Environmental genomics: mechanistic insights into toxicity of and resistance to the herbicide 2,4-D

Coding and non-coding transcripts modulated by transparent and blue PET micro-nanoplastics in Arabidopsis thaliana

To get further insights on the micro-nanoplastic (MNP) effects on plants, the aim of this study was to evaluate the response of hydroponically cultivated Arabidopsis thaliana to the presence of differentially colored polyethylene terephthalate (PET) particles. MNP impacts on the root organ were studied at a molecular level, with a special focus on the role of long non-coding RNAs (lncRNAS) in the regulation of gene expression after PET exposure. MNPs of transparent (Tr-PET) and blue (Bl-PET) material at environmentally realistic concentration caused a significant reduction in root length, while only Bl-PET significantly reduced rosette area. MNPs induced oxidative stress markers. Tr-PET upregulated genes involved in signaling of xenobiotics, whereas Bl-PET scarcely affected root transcriptomic profile, activating few gene categories for abiotic stresses. Regarding hormones, genes involved in ABA response were repressed, while brassinosteroid-related genes were differentially regulated by Tr-PET. Both MNPs, but especially Tr-PET, upregulated major latex protein-related genes. Plant molecular response to MNPs was linked to differential abundance of lncRNAs on both comparisons. Tr-PET affected the expression of much more lncRNAs than bl-PET (80 and 11 respectively). These lncRNAs were predicted to interact with several repressed protein-coding genes (i.e. glucosyltransferase UGT2, oxidative stress genes etc.), with possible effects on their regulation. A lncRNA (AT1G09297) interacted with CYP81D8, a key gene of cytochrome P450 gene family involved in xenobiotics detoxification. Two lncRNAs interacted with two members of repressed HSP (HSP90 and HSP17.4) family. Finally, genes involved in redox detoxification and stress responses were inhibited by the interaction with two microplastics-regulated lncRNAs. These data highlighted the need of investigating non-coding RNAs in the future in addition to the mostly studied protein coding transcriptome.

Genome-wide characterization of the WRKY gene family and the role of LsfWRKY29 in regulating somatic embryogenesis in hybrid sweetgum (Liquidambar styraciflua × L. formosana)

Hybrid sweetgum (Liquidambar styraciflua × L. formosana) is a globally significant forest tree resource, exhibiting significant economic, ornamental, ecological and medicinal values. Somatic embryogenesis (SE) is an effective reproductive strategy, having great application potential and economic value in large-scale propagation, artificial seed production, genetic transformation, germplasm preservation and biotechnology. It's an essential technical approach for the industrial application of hybrid sweetgum. The WRKY gene family, one of the largest groups in plants, is crucial for regulating responses related to plant growth, while its function and molecular mechanism in SE are unknown. Here, we identified 61 members of the WRKY gene family from the genome of hybrid sweetgum and characterized their amino acid sequence characteristics, phylogenetic relationships, conserved motifs, cis-acting elements and gene structures at the genome-wide level. LsfWRKY29, identified as a key gene in Weighted Gene Co-expression Network Analysis (WGCNA), is significantly expressed during the morphogenesis stage of SE. Subcellular localization studies indicate that WRKY29 is located in the nucleus. Functional assays indicate that overexpression of LsfWRKY29 leads to more abnormal embryos and subsequent developmental arrest, suggesting its negative role during SE. Yeast two-hybrid (Y2H) and luciferase complementation imaging (LCI) assays validate the interaction between LsfWRKY29 and the growth regulator LsfGRF2, a member of the growth regulators that has been extensively proven to boost plant regeneration. This interaction implies that the WRKY29-GRF2 might be an important regulatory module in SE of hybrid sweetgum. These findings provide new insights into the role of WRKY genes in regulating SE in plants.

Transcriptome and Gene Expression Analysis Revealed CeNA1: A Potential New Marker for Somatic Embryogenesis in Common Centaury (Centaurium erythraea Rafn.)

Centaurium erythraea Rafn. is a medicinal plant used as a model for studying plant developmental processes due to its developmental plasticity and ease of manipulation in vitro. Identifying the genes involved in its organogenesis and somatic embryogenesis (SE) is the first step toward unraveling the molecular mechanisms underlying its morphogenic plasticity. Although SE is the most common method of centaury regeneration, the genes involved in this have not yet been identified. The aim of this study was to identify the differentially expressed genes (DEGs) during key stages of SE and organogenesis using transcriptome data, with a focus on novel SE-related genes. The transcriptomic analysis revealed a total of 4040 DEGs during SE and 12,708 during organogenesis. Gene Ontology (GO) annotation showed that the highest number of SE-related genes was involved in defense responses. The expression of fifteen selected SE-related candidate genes was assessed by RT-qPCR across nine centaury developmental stages, including embryogenic tissues. Notably, a newly reported transcript, named CeNA1, was specifically activated during embryogenic callus (ec) induction, making it a potential novel marker for early SE. These findings provide, for the first time, insight into SE-related transcriptional patterns, representing a step closer to uncovering the molecular basis of centaury's developmental plasticity.

Synergistic effects of elevated temperature with pesticides on reproduction, development and survival of dung beetles

In times of global change, high temperatures can increase the negative effects of pesticides and other stressors. The goal of this study was to evaluate, under controlled laboratory conditions, the effect of a moderate increase in temperature in combination with ivermectin (an antiparasitic medication used in cattle that is excreted in dung), an herbicide, and parasitic pressure, on the reproductive success, development time and adult survival of dung beetles Euoniticellus intermedius. Whereas high temperature increased the number and proportion of emerged offspring, it had synergistic negative effects in combination with the ivermectin, herbicide and parasite treatments. Moreover, high temperature in combination with ivermectin and with parasitism caused a synergistic increase of adult offspring mortality and, in combination with the herbicide, it synergistically accelerated development. These results indicate that high temperatures can enhance the negative effects of other stressors and act synergistically with them, harming dung beetles, a group with high ecological and economic value in natural and productive ecosystems. Although adult sex ratio was not affected by experimental treatments, contrasting responses were found between males and females, supporting the idea that both sexes use different physiological mechanisms to cope with the same environmental challenges. The effects that combined stressors have on insects deepen our understanding of why we are losing beneficial species and their functions in times of drastic environmental changes.

DNA adduct formation in Saccharomyces cerevisiae following exposure to environmental pollutants, as in vivo model for molecular toxicity studies

DNA adduction in the model yeast Saccharomyces cerevisiae was investigated after exposure to the fungicide penconazole and the reference genotoxic compound benzo(a)pyrene, for validating yeasts as a tool for molecular toxicity studies, particularly of environmental pollution. The effect of the toxicants on the yeast's growth kinetics was determined as an indicator of cytotoxicity. Fermentative cultures of S. cerevisiae were exposed to 2 ppm of Penconazole during different phases of growth; while 0.2 and 2 ppm of benzo(a)pyrene were applied to the culture medium before inoculation and on exponential cultures. Exponential respiratory cultures were also exposed to 0.2 ppm of B(a)P for comparison of both metabolisms. Penconazole induced DNA adducts formation in the exponential phase test; DNA adducts showed a peak of 54.93 adducts/109 nucleotides. Benzo(a)pyrene induced the formation of DNA adducts in all the tests carried out; the highest amount of 46.7 adducts/109 nucleotides was obtained in the fermentative cultures after the exponential phase exposure to 0.2 ppm; whereas in the respiratory cultures, 14.6 adducts/109 nucleotides were detected. No cytotoxicity was obtained in any experiment. Our study showed that yeast could be used to analyse DNA adducts as biomarkers of exposure to environmental toxicants.

Cyanobacterial degradation of herbicide 2,4-dichlorophenoxyacetic acid (2,4-D): Its response to the oxidative stress induced by the primary degradation product 2,4-dichlorophenol (2,4-DCP)

Excessive use of herbicides in agricultural fields has become a major environmental concern due to the negative effects on the ecosystem. Microbial degradation has been well-known as an effective approach for combating such non-natural substances in soil. In the present study, the degradation of 2,4-Dichlorophenoxyacetic acid (2,4-D) as a result of metabolic activities of a cyanobacterium Nostoc muscorum Meg 1 was investigated using GC-MS analysis. After seven days of 2,4-D exposure, the main residue obtained was 2,4-dichlorophenol (2,4-DCP) at RT: 8.334 (confirmed using NIST library). The effects of 2,4-DCP were studied in a cyanobacterium Nostoc muscorum Meg 1 isolated from a rice field where 2,4-D is commonly used. Exposure to 2,4-DCP at 20, 40, and 80 ppm significantly increased ROS production in the cyanobacterium by 74, 107, and 211 % (p < 0.001). With rising 2,4-DCP concentrations in the surroundings, lipid peroxidation and protein oxidation in the organism correspondingly increased, indicating cellular injury. The mRNA and protein contents, and also the activities of different oxidant neutralizing enzymes such as CAT, SOD, GR, and GPx and the non-enzymatic antioxidants (proline, GSH, thiol and phytochelatin content) were found augmented in 20 ppm 2,4-DCP exposed cultures. However, in the presence of 40 and 80 ppm 2,4-DCP, most enzymatic and non-enzymatic antioxidants were severely compromised. At higher exposures, the organism's attempt to mitigate the oxidants was still visible, as both proline and TSH levels increased. SEM and TEM analysis aided in visualizing the effects of 2,4-DCP on the morphology and ultrastructures of the organism.

Environmental performance of phytosanitary control techniques on soybean crop estimated by life cycle assessment (LCA)

Phytosanitary control is essential to ensure agricultural productivity and quality. However, approaches based on scheduled use of pesticides, overuse of harmful molecules produce impacts on different types of living organisms. Integrated Pest and Disease Management (IPM-IDM) may significantly reduce the burden of pesticides in the environment. Plant resistance may also be included in the IPM-IDM and even in conventional management due to little requirement of additional knowledge and changes in agricultural practices. Robust environmental assessments using methodology of universal use, life cycle assessment (LCA), may estimate the impacts of specific pesticides that cause major damages, including remarkable category impacts. Therefore the objective of this study was to determine the impacts and (eco)toxicological effects of phytosanitary strategies (IPM-IDM including or not lepidopteran resistant transgenic cultivars) vs. the scheduled approach. Two inventory modeling methods were also applied to gather information on the use and applicability of these methods. Life cycle assessment (LCA) was applied using two inventory modeling methods: 100%Soil and PestLCI (Consensus) using data from Brazilian croplands under tropical conditions, by combining phytosanitary approaches (IPM-IDM, IPM-IDM + transgenic cultivar, conventional, conventional + transgenic cultivar) and modeling methods. Hence, eight soybean production scenarios were established. The IPM-IDM was efficient to reduce the (eco)toxicity impacts of soybean production mainly for freshwater ecotoxicity category. Due to the dynamic character of IPM-IDM approaches, the inclusion of recently introduced strategies (plant resistant and biological control to stink bugs and plant fungal diseases) may diminish even more the principal impacting substances throughout the Brazilian croplands. The PestLCI Consensus method, although its development is yet in progress, to date can be suggested to estimate the agriculture environmental impacts more properly under tropical conditions.

Insights into ROS-dependent signalling underlying transcriptomic plant responses to the herbicide 2,4-D

The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) functions as an agronomic weed control herbicide. High concentrations of 2,4-D induce plant growth defects, particularly leaf epinasty and stem curvature. Although the 2,4-D triggered reactive oxygen species (ROS) production, little is known about its signalling. In this study, by using a null mutant in peroxisomal acyl CoA oxidase 1 (acx1-2), we identified acyl-coenzyme A oxidase 1 (ACX1) as one of the main sources of ROS production and, in part, also causing the epinastic phenotype following 2,4-D application. Transcriptomic analyses of wild type (WT) plants after treatment with 2,4-D revealed a ROS-related peroxisomal footprint in early plant responses, while other organelles, such as mitochondria and chloroplasts, are involved in later responses. Interestingly, a group of 2,4-D-responsive ACX1-dependent transcripts previously associated with epinasty is related to auxin biosynthesis, metabolism, and signalling. We found that the auxin receptor auxin signalling F-box 3 (AFB3), a component of Skp, Cullin, F-box containing complex (SCF) (ASK-cullin-F-box) E3 ubiquitin ligase complexes, which mediates auxin/indole acetic acid (AUX/IAA) degradation by the 26S proteasome, acts downstream of ACX1 and is involved in the epinastic phenotype induced by 2,4-D. We also found that protein degradation associated with ubiquitin E3-RING and E3-SCF-FBOX in ACX1-dependent signalling in plant responses to 2,4-D is significantly regulated over longer treatment periods.

Highly specific nanobody against herbicide 2,4-dichlorophenoxyacetic acid for monitoring of its contamination in environmental water

2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide, is a small organic chemical pollutant in the environment. To develop a nanobody-based immunoassay for monitoring trace levels of 2,4-D, a step-wise strategy for the generation of nanobodies highly specific against this small chemical was employed. Firstly, we synthesized three novel haptens mimicking 2,4-D and assessed their influence on the sensitivity and specificity of the existing antibody-based assay. Polyclonal antibodies (pAb) from rabbits showed good sensitivity and moderate specificity for 2,4-D, pAb from llama based on selected haptens showed similar performance when compared to those from rabbits. Secondly, nanobodies derived from llama were generated for 2,4-D by an effective procedure, including serum monitoring and one-step library construction. One nanobody, NB3-9, exhibited good sensitivity against 2,4-D (IC₅₀ = 29.2 ng/mL) had better specificity than the rabbit pAb#1518, with no cross-reactivities against the 2,4-D analogs tested. Thirdly, one-step fluorescent enzyme immunoassay (FLEIA) for 2,4-D based on a nanobody-alkaline phosphatase (AP) fusion was developed with IC₅₀ of 1.9 ng/mL and a linear range of 0.4-8.6 ng/mL. Environmental water samples were analyzed by FLEIA and LC-MS/MS for comparison, and the results were consistent between both methods. Therefore, the proposed step-wise strategy from hapten design to nanobody-AP fusion production was successfully conducted, and the resulting nanobody based FLEIA was demonstrated as a convenient tool to monitor 2,4-D residuals in the environment.

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.

Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover

Herbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In this study, we used populations of the forage legume crop red clover (Trifolium pratense L.) that were recurrently selected for 2,4-D resistance to detect genome-wide signatures of adaptation. Four susceptible and six derived resistant populations were sequenced using a less costly approach by combining targeted sequencing (Capture-Seq) with pooled individuals (Pool-Seq). Genomic signatures of selection were identified using: (i) pairwise allele frequency differences; (ii) genome scan for overly differentiated loci; and (iii) genome‐wide association. Fifty significant SNPs were consistently detected, most located in a single chromosome, which can be useful for marker assisted selection. Additionally, we searched for candidate genes at these genomic regions to gain insights into potential molecular mechanisms underlying 2,4-D resistance. Among the predicted functions of candidate genes, we found some related to the auxin metabolism, response to oxidative stress, and detoxification, which are also promising for further functional validation studies.

ERF-VII transcription factors induce ethanol fermentation in response to amino acid biosynthesis-inhibiting herbicides

Herbicides inhibiting either aromatic or branched-chain amino acid biosynthesis trigger similar physiological responses in plants, despite their different mechanism of action. Both types of herbicides are known to activate ethanol fermentation by inducing the expression of fermentative genes; however, the mechanism of such transcriptional regulation has not been investigated so far. In plants exposed to low-oxygen conditions, ethanol fermentation is transcriptionally controlled by the ethylene response factors-VII (ERF-VIIs), whose stability is controlled in an oxygen-dependent manner by the Cys-Arg branch of the N-degron pathway. In this study, we investigated the role of ERF-VIIs in the regulation of the ethanol fermentation pathway in herbicide-treated Arabidopsis plants grown under aerobic conditions. Our results demonstrate that these transcriptional regulators are stabilized in response to herbicide treatment and are required for ethanol fermentation in these conditions. We also observed that mutants with reduced fermentative potential exhibit higher sensitivity to herbicide treatments, thus revealing the existence of a mechanism that mimics oxygen deprivation to activate metabolic pathways that enhance herbicide tolerance. We speculate that this signaling pathway may represent a potential target in agriculture to affect tolerance to herbicides that inhibit amino acid biosynthesis.

Population Genomic Approaches for Weed Science

Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.

Physiological Genomics of Multistress Resistance in the Yeast Cell Model and Factory: Focus on MDR/MXR Transporters

The contemporary approach of physiological genomics is vital in providing the indispensable holistic understanding of the complexity of the molecular targets, signalling pathways and molecular mechanisms underlying the responses and tolerance to stress, a topic of paramount importance in biology and biotechnology. This chapter focuses on the toxicity and tolerance to relevant stresses in the cell factory and eukaryotic model yeast Saccharomyces cerevisiae. Emphasis is given to the function and regulation of multidrug/multixenobiotic resistance (MDR/MXR) transporters. Although these transporters have been considered drug/xenobiotic efflux pumps, the exact mechanism of their involvement in multistress resistance is still open to debate, as highlighted in this chapter. Given the conservation of transport mechanisms from S. cerevisiae to less accessible eukaryotes such as plants, this chapter also provides a proof of concept that validates the relevance of the exploitation of the experimental yeast model to uncover the function of novel MDR/MXR transporters in the plant model Arabidopsis thaliana. This knowledge can be explored for guiding the rational design of more robust yeast strains with improved performance for industrial biotechnology, for overcoming and controlling the deleterious activities of spoiling yeasts in the food industry, for developing efficient strategies to improve crop productivity in agricultural biotechnology.

Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae

Accidental spills and misuse of pesticides may lead to current and/or legacy environmental contamination and may pose concerns regarding possible risks towards non-target microbes and higher eukaryotes in ecosystems. The present study was aimed at comparing transcriptomic responses to effects of sub-lethal levels of six environmentally relevant pesticide active substances in the Saccharomyces cerevisiae eukaryotic model. The insecticide carbofuran, the fungicide pyrimethanil and the herbicides alachlor, S-metolachlor, diuron and methyl(4-chloro-2-methylphenoxy)acetate were studied. Some are currently used agricultural pesticides, while others are under restricted utilization or banned in Europe and/or North America albeit being used in other geographical locations. In the present work transcriptional profiles representing genome-wide responses in a standardized yeast population upon 2 h of exposure to concentrations of each compound exerting equivalent toxic effects, i.e., inhibition of growth by 20% relative to the untreated control cells, were examined. Hierarchical clustering and Venn analyses of the datasets of differentially expressed genes pointed out transcriptional patterns distinguishable between the six active substances. Functional enrichment analyses allowed predicting mechanisms of pesticide toxicity and response to pesticide stress in the yeast model. In general, variations in transcript numbers of selected genes assessed by Real-Time quantitative reverse transcription polymerase chain reaction confirmed microarray data and correlated well with growth inhibitory effects. A possible biological relevance of mechanistic predictions arising from these comparative transcriptomic analyses is discussed in the context of better understanding potential modes of action and adverse side-effects of pesticides.

Exposure to the herbicide 2,4-D produces different toxic effects in two different phytoplankters: A green microalga (Ankistrodesmus falcatus) and a toxigenic cyanobacterium (Microcystis aeruginosa)

The extensive use of 2,4-dichlorophenoxiacetic acid (2,4-D) in agriculture is an important source of pollution to water and soil. Toxicity of commonly used herbicides to non-target, planktonic photosynthetic organisms has not been described completely yet. Therefore, we determined the effect of subinhibitory 2,4-D concentrations on the Chlorophycean alga Ankistrodesmus falcatus and on a toxigenic strain of the cyanobacterium Microcystis aeruginosa. Population growth, photosynthetic pigments, macromolecular biomarkers (carbohydrates, lipids, and protein), and antioxidant enzymes (catalase [CAT], glutathione peroxidase [GPx], and superoxide dismutase [SOD]) were quantified, and the integrated biomarker response (IBR) was calculated. Scanning electron microscope (SEM) and transmission electron microscope (TEM) observations were also performed. The 96-h median inhibitory concentration (IC₅₀) for 2,4-D was 1353.80 and 71.20mgL^-1 for the alga and the cyanobacterium, respectively. Under 2,4-D stress, both organisms increased pigments and macromolecules concentration, modified the activity of all the evaluated enzymes, and exhibited ultrastructural alterations. M. aeruginosa also increased microcystins production, and A. falcatus showed external morphological alterations. The green alga was tolerant to high concentrations of the herbicide, whereas the cyanobacterium exhibited sensitivity comparable to other phytoplankters. Both organisms were tolerant to comparatively high concentrations of the herbicide; however, negative effects on the assessed biomarkers and cell morphology were significant. Moreover, stimulation of the production of cyanotoxins under chemical stress could increase the risk for the biota in aquatic environments, related to herbicides pollution in eutrophic freshwater ecosystems.

Optimization of diazinon biodegradation from aqueous solutions by Saccharomyces cerevisiae using response surface methodology

Diazinon is an organophosphate compound that inhibits the activity of acetylcholinesterase. Standards of the World Health Organization and Environmental Protection Agency for diazinon concentration in water are 0.1 and 9 × 10⁻⁶ mg/L, respectively. The aim of this study was the optimization of diazinon biodegradation from aqueous solutions by Saccharomyces cerevisiae using the response surface methodology (RSM). Harvested cells of S. cerevisiae were locally purchased from the Iranian Research Organization for Science and Technology. To obtain the optimum condition for diazinon biodegradation using RSM, input parameters included the initial concentration of diazinon (0.01–10 mg/L), concentration of S. cerevisiae (0.5–5%), pH (4–10), and retention time (1–30 h). The research study had a central composite design where one of the methods was RSM. According to the results, the observed values of the removal efficiency of diazinon were variable in the range of 23–96. The highest removal rate was obtained as 96% under the initial diazinon concentration of 2.5 mg/L, S. cerevisiae concentration of 3.88%, pH of 5.5, and retention time of 22.75 h. The results displayed that the removal efficiency of diazinon had a direct relationship with the concentration of S. cerevisiae and retention time, and an inverse relationship with pH and the initial concentration of diazinon. We can conclude that S. cerevisiae has the ability to remove diazinon with the lowest cost and a high efficiency.

A New Determinant of Candida glabrata Virulence: The Acetate Exporter CgDtr1

Persistence and virulence of Candida glabrata infections are multifactorial phenomena, whose understanding is crucial to design more suitable therapeutic strategies. In this study, the putative multidrug transporter CgDtr1, encoded by ORF CAGL0M06281g, is identified as a determinant of C. glabrata virulence in the infection model Galleria mellonella. CgDTR1 deletion is shown to decrease the ability to kill G. mellonella larvae by decreasing C. glabrata ability to proliferate in G. mellonella hemolymph, and to tolerate the action of hemocytes. The possible role of CgDtr1 in the resistance to several stress factors that underlie death induced by phagocytosis was assessed. CgDTR1 was found to confer resistance to oxidative and acetic acid stress. Consistently, CgDtr1 was found to be a plasma membrane acetic acid exporter, relieving the stress induced upon C. glabrata cells within hemocytes, and thus enabling increased proliferation and virulence against G. mellonella larvae.

Induction of the PDH bypass and upregulation of the ALDH7B4 in plants treated with herbicides inhibiting amino acid biosynthesis

Imazamox and glyphosate represent two classes of herbicides that inhibit the activity of acetohydroxyacid synthase in the branched-chain amino acid biosynthesis pathway and the activity of 5-enolpyruvylshikimate-3-phosphate synthase in the aromatic amino acid biosynthesis pathway, respectively. However, it is still unclear how imazamox and glyphosate lead to plant death. Both herbicides inhibit amino-acid biosynthesis and were found to induce ethanol fermentation in plants, but an Arabidopsis mutant deficient in alcohol dehydrogenase 1 was neither more susceptible nor more resistant than the wild-type to the herbicides. In this study, we investigated the effects of the amino acid biosynthesis inhibitors, imazamox and glyphosate, on the pyruvate dehydrogenase bypass reaction and fatty acid metabolism in A. thaliana. We found that the pyruvate dehydrogenase bypass was upregulated following the treatment by the two herbicides. Our results suggest that the Arabidopsis aldehyde dehydrogenase 7B4 gene might be participating in the pyruvate dehydrogenase bypass reaction. We evaluated the potential role of the aldehyde dehydrogenase 7B4 upon herbicide treatment in the plant defence mechanism. Plants that overexpressed the ALDH7B4 gene accumulated less soluble sugars, starch, and fatty acids and grew better than the wild-type after herbicide treatment. We discuss how the upregulation of the ALDH7B4 alleviates the effects of the herbicides, potentially through the detoxification of the metabolites produced in the pyruvate dehydrogenase bypass.

Intensive herbicide use has selected for constitutively elevated levels of stress-responsive mRNAs and proteins in multiple herbicide-resistant Avena fatua L

BACKGROUND

Intensive use of herbicides has led to the evolution of two multiple herbicide-resistant (MHR) Avena fatua (wild oat) populations in Montana that are resistant to members of all selective herbicide families available for A. fatua control in US small grain crops. We used transcriptome and proteome surveys to compare constitutive changes in MHR and herbicide-susceptible (HS) plants associated with non-target site resistance.

RESULTS

Compared to HS plants, MHR plants contained constitutively elevated levels of differentially expressed genes (DEGs) with functions in xenobiotic catabolism, stress response, redox maintenance and transcriptional regulation that are similar to abiotic stress-tolerant phenotypes. Proteome comparisons identified similarly elevated proteins including biosynthetic and multifunctional enzymes in MHR plants. Of 25 DEGs validated by RT-qPCR assay, differential regulation of 21 co-segregated with flucarbazone-sodium herbicide resistance in F₃ families, and a subset of 10 of these were induced or repressed in herbicide-treated HS plants.

CONCLUSION

Although the individual and collective contributions of these DEGs and proteins to MHR remain to be determined, our results support the idea that intensive herbicide use has selected for MHR populations with altered, constitutively regulated patterns of gene expression that are similar to those in abiotic stress-tolerant plants. © 2017 Society of Chemical Industry.

Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

Background

The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level.

Results

In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization.

Conclusions

In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3896-y) contains supplementary material, which is available to authorized users.

Phytohormone Behavior in the Model Environment of Plant and Human Lipid Membranes

Interactions between three auxins (indole-3-acetic acid (IAA), 2-naphthoxyacetic acid (BNOA), and 2,4-dichlorophenoxyacetic acid (2,4-D)) and model two-dimensional lipid systems mimicking plant and human cell membranes were investigated in monolayers formed at the air/water solution interface. The analysis was based on the recorded π-A isotherm characteristics complemented with Brewster angle microscopy. The influence of auxins on model membranes was discussed on the basis of condensation changes, modification of mutual lipid-lipid interactions in the mixed films, and morphological alteration of the surface domains on the microscopic scale. It was demonstrated that the lipid composition and mutual proportion of the artificial membranes together with sterol to main the phospholipid ratio play a crucial role in the context of auxin behavior in the membrane-mimicking environment. Apart from specific molecular interactions between studied phytohormones represented by auxins and lipids, the condensation of the investigated monolayers was found to be a regulative factor of model systems' susceptibility toward auxin action. Two effects were recognized: fluidizing of monolayers being in the liquid state (model membranes) and initialization of the three-dimensional structure formation in ordered sterol films at high surface pressure. The influence of auxin molecules on lipid interactions in the monolayer and diminishing of the film condensation was the largest for BNOA, due to the presence of the most bulky nonpolar, aromatic fragment in the molecule. It was also demonstrated that auxins interact with model plant membranes more selectively, stronger, and at markedly lower concentration than with the human membrane models.

Yeast response and tolerance to benzoic acid involves the Gcn4- and Stp1-regulated multidrug/multixenobiotic resistance transporter Tpo1

The action of benzoic acid in the food and beverage industries is compromised by the ability of spoilage yeasts to cope with this food preservative. Benzoic acid occurs naturally in many plants and is an intermediate compound in the biosynthesis of many secondary metabolites. The understanding of the mechanisms underlying the response and resistance to benzoic acid stress in the eukaryotic model yeast is thus crucial to design more suitable strategies to deal with this toxic lipophilic weak acid. In this study, the Saccharomyces cerevisiae multidrug transporter Tpo1 was demonstrated to confer resistance to benzoic acid. TPO1 transcript levels were shown to be up-regulated in yeast cells suddenly exposed to this stress agent. This up-regulation is under the control of the Gcn4 and Stp1 transcription factors, involved in the response to amino acid availability, but not under the regulation of the multidrug resistance transcription factors Pdr1 and Pdr3 that have binding sites in TPO1 promoter region. Benzoic acid stress was further shown to affect the intracellular pool of amino acids and polyamines. The observed decrease in the concentration of these nitrogenous compounds, registered upon benzoic acid stress exposure, was not found to be dependent on Tpo1, although the limitation of yeast cells on nitrogenous compounds was found to activate Tpo1 expression. Altogether, the results described in this study suggest that Tpo1 is one of the key players standing in the crossroad between benzoic acid stress response and tolerance and the control of the intracellular concentration of nitrogenous compounds. Also, results can be useful to guide the design of more efficient preservation strategies and the biotechnological synthesis of benzoic acid or benzoic acid-derived compounds.

Effects of an herbicide on physiology, morphology, and fitness of the dung beetle Euoniticellus intermedius (Coleoptera: Scarabaeidae)

Some agrochemical compounds threaten nontarget organisms and their functions in the ecosystem. The authors experimentally evaluated the effects of one of the most common herbicide mixtures used worldwide, containing 2,4-dichlorophenoxyacetic acid and picloram, on dung beetles, which play fundamental roles in the function of natural and managed ecosystems. The present study employed techniques of physiology and geometric morphometrics, besides including fitness measurements, to assess the effects of the herbicide in the introduced beetle Euoniticellus intermedius. Because herbicide components promote oxidative stress and affect survival in certain insects, the authors predicted negative effects on the beetles. Unexpectedly, no effect of herbicide concentration was found on clutch size, sex ratio, and fluctuating asymmetry, and it even increased physiological condition and body size in exposed beetles. Because the studied species presents 2 male morphs, the authors, for the first time, evaluated the effect of a pollutant on the ratio of these morphs. Contrary to the prediction, the herbicide mixture increased the proportion of major males. Thus, the herbicide does not threaten populations of the studied beetles. The present study discusses how both negative and positive effects of pollutants on wild animals modify natural and sexual selection processes occurring in nature, which ultimately impact population dynamics. The authors recommend the use of physiological and geometric morphometrics techniques to assess the impact of pollutants on nontarget animals. Environ Toxicol Chem 2017;36:96-102. © 2016 SETAC.

Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

Herbicide impact is usually assessed as the result of a unilinear mode of action on a specific biochemical target with a typical dose-response dynamics. Recent developments in plant molecular signaling and crosstalk between nutritional, hormonal and environmental stress cues are however revealing a more complex picture of inclusive toxicity. Herbicides induce large-scale metabolic and gene-expression effects that go far beyond the expected consequences of unilinear herbicide-target-damage mechanisms. Moreover, groundbreaking studies have revealed that herbicide action and responses strongly interact with hormone signaling pathways, with numerous regulatory protein-kinases and -phosphatases, with metabolic and circadian clock regulators and with oxidative stress signaling pathways. These interactions are likely to result in mechanisms of adjustment that can determine the level of sensitivity or tolerance to a given herbicide or to a mixture of herbicides depending on the environmental and developmental status of the plant. Such regulations can be described as rheostatic and their importance is discussed in relation with herbicide use strategies, environmental risk assessment and global change assessment challenges.

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.

Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis

Transcriptional regulation is one of the key steps in the control of gene expression, with huge impact on the survival, adaptation, and fitness of all organisms. However, it is becoming increasingly clear that transcriptional regulation is far more complex than initially foreseen. In model organisms such as the yeast Saccharomyces cerevisiae evidence has been piling up showing that the expression of each gene can be controlled by several transcription factors, in the close dependency of the environmental conditions. Furthermore, transcription factors work in intricate networks, being themselves regulated at the transcriptional, post-transcriptional, and post-translational levels, working in cooperation or antagonism in the promoters of their target genes.In this chapter, a step-by-step guide using the YEASTRACT database is provided, for the prediction and ranking of the transcription factors required for the regulation of the expression a single gene and of a genome-wide response. These analyses are illustrated with the regulation of the PDR18 gene and of the transcriptome-wide changes induced upon exposure to the herbicide 2,4-Dichlorophenoxyacetic acid (2,4-D), respectively. The newest potentialities of this information system are explored, and the various results obtained in the dependency of the querying criteria are discussed in terms of the knowledge gathered on the biological responses considered as case studies.

Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective

The budding yeast Saccharomyces cerevisiae represents a well-consolidated and widely used eukaryotic model, with a number of features that make it an ideal organism to carry out functional toxicological studies. Several advantages are permitted by the use of yeast cells, as the possibility to identify molecular biomarkers, unknown mechanisms of action and novel potential targets. Thanks to the evolutionary conservation, yeast can provide also useful clues allowing the prioritization of more complex analyses and toxicity predictions in higher eukaryotes. The last two decades were incredibly fruitful for yeast "omics", but referring to the analysis of the effects of pesticides on yeast much still remains to be done. Furthermore, a deeper knowledge of the effects of environmental pollutants on biotechnological processes associated with the use of yeasts is to be hoped.

The studies on the toxicity mechanism of environmentally hazardous natural (IAA) and synthetic (NAA) auxin--The experiments on model Arabidopsis thaliana and rat liver plasma membranes

This paper concerns the studies towards membrane-damage effect of two auxins: indole-3-acetic acid - IAA and 1-naphthaleneacetic acid - NAA on plant (Arabidopsis thaliana) and animal (rat liver) model membranes. The foregoing auxins are plant growth regulators widely used in agriculture to control the quality of the crop. However, their accumulation in the environment makes them hazardous for the living organisms. The aim of our investigations was to compare the effect of natural (IAA) vs. synthetic (NAA) auxin on the organization of plant and animal model membranes and find a possible correlation between membrane-disturbing effect of these compounds and their toxicity. The collected data evidenced that auxins cause destabilization of membranes, decrease their condensation and weakens interactions of molecules. The alterations in the morphology of model systems were also noticed. The foregoing effects of auxins are concentration-dependent and additionally NAA was found to act on animal vs. plant membranes more selectively than IAA. Interestingly, both IAA and NAA induce the strongest disordering in model lipid system at the concentration, which is frequently reported as toxic to animal and plants. Based on the above findings it was proposed that membrane-damage effect induced by IAA and NAA may be important from the point of view of the mechanism of toxicity of these compounds and cannot be ignored in further investigations in this area.

The phenotype of grape leaves caused by acetochlor or fluoroglycofen, and effects of latter herbicide on grape leaves

Fluoroglycofen and acetochlor are two different herbicides used in vineyards to eradicate weeds. This present study first characterized the effects of these chemicals on phenotype of grape leaves. Results showed that acetochlor caused the middle- and upper-node grape leaves become yellow at 60th day after treatment, while fluoroglycofen caused the ones became dark green. Then the effects of fluoroglycofen on photosynthetic pigments and chloroplast ultrastructure were characterized. Results showed that fluoroglycofen increased the chlorophyll and carotenoid contents by different extent in different node leaves, while it did not affect the net photosynthesis rate significantly. Chloroplast ultrastructure analysis showed that the gap between thylakoids layers in few chloroplasts of middle-node leaves increased, which was also observed in ones of upper-node leaves; the number and size of chloroplast increased. Analysis on the deformed leaves of grapevines treated with 375 g ai ha(-1) fluoroglycofen showed that the starch grain per cell was much more and larger than that in the same size control leaves; the dark green and yellow parts had more or fewer chloroplast than the control, respectively, but both with more grana per chloroplast and less layers per granum. Chloroplasts went larger and round. Taken together, these results suggested that fluoroglycofen caused the grape leaves become dark green, which might be associated with the changes of chloroplast; the growth inhibition in the second year might be due to accumulation of starch.

2,4-Dichlorophenoxyacetic acid promotes S-nitrosylation and oxidation of actin affecting cytoskeleton and peroxisomal dynamics

2,4-Dichlorophenoxyacetic acid (2,4-D) is a synthetic auxin used as a herbicide to control weeds in agriculture. A high concentration of 2,4-D promotes leaf epinasty and cell death. In this work, the molecular mechanisms involved in the toxicity of this herbicide are studied by analysing in Arabidopsis plants the accumulation of reactive oxygen species (ROS) and nitric oxide (NO), and their effect on cytoskeleton structure and peroxisome dynamics. 2,4-D (23 mM) promotes leaf epinasty, whereas this process was prevented by EDTA, which can reduce ·OH accumulation. The analysis of ROS accumulation by confocal microscopy showed a 2,4-D-dependent increase in both H2O2 and O2·(-), whereas total NO was not affected by the treatment. The herbicide promotes disturbances on the actin cytoskeleton structure as a result of post-translational modification of actin by oxidation and S-nitrosylation, which could disturb actin polymerization, as suggested by the reduction of the F-actin/G-actin ratio. These effects were reduced by EDTA, and the reduction of ROS production in Arabidopsis mutants deficient in xanthine dehydrogenase (Atxdh) gave rise to a reduction in actin oxidation. Also, 2,4-D alters the dynamics of the peroxisome, slowing the speed and shortening the distances by which these organelles are displaced. It is concluded that 2,4-D promotes oxidative and nitrosative stress, causing disturbances in the actin cytoskeleton, thereby affecting the dynamics of peroxisomes and some other organelles such as the mitochondria, with xanthine dehydrogenase being involved in ROS production under these conditions. These structural changes in turn appear to be responsible for the leaf epinasty.

The effects of sublethal levels of 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) on feeding behaviors of the crayfish O. rusticus

The widespread use of herbicides across the globe has increased the probability of synthetic chemicals entering freshwater habitats. On entering aquatic habitats, these chemicals target and disrupt both physiological and behavioral functioning in various aquatic organisms. Herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D), can have negative impacts on chemoreception because these receptor cells are in direct contact with water-soluble chemicals in the environment. Studies focusing on lethal concentration (LC50) levels may understate the impact of herbicides within aquatic habitats because damage to the chemoreceptors can result in modified behaviors or lack of appropriate responses to environmental or social cues. The purpose of this experiment was to determine whether exposure to sublethal levels of 2,4-D alters the foraging behaviors of crayfish Orconectes rusticus. We hypothesized that crayfish exposed to greater concentrations of 2,4-D would be less successful in locating food or on locating food would consume smaller amounts possibly due to an inability to recognize the food odors in the contaminated waters. Crayfish were exposed to three sublethal levels of 2,4-D for 96 h and placed into a Y-maze system with a fish gelatin food source placed randomly in the right or left arm. Average walking speed, average time spent in the correct arm, and percent consumption were analyzed. Our data show that crayfish were impaired in their ability to forage effectively. These inabilities to locate and consume adequate amounts of food could result in lower body weights and decreased fitness in populations of crayfish exposed to 2,4-D in natural habitats.

Physiology and toxicology of hormone-disrupting chemicals in higher plants

Higher plants are exposed to natural environmental organic chemicals, associated with plant-environment interactions, and xenobiotic environmental organic chemicals, associated with anthropogenic activities. The effects of these chemicals result not only from interaction with metabolic targets, but also from interaction with the complex regulatory networks of hormone signaling. Purpose-designed plant hormone analogues thus show extensive signaling effects on gene regulation and are as such important for understanding plant hormone mechanisms and for manipulating plant growth and development. Some natural environmental chemicals also act on plants through interference with the perception and transduction of endogenous hormone signals. In a number of cases, bioactive xenobiotics, including herbicides that have been designed to affect specific metabolic targets, show extensive gene regulation effects, which are more in accordance with signaling effects than with consequences of metabolic effects. Some of these effects could be due to structural analogies with plant hormones or to interference with hormone metabolism, thus resulting in situations of hormone disruption similar to animal cell endocrine disruption by xenobiotics. These hormone-disrupting effects can be superimposed on parallel metabolic effects, thus indicating that toxicological characterisation of xenobiotics must take into consideration the whole range of signaling and metabolic effects. Hormone-disruptive signaling effects probably predominate when xenobiotic concentrations are low, as occurs in situations of residual low-level pollutions. These hormone-disruptive effects in plants may thus be of importance for understanding cryptic effects of low-dosage xenobiotics, as well as the interactive effects of mixtures of xenobiotic pollutants.

Fetotoxicity of 2,4-dichlorophenoxyacetic acid in rats and the protective role of vitamin E

The present study was conducted to investigate the potential role of 2,4-dichlorophenoxyacetic acid (2,4-D) in inducing developmental toxicity and oxidative damage in pregnant rats and their fetuses as well as to assess the efficacy of vitamin E to prevent or alleviate such defects. Pregnant rats received 2,4-D (100 mg/kg bw) alone or in combination with vitamin E (100 mg/kg bw) daily from gestation day 1 to 19. The number of implantations, viable and resorbed fetuses and sex ratio were not statistically different among groups. However, fetuses maternally treated with 2,4-D were characterized by lower body weight and higher morphologic and skeletal defect rate. 2,4-D induced oxidative stress in the liver of mothers and fetuses which was indicated by a significant elevation of malondialdehyde level with reduction in catalase activity and total antioxidant capacity. Coadministration of vitamin E can counteract the deleterious effects of 2,4-D by successive reduction in the oxidative stress.

Xenobiotic sensing and signalling in higher plants

Anthropogenic changes and chemical pollution confront plant communities with various xenobiotic compounds or combinations of xenobiotics, involving chemical structures that are at least partially novel for plant species. Plant responses to chemical challenges and stimuli are usually characterized by the approaches of toxicology, ecotoxicology, and stress physiology. Development of transcriptomics and proteomics analysis has demonstrated the importance of modifications to gene expression in plant responses to xenobiotics. It has emerged that xenobiotic effects could involve not only biochemical and physiological disruption, but also the disruption of signalling pathways. Moreover, mutations affecting sensing and signalling pathways result in modifications of responses to xenobiotics, thus confirming interference or crosstalk between xenobiotic effects and signalling pathways. Some of these changes at gene expression, regulation and signalling levels suggest various mechanisms of xenobiotic sensing in higher plants, in accordance with xenobiotic-sensing mechanisms that have been characterized in other phyla (yeast, invertebrates, vertebrates). In higher plants, such sensing systems are difficult to identify, even though different lines of evidence, involving mutant studies, transcription factor analysis, or comparative studies, point to their existence. It remains difficult to distinguish between the hypothesis of direct xenobiotic sensing and indirect sensing of xenobiotic-related modifications. However, future characterization of xenobiotic sensing and signalling in higher plants is likely to be a key element for determining the tolerance and remediation capacities of plant species. This characterization will also be of interest for understanding evolutionary dynamics of stress adaptation and mechanisms of adaptation to novel stressors.

Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology

The emerging transdisciplinary field of Toxicogenomics aims to study the cell response to a given toxicant at the genome, transcriptome, proteome, and metabolome levels. This approach is expected to provide earlier and more sensitive biomarkers of toxicological responses and help in the delineation of regulatory risk assessment. The use of model organisms to gather such genomic information, through the exploitation of Omics and Bioinformatics approaches and tools, together with more focused molecular and cellular biology studies are rapidly increasing our understanding and providing an integrative view on how cells interact with their environment. The use of the model eukaryote Saccharomyces cerevisiae in the field of Toxicogenomics is discussed in this review. Despite the limitations intrinsic to the use of such a simple single cell experimental model, S. cerevisiae appears to be very useful as a first screening tool, limiting the use of animal models. Moreover, it is also one of the most interesting systems to obtain a truly global understanding of the toxicological response and resistance mechanisms, being in the frontline of systems biology research and developments. The impact of the knowledge gathered in the yeast model, through the use of Toxicogenomics approaches, is highlighted here by its use in prediction of toxicological outcomes of exposure to pesticides and pharmaceutical drugs, but also by its impact in biotechnology, namely in the development of more robust crops and in the improvement of yeast strains as cell factories.

The broad-leaf herbicide 2,4-dichlorophenoxyacetic acid turns rice into a living trap for a major insect pest and a parasitic wasp

Synthetic chemical elicitors of plant defense have been touted as a powerful means for sustainable crop protection. Yet, they have never been successfully applied to control insect pests in the field. We developed a high-throughput chemical genetics screening system based on a herbivore-induced linalool synthase promoter fused to a β-glucuronidase (GUS) reporter construct to test synthetic compounds for their potential to induce rice defenses. We identified 2,4-dichlorophenoxyacetic acid (2,4-D), an auxin homolog and widely used herbicide in monocotyledonous crops, as a potent elicitor of rice defenses. Low doses of 2,4-D induced a strong defensive reaction upstream of the jasmonic acid and ethylene pathways, resulting in a marked increase in trypsin proteinase inhibitor activity and volatile production. Induced plants were more resistant to the striped stem borer Chilo suppressalis, but became highly attractive to the brown planthopper Nilaparvata lugens and its main egg parasitoid Anagrus nilaparvatae. In a field experiment, 2,4-D application turned rice plants into living traps for N. lugens by attracting parasitoids. Our findings demonstrate the potential of auxin homologs as defensive signals and show the potential of the herbicide to turn rice into a selective catch crop for an economically important pest.

Oxidative stress induced by 2,4-phenoxyacetic acid in liver of female rats and their progeny: biochemical and histopathological studies

The 2,4-Dichlorophenoxyacetic acid (2,4-D) was used in agriculture as an herbicide in many countries including Tunisia. The aim of this study was to evaluate the effects of 2,4-D on liver function of adult rats and their progeny. Female Wistar rats were divided into two groups: the controls and the treated rats which received 600 ppm of 2,4-D in their drinking water from the 14th day of pregnancy until day 14 after delivery. In 2,4-D group, a significant decrease in body weight of pups was noted, when compared to controls. Liver antioxidant enzyme activities, superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) decreased, while malondialdehyde (MDA) levels increased in dams and pups. Moreover, plasma aminotransferases (ALT, AST), gamma glutamil transpeptidase (GGT), lactate dehydrogenase (LDH), bilirubin and albumin levels were increased significantly. The biochemical modifications were correlated with histopathological studies. We concluded that 2,4-D induced hepatotoxicity in adult and suckling rats.

The yeast ABC transporter Pdr18 (ORF YNR070w) controls plasma membrane sterol composition, playing a role in multidrug resistance

The action of multidrug efflux pumps in MDR (multidrug resistance) acquisition has been proposed to partially depend on the transport of physiological substrates which may indirectly affect drug partition and transport across cell membranes. In the present study, the PDR18 gene [ORF (open reading frame) YNR070w], encoding a putative PDR (pleiotropic drug resistance) transporter of the ATP-binding cassette superfamily, was found to mediate plasma membrane sterol incorporation in yeast. The physiological role of Pdr18 is demonstrated to affect plasma membrane potential and is proposed to underlie its action as a MDR determinant, conferring resistance to the herbicide 2,4-D (2,4-dichlorophenoxyacetic acid). The action of Pdr18 in yeast tolerance to 2,4-D, which was found to contribute to reduce [(14)C]2,4-D intracellular accumulation, may be indirect, given the observation that 2,4-D exposure deeply affects the sterol plasma membrane composition, this effect being much stronger in a Δpdr18 background. PDR18 activation under 2,4-D stress is regulated by the transcription factors Nrg1, controlling carbon source availability and the stress response, and, less significantly, Yap1, involved in oxidative stress and MDR, and Pdr3, a key regulator of the yeast PDR network, consistent with a broad role in stress defence. Taken together, the results of the present study suggest that Pdr18 plays a role in plasma membrane sterol incorporation, this physiological trait contributing to an MDR phenotype.

Differential response of young and adult leaves to herbicide 2,4-dichlorophenoxyacetic acid in pea plants: role of reactive oxygen species

In this work the differential response of adult and young leaves from pea (Pisum sativum L.) plants to the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) (23 mm) applied by foliar spraying was investigated. The concentration of 2,4-D (23 mm) and the time of treatment (72 h) were previously optimized in order to visualize its toxic effects on pea plants. Under these conditions, the herbicide induced severe disturbances in mesophyll cells structure and proliferation of vascular tissue in young leaves and increased acyl-CoA oxidase (ACX), xanthine oxidase (XOD) and lipoxygenase (LOX) activities in young leaves, and only ACX and LOX in adult leaves. This situation produced reactive oxygen species (ROS) over-accumulation favoured by the absence of significant changes in the enzymatic antioxidants, giving rise to oxidative damages to proteins and membrane lipids. An increase of ethylene took place in both young and adult leaves and the induction of genes encoding the stress proteins, PRP4A and HSP 71,2, was observed mainly in young leaves. These results suggest that ROS overproduction is a key factor in the effect of high concentrations of 2,4-D, and ROS can trigger a differential response in young and adult leaves, either epinasty development in young leaves or senescence processes in adult tissues.

Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity

Alachlor has been a commonly applied herbicide and is a substance of ecotoxicological concern. The present study aims to identify molecular biomarkers in the eukaryotic model Saccharomyces cerevisiae that can be used to predict potential cytotoxic effects of alachlor, while providing new mechanistic clues with possible relevance for experimentally less accessible eukaryotes. It focuses on genome-wide expression profiling in a yeast population in response to two exposure scenarios exerting effects from slight to moderate magnitude at phenotypic level. In particular, 100 and 264 genes, respectively, were found as differentially expressed on a 2-h exposure of yeast cells to the lowest observed effect concentration (110 mg/L) and the 20% inhibitory concentration (200 mg/L) of alachlor, in comparison with cells not exposed to the herbicide. The datasets of alachlor-responsive genes showed functional enrichment in diverse metabolic, transmembrane transport, cell defense, and detoxification categories. In general, the modifications in transcript levels of selected candidate biomarkers, assessed by quantitative reverse transcriptase polymerase chain reaction, confirmed the microarray data and varied consistently with the growth inhibitory effects of alachlor. Approximately 16% of the proteins encoded by alachlor-differentially expressed genes were found to share significant homology with proteins from ecologically relevant eukaryotic species. The biological relevance of these results is discussed in relation to new insights into the potential adverse effects of alachlor in health of organisms from ecosystems, particularly in worst-case situations such as accidental spills or careless storage, usage, and disposal.

2D electrophoresis-based expression proteomics: a microbiologist's perspective

Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.

Adaptive response and tolerance to weak acids in Saccharomyces cerevisiae: a genome-wide view

Weak acids are widely used as food preservatives (e.g., acetic, propionic, benzoic, and sorbic acids), herbicides (e.g., 2,4-dichlorophenoxyacetic acid), and as antimalarial (e.g., artesunic and artemisinic acids), anticancer (e.g., artesunic acid), and immunosuppressive (e.g., mycophenolic acid) drugs, among other possible applications. The understanding of the mechanisms underlying the adaptive response and resistance to these weak acids is a prerequisite to develop more effective strategies to control spoilage yeasts, and the emergence of resistant weeds, drug resistant parasites or cancer cells. Furthermore, the identification of toxicity mechanisms and resistance determinants to weak acid-based pharmaceuticals increases current knowledge on their cytotoxic effects and may lead to the identification of new drug targets. This review integrates current knowledge on the mechanisms of toxicity and tolerance to weak acid stress obtained in the model eukaryote Saccharomyces cerevisiae using genome-wide approaches and more detailed gene-by-gene analysis. The major features of the yeast response to weak acids in general, and the more specific responses and resistance mechanisms towards a specific weak acid or a group of weak acids, depending on the chemical nature of the side chain R group (R-COOH), are highlighted. The involvement of several transcriptional regulatory networks in the genomic response to different weak acids is discussed, focusing on the regulatory pathways controlled by the transcription factors Msn2p/Msn4p, War1p, Haa1p, Rim101p, and Pdr1p/Pdr3p, which are known to orchestrate weak acid stress response in yeast. The extrapolation of the knowledge gathered in yeast to other eukaryotes is also attempted.