Sanjay Dwivedi

Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress

BackgroundWidespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of paints and pigments, tanning, and wood preservation elevates its concentration in surface soil and eventually into rice plants and grains. In spite of many previous studies having been conducted on the effects of chromium stress, the precise molecular mechanisms related to both the effects of chromium phytotoxicity, the defense reactions of plants against chromium exposure as well as translocation and accumulation in rice remain poorly understood.ResultsDetailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. To check whether the Cr-specific motifs were indeed significantly over represented in the promoter regions of Cr-responsive genes, occurrence of these motifs in whole genome sequence was carried out. In the background of whole genome, the lift value for these 14 and 13 motifs was significantly high in the test dataset. Though no functional role has been assigned to any of the motifs, but all of these are present as promoter motifs in the Database of orthologus promoters.ConclusionThese findings clearly suggest that a complex network of regulatory pathways modulates Cr-response of rice. The integrated matrix of both transcriptome and metabolome data after suitable normalization and initial calculations provided us a visual picture of the correlations between components. Predominance of different motifs in the subsets of genes suggests the involvement of motif-specific transcription modulating proteins in Cr stress response of rice.

Lead bioaccumulation potential of an aquatic macrophyte Najas indica are related to antioxidant system.

Plants of Najas indica bioaccumulated significantly higher amounts of Pb (3554 microg g(-1) dw) when, exposed to varying concentrations of Pb(NO(3))(2).This also led to increased malondialdehyde (MDA), electrical conductivity (EC) and H(2)O(2) content. In response to this, the activities of antioxidant enzymes such as superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT) and glutathione reductase (GR) were elevated along with the induction of various molecular antioxidants including GSH, cysteine, ascorbic acid and proline. Further, Pb exposed plants showed significantly increased cysteine synthase and glutathione-S-transferase activity. Visible symptoms of toxicity were evident at 50 microM after 4d showing chlorosis and fragmentation of leaves with mucilaginous discharge. It seems that bioaccumulated Pb is efficiently tolerated by Najas plants through activation of antioxidant system and thiolic pathways which was evident by the increased biomass up to 10 microM Pb. Therefore, it appears that due to metal tolerance characteristics with high concentration factor these plants can find use in phytoremediation of aquatic system highly contaminated by Pb.

Thiol metabolism play significant role during cadmium detoxification by Ceratophyllum demersum L.

In the present study, the level of thiols and activity of related enzymes were investigated in coontail (Ceratophyllum demersum L.) plants to analyze their role in combating the stress caused upon exposure to cadmium (Cd; 0-10 microM) for a duration up to 7d. Plants showed the maximum accumulation of 1293 microg Cd g(-1)dw after 7d at 10 microM. Significant increases in the level of total non-protein thiols (NP-SH) including phytochelatins (PCs) as well as upstream metabolites of the PC biosynthetic pathway, cysteine and glutathione (GSH) were observed. In addition, significant increases in the activities of cysteine synthase (CS), glutathione-S-transferase (GST), glutathione reductase (GR), as well as in vitro activation of phytochelatin synthase (PCS), were noticed in response to Cd. In conclusion, under Cd stress, plants adapted to a new metabolic equilibrium of thiols through coordinated synthesis and consumption to combat Cd toxicity and to accumulate it.

Arsenic tolerances in rice (Oryza sativa) have a predominant role in transcriptional regulation of a set of genes including sulphur assimilation pathway and antioxidant system.

World wide arsenic (As) contamination of rice has raised much concern as it is the staple crop for millions. Four most commonly cultivated rice cultivars, Triguna, IR-36, PNR-519 and IET-4786, of the West Bengal region were taken for a hydroponic study to examine the effect of arsenate (As(V)) and arsenite (As(III)) on growth response, expression of genes and antioxidants vis-à-vis As accumulation. The rice genotypes responded differentially under As(V) and As(III) stress in terms of gene expression and antioxidant defences. Some of the transporters were up-regulated in all rice cultivars at lower doses of As species, except IET-4786. Phytochelatin synthase, GST and γ-ECS showed considerable variation in their expression pattern in all genotypes, however in IET-4786 they were generally down-regulated in higher As(III) stress. Similarly, most of antioxidants such as superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) increased significantly in Triguna, IR-36 and PNR-519 and decreased in IET-4786. Our study suggests that Triguna, IR-36 and PNR-519 are tolerant rice cultivars accumulating higher arsenic; however IET-4786 is susceptible to As-stress and accumulates less arsenic than other cultivars.

Biological removal of arsenic pollution by soil fungi

Fifteen fungal strains were isolated from arsenic contaminated (range 9.45-15.63 mg kg(-1)) agricultural soils from the state of West Bengal, India. Five fungal strains were belonged to the Aspergillus and Trichoderma group each, however, remaining five were identified as the Neocosmospora, Sordaria, Rhizopus, Penicillium and sterile mycelial strain. All these fungal strains were cultivated on medium supplemented with 100, 500, 1000, 5000 and 10,000 mg l(-1) of sodium arsenate. After 30-day cultivation under laboratory conditions, radial growth of these strains was determined and compared with control. Toxicity and tolerance of these strains to arsenate were evaluated on the basis of tolerance index. Out of fifteen, only five fungal strains were found resistant and survived with tolerance index pattern as 0.956 (sterile mycelial strain)>0.311 (Rhizopus sp.)>0.306 (Neocosmospora sp.)>0.212 (Penicillium sp.)>0.189 (Aspergillus sp.) at 10,000 mg l(-1) of arsenate. The arsenic removal efficacy of ten fungal strains, tolerant to 5000 mg l(-1) arsenate, was also assayed under laboratory conditions for 21 days. All these strains were cultivated individually on mycological broth enriched with 10 mg l(-1) of arsenic. The initial and final pH of cultivating medium, fungal biomass and removal of arsenic by each fungal strain were evaluated. Fungal biomass of ten strains removed arsenic biologically from the medium which were ranged from 10.92 to 65.81% depending on fungal species. The flux of biovolatilized arsenic was determined indirectly by estimating the sum of arsenic content in fungal biomass and medium. The mean percent removal as flux of biovolatilized arsenic ranged from 3.71 to 29.86%. The most effective removal of arsenic was observed in the Trichoderma sp., sterile mycelial strain, Neocosmospora sp. and Rhizopus sp. fungal strains. These fungal strains can be effectively used for the bioremediation of arsenic-contaminated agricultural soils.

Arsenate Exposure Affects Amino Acids, Mineral Nutrient Status and Antioxidants in Rice (Oryza sativa L.) Genotypes

Simulated pot experiments were conducted on four rice (Oryza sativa L.) genotypes (Triguna, IR-36, PNR-519, and IET-4786) to examine the effects of As(V) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. Rice genotypes responded differentially to As(V) exposure in terms of amino acids and antioxidant profiles. Total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. While, most of the essential amino acids increased in all cultivars except IR-36, glutamic acid and glycine increased in IET-4786 and PNR-519. The level of nonprotein thiols (NPTs) and the activities of superoxide dismutase (SOD; EC 1.15.1.1), glutathione reductase (GR; EC 1.6.4.2) and ascorbate peroxidase (APX; EC 1.11.1.11) increased in all rice cultivars except IET-4786. A significant genotypic variation was also observed in specific arsenic uptake (SAU; mg kg(-1)dw), which was in the order of Triguna (134) > IR-36 (71) > PNR-519 (53) > IET-4786 (29). Further, application of As(V) at lower doses (4 and 8 mg L(-1) As) enhanced the accumulation of selenium (Se) and other nutrients (Fe, P, Zn, and S), however, higher dose (12 mg L(-1) As) limits the nutrient uptake in rice. In conclusion, low As accumulating genotype, IET-4786, which also had significantly induced level of essential amino acids, seems suitable for cultivation in moderately As contaminated soil and would be safe for human consumption.

Differential response of oxidative stress and thiol metabolism in contrasting rice genotypes for arsenic tolerance.

The mechanism of arsenic (As) tolerance was investigated on two contrasting rice (Oryza sativa L.) genotypes, selected for As tolerance and accumulation. One tolerant (Triguna) and one sensitive (IET-4786) variety were exposed to various arsenate (0-50 μM) levels for 7 d for biochemical analyses. Arsenic induced oxidative stress was more pronounced in IET-4786 than Triguna especially in terms of reactive oxygen species, lipid peroxidation, EC and pro-oxidant enzymes (NADPH oxidase and ascorbate oxidase). However, Triguna tolerated As stress through the enhanced enzymes activities particularly pertaining to thiol metabolism such as serine acetyl transferase (SAT), cysteine synthase (CS), γ-glutamyl cysteine synthase (γ-ECS), γ-glutamyl transpeptidase (γ-GT), and glutathione-S-transferase (GST) as well as arsenate reductase (AR). Besides maintaining the ratio of redox couples GSH/GSSG and ASC/DHA, the level of phytochelatins (PCs) and phytochelatin synthase (PCS) activity were more pronounced in Triguna, in which harmonized responses of thiol metabolism was responsible for As tolerance in contrast to IET-4786 showing its susceptible nature towards As exposure.

Arsenomics: omics of arsenic metabolism in plants

Arsenic (As) contamination of drinking water and groundwater used for irrigation can lead to contamination of the food chain and poses serious health risk to people worldwide. To reduce As intake through the consumption of contaminated food, identification of the mechanisms for As accumulation and detoxification in plant is a prerequisite to develop efficient phytoremediation methods and safer crops with reduced As levels. Transcriptome, proteome, and metabolome analysis of any organism reflects the total biological activities at any given time which are responsible for the adaptation of the organism to the surrounding environmental conditions. As these approaches are very important in analyzing plant As transport and accumulation, we termed “Arsenomics” as approach which deals transcriptome, proteome, and metabolome alterations during As exposure. Although, various studies have been performed to understand modulation in transcriptome in response to As, many important questions need to be addressed regarding the translated proteins of plants at proteomic and metabolomic level, resulting in various ecophysiological responses. In this review, the comprehensive knowledge generated in this area has been compiled and analyzed. There is a need to strengthen Arsenomics which will lead to build up tools to develop As-free plants for safe consumption.

Expression in Arabidopsis and cellular localization reveal involvement of rice NRAMP, OsNRAMP1, in arsenic transport and tolerance

Irrigation of paddy fields to arsenic (As) containing groundwater leads to As accumulation in rice grains and causes serious health risk to the people worldwide. To reduce As intake via consumption of contaminated rice grain, identification of the mechanisms for As accumulation and detoxification in rice is a prerequisite. Herein, we report involvement of a member of rice NRAMP (Natural Resistance-Associated Macrophage Protein) transporter, OsNRAMP1, in As, in addition to cadmium (Cd), accumulation through expression in yeast and Arabidopsis. Expression of OsNRAMP1 in yeast mutant (fet3fet4) rescued iron (Fe) uptake and exhibited enhanced accumulation of As and Cd. Expression of OsNRAMP1 in Arabidopsis provided tolerance with enhanced As and Cd accumulation in root and shoot. Cellular localization revealed that OsNRAMP1 resides on plasma membrane of endodermis and pericycle cells and may assist in xylem loading for root to shoot mobilization. This is the first report demonstrating role of NRAMP in xylem mediated loading and enhanced accumulation of As and Cd in plants. We propose that genetic modification of OsNRAMP1 in rice might be helpful in developing rice with low As and Cd content in grain and minimize the risk of food chain contamination to these toxic metals.

Sulfur mediated reduction of arsenic toxicity involves efficient thiol metabolism and the antioxidant defense system in rice

Arsenic (As) contamination is a global issue, with South Asia and South East Asia being worst affected. Rice is major crop in these regions and can potentially pose serious health risks due to its known As accumulation potential. Sulfur (S) is an essential macronutrient and a vital element to combat As toxicity. The aim of this study was to investigate the role of S with regards to As toxicity in rice under different S regimes. To achieve this aim, plants were stressed with AsIII and AsV under three different S conditions (low sulfur (0.5mM), normal sulfur (3.5mM) and high sulfur (5.0mM)). High S treatment resulted in increased root As accumulation, likely due to As complexation through enhanced synthesis of thiolic ligands, such as non-protein thiols and phytochelatins, which restricted As translocation to the shoots. Enzymes of S assimilatory pathways and downstream thiolic metabolites were up-regulated with increased S supplementation; however, to maintain optimum concentrations of S, transcript levels of sulfate transporters were down-regulated at high S concentration. Oxidative stress generated due to As was counterbalanced in the high S treatment by reducing hydrogen peroxide concentration and enhancing antioxidant enzyme activities. The high S concentration resulted in reduced transcript levels of Lsi2 (a known transporter of As). This reduction in Lsi2 expression level is a probable reason for low shoot As accumulation, which has potential implications in reducing the risk of As in the food chain.