Desensitizing plant EPSP synthase to glyphosate: Optimized global sequence context accommodates a glycine-to-alanine change in the active site

Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design

Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the in-silico analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized in-silico validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level via molecular dynamic (MD) simulation.Communicated by Ramaswamy H. Sarma.

Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate

Gene mutation is a basic evolutionary mechanism in plants under selection pressure of herbicides. Such mutation has pleiotropic effects on plant growth. We systemically investigated the effects of Pro106Leu (P106L), Pro106Ser (P106S), and Thr102Ile + Pro106Ser (TIPS) mutations on EPSPS functionality and fitness traits in Eleusine indica at the biochemical and physiological levels. The affinity of natural EPSPS for glyphosate was 53.8 times higher than that for phosphoenolpyruvate (PEP), as revealed by the dissociation constant; the constant decreased in both the P106L (39.9-fold) and P106S (46.9-fold) mutants but increased in the TIPS (87.5-fold) mutant. The Km (PEP) values of the P106L, P106S, and TIPS mutants were 2.4-, 0.7-, and 4.1-fold higher than that of natural EPSPS, corresponding to resistance levels of 2.5, 1.9, and 11.4, respectively. The catalytic efficiency values (maximum reaction rates) were 0.89-, 0.94-, and 0.26-fold higher than that of natural EPSPS. The levels of metabolites related to amino acids and nucleotides were significantly reduced in the mutated plants. The fitness costs were substantial for the biomass, total leaf area, seed number, and seedling emergence throughout the growth period in the plants with P106L and TIPS mutations. These results provide insights into EPSPS kinetics and their effect on plant growth.

CRISPR/Cas9-mediated homology donor repair base editing confers glyphosate resistance to rice (Oryza sativa L.)

Globally, CRISPR-Cas9-based genome editing has ushered in a novel era of crop advancements. Weeds pose serious a threat to rice crop productivity. Among the numerous herbicides, glyphosate [N-(phosphonomethyl)-glycine] has been employed as a post-emergent, broad-spectrum herbicide that represses the shikimate pathway via inhibition of EPSPS (5'-enolpyruvylshikimate-3-phosphate synthase) enzyme in chloroplasts. Here, we describe the development of glyphosate-resistant rice lines by site-specific amino acid substitutions (G172A, T173I, and P177S: GATIPS-mOsEPSPS) and modification of phosphoenolpyruvate-binding site in the native OsEPSPS gene employing fragment knockout and knock-in of homology donor repair (HDR) template harboring desired mutations through CRISPR-Cas9-based genome editing. The indigenously designed two-sgRNA OsEPSPS-NICTK-1_pCRISPR-Cas9 construct harboring rice codon-optimized SpCas9 along with OsEPSPS-HDR template was transformed into rice. Stable homozygous T₂ edited rice lines revealed significantly high degree of glyphosate-resistance both in vitro (4 mM/L) and field conditions (6 ml/L; Roundup Ready) in contrast to wild type (WT). Edited T₂ rice lines (ER_1-6) with enhanced glyphosate resistance revealed lower levels of endogenous shikimate (14.5-fold) in contrast to treated WT but quite similar to WT. ER_1-6 lines exhibited increased aromatic amino acid contents (Phe, two-fold; Trp, 2.5-fold; and Tyr, two-fold) than WT. Interestingly, glyphosate-resistant Cas9-free EL_1-6 rice lines displayed a significant increment in grain yield (20%-22%) in comparison to WT. Together, results highlighted that the efficacy of GATIPS mutations in OsEPSPS has tremendously contributed in glyphosate resistance (foliar spray of 6 ml/L), enhanced aromatic amino acids, and improved grain yields in rice. These results ensure a novel strategy for weed management without yield penalties, with a higher probability of commercial release.

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

The invasive species Lonicera maackii (Amur Honeysuckle) is an increasing problem sweeping from the eastern United States toward the west, impacting normal forest development and animal survival across multiple taxa. Little is known about the genomics of this species, although a related invasive, Lonicera japonica, has been sequenced. Understanding the genomic foundation of the Lonicera maackii species could help us understand the biochemistry and life history that are the underpinnings of invasive success, as well as potential vulnerabilities and strengths which could guide research and development to control its spread. Here we present a draft, but high-quality, short-read whole-genome sequence, assembly, and annotation of Lonicera maackii, demonstrating that inexpensive and rapid short-read technologies can be successfully used in invasive species research. Despite being a short-read assembly, the genome length (7.93 × 10⁸) and completeness (estimated as 90.2-92.1% by BUSCO and Merqury) are close to the previously published chromosome-level sequencing of L. japonica. No bias, by means of a Gene Ontology analysis, was identified among missing BUSCOs. A duplication of the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene in both Lonicera species is identified, and the potential impact on controlling these invasive species is discussed. Future prospects for a diversity analysis of invasive species is also discussed.

Rapeseed Transformation with aroA Bacterial Gene Containing P101S Mutation Confers Glyphosate Resistance

Field weed infestations can cause serious problems and require regular and planned programs to control them. Glyphosate is a broad-spectrum herbicide that inactivates the 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) enzyme and causes plant death. It has been reported that the mutation of proline 101 to serine in EPSPS is one of the effective mutations to reduce the affinity of glyphosate to EPSPS enzyme. In this study, we investigated the effect of the bacterial P101S mutant aromatic acid (aroA) gene on glyphosate resistance in transgenic rapeseeds. For this purpose, the mutant gene was synthesized and cloned into the pUC18 and pBI121 vectors. The gene was transferred to rapeseed by the Agrobacterium-mediated method. In this experiment, three generations of transgenic plants (T0, T1, and T2) were studied under in vitro and in vivo conditions. After the treatment of 75 putative transgenic plants with 10 mM glyphosate in T0 generation, resistant plants were identified and their seeds were harvested. In the T1 generation, out of 200 cultivated plants, 141 showed resistance. After the plants were treated with herbicides and resistance was determined, the seeds were harvested when they mature. In the T2 generation, most plants (162 plants of 200) were resistant to glyphosate. Therefore, the inheritance of resistance followed Mendel's first law, which is a sign of the monogenic character of resistance. Purification and increasing the percentage of resistant plants will be carried out in the next generations. It is concluded that P101S mutation guarantees glyphosate resistance of rapeseed and is recommended to study it in other plants.

Development of non-transgenic glyphosate tolerant wheat by TILLING

Glyphosate (N-phosphonomethyl-glycine) is the world's most widely used broad spectrum, post-emergence herbicide. It inhibits the chloroplast-targeted enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), a component of the plant and microorganism-specific shikimate pathway and a key catalyst in the production of aromatic amino acids. Variants of EPSPS that are not inhibited by glyphosate due to particular amino acid alterations in the active site of the enzyme are known. Some of these variants have been identified in weed species that have developed resistance to glyphosate because of the strong selective pressure of continuous, heavy glyphosate use. We have used TILLING (Targeting Induced Local Lesions in Genomes), a non-transgenic, target-selected, reverse genetics, mutation breeding technique, and conventional genetic crosses, to identify and combine, through two rounds of mutagenesis, wheat lines having both T102I and P106S (so-called TIPS enzyme) mutations in both the A and the D sub-genome homoeologous copies of the wheat EPSPS gene. The combined effects of the T102I and P106S mutations are known from previous work in multiple species to minimize the binding of the herbicide while maintaining the affinity of the catalytic site for its native substrates. These novel wheat lines exhibit substantial tolerance to commercially relevant levels of glyphosate.

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.

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.

Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance

To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. To overcome the complexity of the maize genome, two sequencing technologies were employed: Illumina and Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs and approximately 800 thousand indels differentiating the two genomes were identified. Detailed analyses allowed to identify 20 variations within the EPSPS gene, but all of them were predicted to have moderate or unknown effects on gene expression. Other genes of the shikimate pathway encoding bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase and chorismate synthase were altered by variants predicted to have a high impact on gene expression. Additionally, high-impact variants located within the genes involved in the active transport of glyphosate through the cell membrane encoding phosphate transporters as well as multidrug and toxic compound extrusion have been identified.

Investigation of the target-site resistance of EPSP synthase mutants P106T and T102I/P106S against glyphosate

The shikimate pathway enzyme 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) catalyzes the reaction involved in the production of amino acids essential for plant growth and survival. Thus, EPSPS is the main target of various herbicides, including glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor of phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. However, punctual mutations in the EPSPS gene have led to glyphosate resistance in some plants. Here, we investigated the mechanism of EPSPS resistance to glyphosate in mutants of two weed species, Conyza sumatrensis (mutant, P106T) and Eleusine indica (mutant, T102I/P106S), both of which have an economic impact on industrial crops. Molecular dynamics (MD) simulations and binding free energy calculations revealed the influence of the mutations on the affinity of glyphosate in the PEP-binding site. The amino acid residues of the EPSPS protein in both species involved in glyphosate resistance were elucidated as well as other residues that could be useful for protein engineering. In addition, during MD simulations, we identified conformational changes in glyphosate when complexed with resistant EPSPS, related to loss of herbicide activity and binding affinity. Our computational findings are consistent with previous experimental results and clarify the inhibitory activity of glyphosate as well as the structural target-site resistance of EPSPS against glyphosate.

Single or double EPSP synthase mutations lead glyphosate to undergo conformational changes that limit its inhibitory action.

Glyphosate's Synergistic Toxicity in Combination with Other Factors as a Cause of Chronic Kidney Disease of Unknown Origin

Chronic kidney disease of unknown etiology (CKDu) is a global epidemic. Sri Lanka has experienced a doubling of the disease every 4 or 5 years since it was first identified in the North Central province in the mid-1990s. The disease primarily affects people in agricultural regions who are missing the commonly known risk factors for CKD. Sri Lanka is not alone: health workers have reported prevalence of CKDu in Mexico, Nicaragua, El Salvador, and the state of Andhra Pradesh in India. A global search for the cause of CKDu has not identified a single factor, but rather many factors that may contribute to the etiology of the disease. Some of these factors include heat stroke leading to dehydration, toxic metals such as cadmium and arsenic, fluoride, low selenium, toxigenic cyanobacteria, nutritionally deficient diet and mycotoxins from mold exposure. Furthermore, exposure to agrichemicals, particularly glyphosate and paraquat, are likely compounding factors, and may be the primary factors. Here, we argue that glyphosate in particular is working synergistically with most of the other factors to increase toxic effects. We propose, further, that glyphosate causes insidious harm through its action as an amino acid analogue of glycine, and that this interferes with natural protective mechanisms against other exposures. Glyphosate's synergistic health effects in combination with exposure to other pollutants, in particular paraquat, and physical labor in the ubiquitous high temperatures of lowland tropical regions, could result in renal damage consistent with CKDu in Sri Lanka.

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.

How Glyphosate Impairs Liver Condition in the Field Lizard Podarcis siculus (Rafinesque-Schmaltz, 1810): Histological and Molecular Evidence

The potential toxicity of glyphosate, a widely used broad-spectrum herbicide, is currently a great matter of debate. As vertebrate insectivores, lizards protect plants from herbivorous insects increasing plant biomass via the trophic cascade and represent an important link between invertebrates and higher predators. A negative effect of glyphosate on lizards' survival could have major impacts at the ecological levels. In this study, we investigated the effects of the exposure to low doses of glyphosate on the liver of the wall lizard Podarcis siculus, a suitable bioindicator of soil pollution. Two different doses of pure glyphosate (0.05 and 0.5 μg/kg body weight) were orally administered every other day for 3 weeks to sexually mature males and females. The results demonstrated that both doses, despite being very low, are toxic for the liver that showed clear signs of suffering, regardless of sex. The histological analysis provided a scenario of severe hepatic condition, which degenerated until the appearance of fibrotic formations. The morphological observations were consistent with a loss of liver physiological functions. Immunocytochemical investigations allowed us to detect an involvement of antioxidant/cytoprotective proteins, such as superoxide dismutase 1 (Cu/Zn SOD, known as SOD1), glutathione peroxidase 1 (GPx1), metallothionein (MT), and tumor suppressor protein 53, (p53) suggesting that the liver was trying to react against stress signals and damage induced by glyphosate. Finally, in situ hybridization and Real-Time PCR analysis showed the upregulation of estrogen receptor α and vitellogenin gene expression, thus demonstrating the xenoestrogenic action of glyphosate. The imbalance of the hormonal homeostasis could threaten the lizards' reproductive fitness and survival, altering the trophic cascade.