Comparison of herbicide specificity of CYP81A cytochrome P450s from rice and a multiple-herbicide resistant weed, Echinochloa phyllopogon

Effects of Amino Acid Mutation in Cytochrome P450 (CYP96A146) of Descurainia sophia on the Metabolism and Resistance to Tribenuron-Methyl

Cytochrome P450 monooxygenases (P450s) play important roles in herbicide resistance. In this study, there are four amino acid mutations (F39Y, H163Y, S203A, and V361E) between CYP96A146-S and CYP96A146-R, which were cloned, respectively, from susceptible (S) and tribenuron-methyl-resistant (TR) Descurainia sophia. The Arabidopsis expressing CYP96A146-S or CYP96A146-R showed resistance to tribenuron-methyl, carfentrazone-ethyl, and oxyfluorfen, while Arabidopsis transformed with CYP96A146-R or CYP96A146 with any two or three mutations of H163Y, S203A, or V361E exhibited significantly higher resistance to tribenuron-methyl than Arabidopsis expressing CYP96A146-S. The metabolic rates of tribenuron-methyl were significantly faster in Arabidopsis expressing CYP96A146-R than that with CYP96A146-S. The molecular dynamics simulation demonstrated that amino acid mutations did not affect the domain of the HEM ring, which could significantly enhance the volume of the catalytic pocket in P450 (CYP96A146), thereby increasing the collision rate between the catalytic pocket and tribenuron-methyl. Hence, the amino acid mutations may be one of the mechanisms underlying P450-mediated herbicide resistance.

Mutations in target gene confers resistance to acetolactate synthase inhibitors in Echinochloa phyllopogon

Echinochloa phyllopogon is a noxious weed that can harm rice over prolonged periods. Recently, a penoxsulam-resistant variant of E. phyllopogon with a mutation in the acetolactate synthase (ALS) gene was collected in Northeastern China. In the present study, the molecular mechanism underlying herbicide resistance in mutant populations was evaluated. The GR50 and IC50 values of the herbicide-resistant mutant 1-11 were 27.0- and 21.4-fold higher than those of the susceptible population 2-31, respectively. In addition, pre-application of malathion reduced the GR50 value of the resistant population. Additionally, mutant populations developed cross-resistance to other ALS inhibitors. E. phyllopogon ALS sequencing showed a Trp-574-Leu mutation in ALS2 variant 1-11. Molecular docking showed that the Trp-574-Leu substitution reduced the number of hydrogen bonds and altered the interaction between penoxsulam and ALS2. Transgenic Arabidopsis plants harboring the ALS2 mutant gene also showed resistance to penoxsulam and other ALS inhibitors. Overall, our study demonstrated that the Trp-574-Leu mutation and P450-mediated metabolic resistance lead to the cross-resistance of E. phyllopogon to ALS inhibitors.

Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review

Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.

Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance

The emergence of herbicide-resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern owing to its unpredictability. Nontarget-site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC-seq and DAP-seq to identify transcription factors and cis-regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exploration and utilization of novel aldoxime, nitrile, and nitro compounds metabolizing enzymes from plants and arthropods

Aldoxime (R1R2C=NOH) and nitrile (R-C≡N) are nitrogen-containing compounds that are found in species representing all kingdoms of life. The enzymes discovered from the microbial "aldoxime-nitrile" pathway (aldoxime dehydratase, nitrile hydratase, amidase, and nitrilase) have been thoroughly studied because of their industrial importance. Although plants utilize cytochrome P450 monooxygenases to produce aldoxime and nitrile, many biosynthetic pathways are yet to be studied. Cyanogenic millipedes accumulate various nitrile compounds, such as mandelonitrile. However, no such aldoxime- and nitrile-metabolizing enzymes have been identified in millipedes. Here, I review the exploration of novel enzymes from plants and millipedes with characteristics distinct from those of microbial enzymes, the catalysis of industrially useful reactions, and applications of these enzymes for nitrile compound production.

Molecular Responses and Degradation Mechanisms of the Herbicide Diuron in Rice Crops

Diuron [DU; 3-(3,4-dichlorophenyl)-1,1-dimethylurea], a widely used herbicide for weed control, arouses ecological and health risks due to its environment persistence. Our findings revealed that DU at 0.125-2.0 mg L^-1 caused oxidative damage to rice. RNA-sequencing profiles disclosed a globally genetic expression landscape of rice under DU treatment. DU mediated downregulated gene encoding photosynthesis and biosynthesis of protein, fatty acid, and carbohydrate. Conversely, it induced the upregulation of numerous genes involved in xenobiotic metabolism, detoxification, and anti-oxidation. Furthermore, 15 DU metabolites produced by metabolic genes were identified, 7 of which include two Phase I-based and 5 Phase II-based derivatives, were reported for the first time. The changes of resistance-related phytohormones, like JA, ABA, and SA, in terms of their contents and molecular-regulated signaling pathways positively responded to DU stress. Our work provides a molecular-scale perspective on the response of rice to DU toxicity and clarifies the biotransformation and degradation fate of DU in rice crops.