Overexpressing Exogenous 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) Genes Increases Fecundity and Auxin Content of Transgenic Arabidopsis Plants

Reduced Carbon Dioxide by Overexpressing EPSPS Transgene in Arabidopsis and Rice: Implications in Carbon Neutrality through Genetically Engineered Plants

With the increasing challenges of climate change caused by global warming, the effective reduction of carbon dioxide (CO2) becomes an urgent environmental issue for the sustainable development of human society. Previous reports indicated increased biomass in genetically engineered (GE) Arabidopsis and rice overexpressing the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, suggesting the possibility of consuming more carbon by GE plants. However, whether overexpressing the EPSPS gene in GE plants consumes more CO2 remains a question. To address this question, we measured expression of the EPSPS gene, intercellular CO2 concentration, photosynthetic ratios, and gene expression (RNA-seq and RT-qPCR) in GE (overexpression) and non-GE (normal expression) Arabidopsis and rice plants. Results showed substantially increased EPSPS expression accompanied with CO2 consumption in the GE Arabidopsis and rice plants. Furthermore, overexpressing the EPSPS gene affected carbon-fixation related biological pathways. We also confirmed significant upregulation of four key carbon-fixation associated genes, in addition to increased photosynthetic ratios, in all GE plants. Our finding of significantly enhanced carbon fixation in GE plants overexpressing the EPSPS transgene provides a novel strategy to reduce global CO2 for carbon neutrality by genetic engineering of plant species, in addition to increased plant production by enhanced photosynthesis.

Recommendations for the Assessment of Potential Environmental Effects of Genome-Editing Applications in Plants in the EU

The current initiative of the European Commission (EC) concerning plants produced using certain new genomic techniques, in particular, targeted mutagenesis and cisgenesis, underlines that a high level of protection for human and animal health and the environment needs to be maintained when using such applications. The current EU biosafety regulation framework ensures a high level of protection with a mandatory environmental risk assessment (ERA) of genetically modified (GM) products prior to the authorization of individual GMOs for environmental release or marketing. However, the guidance available from the European Food Safety Authority (EFSA) for conducting such an ERA is not specific enough regarding the techniques under discussion and needs to be further developed to support the policy goals towards ERA, i.e., a case-by-case assessment approach proportionate to the respective risks, currently put forward by the EC. This review identifies important elements for the case-by-case approach for the ERA that need to be taken into account in the framework for a risk-oriented regulatory approach. We also discuss that the comparison of genome-edited plants with plants developed using conventional breeding methods should be conducted at the level of a scientific case-by-case assessment of individual applications rather than at a general, technology-based level. Our considerations aim to support the development of further specific guidance for the ERA of genome-edited plants.

Deficiencies in the Risk Assessment of Genetically Engineered Bt Cowpea Approved for Cultivation in Nigeria: A Critical Review

We analyze the application filed for the marketing and cultivation of genetically engineered Bt cowpea (event AAT 709A) approved in Nigeria in 2019. Cowpea (Vigna ungiguiculata) is extensively grown throughout sub-Saharan Africa and consumed by around two hundred million people. The transgenic plants produce an insecticidal, recombinant Bt toxin meant to protect the plants against the larvae of Maruca vitrata, which feed on the plants and are also known as pod borer. Our analysis of the application reveals issues of concern regarding the safety of the Bt toxins produced in the plants. These concerns include stability of gene expression, impact on soil organisms, effects on non-target species and food safety. In addition, we show deficiencies in the risk assessment of potential gene flow and uncontrolled spread of the transgenes and cultivated varieties as well as the maintenance of seed collections. As far as information is publicly available, we analyze the application by referring to established standards of GMO risk assessment. We take the provisions of the Cartagena Protocol on Biosafety (CPB) into account, of which both Nigeria and the EU are parties. We also refer to the EU standards for GMO risk assessment, which are complementary to the provisions of the CPB.

Vegetative and Fecundity Fitness Benefit Found in a Glyphosate-Resistant Eleusine indica Population Caused by 5-Enolpyruvylshikimate-3-Phosphate Synthase Overexpression

Fitness is an important trait in weed species that have developed herbicide resistance, including resistance to the popular herbicide glyphosate. Fitness cost is commonly found in weeds with glyphosate resistance, which is caused by target-site mutations. In this study, the vegetative and fecundity fitness traits in a glyphosate-resistant (GR) Eleusine indica population caused by 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression were investigated under glyphosate-free conditions. The results showed that the resistance index of the population resistant (R) to glyphosate compared with that of the population susceptible (WT) to it was approximately 4.0. Furthermore, EPSPS expression level in the R plants was 20.1-82.7 times higher than that in the WT plants. The dry weight of the R population was significantly higher than that of the WT population at the later growth stage after planting; a similar trend was observed for leaf area. In addition, seed production in the R population was 1.4 times higher than that in the WT population. The R and WT populations showed similar maximum germination rates and T₅₀ values. UPLC-MS/MS was performed for the metabolic extracts prepared from the leaves of R and WT populations to address changes in the metabolome. A total of 121 differential metabolites were identified between R and WT individuals. The levels of 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde, which are associated with auxin synthesis, were significantly higher in plants of the R population than in those of the WT population. However, some secondary metabolite levels were slightly lower in the R population than in the WT population. To conclude, in this study, vegetative and fecundity fitness benefits were found in the GR E. indica population. The results of metabolome analysis indicate that the increase in 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde levels may be the result of fitness benefit. Further studies should be conducted to confirm the functions of these metabolites.

A Metabolic Profiling Analysis Revealed a Primary Metabolism Reprogramming in Arabidopsis glyI4 Loss-of-Function Mutant

Methylglyoxal (MG) is a cytotoxic compound often produced as a side product of metabolic processes such as glycolysis, lipid peroxidation, and photosynthesis. MG is mainly scavenged by the glyoxalase system, a two-step pathway, in which the coordinate activity of GLYI and GLYII transforms it into D-lactate, releasing GSH. In Arabidopsis thaliana, a member of the GLYI family named GLYI4 has been recently characterized. In glyI4 mutant plants, a general stress phenotype characterized by compromised MG scavenging, accumulation of reactive oxygen species (ROS), stomatal closure, and reduced fitness was observed. In order to shed some light on the impact of gly4 loss-of-function on plant metabolism, we applied a high resolution mass spectrometry-based metabolomic approach to Arabidopsis Col-8 wild type and glyI4 mutant plants. A compound library containing a total of 70 metabolites, differentially synthesized in glyI4 compared to Col-8, was obtained. Pathway analysis of the identified compounds showed that the upregulated pathways are mainly involved in redox reactions and cellular energy maintenance, and those downregulated in plant defense and growth. These results improved our understanding of the impacts of glyI4 loss-of-function on the general reprogramming of the plant's metabolic landscape as a strategy for surviving under adverse physiological conditions.

Increased Longevity and Dormancy of Soil-Buried Seeds from Advanced Crop–Wild Rice Hybrids Overexpressing the EPSPS Transgene

Simple Summary

Estimating the survival and reproductive ability caused by a transgene moved from a genetically engineered (GE) crop to its wild relative populations through gene flow plays an important role in assessing the potential environmental risks of the GE crop. Such estimation has essentially focused on the survival and reproduction-related characteristics above the ground, but with little attention to the GE seeds shattered in the soil seed banks. We demonstrated that the herbicide-resistant transgene overexpressing the rice endogenous EPSP enzyme increased the survival and longevity of the GE crop–wild (Oryza rufipogon) hybrid seeds in soil seed banks. In addition, enhanced survival and longevity of the GE hybrid seeds are likely associated with increases in seed dormancy and a growth hormone (auxin) via overexpressing the EPSPS transgene. Therefore, the EPSPS transgene can persist in the soil seed banks and spread in the environment, causing unwanted environmental impacts.

Abstract

Estimating the fitness effect conferred by a transgene introgressed into populations of wild relative species from a genetically engineered (GE) crop plays an important role in assessing the potential environmental risks caused by transgene flow. Such estimation has essentially focused on the survival and fecundity-related characteristics measured above the ground, but with little attention to the fate of GE seeds shattered in the soil seed banks after maturation. To explore the survival and longevity of GE seeds in soil, we examined the germination behaviors of crop–wild hybrid seeds (F₄–F₆) from the lineages of a GE herbicide-tolerant rice (Oryzasativa) line that contains an endogenous EPSPS transgene hybridized with two wild O. rufipogon populations after the seeds were buried in soil. The results showed significantly increased germination of the GE crop–wild hybrid seeds after soil burial, compared with that of the non-GE hybrid seeds. Additionally, the proportion of dormant seeds and the content of the growth hormone auxin (indole-3-acetic acid, IAA) in the GE crop–wild hybrid seeds significantly increased. Evidently, the EPSPS transgene enhances the survival and longevity of GE crop–wild rice seeds in the soil seed banks. The enhanced survival and longevity of the GE hybrid seeds is likely associated with the increases in seed dormancy and auxin (IAA) by overexpressing the rice endogenous EPSPS transgene. Thus, the fate of GE seeds in the soil seed banks should be earnestly considered when assessing the environmental risks caused by transgene flow.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

Glyphosate Accelerates the Proliferation of Microcystis aeruginosa, a Dominant Species in Cyanobacterial Blooms

Glyphosate is a commonly used herbicide known for its high performance in killing certain plants and grasses; however, its use is regulated due to its harmful effects on the aquatic environment. The present study investigated and compared the toxic mechanisms of glyphosate on Microcystis aeruginosa (a toxin-producing cyanobacterium) under 2 conditions: 0‰ saline media (experiment I) and 2.5‰ saline media (experiment II). The results indicated that an appropriate concentration of glyphosate provided a phosphate source for M. aeruginosa, resulting in an increased specific growth rate in both experimental groups compared with the controls. Glyphosate-enhanced alkaline phosphatase (ALP) activity increased by up to 1.37-fold in experiment I and 1.68-fold in experiment II. Moreover, the activities of superoxide dismutase (SOD) and catalase (CAT) decreased at glyphosate concentrations below 1.2 mg L-1 but increased at concentrations greater than 1.2 mg L-1 in experiment I, whereas SOD and CAT activities decreased in experiment II and declined by 64 and 49% in the 30 mg L-1 treatments. Furthermore, the transcript abundances of the pyruvate carboxylase (pcB), microcystin synthetase B (mcyB), and paired-like homeobox (phoX) genes were up-regulated by up to 6.92-, 3.63-, and 2.27-fold in experiment I and 6.74-, 6.55-, and 4.86-fold in experiment II after 96 h of incubation. The addition of glyphosate stimulated the production of dissolved organic matter including tryptophan-like substances, fulvic acid-like substances, (marine) humic acid-like substances, and microcystin-leucine-arginine in the culture. In conclusion, glyphosate stimulates the proliferation of M. aeruginosa and enhances the release of dissolved organic matter in saltwater ecosystems. Environ Toxicol Chem 2021;40:342-351. © 2020 SETAC.

Spatiotemporal Controllability and Environmental Risk Assessment of Genetically Engineered Gene Drive Organisms from the Perspective of European Union Genetically Modified Organism Regulation

Gene drive organisms are a recent development created by using methods of genetic engineering; they inherit genetic constructs that are passed on to future generations with a higher probability than with Mendelian inheritance. There are some specific challenges inherent to the environmental risk assessment (ERA) of genetically engineered (GE) gene drive organisms because subsequent generations of these GE organisms might show effects that were not observed or intended in the former generations. Unintended effects can emerge from interaction of the gene drive construct with the heterogeneous genetic background of natural populations and/or be triggered by changing environmental conditions. This is especially relevant in the case of gene drives with invasive characteristics and typically takes dozens of generations to render the desired effect. Under these circumstances, "next generation effects" can substantially increase the spatial and temporal complexity associated with a high level of uncertainty in ERA. To deal with these problems, we suggest the introduction of a new additional step in the ERA of GE gene drive organisms that takes 3 criteria into account: the biology of the target organisms, their naturally occurring interactions with the environment (biotic and abiotic), and their intended biological characteristics introduced by genetic engineering. These 3 criteria are merged to form an additional step in ERA, combining specific "knowns" and integrating areas of "known unknowns" and uncertainties, with the aim of assessing the spatiotemporal controllability of GE gene drive organisms. The establishment of assessing spatiotemporal controllability can be used to define so-called "cut-off criteria" in the risk analysis of GE gene drive organisms: If it is likely that GE gene drive organisms escape spatiotemporal controllability, the risk assessment cannot be sufficiently reliable because it is not conclusive. Under such circumstances, the environmental release of the GE gene drive organisms would not be compatible with the precautionary principle (PP). Integr Environ Assess Manag 2020;16:555-568. © 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate

Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10^-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.

Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate

Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.

Enhanced yield performance of transgenic cry1C* rice in saline-alkaline soil

China has a large area of saline-alkaline land that can be utilized for the cultivation of transgenic rice. Therefore, the growth and reproductive behavior of transgenic rice are not only a problem for production that needs to be resolved, but also an important aspect of environmental risk assessment for saline alkali soil. In the present study, an insect-resistant transgenic cry1C* rice, T1C-19, was grown in farmland and saline-alkaline soils. The transcription and translation of the exogenous cry1C*, and vegetative and reproductive fitness, such as plant height, tiller number, biomass, filled grain number and weight per plant, were assessed. Our findings indicated that the transcription and translation of exogenous cry1C* gene in T1C-19 rice grown in saline-alkaline soil were lower than that grown in farmland; however, the correlation was not significant. The vegetative and reproductive growth abilities of T1C-19 were lower than that of the parental rice, Minghui63 (MH63), in farmland. In alkaline-saline soil, except for tiller number and biomass, there were no significant differences between T1C-19 and MH63 in other vegetative indices. In contrast, the reproductive indices of T1C-19 were significantly higher than those of MH63. The results suggested that T1C-19 had a strong reproductive capacity, and significantly reduced the loss of yield caused by insects, thereby leading to a higher yield than that of MH63 grown in saline-alkaline soils. This may promote the cultivation of saline-alkaline soil to permit farming of T1C-19 in China in the future, despite the possible increased ecological risks.

A thermostable 5-enolpyruvylshikimate-3-phosphate synthase from Thermotoga maritima enhances glyphosate tolerance in Escherichia coli and transgenic Arabidopsis

5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression, attempting to provide excess EPSPS to combine with glyphosate, is one way to improve glyphosate resistance of plants. The EPSPS in extremophiles which is selected by nature to withstand the evolutionary pressure may possess some potential-specific biological functions. In this study, we reported the cloning, expression and enzymatic characterization of a novel Class II EPSPS AroAT. maritima from Thermotoga maritima MSB8. The enzyme showed low sequence identities with other EPSPSs, and was one of the most thermostable EPSPSs so far, which showed the optimum enzyme activity at 80 °C. The enzyme maintains the activity below 50 °C and in a wide range of pH 4.0-10, which indicated its stability under rough environment, especially in tropical regions and alkaline soil. Excellent Ki/Km value of AroAT. maritima suggested that the enzyme showed powerful competitive binding capacity of PEP over glyphosate and high glyphosate tolerance. Furthermore, aroAT. maritima gene was transformed into Arabidopsis thaliana. The transgenic lines were resistant to 15 mM glyphosate, which proved the application value in the cultivation of glyphosate-tolerant plants.

Do plants pay a fitness cost to be resistant to glyphosate?

We reviewed the literature to understand the effects of glyphosate resistance on plant fitness at the molecular, biochemical and physiological levels. A number of correlations between enzyme characteristics and glyphosate resistance imply the existence of a plant fitness cost associated with resistance-conferring mutations in the glyphosate target enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). These biochemical changes result in a tradeoff between the glyphosate resistance of the EPSPS enzyme and its catalytic activity. Mutations that endow the highest resistance are more likely to decrease catalytic activity by reducing the affinity of EPSPS for its natural substrate, and/or slowing the velocity of the enzyme reaction, and are thus very likely to endow a substantial plant fitness cost. Prediction of fitness costs associated with EPSPS gene amplification and overexpression can be more problematic. The validity of cost prediction based on the theory of evolution of gene expression and resource allocation has been cast into doubt by contradictory experimental evidence. Further research providing insights into the role of the EPSPS cassette in weed adaptation, and estimations of the energy budget involved in EPSPS amplification and overexpression are required to understand and predict the biochemical and physiological bases of the fitness cost of glyphosate resistance.

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.