the phosphoproteome of tomato plants by performing a comparative analysis of tomato genotypes with contrasting cadmium tolerance.

Comparative transcriptomic analysis reveals the coordinated mechanisms of Populus × canadensis 'Neva' leaves in response to cadmium stress

Cadmium (Cd), a heavy metal element has strong toxicity to living organisms. Excessive Cd accumulation directly affects the absorption of mineral elements, inhibits plant tissue development, and even induces mortality. Populus × canadensis 'Neva', the main afforestation variety planted widely in northern China, was a candidate variety for phytoremediation. However, the genes relieving Cd toxicity and increasing Cd tolerance of this species were still unclear. In this study, we employed transcriptome sequencing on two Cd-treated cuttings to identify the key genes involved in Cd stress responses of P. × canadensis 'Neva' induced by 0 (CK), 10 (C10), and 20 (C20) mg/L Cd(NO3)2 4H2O. We discovered a total of 2,656 (1,488 up-regulated and 1,168 down-regulated) and 2,816 DEGs (1,470 up-regulated and 1,346 down-regulated) differentially expressed genes (DEGs) between the CK vs C10 and CK vs C20, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses in response to the Cd stress indicated that many DEGs identified were involved in the catalytic activity, the oxidoreductase activity, the transferase activity, and the biosynthesis of secondary metabolites. Based on the enrichment results, potential candidate genes were identified related to the calcium ion signal transduction, transcription factors, the antioxidant defense system, and transporters and showed divergent expression patterns under the Cd stress. We also validated the reliability of transcriptome data with the real-time PCR. Our findings deeper the understanding of the molecular responsive mechanisms of P. × canadensis 'Neva' on Cd tolerance and further provide critical resources for phytoremediation applications.

Phosphoproteomic Profiling Reveals Early Salt-Responsive Mechanisms in Two Foxtail Millet Cultivars

Excess soluble salts in saline soils are harmful to most plants. Understanding the biochemical responses to salts in plants and studying the salt tolerance-associated genetic resources in nature will contribute to the improvement of salt tolerance in crops. As an emerging model crop, foxtail millet (Setaria italica L.) has been regarded as a novel species for stress resistance investigation. Here, the dynamic proteomic and phosphoproteomic profiling of two foxtail millet varieties of An04 and Yugu2 with contrasting salt tolerance characteristics were investigated under salt stress. In total, 10,366 sites representing to 2,862 proteins were detected and quantified. There were 759 and 990 sites corresponding to 484 and 633 proteins identified under salinity in An04 and Yugu2, respectively, and 1,264 and 1,131 phosphorylation sites corresponding to 789 and 731 proteins were identified between these two varieties before and after salt stress, respectively. The differentially-regulated phosphoproteins (DRPPs) were mainly involved in signal transduction, regulation of gene expression, translation, ion transport, and metabolism processes. Yugu2 possessed signal perception and transduction capabilities more rapidly and had a more intense response compared with An04 upon salinity. The sucrose metabolism pathway, in particularly, might play a vital role in salt response in foxtail millet, which not only provides UDP-glucose for the cellulose synthesis and energy production, but also promotes flavonoid related synthesis to enhance the salt tolerance ability. Over-expressing the phospho-mimic sucrose synthase (SuS) (SuS ^S10D ) in soybean roots enhanced salt tolerance compared with over-expressing SuS lines. The knowledge of this research will shed light on elucidating the mechanisms of salt response, and pave the way for crop varieties innovation and cultivation under salinity and stresses.

Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply

Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.

Protein Phosphorylation Response to Abiotic Stress in Plants

Plants are an important part of nature because as photoautotrophs, they provide a nutrient source for many other living organisms. Due to their sessile nature, to overcome both biotic and abiotic stresses, plants have developed intricate mechanisms for perception of and reaction to these stresses, both on an external level (perception) and on an internal level (reaction). Specific proteins found within cells play crucial roles in stress mitigation by enhancing cellular processes that facilitate the plants survival during the unfavorable conditions. Well before plants are able to synthesize nascent proteins in response to stress, proteins which already exist in the cell can be subjected to an array of posttranslation modifications (PTMs) that permit a rapid response. These activated proteins can, in turn, aid in further stress responses. Different PTMs have different functions in growth and development of plants. Protein phosphorylation, a reversible form of modification has been well elucidated, and its role in signaling cascades is well documented. In this mini-review, we discuss the integration of protein phosphorylation with other components of abiotic stress-responsive pathways including phytohormones and ion homeostasis. Overall, this review demonstrates the high interconnectivity of the stress response system in plants and how readily plants are able to toggle between various signaling pathways in order to survive harsh conditions. Most notably, fluctuations of the cytosolic calcium levels seem to be a linking component of the various signaling pathways.

Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods

BACKGROUND

Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers.

RESULTS

To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10^- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods.

CONCLUSIONS

While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.

Phytoremediation of Cadmium: Physiological, Biochemical, and Molecular Mechanisms

Cadmium (Cd) is one of the most toxic metals in the environment, and has noxious effects on plant growth and production. Cd-accumulating plants showed reduced growth and productivity. Therefore, remediation of this non-essential and toxic pollutant is a prerequisite. Plant-based phytoremediation methodology is considered as one a secure, environmentally friendly, and cost-effective approach for toxic metal remediation. Phytoremediating plants transport and accumulate Cd inside their roots, shoots, leaves, and vacuoles. Phytoremediation of Cd-contaminated sites through hyperaccumulator plants proves a ground-breaking and profitable choice to combat the contaminants. Moreover, the efficiency of Cd phytoremediation and Cd bioavailability can be improved by using plant growth-promoting bacteria (PGPB). Emerging modern molecular technologies have augmented our insight into the metabolic processes involved in Cd tolerance in regular cultivated crops and hyperaccumulator plants. Plants’ development via genetic engineering tools, like enhanced metal uptake, metal transport, Cd accumulation, and the overall Cd tolerance, unlocks new directions for phytoremediation. In this review, we outline the physiological, biochemical, and molecular mechanisms involved in Cd phytoremediation. Further, a focus on the potential of omics and genetic engineering strategies has been documented for the efficient remediation of a Cd-contaminated environment.

Calcium-Regulated Phosphorylation Systems Controlling Uptake and Balance of Plant Nutrients

Essential elements taken up from the soil and distributed throughout the whole plant play diverse roles in different tissues. Cations and anions contribute to maintenance of intracellular osmolarity and the formation of membrane potential, while nitrate, ammonium, and sulfate are incorporated into amino acids and other organic compounds. In contrast to these ion species, calcium concentrations are usually kept low in the cytosol and calcium displays unique behavior as a cytosolic signaling molecule. Various environmental stresses stimulate increases in the cytosolic calcium concentration, leading to activation of calcium-regulated protein kinases and downstream signaling pathways. In this review, we summarize the stress responsive regulation of nutrient uptake and balancing by two types of calcium-regulated phosphorylation systems: CPK and CBL-CIPK. CPK is a family of protein kinases activated by calcium. CBL is a group of calcium sensor proteins that interact with CIPK kinases, which phosphorylate their downstream targets. In Arabidopsis, quite a few ion transport systems are regulated by CPKs or CBL-CIPK complexes, including channels/transporters that mediate transport of potassium (KAT1, KAT2, GORK, AKT1, AKT2, HAK5, SPIK), sodium (SOS1), ammonium (AMT1;1, AMT1;2), nitrate and chloride (SLAC1, SLAH2, SLAH3, NRT1.1, NRT2.4, NRT2.5), and proton (AHA2, V-ATPase). CPKs and CBL-CIPKs also play a role in C/N nutrient response and in acquisition of magnesium and iron. This functional regulation by calcium-dependent phosphorylation systems ensures the growth of plants and enables them to acquire tolerance against various environmental stresses. Calcium serves as the key factor for the regulation of membrane transport systems.

Differential phosphoproteome study of the response to cadmium stress in rice

Cadmium (Cd) is one of the most toxic heavy metals, and its accumulation in plants will seriously affect growth and yield. In this study, Cd-sensitive line D69 and Cd-tolerant line D28 were selected, which the Cd content of D28 was higher than D69 in both above and underground parts after Cd treatment. Using a combination of two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF MS/MS, the differential expression changes of phosphorylated proteins between D69 and D28 in leaves were classified and analyzed after Cd treatment. A total of 53 differentially expressed phosphoproteins were identified, which mainly involved in metabolism, signal transduction, gene expression regulation, material transport, and membrane fusion. The phosphorylated proteins of Cd-tolerant and Cd-sensitive lines were all analyzed, and found that some proteins associated with carbon metabolism, proteolytic enzymes, F-box containing transcription factors, RNA helicases, DNA replication/transcription/repair enzymes and ankyrins were detected in Cd-tolerant line D28, which might alleviate the abiotic stress caused by Cd treatment. These results will clarify the phosphorylated pathways in response and resistance to Cd stress in rice.

Phosphoproteomic Analysis of Two Contrasting Maize Inbred Lines Provides Insights into the Mechanism of Salt-Stress Tolerance

Salinity is a major abiotic stress that limits maize yield and quality throughout the world. We investigated phosphoproteomics differences between a salt-tolerant inbred line (Zheng58) and a salt-sensitive inbred line (Chang7-2) in response to short-term salt stress using label-free quantitation. A total of 9448 unique phosphorylation sites from 4116 phosphoproteins in roots and shoots of Zheng58 and Chang7-2 were identified. A total of 209 and 243 differentially regulated phosphoproteins (DRPPs) in response to NaCl treatment were detected in roots and shoots, respectively. Functional analysis of these DRPPs showed that they were involved in carbon metabolism, glutathione metabolism, transport, and signal transduction. Among these phosphoproteins, the expression of 6-phosphogluconate dehydrogenase 2, pyruvate dehydrogenase, phosphoenolpyruvate carboxykinase, glutamate decarboxylase, glutamate synthase, l-gulonolactone oxidase-like, potassium channel AKT1, high-affinity potassium transporter, sodium/hydrogen exchanger, and calcium/proton exchanger CAX1-like protein were significantly regulated in roots, while phosphoenolpyruvate carboxylase 1, phosphoenolpyruvate carboxykinase, sodium/hydrogen exchanger, plasma membrane intrinsic protein 2, glutathione transferases, and abscisic acid-insensitive 5-like protein were significantly regulated in shoots. Zheng58 may activate carbon metabolism, glutathione and ascorbic acid metabolism, potassium and sodium transportation, and the accumulation of glutamate to enhance its salt tolerance. Our results help to elucidate the mechanisms of salt response in maize seedlings. They also provide a basis for further study of the mechanism underlying salt response and tolerance in maize and other crops.

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets

BACKGROUND

Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed.

METHODS

To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment.

RESULTS

We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr).

CONCLUSION

In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.

Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality

Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.