Biomonitoring the genotoxicity of environmental factors with transgenic plants

Glyphosate Separating and Sensing for Precision Agriculture and Environmental Protection in the Era of Smart Materials

The present article critically and comprehensively reviews the most recent reports on smart sensors for determining glyphosate (GLP), an active agent of GLP-based herbicides (GBHs) traditionally used in agriculture over the past decades. Commercialized in 1974, GBHs have now reached 350 million hectares of crops in over 140 countries with an annual turnover of 11 billion USD worldwide. However, rolling exploitation of GLP and GBHs in the last decades has led to environmental pollution, animal intoxication, bacterial resistance, and sustained occupational exposure of the herbicide of farm and companies' workers. Intoxication with these herbicides dysregulates the microbiome-gut-brain axis, cholinergic neurotransmission, and endocrine system, causing paralytic ileus, hyperkalemia, oliguria, pulmonary edema, and cardiogenic shock. Precision agriculture, i.e., an (information technology)-enhanced approach to crop management, including a site-specific determination of agrochemicals, derives from the benefits of smart materials (SMs), data science, and nanosensors. Those typically feature fluorescent molecularly imprinted polymers or immunochemical aptamer artificial receptors integrated with electrochemical transducers. Fabricated as portable or wearable lab-on-chips, smartphones, and soft robotics and connected with SM-based devices that provide machine learning algorithms and online databases, they integrate, process, analyze, and interpret massive amounts of spatiotemporal data in a user-friendly and decision-making manner. Exploited for the ultrasensitive determination of toxins, including GLP, they will become practical tools in farmlands and point-of-care testing. Expectedly, smart sensors can be used for personalized diagnostics, real-time water, food, soil, and air quality monitoring, site-specific herbicide management, and crop control.

Cytogenetic toxicity from pesticide and trace element mixtures in soils used for conventional and organic crops of Allium cepa L

Pesticides and trace elements occur in complex mixtures in agroecosystems, affecting soil health and food security. Hence, it is necessary to determine their toxicity in field conditions and to develop monitoring approaches to assess conventional and organic agriculture. The aim of this research was to evaluate the associations between Allium cepa L. cytogenetic biomarkers and the realistic mixture of pesticides and trace elements found in soils of conventional, conversion, and organic crops in an intensive agricultural region in Colombia. Pesticide screening was conducted using GC-MS/MS and LC-MS/MS methods. Arsenic, cadmium, lead, and zinc were analyzed by ICP-MS; chromium, copper, nickel, and selenium by ICP-OES; and mercury by a direct analyzer. The meristematic cells in roots of Allium cepa L. were analyzed through microscopic observations to quantify cytogenetic effects. In conventional crops, 26 pesticides were detected in the soil samples, and those were below the limit of quantification in organic crops. The mean levels of As, Cd, Cr, Ni, Pb, and Se were also greater in soils of conventional crops compared to the organics. In addition, the biomarkers of cytotoxicity and genotoxicity appeared augmented in conventional samples, and those were correlated with pesticide and trace element concentrations, pollution indices, and hazard quotients. Subsequently, a discriminant function based on the mitotic index, chromosomal aberrations, and nuclear abnormalities was suitable to classify the samples by crop type. These results demonstrate the sensitivity of Allium cepa L. to the toxicity of complex mixtures in field crops and its potential as an in-situ approach for soil health monitoring in organic and conventional crop systems.

Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants

Plants orchestrate various DNA damage responses (DDRs) to overcome the deleterious impacts of genotoxic agents on genetic materials. Ionizing radiation (IR) is widely used as a potent genotoxic agent in plant DDR research as well as plant breeding and quarantine services for commercial uses. This review aimed to highlight the recent advances in cellular and phenotypic DDRs, especially those induced by IR. Various physicochemical genotoxic agents damage DNA directly or indirectly by inhibiting DNA replication. Among them, IR-induced DDRs are considerably more complicated. Many aspects of such DDRs and their initial transcriptomes are closely related to oxidative stress response. Although many key components of DDR signaling have been characterized in plants, DDRs in plant cells are not understood in detail to allow comparison with those in yeast and mammalian cells. Recent studies have revealed plant DDR signaling pathways including the key regulator SOG1. The SOG1 and its upstream key components ATM and ATR could be functionally characterized by analyzing their knockout DDR phenotypes after exposure to IR. Considering the potent genotoxicity of IR and its various DDR phenotypes, IR-induced DDR studies should help to establish an integrated model for plant DDR signaling pathways by revealing the unknown key components of various DDRs in plants.

Homologous recombination in Arabidopsis seeds along the track of energetic carbon ions

Heavy ion irradiation has been used as radiotherapy of deep-seated tumors, and is also an inevitable health concern for astronauts in space mission. Unlike photons such as X-rays and γ-rays, a high linear energy transfer (LET) heavy ion has a varying energy distribution along its track. Therefore, it is important to determine the correlation of biological effects with the Bragg curve energy distribution of heavy ions. In this study, a continuous biological tissue equivalent was constructed using a layered cylinder of Arabidopsis seeds, which was irradiated with carbon ions of 87.5MeV/nucleon. The position of energy loss peak in the seed pool was determined with CR-39 track detectors. The mutagenic effect in vivo along the path of carbon ions was investigated with the seeds in each layer as an assay unit, which corresponded to a given position in physical Bragg curve. Homologous recombination frequency (HRF), expression level of AtRAD54 gene, germination rate of seeds, and survival rate of young seedlings were used as checking endpoints, respectively. Our results showed that Arabidopsis S0 and S1 plants exhibited significant increases in HRF compared to their controls, and the expression level of AtRAD54 gene in S0 plants was significantly up-regulated. The depth-biological effect curves for HRF and the expression of AtRAD54 gene were not consistent with the physical Bragg curve. Differently, the depth-biological effect curves for the developmental endpoints matched generally with the physical Bragg curve. The results suggested a different response pattern of various types of biological events to heavy ion irradiation. It is also interesting that except for HRF in S0 plants, the depth-biological effect curves for each biological endpoint were similar for 5Gy and 30Gy of carbon irradiation.

Genotoxicity studies performed in the ecuadorian population

Genotoxicity studies in Ecuador have been carried out during the past two decades. The focuses of the research were mainly the area of environmental issues, where the populations have been accidentally exposed to contaminants and the area of occupational exposure of individuals at the workplace. This paper includes studies carried out in the population of the Amazon region, a zone known for its rich biodiversity as well as for the ecological damage caused by oil spills and chemical sprayings whose consequences continue to be controversial. Additionally, we show the results of studies comprised of individuals occupationally exposed to toxic agents in two very different settings: flower plantation workers exposed to pesticide mixtures and X-ray exposure of hospital workers. The results from these studies confirm that genotoxicity studies can help evaluate current conditions and prevent further damage in the populations exposed to contaminants. As such, they are evidence of the need for biomonitoring employers at risk, stricter law enforcement regarding the use of pesticides, and increasingly conscientious oil extraction activities.

Reversion-reporter transgenes to analyze all six base-substitution pathways in Arabidopsis

To expand the repertoire of Arabidopsis (Arabidopsis thaliana) mutation-reporter transgenes, we constructed six mutant alleles in the same codon of the β-glucuronidase-encoding GUS transgene. Each allele reverts to GUS+ only via a particular one of the six transition/transversion pathways. AcV5 epitope tags, fused carboxyl terminal to the inactive GUS- proteins, enabled semiquantitative immunoassays in plant protein extracts. Spontaneous G:C→T:A transversions, previously not measured using reporter transgenes, were quite frequent. This may reflect mispairing of adenine with 8-oxoguanine in DNA attacked by endogenous oxyradicals. Spontaneous G:C→A:T was modest and other reversions were relatively low, as reported previously. Frequencies of ultraviolet C-induced TT→TC and TC→TT reversions were both high. With increased transgene copy number, spontaneous G:C→T:A reversions increased but ultraviolet C-induced reversions decreased. Frequencies of some reversion events were reduced among T4 versus T3 generation plants. Based on these and other analyses of sources of experimental variation, we propose guidelines for the employment of these lines to study genotoxic stress in planta.

Genotoxicity/mutagenicity of formaldehyde revealed by the Arabidopsis thaliana plants transgenic for homologous recombination substrates

Formaldehyde (FA) is a major industrial chemical and has been extensively used in the manufacture of synthetic resins and chemicals. The use of FA-containing industrial materials in daily life exposes human to FA extensively. Numerous studies indicate that FA is genotoxic, and can induce various genotoxic effects in vitro and in vivo. The primary DNA lesions induced by FA are DNA-protein crosslinks (DPCs). Recently, it has been reported that the homologous recombination (HR) mechanism is involved in the repair of DPCs, suggesting the homologous recombination could be a potential indicator for the genotoxicity/mutagenicity of FA. However, it has not yet been reported that organisms harboring recombination substrates are used for the detection of genotoxic/mutagenic effects of FA. In this present study, an Arabidopsis thaliana-line transgenic for GUS recombination substrates was used to study the genotoxicity/mutagenicity of FA, and the results showed that FA-exposure significantly increased the induction of HR in growing plants, but not in dormant seeds. We also observed an early up-regulation of expression of HR-related gene, AtRAD54, after FA-exposure. Moreover, the pretreatment with glutathione (GSH) suppressed drastically the induction of HR by FA-exposure.

Development and application of novel constructs to score C:G-to-T:A transitions and homologous recombination in Arabidopsis

We report on the development of five missense mutants and one recombination substrate of the beta-glucuronidase (GUS)-encoding gene of Escherichia coli and their use for detecting mutation and recombination events in transgenic Arabidopsis (Arabidopsis thaliana) plants by reactivation of GUS activity in clonal sectors. The missense mutants were designed to find C:G-to-T:A transitions in a symmetrical sequence context and are in that respect complementary to previously published GUS point mutants. Small peptide tags (hemagglutinin tag and Strep tag II) and green fluorescent protein were translationally fused to GUS, which offers possibilities to check for mutant GUS production levels. We show that spontaneous mutation and recombination events took place. Mutagenic treatment of the plants with ethyl methanesulfonate and ultraviolet-C increased the number of mutations, validating the use of these constructs to measure mutation and recombination frequencies in plants exposed to biotic or abiotic stress conditions, or in response to different genetic backgrounds. Plants were also subjected to heavy metals, methyl jasmonate, salicylic acid, and heat stress, for which no effect could be seen. Together with an ethyl methanesulfonate mutation induction level much higher than previously described, the need is illustrated for many available scoring systems in parallel. Because all GUS missense mutants were cloned in a bacterial expression vector, they can also be used to score mutation events in E. coli.

Transformed roots of Crepis capillaries — a sensitive system for the evaluation of the clastogenicity of abiotic agents

The presence of a large number of pollutants, including mutagenic agents in the environment is a problem of a major concern. Rapid progress in plant biotechnology, especially in the development of cell transformation methods, including the production of transformed roots -- 'hairy roots' -- has opened new possibilities to use transformed root cultures in plant bioassays for the evaluation mutagenic effects of different agents. We have used Crepis capillaris hairy roots for evaluation of cytogenetic effects of mutagenic treatment. Effects of maleic acid hydrazide (MH) and X-ray treatment were analysed in chromosomal aberration, sister chromatid exchange (SCE) and TUNEL tests. Comparison of cytogenetic effects in hairy roots and roots of seedlings showed a much higher sensitivity of hairy roots, which makes them convenient material for monitoring DNA damage after mutagenic treatment.

Systemic plant signal triggers genome instability

Previously, we have shown that infection of tobacco plants with a viral pathogen triggers local and systemic induction of homologous recombination (HR). Here, we have tested the hypothesis of whether free radicals are potentially involved in the induction of the systemic effect. We report a significant induction of HR in tobacco plants treated with radical-generating agents, UVC or rose Bengal (RB). Importantly, the recombination increase was observed in local (treated) as well as systemic (non-treated) tissue. The systemic increase in recombination implies the existence of a signal that is transmitted to non-treated tissue. Several sets of grafting experiments proved the generation of said signal by both RB and UVC exposure. A statistically significant increase in HR was observed in tissue that received a systemic signal via a grafted leaf. Similar data were obtained from transgenic plants naphthalene degrading salicylate 1-hydroxylase (NahG) unable to accumulate salicylic acid (SA). Interestingly, pre-treatment of plants with the radical-scavenging compound N-acetyl-l-cysteine (NAC) led to a significantly lower recombination increase upon grafting after treatment with UVC and RB. Moreover, leaves taken for grafting from NAC-pre-treated plants exhibited a lower level of oxidized organic compounds. Our data suggest the involvement of free radical production in either generation or maintenance of the recombination signal. We discuss potential mechanisms for generation of the signal and possible adaptive advantages of enhanced genomic flexibility following exposure to DNA-damaging agents.

Genotoxicity of 2,4-D and dicamba revealed by transgenic Arabidopsis thaliana plants harboring recombination and point mutation markers

The phenoxy herbicides 2,4-D and dicamba are released daily into the environment in large amount. The mechanisms of genotoxicity and mutagenicity of these herbicides are poorly understood, and the available genotoxicity data is controversial. There is a cogent need for a novel genotoxicity monitoring system that could provide both reliable information at the molecular level, and complement existing systems.We employed the transgenic Arabidopsis thaliana 'point mutation' and 'recombination' plants to monitor the genetic effects of the herbicides 2,4-D and dicamba. We found that both herbicides had a significant effect on the frequency of homologous recombination A-->G mutation. Neither herbicides affected the T-->G mutation frequency. Interestingly, these transgenic biomonitoring plants were able to detect the presence of phenoxy herbicides at concentrations that were lower than the guideline levels for Drinking Water Quality. The results of our studies suggest that our transgenic system may be ideal for the evaluation of the genotoxicity of herbicide-contaminated water. Moreover, the unique ability of the plants to detect both double-strand breaks (homologous recombination) and point mutations provides tremendous potential in the study of molecular mechanisms of genotoxicity and mutagenicity of phenoxy herbicides.

Genome hypermethylation in Pinus silvestris of Chernobyl--a mechanism for radiation adaptation?

Adaptation is a complex process by which populations of organisms respond to long-term environmental stresses by permanent genetic change. Here we present data from the natural "open-field" radiation adaptation experiment after the Chernobyl accident and provide the first evidence of the involvement of epigenetic changes in adaptation of a eukaryote-Scots pine (Pinus silvestris), to chronic radiation exposure. We have evaluated global genome methylation of control and radiation-exposed pine trees using a method based on cleavage by a methylation-sensitive HpaII restriction endonuclease that leaves a 5' guanine overhang and subsequent single nucleotide extension with labeled [3H] dCTP. We have found that genomic DNA of exposed pine trees was considerably hypermethylated. Moreover, hypermethylation appeared to be dependent upon the radiation dose absorbed by the trees. Such hypermethylation may be viewed as a defense strategy of plants that prevents genome instability and reshuffling of the hereditary material, allowing survival in an extreme environment. Further studies are clearly needed to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of radiation stress and adaptive response.

Homologous recombination and gene targeting in plant cells

Gene targeting has become an indispensable tool for functional genomics in yeast and mouse; however, this tool is still missing in plants. This review discusses the gene targeting problem in plants in the context of general knowledge on recombination and gene targeting. An overview on the history of gene targeting is followed by a general introduction to genetic recombination of bacteria, yeast, and vertebrates. This abridged discussion serves as a guide to the following sections, which cover plant-specific aspects of recombination assay systems, the mechanism of recombination, plant recombination genes, the relationship of recombination to the environment, approaches to stimulate homologous recombination and gene targeting, and a description of two plant systems, the moss Physcomitrella patens and the chloroplast, that naturally have high efficiencies of gene targeting. The review concludes with a discussion of alternatives to gene targeting.