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

Physiological effects of maize stressed by HPPD inhibitor herbicides via multi-spectral technology and two-dimensional correlation spectrum technology

Understanding the physiological effects of herbicides on crops is crucial for crop production and environmental management. The effects of 4-hydroxyphenylpyruvate dioxygenase inhibitor (HPPDi) herbicides at different concentrations on chlorophyll content in maize leaves, fresh weight of roots, stems and leaves, and fluorescence substances and functional groups in root exudates (REs) were studied by UV-Vis absorption spectroscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR) and two-dimensional correlation analysis (2D-COS). The results showed that 5 mg/L and 10 mg/L HPPDi herbicides inhibited the synthesis of chlorophyll in maize leaves. The weight of roots, stems and leaves of maize after application was lighter than that of the control group. HPPDi herbicides affected the early growth of maize seedlings, and the effect was most obvious at high concentration. Synchronous fluorescence spectrum and three-dimensional (3D) fluorescence spectrum revealed that the fluorescence intensity of protein, fulvic acid and humic acid in maize REs changed prominently. With the increase of HPPDi herbicides concentration, the fluorescence intensity decreased gradually. Through FTIR and 2D-COS, functional groups such as C-H, CO, Cl, NO3-, C-O and O-H were found to participate in the interaction between HPPDi herbicides and maize REs as binding sites. C-O, C-Cl and C-C have the strongest binding ability, while CC and CO of aromatic rings, quinones or ketones first take part in the binding between HPPDi herbicides and maize REs. The results can provide a theoretical basis for evaluating the safety of HPPDi herbicides on maize and a method for discovering the effects of pesticides on environmental media and plant physiological effects.

"Structural responses of non-targeted bacterial and hppd communities to the herbicide tembotrione in soil"

Tembotrione (TBT) is a β-triketone herbicide targeting the 4-Hydroxyphenylpyruvate dioxygenase enzyme (4-HPPD) of weeds. This molecule can also affect soil microorganisms, either through both direct and indirect toxic effects for microorganisms expressing 4-HPPD, or by promoting tolerant and/or degrading microbial populations. Our study aimed to characterize the impacts of TBT on the diversity of total- and hppd (coding for 4-HPPD) -soil bacterial communities. Soil microcosms were treated with the active ingredient TBT at the recommended field dose (100 g a.i/ha; D1) or the tenfold dose (D10). Soil samples were collected from 0 to 55 days post-treatment to study: (i) total- and hppd-bacterial diversities using 16SrRNA and hppd amplicons sequencing, respectively; (ii) TBT dissipation in soil. Both total- and hppd-bacterial community composition was not affected by TBT treatments (D1 and D10). However, D10 treatment slightly increased richness and phylogenetic diversity of the total bacterial community while decreasing hppd richness. Overall, the highest dose of TBT seemed to promote TBT-tolerant or TBT-degrading bacterial populations and to deplete TBT-sensitive ones. These effects were transient as TBT was rapidly dissipated with a DT50 of 7 days and 15 days for D1 and D10, respectively. Differential abundance analysis with a Generalized Linear Model allowed the identification of Sphingomonas, Steroidobacter and Lysobacter as genus that were influenced by TBT, and which could be used as a new class of exposure biomarkers.

Improving the Herbicide Resistance of Rice 4-Hydroxyphenylpyruvate Dioxygenase by DNA Shuffling Basis-Directed Evolution

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an ideal target for herbicide resistance genetic engineering. In this study, a mutant MFRR-2 with mesotrione resistance was screened from an Oryza sativa HPPD and mutant-Zea mays HPPD DNA shuffling library. The enzyme properties showed that although the stability of the mutant decreased in vitro, the enzyme activity of MFRR-2 at the optimum temperature of 25 °C was still equivalent to that of OsHPPD. Under 50 μM mesotrione treatment, MFRR-2 enzyme activity remained at approximately 90%, while the enzyme activity of OsHPPD decreased by approximately 50%. Surprisingly, Fe2+ was found to have an inhibitory effect on the enzyme activity. Then, the transgenic rice of the MFRR-2 gene showed approximately 1.5 times mesotrione resistance compared to OsHPPD transgenic rice. In conclusion, this study has conducted a beneficial exploration on the use of DNA shuffling for HPPD-directed evolution, and the mutant has potential application value for herbicide resistance genetic engineering.

Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches

4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.

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.

Vibrio splendidus virulence to Apostichopus japonicus is mediated by hppD through glutamate metabolism and flagellum assembly

Vibrio splendidus is the main opportunistic pathogen that causes skin ulcer syndrome in Apostichopus japonicus. hppDIn the present study, mutant V. splendidus with an in-frame deletion of hppDV.s. (MTVs) was constructed. The median lethal doses of wild-type V. splendidus (WTVs) and MTVs were 5.129 × 10⁶ and 2.606 × 10¹⁰ CFU mL⁻¹, respectively. RNA-Seq was performed using WTVs and MTVs cells at different growth stages to explore the mechanisms of the pathogenesis mediated by hppDV.s. Gene Ontology analysis showed that the expression levels of 105 genes involved in amino acid metabolism and protein binding were remarkably different between MTVs and WTVs. Kyoto Encyclopedia of Genes and Genomes analysis showed that the pathways of glutamate metabolism and flagellum assembly involved in biofilm formation and swarming motility were suppressed in MTVs. Correspondingly, the swarming motility, biofilm formation and colonisation of MTVs were remarkably decreased compared with those of WTVs. The results showed that 4-hppD catalyses tyrosine into fumarate, which could enhance glutamate metabolism and ATP production; promote flagellum assembly through the TCA cycle and lead to higher swarming, biofilm formation and colonisation abilities, to contribute to the pathogenesis of V. splendidus.

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.

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.