Comparative transcriptome analysis of Zea mays in response to petroleum hydrocarbon stress

Transcriptome analysis of a springtail, Folsomia candida, reveals energy constraint and oxidative stress during petroleum hydrocarbon exposure

Petroleum hydrocarbon (PHC) contamination in soil is ubiquitous and poses harmful consequences to many organisms. The toxicity of PHC-impacted soil is difficult to predict due to variations in mixture composition and the impacts of natural weathering processes. Hence, high-throughput methods to assess PHC-impacted soils is required to expedite land management decisions. Next-generation sequencing is a robust tool that allows researchers to investigate the effects of contaminants on the transcriptome of organisms and identify molecular biomarkers. In this study, the effects of PHCs on conventional endpoints (i.e., survival and reproduction) and gene expression rates of a model springtail species, Folsomia candida were investigated. Age-synchronized F. candida were exposed to ecologically-relevant concentrations of soils spiked with fresh crude oil to calculate the reproductive EC25 and EC50 values using conventional toxicity testing. Soils spiked to these concentrations were then used to evaluate effects on the F. candida transcriptome over a 7-day exposure period. RNA-seq analysis found 98 and 132 differentially expressed genes when compared to the control for the EC25 and EC50 treatment groups, respectively. The majority of up-regulated genes were related to xenobiotic biotransformation reactions and oxidative stress response, while down-regulated genes coded for carbohydrate and peptide metabolic processes. Promotion of the pentose phosphate pathway was also found. Results suggest that the decreased reproduction rates of F. candida exposed to PHCs is due to energy constraints caused by inhibition of carbohydrate metabolic processes and allocation of remaining energy to detoxify xenobiotics. These findings provide insights into the molecular effects in F. candida following exposure to crude oil for seven days and highlight their potential to be used as a high-throughput screening test for PHC-contaminated sites. Adverse molecular effects can be measured as early as 24 h following exposure, whereas conventional toxicity tests may require a minimum of four weeks.

Physiological and Biochemical Responses of Solanum lycopersicum L. to Benzo[a]pyrene Contaminated Soils

Benzo[a]pyrene (BaP) is noted as one of the main cancer-causing pollutants in human beings and may damage the development of crop plants. The present work was designed to explore more insights into the toxic effects of BaP on Solanum lycopersicum L. at various doses (20, 40, and 60 MPC) spiked in Haplic Chernozem. A dose-dependent response in phytotoxicity were noted, especially in the biomass of the roots and shoots, at doses of 40 and 60 MPC BaP and the accumulation of BaP in S. lycopersicum tissues. Physiological and biochemical response indices were severely damaged based on applied doses of BaP. During the histochemical analysis of the localization of superoxide in the leaves of S. lycopersicum, formazan spots were detected in the area near the leaf's veins. The results of a significant increase in malondialdehyde (MDA) from 2.7 to 5.1 times, proline 1.12- to 2.62-folds, however, a decrease in catalase (CAT) activity was recorded by 1.8 to 1.1 times. The activity of superoxide dismutase (SOD) increased from 1.4 to 2, peroxidase (PRX) from 2.3 to 5.25, ascorbate peroxidase (APOX) by 5.8 to 11.5, glutathione peroxidase (GP) from 3.8 to 7 times, respectively. The structure of the tissues of the roots and leaves of S. lycopersicum in the variants with BaP changed depending on the dose: it increased the intercellular space, cortical layer, and the epidermis, and the structure of the leaf tissues became looser.

Thermodynamics of benzoquinone-induced conformational changes in nucleic acids and human serum albumin

Biological macromolecules such as proteins, nucleic acids, carbohydrates and lipids, play a crucial role in biochemical and molecular processes. Thus, the study of the structure-function relationship of biomolecules in presence of ligands is an important aspect of structural biology. The current communication describes the chemico-biological interaction between benzene metabolite para-benzoquinone (BQ) with B-form of nucleic acids (B-DNA) and human serum albumin (HSA). The binding ability of HSA towards bromocresol green (BCG) was significantly suppressed when exposed to increasing concentrations of BQ in the presence of various physiological buffers. Further, the native fluorescence of HSA was drastically reduced and the secondary structures of HSA were significantly compromised with increasing concentrations of BQ. In vitro and in silico studies also revealed that BQ binds to domains I and II of HSA and thus altering the conformation of HSA which may potentially affect plasma osmotic pressure, as well as the binding and transport of numerous endogenous and exogenous molecules. Similarly, BQ interacts directly to the GC region of B-DNA particularly in the minor groove which was also assessed by computational docking studies. Isothermal titration calorimetry data suggest higher binding affinity of BQ towards DNA than HSA. Various spectroscopic observations also suggest that BQ binds to DNA preferably in the minor grooves. Thus, the results revealed that BQ may play a key role in inducing mutagenicity, either by formation of adducts on GC regions or by accelerating oxidative damage to biomacromolecules through chemico-biological interactions.

Comparative transcriptome combined with transgenic analysis reveal the involvement of salicylic acid pathway in the response of Nicotiana tabacum to triclosan stress

Triclosan (TCS) is a highly effective antibacterial agent, which is widely distributed in wastewater and sludge. The application of sludge containing high concentration TCS in agriculture will cause physiological damage to plants. Nevertheless, little is known about the physiological and molecular mechanism of TCS to plants. So firstly the physiological and biochemical indexes of tobacco with treatment of different concentrations of TCS were evaluated in this study. The results showed that tobacco plants with TCS treatment exhibited lower germination rate, root development, photosynthesis efficiency, and higher ROS accumulation in comparison with control group. The transcriptome analysis of tobacco plants was then performed to reveal the molecular mechanism in the response of tobacco to TCS. There were 3, 819 differentially expressed genes (DEGs) were identified between groups with or without TCS treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these DEGs were mainly enriched in groups of the plant hormone signal transduction pathway. To further investigate the role of plant hormone, transgenic tobacco overexpressing a homologous of salicylic acid (SA) binding protein gene was used to assess the SA-mediate TCS tolerance in plant. The results showed that transgenic plants exhibited enhanced activities of antioxidant enzymes and stronger TCS resistance than wild-type ones, which verify the important role of SA signal pathway in TCS response of tobacco plants. This study could be used to better understand the key roles of plant hormones in the TCS stress response of higher plants, and find key pathways and candidate genes for phytoremediation.

Dopamine Alleviates Hydrocarbon Stress in Brassica oleracea through Modulation of Physio-Biochemical Attributes and Antioxidant Defense Systems

Hydrocarbon stress has become one of the most restrictive factors for crop choice and productivity in most parts of the world. Dopamine (DA) has positively influenced the metabolic, physiological and biochemical activities besides the growth of plants under numerous abiotic stress conditions. The current study was performed to analyze the potential of DA to alleviate hydrocarbon stress and improve growth of Brassica oleracea plants. Hydrocarbon stress in plants was induced by growing in 5% and 10% crude oil contaminated soil. Crude oil stressed plants exhibited reduced growth besides decreased level of photosynthetic pigments and gas exchange attributes. Moreover, oil stressed plants showed elevated level of hydrogen peroxide (H₂O₂), electrolyte leakage (EL), malondialdehyde (MDA) and superoxide radical (O^2-). However, exogenous application of 50, 100 and 200 μmol L^-1 DA improved photosynthesis, shoot and root dry weight of B. oleracea seedlings growing in hydrocarbon amended soil. Additionally, DA100 treatments improved non-enzymatic and enzymatic antioxidants of treated seedlings. Our results demonstrate that increased gas exchange attributes, modulation of osmoregulators and improved activity of the antioxidative enzymes alleviated hydrocarbon stress in DA supplemented B. oleracea plants. Consequently, the first time observed ameliorative role of DA in hydrocarbon stress opens a new arena for application of this dynamic biomolecule for sustainable crop production.

Anthracene induces oxidative stress and activation of antioxidant and detoxification enzymes in Ulva lactuca (Chlorophyta)

In order to analyze whether the marine macroalga Ulva lactuca can absorb and metabolize anthracene (ANT), the alga was cultivated with 5 µM ANT for 0-72 h, and the level of ANT was detected in the culture medium, and in the alga. The level of ANT rapidly decreased in the culture medium reaching a minimal level at 6 h, and rapidly increased in the alga reaching a maximal level at 12 h and then decreased to reach a minimal level at 48 h of culture. In addition, ANT induced an increase in hydrogen peroxide that remained until 72 h and a higher increase in superoxide anions that reach a maximal level at 24 h and remained unchanged until 72 h, indicating that ANT induced an oxidative stress condition. ANT induced an increase in lipoperoxides that reached a maximal level at 24 h and decreased at 48 h indicating that oxidative stress caused membrane damage. The activity of antioxidant enzymes SOD, CAT, AP, GR and GP increased in the alga treated with ANT whereas DHAR remained unchanged. The level of transcripts encoding these antioxidant enzymes increased and those encoding DHAR did not change. Inhibitors of monooxygenases, dioxygenases, polyphenol oxidases, glutathione-S-transferases and sulfotransferases induced an increase in the level of ANT in the alga cultivated for 24 h. These results strongly suggest that ANT is rapidly absorbed and metabolized in U. lactuca and the latter involves Phase I and II metabolizing enzymes.

Effect of Crude Oil on Growth, Oxidative Stress and Response of Antioxidative System of Two Rye (Secale cereale L.) Varieties

Rye (Secale cereale L.) is one of the most important cereal crops in Eastern and Northern Europe, showing better tolerance to environmental stress factors compared to wheat and triticale. Plant response to the crude oil-polluted soil depends on plant species, oil concentration, time of exposure, etc. The current study is aimed at investigating the growth, oxidative stress and the response of antioxidative system of two rye varieties (Krona and Valdai) cultivated on crude oil-contaminated soils at different concentrations (1.5, 3.0, 6.0, and 12.0%). Inhibition of rye growth was observed at crude oil concentrations of above 3% for above-ground plant parts and of above 1.5% for roots. A decrease in content of chlorophyll a and total chlorophylls in Krona variety was detected at 1.5% oil concentration in soil and in Valdai variety at 3% oil concentration. Compared with the control, the content of malondialdehyde was significantly increased in the Krona variety at 3% oil concentration and in Valdai variety at 6% oil concentration. The crude oil-induced oxidative stress was minimized in rye plants by the enhanced contents of low-molecular antioxidants (proline, non-protein thiols, ascorbic acid, phenolic compounds) and activities of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione peroxidase. The strongest positive correlation was detected between the content of malondialdehyde and contents of proline (r = 0.89–0.95, p ≤ 0.05) and phenolic compounds (r = 0.90–0.94, p ≤ 0.05) as well as superoxide dismutase activity (r = 0.81–0.90, p ≤ 0.05). Based on the results of a comprehensive analysis of growth and biochemical parameters and of the cluster analysis, Valdai variety proved to be more resistant to oil pollution. Due to this, Valdai variety is considered to be a promising rye variety for cultivation on moderately oil-polluted soils in order to decontaminate them. At the same time, it is necessary to conduct further studies aimed at investigating oil transformation processes in the soil-rye system, which would make it possible to determine the efficiency of using this cereal for soil remediation.

Benzopyrene induces oxidative stress and increases expression and activities of antioxidant enzymes, and CYP450 and GST metabolizing enzymes in Ulva lactuca (Chlorophyta)

Benzopyrene is rapidly incorporated and metabolized, and induces oxidative stress and activation of antioxidant enzymes, and CYP450 and GST metabolizing enzymes in Ulva lactuca. To analyze absorption and metabolism of benzo[a]pyrene (BaP) in Ulva lactuca, the alga was cultivated with 5 µM of BaP for 72 h. In the culture medium, BaP level rapidly decreased reaching a minimal level at 12 h and, in the alga, BaP level increased until 6 h, remained stable until 24 h, and decreased until 72 h indicating that BaP is being metabolized in U. lactuca. In addition, BaP induced an initial increase in hydrogen peroxide decreasing until 24 h, superoxide anions level that remained high until 72 h, and lipoperoxides that initially increased and decreased until 72 h, showing that BaP induced oxidative stress. Activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (AP), glutathione reductase (GR) and glutathione peroxidase (GP) were increased, whereas dehydroascorbate reductase (DHAR) activity was unchanged. The level of transcripts encoding these antioxidant enzymes was increased, but transcripts encoding DHAR remained unchanged. Interestingly, the activity of glutathione-S-transferase (GST) was also increased, and inhibitors of cytochrome P450 (CYP450) and GST activities enhanced the level of BaP in algal tissue, suggesting that these enzymes participate in BaP metabolism.

Enhanced performance of Bacillus megaterium OSR-3 in combination with putrescine ammeliorated hydrocarbon stress in Nicotiana tabacum

Hydrocarbon stress (HS) has been causing decreased plant growth and productivity. Putrescine (Put) and growth promoting microbes are vital for plant growth and development under hydrocarbon stress. Current research work was carried out to evaluate the potential of Bacillus megaterium OSR-3 alone and in combination with Put to alleviate HS in Nicotiana tabacum (L.). The crude petroleum contaminated soil significantly reduced growth attributes of N. tabacum. B. megaterium OSR-3 inoculated plants subjected to HS exhibited improved photosynthetic rate, gas exchange characteristics, poline contents and protein level. Furthermore, bacterial inoculation enhanced the antioxidative activity of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) in tobacco plants subjected to HS. The HS alleviation in B. megaterium OSR-3 inoculated N. tabacum can be credited to the heightened activity of antioxidative enzymes, reduction in hydrogen peroxide (H2O2) and abridged synthesis of malondialdehyde (MDA). The increased synthesis of indole acetic acid (IAA) in HS stressed N. tabacum plants treated with co-application of B. megaterium OSR-3 and Put attenuated toxicity and amplified growth of plants. Additionally, the co-application of B. megaterium OSR-3 and Put also upregulated the activity of antioxidative enzymes and induced augmented level of proline and IAA in plants under HS regimes. Current research provides novel insight into the potential and mechanism of B. megaterium OSR-3 and Put in mitigation of HS in N. tabacum plants.