Characterization and safety evaluation of HPPD W336, a modified 4-hydroxyphenylpyruvate dioxygenase protein, and the impact of its expression on plant metabolism in herbicide-tolerant MST-FGØ72-2 soybean

Comparative transcriptomic and proteomic analysis reveals common molecular factors responsive to heat and drought stresses in sweetpotaoto (Ipomoea batatas)

Introduction

Crops are affected by various abiotic stresses, among which heat (HT) and drought (DR) stresses are the most common in summer. Many studies have been conducted on HT and DR, but relatively little is known about how drought and heat combination (DH) affects plants at molecular level.

Methods

Here, we investigated the responses of sweetpotato to HT, DR, and DH stresses by RNA-seq and data-independent acquisition (DIA) technologies, using controlled experiments and the quantification of both gene and protein levels in paired samples.

Results

Twelve cDNA libraries were created under HT, DR, and DH conditions and controls. We identified 536, 389, and 907 DEGs in response to HT, DR, and DH stresses, respectively. Of these, 147 genes were common and 447 were specifically associated with DH stress. Proteomic analysis identified 1609, 1168, and 1535 DEPs under HT, DR, and DH treatments, respectively, compared with the control, of which 656 were common and 358 were exclusive to DH stress. Further analysis revealed the DEGs/DEPs were associated with heat shock proteins, carbon metabolism, phenylalanine metabolism, starch and cellulose metabolism, and plant defense, amongst others. Correlation analysis identified 6465, 6607, and 6435 co-expressed genes and proteins under HT, DR, and DH stresses respectively. In addition, a combined analysis of the transcriptomic and proteomic data identified 59, 35, and 86 significantly co-expressed DEGs and DEPs under HT, DR, and DH stresses, respectively. Especially, top 5 up-regulated co-expressed DEGs and DEPs (At5g58770, C24B11.05, Os04g0679100, BACOVA_02659 and HSP70-5) and down-regulated co-expressed DEGs and DEPs (AN3, PMT2, TUBB5, FL and CYP98A3) were identified under DH stress.

Discussion

This is the first study of differential genes and proteins in sweetpotato under DH stress, and it is hoped that the findings will assist in clarifying the molecular mechanisms involved in sweetpotato resistance to heat and drought stress.

Identification and Characterization of Mesotrione-Resistant Grain Sorghum [Sorghum bicolor (L.) Moench]: A Viable Option for Postemergence Grass Weed Control

Mesotrione is effective in controlling a wide spectrum of weeds in corn but not registered for postemergence use in sorghum because of crop injury. We screened a sorghum germplasm collection and identified two mesotrione-resistant sorghum genotypes (G-1 and G-10) and one susceptible genotype (S-1) in an in vitro plate assay. A mesotrione dose-response assay under greenhouse and field conditions confirmed that G-1 and G-10 are highly resistant compared to S-1. We found enhanced metabolism of mesotrione in G-1 and G-10 using HPLC assay, and a significant reduction in biomass accumulation was found in G-1 and G-10 plants pretreated with cytochrome P450 (CYP)-inhibitors malathion or piperonyl butoxide, indicating the involvement of CYPs in the metabolism of mesotrione. Genetic analyses using F₁ and F₂ progenies generated by crossing G-1 and G-10 separately with S-1 revealed that mesotrione resistance in sorghum is controlled by a single dominant gene along with several genes with minor effects.

Ecotoxicological implications of residual pesticides to beneficial soil bacteria: A review

Optimization of crop production in recent times has become essential to fulfil food demands of constantly increasing human populations worldwide. To address this formidable challenge, application of agro-chemicals including synthetic pesticides in intensive farm practices has increased alarmingly. The excessive and indiscriminate application of pesticides to foster food production however, leads to its exorbitant deposition in soils. After accumulation in soils beyond threshold limits, pesticides harmfully affect the abundance, diversity and composition and functions of rhizosphere microbiome. Also, the cost of pesticides and emergence of resistance among insect-pests against pesticides are other reasons that require attention. Due to this, loss in soil nutrient pool cause a substantive reduction in agricultural production which warrant the search for newer environmentally friendly technology for sustainable crop production. Rhizosphere microbes, in this context, play vital roles in detoxifying the polluted environment making soil amenable for cultivation through detoxification of pollutants, rhizoremediation, bioremediation, pesticide degradation, and stress alleviation, leading to yield optimization. The response of soil microorganisms to range of chemical pesticides is variable ranging from unfavourable to the death of beneficial microbes. At cellular and biochemical levels, pesticides destruct the morphology, ultrastructure, viability/cellular permeability, and many biochemical reactions including protein profiles of soil bacteria. Several classes of pesticides also disturb the molecular interaction between crops and their symbionts impeding the overall useful biological processes. The harmful impact of pesticides on soil microbes, however, is poorly researched. In this review, the recent findings related with potential effects of synthetic pesticides on a range of soil microbiota is highlighted. Emphasis is given to find and suggest strategies to minimize the chemical pesticides usage in the real field conditions to preserve the viability of soil beneficial bacteria and soil quality for safe and sustainable crop production even in pesticide contaminated soils.

Mutations of Asn321 and Glu322 Improve Resistance of 4-Hydroxyphenylpyruvate Dioxygenase SpHPPDm to Topramezone

As a highly efficient 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide, topramezone is an ideal target for herbicide-resistant genetic engineering. In this study, two mutants, K-19 (N321Y) and K-63 (Q166R/E322V), with topramezone resistance increased by 205.3 and 58.5%, respectively, were screened from the random mutation library of SpHPPDm, a topramezone-resistant HPPD mutant that we previously obtained. Sites N321 and E322 were identified as key sites for increased topramezone resistance by single-site mutation analysis. A mutant KB-145 (N321Y/E322K) was further obtained by saturation mutation at sites N321 and E322. The topramezone resistance of KB-145 increased by 955.3% compared to mutant SpHPPDm. In conclusion, this study identifies two new sites that significantly affect the topramezone resistance of SpHPPDm, which provides new insights into the molecular mechanism of herbicide resistance of HPPD, and the acquired mutants have great application potential in the construction of herbicide-resistant crops.

Ectopic expression of a rice triketone dioxygenase gene confers mesotrione tolerance in soybean

BACKGROUND

Herbicide-resistant weeds pose a challenge to agriculture and food production. New herbicide tolerance traits in crops will provide farmers with more options to effectively manage weeds. Mesotrione, a selective pre- and post-emergent triketone herbicide used in corn production, controls broadleaf and some annual grass weeds via hydroxyphenylpyruvate dioxygenase (HPPD) inhibition. Recently, the rice HIS1 gene, responsible for native tolerance to the selective triketone herbicide benzobicyclon, was identified. Expression of HIS1 also confers a modest level of mesotrione resistance in rice. Here we report the use of the HIS1 gene to develop a mesotrione tolerance trait in soybean.

RESULTS

Conventional soybean is highly sensitive to mesotrione. Ectopic expression of a codon-optimized version of the rice HIS1 gene (TDO) in soybean confers a commercial level of mesotrione tolerance. In TDO transgenic soybean plants, mesotrione is rapidly and locally oxidized into noninhibitory metabolites in leaf tissues directly exposed to the herbicide. These metabolites are further converted into compounds similar to known classes of plant secondary metabolites. This rapid metabolism prevents movement of mesotrione from treated leaves into vulnerable emerging leaves. Minimizing the accumulation of the herbicide in vulnerable emerging leaves protects the function of HPPD and carotenoid biosynthesis more generally while providing tolerance to mesotrione.

CONCLUSIONS

Mesotrione has a favorable environmental and toxicological profile. The TDO-mediated soybean mesotrione tolerance trait described here provides farmers with a new option to effectively manage difficult-to-control weeds using familiar herbicide chemistry. This trait can also be adapted to other mesotrione-sensitive crops (e.g. cotton) for effective weed management. © 2022 Bayer Crop Science. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Improving the herbicide resistance of 4-hydroxyphenylpyruvate dioxygenase SpHPPD by directed evolution

Topramezone, a highly efficient 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicide, is an ideal target for herbicide-resistant genetic engineering. However, there is still a lack of HPPD gene that is highly resistant to topramezone. In previous studies, we obtained a topramezone-resistant HPPD (SpHPPDm) gene from Sphingobium sp. TPM-19, however, its resistance strength still could not meet the requirements for construction of herbicide-resistant crop. In this study, random mutagenesis (error-prone PCR) was employed to improve the topramezone resistance of SpHPPDm. Two mutants with improved resistance, K-28 (E322R) and K-113 (K249R, G327C), were screened from the random mutation library of SpHPPDm. The catalytic efficiency (k_cat/K_m) of mutants K-28 and K-113 only slightly decreased by approximately 2%. The half-maximal inhibitory concentration (IC₅₀) of topramezone increased by 58.5% and 195.5% for mutants K-28 and K-113, respectively. Furthermore, mutant K-113 also showed significantly improved resistance to mesotrione and DKN (the active ingredient of isoxaflutole) with the IC₅₀ increasing by 60.3% and 167.5%, respectively; while mutant K-28 only showed increased resistance to mesotrione with IC₅₀ increasing by 77.6%, but reduced resistance to DKN with IC₅₀ declining by 20.9%. Site-directed mutation assays revealed that G327C, but not K249R, contributed to topramezone resistance in mutant K-113. This study provides genetic resources for the genetic engineering of HPPD-inhibitor-resistant crops and a basis for further research on HPPD resistance mechanisms.

Characterization, Genetic Analyses, and Identification of QTLs Conferring Metabolic Resistance to a 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor in Sorghum (Sorghum bicolor)

Postemergence grass weed control continues to be a major challenge in grain sorghum [Sorghum bicolor (L.) Moench], primarily due to lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control can be an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g., mesotrione or tembotrione) can control a broad spectrum of weeds including grasses, which, however, are not registered for postemergence application in sorghum due to crop injury. In this study, we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one susceptible genotype (S-1) by screening 317 sorghum lines from a sorghum association panel (SAP). These tembotrione-resistant and tembotrione-susceptible genotypes were evaluated in a tembotrione dose-response [0, 5.75, 11.5, 23, 46, 92 (label recommended dose), 184, 368, and 736 g ai ha^-1] assay. Compared with S-1, the genotypes G-200 and G-350 exhibited 10- and seven fold more resistance to tembotrione, respectively. To understand the inheritance of tembotrione-resistant trait, crosses were performed using S-1 and G-200 or G-350 to generate F₁ and F₂ progeny. The F₁ and F₂ progeny were assessed for their response to tembotrione treatment. Genetic analyses of the F₁ and F₂ progeny demonstrated that the tembotrione resistance in G-200 and G-350 is a partially dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed QTLs associated with tembotrione resistance in G-200 and G-350 genotypes. Overall, the genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids.

Improved Herbicide Resistance of 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19 through Directed Evolution

4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted extensive interest as a promising target for the genetic engineering of herbicide-resistant crops. However, naturally occurring HPPDs are generally very sensitive to HPPD inhibitors. In this study, random mutagenesis was performed to increase the HPPD inhibitors' resistance of Sphingobium sp. HPPD (SpHPPD). Two mutants, Q258M and Y333F, with improved resistance were obtained. Subsequently, a double-mutant (Q258M/Y333F) was generated through combined mutation. Q258M/Y333F exhibited the highest resistance to four HPPD inhibitors [topramezone, mesotrione, tembotrione, and diketonitrile (DKN)]. The enzyme fitness of Q258M/Y333F to topramezone, mesotrione, tembotrione, and DKN was increased by 4.0-, 4.1-, 4.2-, and 3.2-folds, respectively, in comparison with that of the wild-type. Molecular modeling and docking revealed that Q258M mutation leads to the decrease of enzyme-inhibitor-binding strength by breaking the hydrogen bond between the enzyme and the inhibitor, and Y333F mutation changes the conformational balance of the C-terminal helix H11, which hinders the binding of the inhibitor to the enzyme and thus would contribute to improved herbicide resistance. This study helps to further elucidate the structural basis for herbicide resistance and provides better genetic resources for the genetic engineering of herbicide-resistant crops.

Mechanisms of evolved herbicide resistance

The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and nontarget-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mutations in genes encoding the protein targets of herbicides, affecting the binding of the herbicide either at or near catalytic domains or in regions affecting access to them. Most of these mutations are nonsynonymous SNPs, but polymorphisms in more than one codon or entire codon deletions have also evolved. Some herbicides bind multiple proteins, making the evolution of TSR mechanisms more difficult. Increased amounts of protein target, by increased gene expression or by gene duplication, are an important, albeit less common, TSR mechanism. NTSR mechanisms include reduced absorption or translocation and increased sequestration or metabolic degradation. The mechanisms that can contribute to NTSR are complex and often involve genes that are members of large gene families. For example, enzymes involved in herbicide metabolism-based resistances include cytochromes P450, GSH S-transferases, glucosyl and other transferases, aryl acylamidase, and others. Both TSR and NTSR mechanisms can combine at the individual level to produce higher resistance levels. The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures. These evolutionary processes drive herbicide and herbicide-resistant crop development and resistance management strategies.

Isolation and Characterization of a Topramezone-Resistant 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19

Topramezone is a 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor. Due to its broad-spectrum, high efficiency, and low toxicity, topramezone is a candidate herbicide for the construction of genetically modified (GM) herbicide-resistant crops. In the present study, we screened a topramezone-resistant isolate Sphingobium sp. TPM-19 and cloned a topramezone-resistant HPPD gene (SphppD) from this isolate. SpHPPD shared the highest similarity (53%) with an HPPD from Vibrio vulnificus CMCP6. SpHPPD was synthesized in Escherichia coli BL21(DE3) and purified to homogeneity using Co²⁺-affinity chromatography. SpHPPD was found to be a monomer. The K_m and k_cat of SpHPPD for 4-hydroxyphenylpyruvate (4-HPP) were 82.8 μM and 15.0 s^-1, respectively. SpHPPD showed high resistance to topramezone with half maximal inhibitory concentration (IC₅₀) and K_i values of 5.2 and 2.5 μM, respectively. Additionally, SpHPPD also showed high resistance to isoxaflutole (DKN) (IC₅₀: 8.7 μM; K_i: 6.0 μM) and mesotrione (IC₅₀: 4.2 μM; K_i: 1.3 μM) and moderate resistance to tembotrione (IC₅₀: 2.5 μM; K_i: 1.0 μM). The introduction of the SphppD gene into Arabidopsis thaliana enhanced obvious resistance against topramezone. In conclusion, this study provides a novel topramezone-resistant HPPD gene for the genetic engineering of GM herbicide-resistant crops.

Assessment of genetically modified soybean SYHT0H2 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE-2012-111)

The scope of application EFSA-GMO-DE-2012-111 is for food and feed uses, import and processing of genetically modified (GM) soybean SYHT0H2 in the European Union. Soybean SYHT0H2 was developed to confer tolerance to the herbicidal active substances mesotrione and other p-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides and glufosinate ammonium. The molecular characterisation data and bioinformatic analyses do not identify issues except for sequence similarity of AvHPPD-03 to bacterial haemolysins that was considered in food/feed safety assessment. The outcome of the comparative analysis (agronomic/phenotypic and compositional characteristics) did not need further assessment except for the changes in seed levels of α-tocopherol and γ-tocopherol that were assessed for food and feed relevance. The GMO Panel does not identify toxicological and allergenicity concerns for the AvHPPD-03 and PAT proteins expressed in soybean SYHT0H2 and finds no evidence that the genetic modification would change the overall allergenicity of soybean SYHT0H2. The nutritional impact of food/feed from soybean SYHT0H2 is expected to be the same as that of food/feed from the conventional counterpart and commercial non-GM soybean reference varieties. The GMO Panel concludes that soybean SYHT0H2 is as safe as and nutritionally equivalent to the conventional counterpart and the tested non-GM soybean reference varieties, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable soybean SYHT0H2 grains into the environment, soybean SYHT0H2 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean SYHT0H2. In conclusion, the GMO Panel considers that soybean SYHT0H2, as described in this application, is as safe as its conventional counterpart and the tested non-GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Characterization of 4-hydroxyphenylpyruvate dioxygenases, inhibition by herbicides and engineering for herbicide tolerance in crops

4-Hydroxyphenylpyruvate dioxgenase (HPPD) enzymes from rat and from several plants contained only about a single inhibitor-binding active site per dimer which matched the content of iron in the purified Arabidopsis thaliana and Avena sativa enzymes. The dimeric HPPDs were about 10 fold more catalytically active than the tetrameric P. fluorescens enzyme with k_cat/K_mHPP values ranging from 0.8 to 2.5 s^-1 μM^-1. Most were also highly sensitive to herbicides with, for example, K_i values for mesotrione ranging from 25 to 100 pM. Curiously HPPDs from cool climate grasses were much less herbicide-sensitive. When likewise expressed in Nicotinia tabacum, Avena sativa HPPD, K_i value of 11 nM for mesotrione, conferred far greater tolerance to mesotrione (Callisto^TM) than did any of the more sensitive HPPDs. Targeted mutagenesis of the Avena HPPD led to the discovery of 4 mutations imparting improved inherent tolerance, defined as the ratio of K_i to K_mHPP, by about 16 fold without any loss of catalytic activity. The Nicotinia line with the highest expression of this quadruple mutant exhibited substantial resistance even up to a 3 kg/ha post-emergence application of mesotrione. The maximum observed expression level of heterologous plant HPPDs in tobacco was ca. 0.35% of the total soluble protein whereas the endogenous tobacco HPPD constituted only ca. 0.00075%. At such high expression even HPPDs with impaired catalytic activity could be effective. A quintuple mutant Avena sativa HPPD conferred substantial tolerance across a broad range of HPPD herbicide chemistries despite being only ca. 5 % as catalytically active as the wild type enzyme. Testing various wild type and mutant HPPDs in tobacco revealed that tolerance to field rates of herbicide generally requires about two order of magnitude increases in both inherent herbicide tolerance and expression relative to endogenous levels. This double hurdle may explain why target-site based resistance to HPPD-inhibiting herbicides has been slow to evolve in weeds.

Supplementary data on the characterization and safety evaluation of HPPD W336, a modified 4-hydroxyphenylpyruvate dioxygenase protein, which confers herbicide tolerance, and on the compositional assessment of field grown MST-FGØ72-2 soybean expressing HPPD W336

Supplementary data are provided which are supportive to the research article entitled “Characterization and safety evaluation of HPPD W336, a modified 4-hydroxyphenylpyruvate dioxygenase protein, and the impact of its expression on plant metabolism in herbicide-tolerant MST-FGØ72-2 soybean” (Dreesen et al., 2018) [1]. The conducted supplementary analyses include the characterization of additional Escherichia coli-produced HPPD W336 protein batches used as a surrogate in HPPD W336 safety studies, the assessment of potential glycosylation and monitoring of stability in simulated intestinal fluid and during heating of the HPPD W336 protein. Furthermore, data are provided on conducted field trials and subsequent compositional analysis in MST-FGØ72-2 soybean grain of compounds related to the tyrosine degradation pathway and the metabolism of homogentisate.