Proteomics analysis of flax grown in Chernobyl area suggests limited effect of contaminated environment on seed proteome

Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area

The nuclear reactor accident in Chernobyl, Ukraine, resulted in effects both locally and farther away. Most of the contaminated areas were the agricultural fields and forests. Experimental fields were established near Chernobyl—radioactively contaminated fields localized 5 km from Chernobyl Nuclear Power Plant as well as the remediated soil that is localized directly in the Chernobyl town. Two flax varieties growing under chronic exposition to ionizing radiation were used for this study—the local Ukrainian variety Kyivskyi and a commercial variety Bethune. The screening of the length polymorphism generated by transposable elements insertions were performed. All known types of common flax transposon, retrotransposons and iPBS approach were used. In the iPBS multiplex analyze, for the Kyivskyi variety, a unique addition was found in the seeds from the radioactive contaminated field and for the Bethune variety, a total of five amplicon additions were obtained and one deletion. For the TRIM Cassandra fingerprints, two amplicon additions were generated in the seeds from radioactive contaminated fields for the Bethune variety. In summary, the obtained data represent the genetic diversity between control and irradiated subgroups of flax seeds from Chernobyl area and the presence of activated transposable elements due to the irradiation stress.

Effect of chronic radiation on the flax (Linum usitatissimum L.) genome grown for six consecutive generations in the radioactive Chernobyl area

The growth of plants under chronic radiation stress in the Chernobyl area may cause changes in the genome of plants. To assess the extent of genetic and epigenetic changes in nuclear DNA, seeds of the annual crop flax (Linum usitatissimum L.) of the Kyivskyi variety, sown 21 years after the accident and grown for six generations in radioactive (RAD) and remediated (REM) fields were analysed. Flaxseed used for sowing first generation, which served as a reference (REF), was also analysed. The AFLP (Amplified Fragment Length Polymorphism) revealed a higher number of specific EcoRI-MseI loci (3.4-fold) in pooled flaxseed samples harvested from the RAD field compared with the REM field, indicating a link between the mutation process in the flax genome and the ongoing adaptation process. MSAP (Methylation-Sensitive Amplified Polymorphism) detecting EcoRI-MspI and EcoRI-HpaII loci in flax nuclear DNA genome showed no significant differences in methylation level, reaching about 33% in each of the groups studied. On the other hand, significant changes in the DNA methylation pattern of flaxseed samples harvested from the RAD field compared with controls were detected. Pairwise F_ST comparison revealed within both, EcoRI-MspI and transformed methylation-Sensitive data sets more than a 3-fold increase of genetic divergence in the RAD field compared with both controls. These results indicate that the nuclear genome of flax exposed to chronic radiation for six generations has more mutations and uses DNA methylation as one of the adaptation mechanisms for sustainability under adverse conditions.

Managing soils of environmental significance: A critical review

Globally, environmentally significant soils (ESSs) mainly include acid sulfate, heavy metal(loid)-contaminated, petroleum hydrocarbon-contaminated, pesticide-contaminated, and radionuclide-contaminated soils. These soils are interrelated and have many common characteristics from an environmental management perspective. In this review, we critically evaluate the available literature on individual ESSs, aiming to identify common problems related to environmental quality/risk assessment, remediation approaches, and environmental regulation for these soils. Based on these findings, we highlight the challenges to, and possible solutions for sustainable ESS management. Contaminated land has been rapidly expanding since the first industrial revolution from the industrialized Western countries to the emerging industrialized Asia and other parts of the world. Clean-up of contaminated lands and slowdown of their expansion require concerted international efforts to develop advanced cleaner production and cost-effective soil remediation technologies in addition to improvement of environmental legislation, regulatory enforcement, financial instruments, and stakeholder involvement to create enabling environments. Two particular areas require further action and research efforts: developing a universal system for assessing ESS quality and improving the cost-effectiveness of remediation technologies. We propose an integrated framework for deriving ESS quality indicators and make suggestions for future research directions to improve the performance of soil remediation technologies.

Implications of ionizing radiation on pollen performance in comparison with diverse models of polar cell growth

Research concerning the effects of ionizing radiation (IR) on plant systems is essential for numerous aspects of human society, as for instance, in terms of agriculture and plant breeding, but additionally for elucidating consequences of radioactive contamination of the ecosphere. This comprehensive survey analyses effects of x- and γ-irradiation on male gametophytes comprising primarily in vitro but also in vivo data of diverse plant species. The IR-dose range for pollen performance was compiled and 50% inhibition doses (ID₅₀ ) for germination and tube growth were comparatively related to physiological characteristics of the microgametophyte. Factors influencing IR-susceptibility of mature pollen and polarized tube growth were evaluated, such as dose-rate, environmental conditions, or species-related variations. In addition, all available reports suggesting bio-positive IR-effects particularly on pollen performance were examined. Most importantly, for the first time influences of IR specifically on diverse phylogenetic models of polar cell growth were comparatively analysed, and thus demonstrated that the gametophytic system of pollen is extremely resistant to IR, more than plant sporophytes and especially much more than comparable animal cells. Beyond that, this study develops hypotheses regarding a molecular basis for the extreme IR-resistance of the plant microgametophyte and highlights its unique rank among organismal systems.

A review of the impact on the ecosystem after ionizing irradiation: wildlife population

PURPOSE

On 26 April 1986, reactor 4 at the Chernobyl power plant underwent a catastrophic failure leading to core explosions and open-air fires. On 11 March 2011, a combination of earthquake and tsunami led to a similar disaster at the Fukushima Daiichi power plant. In both cases, radioactive isotopes were released and contaminated the air, soil and water in a substantial area around the power plants. Humans were evacuated from the immediate regions but the wildlife stayed and continued to be affected by the ongoing high radiation exposure initially and later decayed amounts of fallout dusts with time. In this review, we will examine the significant effects of the increased radiation on vegetation, insects, fish, birds and mammals.

CONCLUSIONS

The initial intense radiation in these areas has gradually begun to decrease but still remains high. Adaptation to radiation is evident and the ecosystems have dynamically changed from the periods immediately after the accidents to the present day. Understanding the molecular mechanisms that allow the adaptation and recovery of wildlife to chronic radiation challenges would aid in future attempts at ecosystem remediation in the wake of such incidents.

Does Chernobyl-derived radiation impact the developmental stability of Asellus aquaticus 30years on?

Effects of long-term, environmentally relevant doses of radiation on biota remain unclear due to a lack of studies following chronic exposure in contaminated environments. The 1986 Chernobyl accident dispersed vast amounts of radioactivity into the environment which persists to date. Despite three decades of research, impacts of the incident on non-human organisms continues to be contested within the scientific literature. The present study assessed the impact of chronic radiation exposure from Chernobyl on the developmental stability of the model aquatic isopod, Asellus aquaticus using fluctuating asymmetry (FA) as an indicator. Fluctuating asymmetry, defined as random deviations from the expected perfect bilateral symmetry of an organism, has gained prominence as an indicator of developmental stability in ecotoxicology. Organisms were collected from six lakes along a gradient of radionuclide contamination in Belarus and the Ukraine. Calculated total dose rates ranged from 0.06-27.1μGy/h. Fluctuating asymmetry was assessed in four meristic and one metrical trait. Significant differences in levels of pooled asymmetry were recorded between sample sites independent of sex and specific trait measured. However, there was no correlation of asymmetry with radiation doses, suggesting that differences in asymmetry were not attributed to radionuclide contamination and were driven by elevated asymmetry at a single site. No correlation between FA and measured environmental parameters suggested a biotic factor driving observed FA differences. This study appears to be the first to record no evident increase in developmental stability of biota from the Chernobyl region. These findings will aid in understanding the response of organisms to chronic pollutant exposure and the long term effects of large scale nuclear incidents such as Chernobyl and Fukushima.

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.

Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 10(7)  base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.

Are Organisms Adapting to Ionizing Radiation at Chernobyl?

Numerous organisms have shown an ability to survive and reproduce under low-dose ionizing radiation arising from natural background radiation or from nuclear accidents. In a literature review, we found a total of 17 supposed cases of adaptation, mostly based on common garden experiments with organisms only deriving from typically two or three sampling locations. We only found one experimental study showing evidence of improved resistance to radiation. Finally, we examined studies for the presence of hormesis (i.e., superior fitness at low levels of radiation compared with controls and high levels of radiation), but found no evidence to support its existence. We conclude that rigorous experiments based on extensive sampling from multiple sites are required.

Do Cupins Have a Function Beyond Being Seed Storage Proteins?

Plants continue to flourish around the site of the Chernobyl Nuclear Power Plant disaster. The ability of plants to transcend the radio-contaminated environment was not anticipated and is not well understood. The aim of this study was to evaluate the proteome of flax (Linum usitatissimum L.) during seed filling by plants grown for a third generation near Chernobyl. For this purpose, seeds were harvested at 2, 4, and 6 weeks after flowering and at maturity, from plants grown in either non-radioactive or radio-contaminated experimental fields. Total proteins were extracted and the two-dimensional gel electrophoresis (2-DE) patterns analyzed. This approach established paired abundance profiles for 130 2-DE spots, e.g., profiles for the same spot across seed filling in non-radioactive and radio-contaminated experimental fields. Based on Analysis of Variance (ANOVA) followed by sequential Bonferroni correction, eight of the paired abundance profiles were discordant. Results from tandem mass spectrometry show that four 2-DE spots are discordant because they contain fragments of the cupin superfamily-proteins. Most of the fragments were derived from the N-terminal half of native cupins. Revisiting previously published data, it was found that cupin-fragments were also involved with discordance in paired abundance profiles of second generation flax seeds. Based on these observations we present an updated working model for the growth and reproductive success of flax in a radio-contaminated Chernobyl environment. This model suggests that the increased abundance of cupin fragments or isoforms and monomers contributes to the successful growth and reproduction of flax in a radio-contaminated environment.

Revealing the seed proteome of the health benefitting grain amaranth (Amaranthus cruentus L.)

Amaranth, a staple food source in ancient Aztec, Maya and Inca cultures, has been recognized as a 21st century crop. This superfood, known as Inca wheat, attracts the worldwide attention of researchers and farmers for its superior agronomical and technological properties but especially because of its exceptional nutritive value. A combination of two-dimensional electrophoresis (2-DE) with MS facilitating the effective differentiation of 13 classes of

Using 7 cm immobilized pH gradient strips to determine levels of clinically relevant proteins in wheat grain extracts

The aim of the work was to test a relatively simple proteomics approach based on phenol extraction and two-dimensional gel electrophoresis (2-DE) with 7 cm immobilized pH gradient strips for the determination of clinically relevant proteins in wheat grain. Using this approach, 157 2-DE spots were quantified in biological triplicate, out of which 55 were identified by matrix-assisted laser desorption/ionization - time of flight tandem mass spectrometry. Clinically relevant proteins associated with celiac disease, wheat dependent exercise induced anaphylaxis, baker's asthma, and food allergy, were detected in 24 2-DE spots. However, alcohol-soluble gliadins were not detected with this approach. The comparison with a recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for the detection and quantification of clinically relevant proteins in wheat grain.

Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment

Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk.

Proteomics of field samples in radioactive Chernobyl area

Two serious nuclear accidents during the past quarter of a century contaminated large agricultural areas with radioactivity. The remediation and possible recovery of radio-contaminated areas for agricultural purposes require comprehensive characterization of plants grown in such places. Here we describe the quantitative proteomics method that we use to analyze proteins isolated from seeds of plants grown in radioactive Chernobyl zone.

Radioactive Chernobyl environment has produced high-oil flax seeds that show proteome alterations related to carbon metabolism during seed development

Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for this increase, seed development has been studied. Flax seeds were harvested in biological triplicate at 2, 4, and 6 weeks after flowering and at maturity from plants grown in nonradioactive and radio-contaminated plots in the Chernobyl area for two generations. Quantitative proteomic analyses based on 2-D gel electrophoresis (2-DE) allowed us to establish developmental profiles for 199 2-DE spots in both plots, out of which 79 were reliably identified by tandem mass spectrometry. The data suggest a statistically significant increased abundance of proteins associated with pyruvate biosynthesis via cytoplasmic glycolysis, L-malate decarboxylation, isocitrate dehydrogenation, and ethanol oxidation to acetaldehyde in early stages of seed development. This was followed by statistically significant increased abundance of ketoacyl-[acylcarrier protein] synthase I related to condensation of malonyl-ACP with elongating fatty acid chains. On the basis of these and previous data, we propose a preliminary model for plant adaptation to growth in a radio-contaminated environment. One aspect of the model suggests that changes in carbon assimilation and fatty acid biosynthesis are an integral part of plant adaptation.

The use of proteomic analysis for exploring the phytoremediation mechanism of Scirpus triqueter to pyrene

Scirpus triqueter has been reported to be an effective phytoremediation plant for pyrene dissipation. The study of S. triqueter in response to pyrene is crucial to understand the mechanism of phytoremediation. To gain a certain extent understanding of S. triqueter in response to pyrene, S. triqueter seedlings were exposed to 50 mg kg(-1) pyrene and a comparative proteomic analysis of total proteins was performed. 37 and 55 proteins were significantly differentially expressed in the shoot and root of S. triqueter upon exposure, respectively. 24 proteins (17 proteins in shoot and 7 proteins in root) were identified on the basis of the homology of their peptide profiles with existing protein sequences using mass spectrometry analysis. Analysis of protein expression patterns revealed that proteins in shoot associated with photosynthesis, defense, energy and matter metabolism, coenzyme metabolism and protein metabolism. Moreover, the proteins related photosynthesis accounted for more than 70% of the identified proteins. The proteins in root associated with stress, defense, energy metabolism, protein modification and carbohydrate metabolism. Pyrene appears to have an important deleterious effect on primary carbon metabolism, the synthesis of proteins and signal transduction. The present study demonstrates the use of proteomic approach to help us understand the phytoremediation mechanism of S. triqueter.

Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development

Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.

Global liver proteome analysis using iTRAQ labeling quantitative proteomic technology to reveal biomarkers in mice exposed to perfluorooctane sulfonate (PFOS)

Proteomic analysis allows detection of changes of proteins expression in organisms exposed to environmental pollutants, leading to the discovery of biomarkers of exposure and understanding of the action mechanism of toxicity. In the present study, we applied iTRAQ labeling quantitative proteomic technology for global characterization of the liver proteome in mice exposed to perfluorooctane sulfonate (PFOS). This successfully identified and quantified 1038 unique proteins. Seventy-one proteins showed a significant expression change in the treated groups (1.0, 2.5, 5.0 mg/kg of body weight) compared with the control group, and 16 proteins displayed strong dose-dependent changes. Gene ontology analysis showed that these differential proteins were significantly enriched and mainly involved in lipid metabolism, transport, biosynthetic processes, and response to stimulus. We detected significantly increased expression levels of enzymes regulating peroxisomal β-oxidation-including long-chain acyl-CoA synthetase, acyl-CoA oxidase 1, bifunctional enzyme, and 3-ketoacyl-CoA thiolase A. PFOS also significantly induced cytochrome P450s and glutathione S-transferases that are responsible for the metabolism of xenobiotic compounds. The expressions of several proteins with important biological functions-such as cysteine sulfinic acid decarboxylase, aldehyde dehydrogenase, and apolipoprotein A-I, also correlated with PFOS exposure. Together, the present results provide insight into the molecular mechanism and biomarkers for PFOS-induced effects.

Soybeans grown in the Chernobyl area produce fertile seeds that have increased heavy metal resistance and modified carbon metabolism

Plants grow and reproduce in the radioactive Chernobyl area, however there has been no comprehensive characterization of these activities. Herein we report that life in this radioactive environment has led to alteration of the developing soybean seed proteome in a specific way that resulted in the production of fertile seeds with low levels of oil and β-conglycinin seed storage proteins. Soybean seeds were harvested at four, five, and six weeks after flowering, and at maturity from plants grown in either non-radioactive or radioactive plots in the Chernobyl area. The abundance of 211 proteins was determined. The results confirmed previous data indicating that alterations in the proteome include adaptation to heavy metal stress and mobilization of seed storage proteins. The results also suggest that there have been adjustments to carbon metabolism in the cytoplasm and plastids, increased activity of the tricarboxylic acid cycle, and decreased condensation of malonyl-acyl carrier protein during fatty acid biosynthesis.

Agricultural recovery of a formerly radioactive area: I. Establishment of high-resolution quantitative protein map of mature flax seeds harvested from the remediated Chernobyl area

In recent years there has been an increasing tendency toward remediation of contaminated areas for agriculture purposes. The study described herein is part of a comprehensive, long-term characterization of crop plants grown in the area formerly contaminated with radioactivity. As a first step, we have established a quantitative map of proteins isolated from mature flax (Linum usitatissimum L.) seeds harvested from plants grown in a remediated plot localized directly in Chernobyl town. Flax was selected because it is a crop of economic and historical importance, despite the relative paucity of molecular resources. We used 2-dimensional electrophoresis followed by tandem mass spectrometry to establish a high-resolution seed proteome map. This approach yielded quantitative information for 318 protein spots. Genomic sequence resources for flax are very limited, leaving us with an "unknown function" annotation for 38% of the proteins analyzed including several that comprise very large spots. In addition to the seed storage proteins, we were able to reliably identify 82 proteins many of which are involved with central metabolism.

Agricultural recovery of a formerly radioactive area: II. Systematic proteomic characterization of flax seed development in the remediated Chernobyl area

Molecular characterization of crop plants grown in remediated, formerly radioactive, areas could establish a framework for future agricultural use of these areas. Recently, we have established a quantitative reference map for mature flax seed proteins (Linum usitatissimum L.) harvested from a remediated plot in Chernobyl town. Herein we describe results from our ongoing studies of this subject, and provide a proteomics-based characterization of developing flax seeds harvested from same field. A quantitative approach, based on 2-dimensional electrophoresis (2-DE) and tandem mass spectrometry, yielded expression profiles for 379 2-DE spots through seed development. Despite the paucity of genomic resources for flax, the identity for 102 proteins was reliably determined. These proteins were sorted into 11 metabolic functional classes. Proteins of unknown function comprise the largest group, and displayed a pattern of decreased abundance throughout seed development. Analysis of the composite expression profiles for metabolic protein classes revealed specific expression patterns during seed development. For example, there was an overall decrease in abundance of the glycolytic enzymes during seed development.