Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail

Retinal Toxicity Induced by Chemical Agents

Vision is an important sense for humans, and visual impairment/blindness has a huge impact in daily life. The retina is a nervous tissue that is essential for visual processing since it possesses light sensors (photoreceptors) and performs a pre-processing of visual information. Thus, retinal cell dysfunction or degeneration affects visual ability and several general aspects of the day-to-day of a person's lives. The retina has a blood-retinal barrier, which protects the tissue from a wide range of molecules or microorganisms. However, several agents, coming from systemic pathways, reach the retina and influence its function and survival. Pesticides are still used worldwide for agriculture, contaminating food with substances that could reach the retina. Natural products have also been used for therapeutic purposes and are another group of substances that can get to the retina. Finally, a wide number of medicines administered for different diseases can also affect the retina. The present review aimed to gather recent information about the hazard of these products to the retina, which could be used to encourage the search for more healthy, suitable, or less risky agents.

Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from Eleusine indica (EiEPSPS) as a starting point. First, ligand-based pharmacophore screening was performed to select compounds with a similar pharmacophore to glyphosate. Then, structure-based pharmacophore modeling was applied to build a model which represents the molecular features of glyphosate. Then, consensus docking was performed to rank the best poses of the natural compounds against the PEP binding site, and then molecular dynamics simulations were performed to analyze the stability of EPSPS complexed with the selected ligands. Finally, we have investigated the binding affinity of the complexes using free energy calculations. The selected hit compound, namely AG332841, showed a stable conformation and binding affinity to the EPSPS structure and showed no structural similarity to the already known weed EPSPS inhibitors. Our computational study aims to clarify the inhibition of the mutant EiEPSPS, which is resistant to glyphosate, and identify new potential herbicides from natural products.

In vitro toxicity of glyphosate in Atlantic salmon evaluated with a 3D hepatocyte-kidney co-culture model

A novel 3D Atlantic salmon co-culture model was developed using primary hepatocytes and kidney epithelial cells isolated from the same fish. Mono and co-cultures of primary hepatocytes and kidney epithelial cells were exposed for 48 h to glyphosate (5, 50 and 500 μM). For comparison, cells were also exposed to chlorpyrifos, benzo(a)pyrene and cadmium. Cell staining, cell viability assessments, RT-qPCR and global metabolomic profiling were used to examine the toxicological effects on liver and renal function and to compare responses in 3D and 2D cultures. The 3D hepatocyte cell culture was considered superior to the 2D culture due to the ATP binding cassette subfamily B member 1 (Abcb1) response and was thus used further in co-culture with kidney cells. Metabolomic analysis of co-cultured cells showed that glyphosate exposure (500 μM) altered lipid metabolism in both hepatocytes and kidney cells. Elevated levels of several types of PUFAs and long-chain fatty acids were observed in exposed hepatocytes, owing to increased uptake and phospholipid remodelling. Glyphosate suppressed the expression of estrogen receptor 1 (Esr1) and vitellogenin (Vtg) and altered histidine metabolism in exposed hepatocytes. Increased levels of cholesterol and downregulation of clusterin (Clu) suggest that glyphosate treatment affected membrane stability in Atlantic salmon kidney cells. This study demonstrates the usefulness of applying 3D co-culture models in risk assessment.

Does Glyphosate Affect the Human Microbiota?

Glyphosate is the world’s most widely used agrochemical. Its use in agriculture and gardening has been proclaimed safe because humans and other animals do not have the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). However, increasing numbers of studies have demonstrated risks to humans and animals because the shikimate metabolic pathway is present in many microbes. Here, we assess the potential effect of glyphosate on healthy human microbiota. Our results demonstrate that more than one-half of human microbiome are intrinsically sensitive to glyphosate. However, further empirical studies are needed to determine the effect of glyphosate on healthy human microbiota.

Genome Editing: A Promising Approach for Achieving Abiotic Stress Tolerance in Plants

The susceptibility of crop plants towards abiotic stresses is highly threatening to assure global food security as it results in almost 50% annual yield loss. To address this issue, several strategies like plant breeding and genetic engineering have been used by researchers from time to time. However, these approaches are not sufficient to ensure stress resilience due to the complexity associated with the inheritance of abiotic stress adaptive traits. Thus, researchers were prompted to develop novel techniques with high precision that can address the challenges connected to the previous strategies. Genome editing is the latest approach that is in the limelight for improving the stress tolerance of plants. It has revolutionized crop research due to its versatility and precision. The present review is an update on the different genome editing tools used for crop improvement so far and the various challenges associated with them. It also highlights the emerging potential of genome editing for developing abiotic stress-resilient crops.

Metabolic stability of glyphosate and its environmental metabolite (aminomethylphosphonic acid) in the ruminal content of cattle

Glyphosate (GLY) is one of the most commonly used herbicides worldwide. Both GLY and aminomethylphosphonic acid (AMPA), its main degradation product, may be present in feedstuffs offered to dairy cows. Although the major proportions of ingested GLY and AMPA are eliminated with faeces, a potential degradation of GLY to AMPA in the rumen of dairy cows has been suggested. Considering that the rumen plays a central role in the pre-systemic metabolism of xenobiotics, this research aimed to investigate whether or not GLY and AMPA are metabolised in the ruminal environment of cattle. The distribution of both compounds between the fluid and solid phases of the ruminal content (RC) was also evaluated. RC from 3 steers were collected in an abattoir. Aliquots were incubated (3-6 h) in anaerobiosis with GLY (15 µg/mL) and AMPA (1.5 µg/mL). Metabolic viability of RC was assessed by the measurement of the sulpho-reduction of the anthelmintic derivative albendazole sulphoxide (ABZSO) into albendazole (ABZ) in the absence (controls) or in presence of GLY and AMPA. Incubations of boiled (inactive) RC were used as controls. Samples were analysed by HLPC with fluorescence detection. Neither GLY nor AMPA were metabolised in metabolically active RC from cattle. Both compounds were predominantly found in the fluid phase compared to the solid (particulate) matter of RC. Neither GLY nor AMPA had a negative effect on the metabolic production of ABZ. A high metabolic stability of both compounds within the ruminal environment would be expected in vivo. Their presence in high proportion in the fluid phase of the ruminal content may give rise to a rapid flow of both GLY and AMPA to the posterior gastrointestinal tract. Negative effects on the ruminal biotransformation of therapeutically used drugs would not be expected when the herbicide and its degradation product are consumed with food.

Effects of Phosphonate Herbicides on the Secretions of Plant-Beneficial Compounds by Two Plant Growth-Promoting Soil Bacteria: A Metabolomics Investigation

Plant growth-promoting rhizobacteria (PGPR) that colonize plant roots produce a variety of plant-beneficial compounds, including plant-growth regulators, metal-scavenging compounds, and antibiotics against plant pathogens. Adverse effects of phosphonate herbicides, the most extensively used herbicides, on the growth and metabolism of PGPR species have been widely reported. However, the potential consequence of these effects on the biosynthesis and secretion of PGPR-derived beneficial compounds still remains to be investigated. Here, using high-resolution mass spectrometry and a metabolomics approach, we investigated both the intracellular metabolome and the extracellular secretions of biomass-normalized metabolite levels in two PGPR species (Pseudomonas protegens Pf-5, a Gram-negative bacterium; Priestia megaterium QM B1551, a Gram-positive bacterium) exposed to three common phosphonate herbicides (glyphosate, glufosinate, and fosamine; 0.1-1 mM) in either iron (Fe)-replete or Fe-deficient nutrient media. We quantified secreted auxin-type plant hormone compounds (phenylacetic acid and indole-3-acetic acid), iron-scavenging compounds or siderophores (pyoverdine and schizokinen), and antibiotics (2,4-diacetylphloroglucinol and pyoluteorin) produced by these PGPR species. The Fe-replete cells exposed to the phosphonate herbicides yielded up to a 25-fold increase in the production of both auxin and antibiotic compounds, indicating that herbicide exposure under Fe-replete conditions triggered metabolite secretions. However, the herbicide-exposed Fe-deficient cells exhibited a near 2-fold depletion in the secretion of these auxin and antibiotic compounds as well as a 77% decrease in siderophore production. Intracellular metabolomics analysis of the Fe-deficient cells further revealed metabolic perturbations in biosynthetic pathways consistent with the impaired production of the plant-beneficial compounds. Our findings implied that compromised cellular metabolism during nutrient deficiency may exacerbate the adverse effects of phosphonate herbicides on PGPR species.

Deciphering the Structure of Arabidopsis thaliana 5-enol-Pyruvyl-Shikimate-3-Phosphate Synthase: an Essential Step toward the Discovery of Novel Inhibitors to Supersede Glyphosate

Glyphosate interferes with plant aromatic metabolism through the inhibition of 5-enol-pyruvyl-shikimate-3-phosphate (EPSP) synthase [EPSPS, EC 2.5.1.19]. For this reason, EPSPS has been extensively studied in a vast array of organisms. This notwithstanding, up to date, the crystal structure of the protein has been solved exclusively in a few prokaryotes, while that of the plant enzyme has been only deduced in silico by similarity. This study aimed at determining the structure of EPSPS from the plant model species Arabidopsis thaliana, which has been cloned, heterologously expressed and affinity-purified. The kinetic properties of the enzyme have been determined, as well as its susceptibility to the inhibition brought about by glyphosate. The crystal structure of the protein has been resolved at high resolution (1.4 Å), showing open conformation of the enzyme, which is the state ready for substrate/inhibitor binding. This provides a framework for the structure-based design of novel EPSPS inhibitors. Surface regions near the active-site cleft entrance or at the interdomain hinge appear promising for inhibitor selectivity, while bound chloride near the active site is a potential placeholder for anionic moieties of future herbicides.

High Hydrostatic Pressure to Increase the Biosynthesis and Extraction of Phenolic Compounds in Food: A Review

Phenolic compounds from fruits and vegetables have shown antioxidant, anticancer, anti-inflammatory, among other beneficial properties for human health. All these benefits have motivated multiple studies about preserving, extracting, and even increasing the concentration of these compounds in foods. A diverse group of vegetable products treated with High Hydrostatic Pressure (HHP) at different pressure and time have shown higher phenolic content than their untreated counterparts. The increments have been associated with an improvement in their extraction from cellular tissues and even with the activation of the biosynthetic pathway for their production. The application of HHP from 500 to 600 MPa, has been shown to cause cell wall disruption facilitating the release of phenolic compounds from cell compartments. HPP treatments ranging from 15 to 100 MPa during 10-20 min at room temperature have produced changes in phenolic biosynthesis with increments up to 155%. This review analyzes the use of HHP as a method to increase the phenolic content in vegetable systems. Phenolic content changes are associated with either an immediate stress response, with a consequent improvement in their extraction from cellular tissues, or a late stress response that activates the biosynthetic pathways of phenolics in plants.

Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution

Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.

A pyrene-based ratiometric probe for nanomolar level detection of glyphosate in food and environmental samples and its application for live-cell imaging

An in situ formed copper(ii)-complex is involved in analyzing glyphosate in real-life samples, such as crops, soil, water and biological fluids.

First evaluation of the periphyton recovery after glyphosate exposure

The potential environmental risk of glyphosate has promoted the need for decontamination of glyphosate-polluted water bodies. These treatments should be accompanied by studies of the recovery potential of aquatic communities and ecosystems. We evaluated the potential of freshwater periphyton to recover from glyphosate exposure using microcosms under laboratory conditions. Periphyton developed on artificial substrates was exposed to 0.4 or 4 mg l-1 monoisopropylamine salt of glyphosate (IPA) for 7 days, followed by translocation to herbicide-free water. We sampled the community 1, 2 and 3 weeks after the transfer. Dry weight, ash-free dry weight, chlorophyll a, and periphyton abundances were analysed. The periphyton impacted with the lowest IPA concentration recovered most of the structural parameters within 7 days in clean water, but the taxonomic structure did not entirely recover towards the control structure. Periphyton exposed to 4 mg IPA l-1 could not recover during 21 days in herbicide-free water, reaching values almost four times higher in % of dead diatoms and four times lower in ash-free dry weight concerning the control at the end of the study. Results suggest a long-lasting effect of the herbicide due to the persistence within the community matrix even after translocating periphyton to decontaminated water. We conclude that the exposure concentration modulates the recovery potential of IPA-impacted periphyton. The current research is the first to study the recovery in glyphosate-free water of periphyton exposed to the most commonly used herbicide in the world. Finally, we highlight the need for more studies focused on the recovery potential of freshwater ecosystems and aquatic communities after glyphosate contamination.

Stabilization of glyphosate zwitterions and conformational/tautomerism mechanism in aqueous solution: insights from ab initio and density functional theory-continuum model calculations

In this work, a comparative theoretical conformational analysis of the commercially most successful herbicide compound, glyphosate (N-phosphonomethylglycine), has been made at various quantum chemical levels of theory, in the gas phase and aqueous solution, using the integral equation-formalism polarizable continuum model (IEFPCM) and the solvation model density (SMD) approaches. The stable conformers of non-ionized (NE) and ionized or zwitterionic (ZW) neutral forms of glyphosate and the inter-conversions between them are described. Calculations revealed that several NE conformers of glyphosate exist in the gas phase but the zwitterionic form (ZW) is unstable in vacuo at all levels of theory. In aqueous solution, the stabilization of the zwitterion form of glyphosate was unable to be predicted satisfactorily within the equilibrated framework of the IEFPCM polarizable continuum model and using the standard UFF-radii cavity. However, the calculation with the density-based solvation model (SMD) was consistent with the experimental findings and led to the identification of the phosphonate zwitterionic (ZWP) structure as the global minimum energy in aqueous solution. The ZWP ⇋ NE tautomeric equilibrium between the non-ionized and zwitterionic forms of glyphosate was studied in aqueous solution at the SMD-B3LYP-D3/6-311++(2d,2p) level. Zwitterion formation in solution could occur by means of a concerted intramolecular proton transfer from the nitrogen to the oxygen of the phosphonate group. An analysis of the intermolecular mechanism shows that the addition of one water molecule favours the process either thermodynamically or kinetically. The possibility that the tautomerization process of glyphosate via a nonconcerted mechanism with zwitterion carboxylate (ZWC) as the intermediate can be excluded and the ZWP → ZWC proton transfer conversion can be a nearly barrierless process in PES and FES surfaces. comparison with similarly related biologically active systems was made.

Short exposure to glyphosate induces locomotor, craniofacial, and bone disorders in zebrafish (Danio rerio) embryos

Glyphosate [N-(phosphonomethyl)glycine] is the active ingredient in widely used broad-spectrum herbicides. Even though the toxicity mechanism of this herbicide in vertebrates is poorly understood, evidence suggests that glyphosate is an endocrine disruptor capable of producing morphological anomalies as well as cardiotoxic and neurotoxic effects. We used the zebrafish model to assess the effects of early life glyphosate exposure on the development of cartilage and bone tissues and organismal responses. We found functional alterations, including a reduction in the cardiac rate, significant changes in the spontaneous tail movement pattern, and defects in craniofacial development. These effects were concomitant with alterations in the level of the estrogen receptor alpha osteopontin and bone sialoprotein. We also found that embryos exposed to glyphosate presented spine deformities as adults. These developmental alterations are likely induced by changes in protein levels related to bone and cartilage formation.

In vivo and in vitro evaluation of the effect of glyphosate (Roundup) on Toxoplasma gondii

Apicoplast, a derived non-photosynthetic plastid, which is found in most Apicomplexa, provides essential functions to parasites. The shikimate pathway is localized in the plant chloroplast as a remarkable route for the survival of the Toxoplasma. In this study, in vivo and in vitro effects of glyphosate (Roundup, Herbicide), as an inhibitor of the enzyme, were evaluated on T. gondii. Tachyzoites of RH strain were incubated for 1.5 h in various concentrations (1-128 µg/ml) of glyphosate. The parasite was cultivated in the cell monolayer of the heLa cell, and then the cultures were exposed to various concentrations. To evaluate the therapeutic quality, 2 × 10⁵ tachyzoites were intradermally inoculated into ten mice from each group. Four doses of the compound were daily administrated every 24 h after inoculation due 10 days continuously. Also, two other groups were assigned as the positive and negative control. In flow cytometry, the highest mortality rate was related to concentrations of 128 and 256 μg/ml, 18.29% and 18.64%, respectively, while the mortality rate was 0.03% in the negative control (P value > 0.05). Based on microscopic observation of the stained touch smear of the liver, all treated mice were killed by the parasite. This compound also had no lethal effect on the mice. According to the results of this study, glyphosate is not a good candidate for the treatment of toxoplasmosis. It seems that the parasite has another pathway for providing the essential amino acids.

Molecular mechanisms underlying glyphosate resistance in bacteria

Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.

Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (5-enolpyruvylshikimate-3-phosphate, EPSP) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in bacteria, fungi and plants. Our results reveal that bacteria may easily become resistant to glyphosate through changes in the 5-enolpyruvylshikimate-3-phosphate synthase active site. This indicates the importance of examining how glyphosate affects microbe-mediated ecosystem functions and human microbiomes.

Characterization of a Glyphosate-Tolerant Enzyme from Streptomyces svecius: A Distinct Class of 5-Enolpyruvylshikimate-3-phosphate Synthases

Natural and modified versions of the 5-enolpyruvylshikimate-3-phosphate synthase (epsps) gene have been used to confer tolerance to the broad-spectrum herbicide glyphosate in a variety of commercial crops. The most widely utilized trait was obtained from the Agrobacterium tumefaciens strain CP4 and has been commercialized in several glyphosate-tolerant crops. The EPSPS gene products are enzymes that have been divided into three classes based on sequence similarity, sensitivity to glyphosate, and steady-state catalytic parameters. Herein, we describe the informatics-guided identification and biochemical and structural characterization of a novel EPSPS from Streptomyces sviceus (DGT-28 EPSPS). The data suggest DGT-28 EPSPS and other closely related homologues exemplify a distinct new class (Class IV) of EPSPS enzymes that display intrinsic tolerance to high concentrations of glyphosate (Ki ≥ 5000 μM). We further demonstrate that dgt-28 epsps, when transformed into stable plants, provides robust (≥4× field rates) vegetative/reproductive herbicide tolerance and has utility in weed-control systems comparable to that of commercialized events.

Optimization and validation of a liquid chromatography-tandem mass spectrometry method for the determination of glyphosate in human urine after pre-column derivatization with 9-fluorenylmethoxycarbonyl chloride

In 2015, glyphosate was classified as "Group 2A - probably carcinogenic to humans" by the International Agency for Research on Cancer (IARC). Therefore, public concerns about the environmental and health risks of this substance have rapidly increased. Considering its toxicokinetic characteristics, urinary levels of glyphosate could be a powerful tool for human biomonitoring. Nevertheless, the physicochemical properties of this molecule and the complexity of the matrix make this purpose particularly challenging. In order to solve this problem, the presented study describes a simple LC-MS/MS method for the quantification of glyphosate in human urine after pre-column derivatization with FMOC-Cl. Method development was focused on the optimization of the derivatization reaction in human urine, adjusting critical variables such as pH of borate buffer, FMOC-Cl concentration and derivatization time. Besides, chromatographic separation and spectrometric parameters were also established. The analytical method was fully validated according international guidelines for selectivity, carry over, linearity, accuracy, precision, lower limit of quantitation, matrix effect and stability under different conditions. All performance parameters were within the acceptance criteria. In addition, the method was successfully applied to 52 urine samples obtained from exposed subjects from northern Argentina, laying the foundation for future epidemiological studies.

Glyphosate: How do ongoing controversies, market characteristics, and funding influence the global research landscape?

Glyphosate is a systemic broad-spectrum herbicide that is by now the most extensively used herbicide in the world and has been the source for a still heated controversy about its harmful effects on human health and the environment. The different weighting of scientific studies has led to different attitudes in most countries towards appropriate handling and their regulatory authorities. Therefore, an in-depth analysis of the global research landscape on glyphosate is needed to provide the background for further decisions regarding appropriate and careful use, taking into account the different regional conditions. The present study is based on established bibliometric methodological tools and is extended by glyphosate-specific parameters. Chronological and geographical patterns are revealed to determine the incentives and intentions of international scientific efforts. Research output grew in line with the exponential growth in consumption, with the field of research becoming increasingly multidisciplinary and shifting towards environmental and medical disciplines. The countries with the highest herbicide use are also the leading countries in glyphosate research: USA, Brazil, Canada, China and Argentina. The link between publication output and market parameters is as evident as the association with national grants. The research interest of the manufacturing company Monsanto could be shown as the second largest publishing institution behind the US Department of Agriculture, which interest is underscored by its position among the otherwise government-funded organizations. Developing countries are generally underrepresented in glyphosate research, although the use of glyphosate is increasing dramatically. In conclusion, the incentives are strongly linked to market and agricultural interests, with the scientific infrastructure of the countries forming the basis for financing and conducting research. The existing international network is important and needs to be expanded and strengthened by including the lower economies in order to take into account all regional and social needs and aspects of glyphosate use.

Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats

Health effects of pesticides are not always accurately detected using the current battery of regulatory toxicity tests. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in a subchronic toxicity test of a mixture of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole) in Sprague-Dawley rats. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little effect. Contrastingly, serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested activation of an oxidative stress response. This was not reflected by gut microbial community composition changes evaluated by shotgun metagenomics. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included the regulation of response to steroid hormones and the activation of stress response pathways. Genome-wide DNA methylation analysis of the same liver samples showed that 4,255 CpG sites were differentially methylated. Overall, we demonstrated that in-depth molecular profiling in laboratory animals exposed to low concentrations of pesticides allows the detection of metabolic perturbations that would remain undetected by standard regulatory biochemical measures and which could thus improve the predictability of health risks from exposure to chemical pollutants.

Glyphosate-Modulated Biosynthesis Driving Plant Defense and Species Interactions

Glyphosate has become the best-selling herbicide used in agriculture, horticulture, silviculture, and urban environments. It disrupts the shikimate metabolic pathway and thereby blocks the production of aromatic amino acids, which are the basis for several plant metabolites. Glyphosate residues are reported in soils from diverse environments, but the effects on plant physiology and consequences for species interactions are largely unknown. Here, we emphasize the complexity of these physiological processes, and argue that glyphosate residues modulate biosynthetic pathways, individually or interactively, which may affect interactions between plants and heterotrophic organisms. In this way, glyphosate residues can substantially interfere with plant resistance and the attraction of beneficial insects, both of which are essential elements in integrated pest management and healthy ecosystems.

Herbicide Resistance: Another Hot Agronomic Trait for Plant Genome Editing

Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a rapidly increasing human population. Chemical weed control (herbicides) along with integrated weed management (IWM) practices can be the most effective and reliable method of weed management programs. The application of herbicides for weed control practices calls for the urgency to develop herbicide-resistant (HR) crops. Recently, genome editing tools, especially CRISPR-Cas9, have brought innovation in genome editing technology that opens up new possibilities to provide sustainable farming in modern agricultural industry. To date, several non-genetically modified (GM) HR crops have been developed through genome editing that can present a leading role to combat weed problems along with increasing crop productivity to meet increasing food demand around the world. Here, we present the chemical method of weed control, approaches for herbicide resistance development, and possible advantages and limitations of genome editing in herbicide resistance. We also discuss how genome editing would be effective in combating intensive weed problems and what would be the impact of genome-edited HR crops in agriculture.

Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy

Scytonemin is a promising UV-screen and antioxidant small molecule with commercial value in cosmetics and medicine. It is solely biosynthesized in some cyanobacteria. Recently, its biosynthesis mechanism has been elucidated in the model cyanobacterium Nostoc punctiforme PCC 73102. The direct precursors for scytonemin biosynthesis are tryptophan and p-hydroxyphenylpyruvate, which are generated through the shikimate and aromatic amino acid biosynthesis pathway. More upstream substrates are the central carbon metabolism intermediates phosphoenolpyruvate and erythrose-4-phosphate. Thus, it is a long route to synthesize scytonemin from the fixed atmospheric CO2 in cyanobacteria. Metabolic engineering has risen as an important biotechnological means for achieving sustainable high-efficiency and high-yield target metabolites. In this review, we summarized the biochemical properties of this molecule, its biosynthetic gene clusters and transcriptional regulations, the associated carbon flux-driving progresses, and the host selection and biosynthetic strategies, with the aim to expand our understanding on engineering suitable cyanobacteria for cost-effective production of scytonemin in future practices.

Ecotoxicology of Glyphosate, Its Formulants, and Environmental Degradation Products

The chemical and biological properties of glyphosate are key to understanding its fate in the environment and potential risks to non-target organisms. Glyphosate is polar and water soluble and therefore does not bioaccumulate, biomagnify, or accumulate to high levels in the environment. It sorbs strongly to particles in soil and sediments and this reduces bioavailability so that exposures to non-target organisms in the environment are acute and decrease with half-lives in the order of hours to a few days. The target site for glyphosate is not known to be expressed in animals, which reduces the probability of toxicity and small risks. Technical glyphosate (acid or salts) is of low to moderate toxicity; however, when mixed with some formulants such as polyoxyethylene amines (POEAs), toxicity to aquatic animals increases about 15-fold on average. However, glyphosate and the formulants have different fates in the environment and they do not necessarily co-occur. Therefore, toxicity tests on formulated products in scenarios where they would not be used are unrealistic and of limited use for assessment of risk. Concentrations of glyphosate in surface water are generally low with minimal risk to aquatic organisms, including plants. Toxicity and risks to non-target terrestrial organisms other than plants treated directly are low and risks to terrestrial invertebrates and microbial processes in soil are very small. Formulations containing POEAs are not labeled for use over water but, because POEA rapidly partitions into sediment, risks to aquatic organisms from accidental over-sprays are reduced in shallow water bodies. We conclude that use of formulations of glyphosate under good agricultural practices presents a de minimis risk of direct and indirect adverse effects in non-target organisms.

Use of Shotgun Metagenomics and Metabolomics to Evaluate the Impact of Glyphosate or Roundup MON 52276 on the Gut Microbiota and Serum Metabolome of Sprague-Dawley Rats

BACKGROUND

There is intense debate on whether glyphosate can inhibit the shikimate pathway of gastrointestinal microorganisms, with potential health implications.

OBJECTIVES

We tested whether glyphosate or its representative EU herbicide formulation Roundup MON 52276 affects the rat gut microbiome.

METHODS

We combined cecal microbiome shotgun metagenomics with serum and cecum metabolomics to assess the effects of glyphosate [0.5, 50, 175 mg / kg  body weight  ( BW )  per day ] or MON 52276 at the same glyphosate-equivalent doses, in a 90-d toxicity test in rats.

RESULTS

Glyphosate and MON 52276 treatment resulted in ceca accumulation of shikimic acid and 3-dehydroshikimic acid, suggesting inhibition of 5-enolpyruvylshikimate-3-phosphate synthase of the shikimate pathway in the gut microbiome. Cysteinylglycine, γ -glutamylglutamine , and valylglycine levels were elevated in the cecal microbiome following glyphosate and MON 52276 treatments. Altered cecum metabolites were not differentially expressed in serum, suggesting that the glyphosate and MON 52276 impact on gut microbial metabolism had limited consequences on physiological biochemistry. Serum metabolites differentially expressed with glyphosate treatment were associated with nicotinamide, branched-chain amino acid, methionine, cysteine, and taurine metabolism, indicative of a response to oxidative stress. MON 52276 had similar, but more pronounced, effects than glyphosate on the serum metabolome. Shotgun metagenomics of the cecum showed that treatment with glyphosate and MON 52276 resulted in higher levels of Eggerthella spp., Shinella zoogleoides, Acinetobacter johnsonii, and Akkermansia muciniphila. Shinella zoogleoides was higher only with MON 52276 exposure. In vitro culture assays with Lacticaseibacillus rhamnosus strains showed that Roundup GT plus inhibited growth at concentrations at which MON 52276 and glyphosate had no effect.

DISCUSSION

Our study highlights the power of multi-omics approaches to investigate the toxic effects of pesticides. Multi-omics revealed that glyphosate and MON 52276 inhibited the shikimate pathway in the rat gut microbiome. Our findings could be used to develop biomarkers for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on humans. https://doi.org/10.1289/EHP6990.

History and Outlook for Glyphosate-Resistant Crops

Glyphosate-resistant (GR) crops, commercially referred to as glyphosate-tolerant (GT), started the revolution in crop biotechnology in 1996. Growers rapidly accepted GR crops whenever they became available and made them the most rapidly adopted technology in agriculture history. Adoption usually meant sole reliance on glyphosate [N-(phosphonomethyl)glycine, CAS No. 1071-83-6] for weed control. Not surprisingly, weeds eventually evolved resistance and are forcing growers to change their weed management practices. Today, the widespread dissemination of GR weeds that are also resistant to other herbicide modes-of-action (MoA) has greatly reduced the value of the GR crop weed management systems. However, growers continue to use the technology widely in six major crops throughout North and South America. Integrated chemistry and seed providers seek to sustain glyphosate efficacy by promoting glyphosate combinations with other herbicides and stacking the traits necessary to enable the use of partner herbicides. These include glufosinate {4-[hydroxy(methyl)phosphinoyl]-DL-homoalanine, CAS No. 51276-47-2}, dicamba (3,6-dichloro-2-methoxybenzoic acid, CAS No. 1918-00-9), 2,4-D [2-(2,4-dichlorophenoxy)acetic acid, CAS No. 94-75-7], 4-hydroxyphenyl pyruvate dioxygenase inhibitors, acetyl coenzyme A carboxylase (ACCase) inhibitors, and other herbicides. Unfortunately, herbicide companies have not commercialized a new MoA for over 30 years and have nearly exhausted the useful herbicide trait possibilities. Today, glyphosate-based crop systems are still mainstays of weed management, but they cannot keep up with the capacity of weeds to evolve resistance. Growers desperately need new technologies, but no technology with the impact of glyphosate and GR crops is on the horizon. Although the expansion of GR crop traits is possible into new geographic areas and crops such as wheat and sugarcane and could have high value, the Roundup Ready® revolution is over. Its future is at a nexus and dependent on a variety of issues.

Evolution of Glyphosate-Resistant Weeds

Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.

Gene expression response of the alga Fucus virsoides (Fucales, Ochrophyta) to glyphosate solution exposure

Fucus virsoides is an ecologically important canopy-forming brown algae endemic to the Adriatic Sea. Once widespread in marine coastal areas, this species underwent a rapid population decline and is now confined to small residual areas. Although the reasons behind this progressive disappearance are still a matter of debate, F. virsoides may suffer, like other macroalgae, from the potential toxic effects of glyphosate-based herbicides. Here, through a transcriptomic approach, we investigate the molecular basis of the high susceptibility of this species to glyphosate solution, previously observed at the morphological and eco-physiological levels. By simulating runoff event in a factorial experiment, we exposed F. virsoides to glyphosate (Roundup® 2.0), either alone or in association with nutrient enrichment, highlighting significant alterations of gene expression profiles that were already visible after three days of exposure. In particular, glyphosate exposure determined the near-complete expression shutdown of several genes involved in photosynthesis, protein synthesis and stress response molecular pathways. Curiously, these detrimental effects were partially mitigated by nutrient supplementation, which may explain the survival of relict population in confined areas with high nutrient inputs.

Review: amino acid biosynthesis as a target for herbicide development

There are three amino acid biosynthesis pathways that are targeted by current herbicides, namely those leading to the production of aromatic amino acids, branched chain amino acids and glutamine. However, their efficacy is diminishing as a result of the increasing number of resistant weeds. Indeed, resistance to most classes of herbicides is on the rise, posing a significant threat to the utility of current herbicides to sustain effective weed management. This review provides an overview of potential herbicide targets within amino acid biosynthesis that remain unexploited commercially, and recent inhibitor discovery efforts. Despite contemporary approaches to herbicide discovery, such as chemical repurposing and the use of omics technologies, there have been no new products introduced to the market that inhibit amino acid biosynthesis over the past three decades. This highlights the chasm that exists between identifying a potent inhibitor and introducing a commercial herbicide. The unpredictability of a mode of action at the systemic level, as well as poor physicochemical properties, often contribute to a lack of progression beyond the target inhibition stage. Nevertheless, it will be important to overcome these obstacles for the development of new herbicides to protect our agricultural industry and ensure food security for an increasing world population. © 2020 Society of Chemical Industry.

Overexpression of improved EPSPS gene results in field level glyphosate tolerance and higher grain yield in rice

Glyphosate is a popular, systemic, broad-spectrum herbicide used in modern agriculture. Being a structural analog of phosphoenolpyruvate (PEP), it inhibits 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) which is responsible for the biosynthesis of aromatic amino acids and various aromatic secondary metabolites. Taking a lead from glyphosate-resistant weeds, two mutant variants of the rice EPSPS gene were developed by amino acid substitution (T173I + P177S; TIPS-OsEPSPS and G172A + T173I + P177S; GATIPS-OsEPSPS). These mutated EPSPS genes were overexpressed in rice under the control of either native EPSPS or constitutive promoters (maize ubiquitin [ZmUbi] promoter). The overexpression of TIPS-OsEPSPS under the control of the ZmUbi promoter resulted in higher tolerance to glyphosate (up to threefold of the recommended dose) without affecting the fitness and related agronomic traits of plants in both controlled and field conditions. Furthermore, such rice lines produced 17%-19% more grains compared to the wild type (WT) in the absence of glyphosate application and the phenylalanine and tryptophan contents in the transgenic seeds were found to be significantly higher in comparison with WT seeds. Our results also revealed that the native promoter guided expression of modified EPSPS genes did not significantly improve the glyphosate tolerance. The present study describing the introduction of a crop-specific TIPS mutation in class I aroA gene of rice and its overexpression have potential to substantially improve the yield and field level glyphosate tolerance in rice. This is the first report to observe that the EPSPS has role to play in improving grain yield of rice.

Physiological mechanisms and phytoremediation potential of the macrophyte Salvinia biloba towards a commercial formulation and an analytical standard of glyphosate

Glyphosate (Gly) is the most widely used herbicide in the world and has broad-spectrum and non-selective activity. Its indiscriminate use hence risks contamination of water bodies and can affect living organisms, especially sensitive or resistant non-target plants. Despite this, studies on physiological mechanisms and Gly remediation in Neotropical aquatic plants remain limited. This study aims to evaluate the physiological mechanisms of the aquatic macrophyte Salvinia biloba on exposure to different concentrations of a Gly commercial formulation (Gly-CF) and a Gly analytical standard (Gly-AS). Furthermore, using square-wave voltammetry (SWV), we determined whether the studied plant could remove Gly from water. Our data suggest that Gly-AS and Gly-CF induce similar physiological responses in S. biloba. However, Gly-CF was more phytotoxic. Depending on the concentration, the two forms of Gly affected the plants, decreasing the chlorophyll a and b contents and the photosystem II (PSII) photochemical activity. The data also revealed that Gly promoted oxidative stress and increased the shikimic acid concentration. At the same time, the plants removed Gly from water, with 100% removal for 1 mg L-1 Gly and above 60% removal for the other concentrations studied. Therefore, our results suggest that S. biloba may be a potential phytoremediation agent for low Gly concentrations, since 1 mg L-1 Gly was completely removed and exhibited low phytotoxicity. This study deepens our scientific understanding of the Gly impact on and the phytoremediation potential of S. biloba.

Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors

In this study, we have investigated the enzyme shikimate 5-dehydrogenase from the causative agent of tuberculosis, Mycobacterium tuberculosis. We have employed a mixture of computational techniques, including molecular dynamics, hybrid quantum chemical/molecular mechanical potentials, relaxed surface scans, quantum chemical descriptors and free-energy simulations, to elucidate the enzyme's reaction pathway. Overall, we find a two-step mechanism, with a single transition state, that proceeds by an energetically uphill hydride transfer, followed by an energetically downhill proton transfer. Our mechanism and calculated free energy barrier for the reaction, 64.9 kJ mol^- 1, are in good agreement with those predicted from experiment. An analysis of quantum chemical descriptors along the reaction pathway indicated a possibly important, yet currently unreported, role of the active site threonine residue, Thr65.

Picomolar glyphosate sensitivity of an optical particle-based sensor utilizing biomimetic interaction principles

The continually growing use of glyphosate and its critically discussed health and biodiversity risks ask for fast, low cost, on-site sensing technologies for food and water. To address this problem, we designed a highly sensitive sensor built on the remarkably specific recognition of glyphosate by its physiological target enzyme 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPs). This principle is implemented in an interferometric sensor by using the recently established soft colloidal probe (SCP) technique. EPSPs was site-specifically immobilized on a transparent surface utilizing the self-assembling properties of circadian clock gene 2 hydrophobin chimera and homogeneity of the layer was evidenced by atomic force microscopy. Exposure of the enzyme decorated biochip to glyphosate containing samples causes formation of enzyme-analyte complexes and a competitive loss of available binding sites for glyphosate-functionalized poly(ethylene glycol) SCPs. Functionalization of the SCPs with different types of linker molecules and glyphosate was assessed employing confocal laser scanning microscopy as well as confocal Raman microspectroscopy. Overall, reflection interference contrast microscopy analysis of SCP-biochip interactions revealed a strong influence of linker length and glyphosate coupling position on the sensitivity of the sensor. In employing a combination of pentaglycine linker and tethering glyphosate via its secondary amino group, concentrations in aqueous solutions down to 100 pM could be measured by the differential adhesion between SCP and biochip surface, supported by automated image analysis algorithms. This sensing concept could even prove its exceptional pM sensitivity in combination with a superior discrimination against structurally related compounds.

Chronic High Glyphosate Exposure Delays Individual Worker Bee (Apis mellifera L.) Development under Field Conditions

The ongoing debate about glyphosate-based herbicides (GBH) and their implications for beneficial arthropods gives rise to controversy. This research was carried out to cover possible sublethal GBH effects on the brood and colony development, adult survival, and overwintering success of honey bees (Apis mellifera L.) under field conditions. Residues in bee relevant matrices, such as nectar, pollen, and plants, were additionally measured. To address these questions, we adopted four independent study approaches. For brood effects and survival, we orally exposed mini-hives housed in the "Kieler mating-nuc" system to sublethal concentrations of 4.8 mg glyphosate/kg (T1, low) and 137.6 mg glyphosate/kg (T2, high) over a period of one brood cycle (21 days). Brood development and colony conditions were assessed after a modified OECD method (No. 75). For adult survival, we weighed and labeled freshly emerged workers from control and exposed colonies and introduced them into non-contaminated mini-hives to monitor their life span for 25 consecutive days. The results from these experiments showed a trivial effect of GBH on colony conditions and the survival of individual workers, even though the hatching weight was reduced in T2. The brood termination rate (BTR) in the T2 treatment, however, was more than doubled (49.84%) when compared to the control (22.11%) or T1 (20.69%). This was surprising as T2 colonies gained similar weight and similar numbers of bees per colony compared to the control, indicating an equal performance. Obviously, the brood development in T2 was not "terminated" as expected by the OECD method terminology, but rather "slowed down" for an unknown period of time. In light of these findings, we suggest that chronic high GBH exposure is capable of significantly delaying worker brood development, while no further detrimental effects seem to appear at the colony level. Against this background, we discuss additional results and possible consequences of GBH for honey bee health.

Determination of the Ecotoxicity of Herbicides Roundup® Classic Pro and Garlon New in Aquatic and Terrestrial Environments

Herbicides help increase agricultural yields significantly, but they may negatively impact the life of non-target organisms. Modifying the life cycle of primary producers can affect other organisms in the food chain, and consequently in the whole ecosystem. We investigated the effect of common herbicides Roundup® Classic Pro (active substance glyphosate) and Garlon New (triclopyr and fluroxypyr) on aquatic organisms duckweed Lemna minor and green algae Desmodesmus subspicatus, and on the enzymatic activity of soil. We also compared the effects of Roundup® Classic Pro to that of a metabolite of its active substance, aminomethylphosphonic acid (AMPA). The results of an algal growth test showed that AMPA has a 1.5× weaker inhibitory effect on the growth of D. subspicatus than the Roundup formula, and the strongest growth inhibition was caused by Garlon New (IC50Roundup = 267.3 µg/L, IC50Garlon = 21.0 µg/L, IC50AMPA = 117.8 mg/L). The results of the duckweed growth inhibition test revealed that Roundup and Garlon New caused 100% growth inhibition of L. minor even at significantly lower concentrations than the ready-to-use concentration. The total chlorophyll content in the fronds was lowest when Garlon New was used. The highest dehydrogenase activity was observed in soil treated with Garlon New, and the lowest in soil treated with Roundup® Classic Pro. The results of this study showed that all three tested substances were ecotoxic to the tested organisms.

Targeting shikimate pathway: In silico analysis of phosphoenolpyruvate derivatives as inhibitors of EPSP synthase and DAHP synthase

The shikimate pathway consists of seven enzymatic steps involved in the conversion of erythrose-4-phosphate and phosphoenolpyruvate to chorismate and also responsible to the production of aromatic amino acids, such as phenylalanine, tyrosine, and tryptophan which are essential to the bacterial metabolism. The 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) catalyze important steps in the shikimate pathway using as substrate the phosphoenolpyruvate (PEP). Due to the importance of PEP in shikimate pathway, its structure has been investigated to develop new bioinspired competitive inhibitors against DAHPS and EPSPS. In the present study, we perform a literature survey of 28 PEP derivatives, then we analyzed the selectivity and affinity of these compounds against the EPSPS and DAHPS structures using consensual molecular docking, pharmacophore prediction, molecular dynamics (MD) simulations, and binding free energy calculations. Here, we propose consistent binding modes of the selected ligands and indicate that their structures show interesting pharmacophoric properties related to multi-targets inhibitors for both enzymes. Our computational results are supported by previous experimental findings related to the interactions of PEP derivatives with DAHPS and EPSPS structures.

Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria

BACKGROUND

Non-photosynthetic plastids of plants are known to be involved in a range of metabolic and biosynthetic reactions, even if they have been difficult to study due to their small size and lack of color. The morphology of root plastids is heterogeneous and also the plastid size, density and subcellular distribution varies depending on the cell type and developmental stage, and therefore the functional features have remained obscure. Although the root plastid proteome is likely to reveal specific functional features, Arabidopsis thaliana root plastid proteome has not been studied to date.

RESULTS

In the present study, we separated Arabidopsis root protein fraction enriched with plastids and mitochondria by 2D-PAGE and identified 84 plastid-targeted and 77 mitochondrion-targeted proteins using LC-MS/MS. The most prevalent root plastid protein categories represented amino acid biosynthesis, carbohydrate metabolism and lipid biosynthesis pathways, while the enzymes involved in starch and sucrose metabolism were not detected. Mitochondrion-targeted proteins were classified mainly into the energetics category.

CONCLUSIONS

This is the first study presenting gel-based map of Arabidopsis thaliana root plastid and mitochondrial proteome. Our findings suggest that Arabidopsis root plastids have broad biosynthetic capacity, and that they do not play a major role in a long-term storage of carbohydrates. The proteomic map provides a tool for further studies to compare changes in the proteome, e.g. in response to environmental cues, and emphasizes the role of root plastids in nitrogen and sulfur metabolism as well as in amino acid and fatty acid biosynthesis. The results enable taking a first step towards an integrated view of root plastid/mitochondrial proteome and metabolic functions in Arabidopsis thaliana roots.

Molecular dynamics simulations of two GH74 endo-processive xyloglucanases and the mutated variants to understand better the mechanism of the enzyme action

BACKGROUND

GH74 xyloglucanases are composed of two separate domains connected by two unstructured peptides. Previously, a hypothesis was made that the movement of domains may affect the enzyme mechanism of catalysis.

METHODS

The molecular dynamics (MD) simulations of endo-processive xyloglucanases from Paenibacillus odorifer (PoGH74_cat) and Myceliophthora thermophila (MtXeg74A) were carried out.

RESULTS

MD simulations for both enzymes in complex with XXLG and XGXXLG oligosaccharides confirmed the possibility of domain movement. In the case of MtXeg74A, changes in the distances between C_α atoms of aromatic residues involved in xyloglucan binding in -3 and +3 subsites of the active site cleft and those of selected residues on the opposite side of the cleft reached values up to 10-12 Å. For PoGH74_cat the conformational changes were less pronounced. In MtXeg74A variants, the deletion of loop 1, which partially closes the entrance to the cleft, and the additional double mutation of two Trp residues in +3 and +5 subsites caused the enhanced mobility of the XGXXLG and also induced changes in topography of the cleft.

CONCLUSIONS

These findings demonstrate the possibility of existence of GH74 xyloglucanases in a more open and more closed enzyme conformation. The enzyme in an open conformation may more easily accommodate the branched polysaccharide, while its transition to the closed conformation, together with loop 1 function, should aid processivity.

GENERAL SIGNIFICANCE

Our results provide an insight into a mechanism of action of GH74 xyloglucanases and may be useful for discussing the catalytic mechanisms of glycoside hydrolases from other families.

Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway

Chlorogenic acid (CGA) is a phenolic compound with well-known antibacterial properties against pathogens. In this study, structural and biochemical characterization was used to show the inhibitory role of CGA against the enzyme of the shikimate pathway, a well-characterized drug target in several pathogens. Here, we report the crystal structures of dehydroquinate synthase (DHQS), the second enzyme of the shikimate pathway, from Providencia alcalifaciens (PaDHQS), in binary complex with NAD and ternary complex with NAD and CGA. Structural analyses reveal that CGA occupies the substrate position in the active site of PaDHQS, which disables domain movements, leaving the enzyme in an open and catalysis-incompetent state. The binding analyses by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) show that CGA binds to PaDHQS with KD (equilibrium dissociation constant) values of 6.3 μM and 0.5 μM, respectively. In vitro enzyme inhibition studies show that CGA inhibits PaDHQS with a Ki of 235 ± 21 μM, while it inhibits the growth of Providencia alcalifaciens, Moraxella catarrhalis, Staphylococcus aureus, and Escherichia coli with MIC values of 60 to 100 μM. In the presence of aromatic amino acids supplied externally, CGA does not show the toxic effect. These results, along with the observations of the inhibition of the 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) regulatory domain by CGA in our previous study, suggest that CGA binds to shikimate pathway enzymes with high affinity and inhibits their catalysis and can be further exploited for designing novel drug-like molecules.IMPORTANCE The shikimate pathway is an attractive target for the development of herbicides and antimicrobial agents, as it is essential in plants, bacteria, and apicomplexan parasites but absent in humans. The enzymes of shikimate pathway are conserved among bacteria. Thus, the inhibitors of the shikimate pathway act on wide range of pathogens. We have identified that chlorogenic acid targets the enzymes of the shikimate pathway. The crystal structure of dehydroquinate synthase, the second enzyme of the pathway, in complex with chlorogenic acid and enzymatic inhibition studies explains the mechanism of inhibition of chlorogenic acid. These results suggest that chlorogenic acid has a good chemical scaffold and have important implications for its further development as a potent inhibitor of shikimate pathway enzymes.

Architecture and functional dynamics of the pentafunctional AROM complex

The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.

The Effects of Glyphosate and Its Commercial Formulations to Marine Invertebrates: A Review

Glyphosate is the active ingredient of numerous commercial formulations of herbicides applied in different sectors, from agriculture to aquaculture. Due to its widespread use around the world, relatively high concentrations of glyphosate have been detected in soil and aquatic environments. The presence of glyphosate in aquatic ecosystems has aroused the attention of researchers because of its potential negative effects on living organisms, both animals and plants. In this context, this review intends to summarize results of studies aimed at evaluating the effects of glyphosate (both as active ingredient and component of commercial formulations) on marine invertebrates. Generally, data obtained in acute toxicity tests indicate that glyphosate and its commercial formulations are lethal at high concentrations (not environmentally realistic), whereas results of long-lasting experiments indicate that glyphosate can markedly affect biological responses of marine invertebrates. Consequently, more efforts should be addressed at evaluating chronic or sub-chronic effects of such substances to marine invertebrate species.

Transcriptome Analysis Identifies Candidate Target Genes Involved in Glyphosate-Resistance Mechanism in Lolium multiflorum

Italian ryegrass (Lolium multiflorum; LOLMU) is one of the most troublesome weeds in temperate regions in the world. This weed species interfere with wheat, corn, rye, and oat, causing significant crop yield losses. This species has evolved glyphosate resistance, making it difficult to control. The mechanisms of glyphosate resistance are still unknown, and an understanding thereof will favor the development of new strategies of management. The present study is the first transcriptome study in LOLMU using glyphosate-resistant and -sensitive biotypes, aiming to identify and to provide a list of the candidate target genes related to glyphosate resistance mechanism. The transcriptome was assembled de novo, producing 87,433 contigs with an N50 of 740 bp and an average length of 575 bp. There were 92 and 54 up- and down-regulated genes, respectively, in the resistant biotype, while a total of 1683 were differentially expressed in the sensitive biotype in response to glyphosate treatment. We selected 14 highly induced genes and seven with repressed expression in the resistant biotype in response to glyphosate. Of these genes, a significant proportion were related to the plasma membrane, indicating that there is a barrier making it difficult for glyphosate to enter the cell.

Computational modelling provides insight into the effects of glyphosate on the shikimate pathway in the human gut microbiome

The herbicide active ingredient glyphosate can affect the growth of microorganisms, which rely on the shikimate pathway for aromatic amino acid biosynthesis. However, it is uncertain whether glyphosate exposure could lead to perturbations in the population of human gut microbiota. We have addressed this knowledge gap by analysing publicly available datasets to provide new insights into possible effects of glyphosate on the human gut microbiome. Comparison of the abundance of the shikimate pathway in 734 paired metagenomes and metatranscriptomes indicated that most gut bacteria do not possess a complete shikimate pathway, and that this pathway is mostly transcriptionally inactive in the human gut microbiome. This suggests that gut bacteria are mostly aromatic amino acid auxotrophs and thus relatively resistant to a potential growth inhibition by glyphosate. As glyphosate blocking of the shikimate pathway is via inhibition of EPSPS, we classified E. coli EPSPS enzyme homologues as class I (sensitive to glyphosate) and class II (resistant to glyphosate). Among 44 subspecies reference genomes, accounting for 72% of the total assigned microbial abundance in 2144 human faecal metagenomes, 9 subspecies have class II EPSPS. The study of publicly available gut metagenomes also indicated that glyphosate might be degraded by some Proteobacteria in the human gut microbiome using the carbon-phosphorus lyase pathway. Overall, there is limited experimental evidence available for the effects of glyphosate on the human gut microbiome. Further investigations using more advanced molecular profiling techniques are needed to ascertain whether glyphosate and glyphosate-based herbicides can alter the function of the gut microbiome with consequent health implications.