Characterization of HemY-type protoporphyrinogen IX oxidase genes from cyanobacteria and their functioning in transgenic Arabidopsis

Functional characterization of GAPDH2 through overexpression and dsRNA-mediated RNA interference in Synechocystis

Glyceraldehyde-3-phosphate dehydrogenase 2 (GAPDH2) plays a vital role in cell growth, stress responses, and various cellular processes in organisms. However, its functional characterization in cyanobacteria, particularly in Synechocystis sp. PCC 6803, remains largely unexplored, especially concerning its overexpression and RNA interference (RNAi) via double-stranded RNA (dsRNA). This study aimed to investigate the biological role of GAPDH2 in Synechocystis sp. PCC 6803 by cloning its complete coding sequence (SyGAPDH2). The SyGAPDH2 protein comprises 350 amino acids with a molecular weight of 86.480 kDa and an isoelectric point of 5.03. The sequence alignment analysis revealed two conserved domains: NADH (Nicotinamide Adenine Dinucleotide)-quinone oxidoreductase subunit NuoI and NADH-ubiquinone/plastoquinone oxidoreductase chain 6. Similarly, Phylogenetic analysis demonstrated high sequence similarity of 96 % and 94 % with Coliform (Gammaproteobacteria bacterium), respectively. We further explored the functional significance of SyGAPDH2 through overexpression using the PpsbAII+SyGAPDH2 vector and double stranded RNA (dsRNA)-mediated silencing with dsGAPDH2. Overexpression significantly enhanced cell growth, while dsRNA-mediated suppression resulted in reduced cell proliferation, with effects observed 12 h post-treatment and persisting up to 36 h. These findings emphasize the essential regulatory role of SyGAPDH2 in cellular development and stress response. This study contributes to our understanding of GAPDH2 functional importance in cyanobacteria, providing a foundation for future investigations into its subcellular localization, additional functional roles, and broader regulatory mechanisms within cyanobacterial cellular processes.

Novel N-Phenyltriazinone Carboxylic Acid Derivatives as Promising Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen IX oxidase (PPO) is a critical target for new herbicide development. We used a scaffold hopping strategy to develop 49 novel N-phenyltriazinone carboxylic acid derivatives and assessed their function as PPO inhibitors. Bioassay revealed that compound D5 exhibited excellent inhibitory activity against Nicotiana tabacum PPO (NtPPO) with a Ki of 33.7 nM, comparable to that of trifludimoxazin (Ki = 31.1 nM). Compound D5 also exhibited remarkable postemergence herbicidal activity against five weed species (Setaria faberii, Echinochloa crusgalli, Amaranthus retroflexus, Abutilon juncea, and Portulaca oleracea) at an ultralow concentration (9.375 g a.i./ha), and it showed broad-spectrum herbicidal activity and relatively high safety in wheat, rice, and peanut at 150 and 75 g a.i./ha, respectively. In molecular simulations, compound D5 stably binds NtPPO via π-π stacking with Phe392 and a sandwiched π-alkyl interaction with the key amino acids Leu356 and Leu372. This study shows that the novel N-phenyltriazinone carboxylic acid derivative D5 is a promising PPO inhibitor for agricultural weed control.

Production and characterization of homologous protoporphyrinogen IX oxidase (PPO) proteins: Evidence that small N-terminal amino acid changes do not impact protein function

Transgenic soybean, cotton, and maize tolerant to protoporphyrinogen IX oxidase (PPO)-inhibiting herbicides have been developed by introduction of a bacterial-derived PPO targeted into the chloroplast. PPO is a membrane-associated protein with an intrinsic tendency for aggregation, making expression, purification, and formulation at high concentrations difficult. In this study, transgenic PPO expressed in three crops was demonstrated to exhibit up to a 13 amino acid sequence difference in the N-terminus due to differential processing of the chloroplast transit peptide (CTP). Five PPO protein variants were produced in and purified from E. coli, each displaying equivalent immunoreactivity and functional activity, with values ranging from 193 to 266 nmol min-1 mg-1. Inclusion of an N-terminal 6xHis-tag or differential processing of the CTP peptide does not impact PPO functional activity. Additionally, structural modeling by Alphafold, ESMfold, and Openfold indicates that these short N-terminal extensions are disordered and predicted to not interfere with the mature PPO structure. These results support the view that safety studies on PPO from various crops can be performed from a single representative variant. Herein, we report a novel and robust method for large-scale production of PPO, enabling rapid production of more than 200 g of highly active PPO protein at 99% purity and low endotoxin contamination. We also present a formulation that allows for concentration of active PPO to > 75 mg/mL in a buffer suitable for mammalian toxicity studies.

Discovery of Novel N-Phenyltriazinone Derivatives Containing Oxime Ether or Oxime Ester Moieties as Promising Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) is one of the most important targets for the discovery of green herbicides. In order to find novel PPO inhibitors with a higher herbicidal activity, a series of novel N-phenyltriazinone derivatives containing oxime ether and oxime ester groups were designed and synthesized based on the strategy of pharmacophore and scaffold hopping. Bioassay results revealed that some compounds showed herbicidal activities; especially, compound B16 exhibited broad-spectrum and excellent 100% herbicidal effects to Echinochloa crusgalli, Digitaria sanguinalis, Setaria faberii, Abutilon juncea, Amaranthus retroflexus, and Portulaca oleracea at a concentration of 37.5 g a.i./ha, which were comparable to trifludimoxazin. Nicotiana tabacum PPO (NtPPO) enzyme inhibitory assay indicated that B16 showed an excellent enzyme inhibitory activity with a value of 32.14 nM, which was similar to that of trifludimoxazin (31.33 nM). Meanwhile, compound B16 revealed more safety for crops (rice, maize, wheat, peanut, soybean, and cotton) than trifludimoxazin at a dose of 150 g a.i./ha. Moreover, molecular docking and molecular dynamics simulation further showed that B16 has a very strong and stable binding to NtPPO. It indicated that B16 can be used as a potential PPO inhibitor and herbicide candidate for application in the field.

Development of an immunoassay based on a specific antibody for the detection of diphenyl ether herbicide fomesafen

Fomesafen belongs to the diphenyl ether herbicide, and is widely used in the control of broadleaf weeds in crop fields due to its high efficiency and good selectivity. The residual of fomesafen in soil has a toxic effect on subsequent sensitive crops and the microbial community structure because of its long residual period. Therefore, an efficient method for detecting fomesafen is critical to guide the correct and reasonable use of this herbicide. Rapid and sensitive immunoassay methods for fomesafen is unavailable due to the lack of specific antibody. In this study, a specific antibody for fomesafen was generated based on rational design of haptens and a sensitive immunoassay method was established. The half maximal inhibitory concentration (IC50) of the immunoassay was 39 ng/mL with a linear range (IC10-90) of 1.92-779.8 ng/mL. In addition, the developed assay had a good correlation with the standard UPLC-MS/MS both in the spike-recovery studies and in the detection of real soil samples. Overall, the developed indirect competitive enzyme immunoassay reported here is important for detecting and quantifying fomesafen contamination in soil and other environmental samples with good sensitivity and high reproducibility.

Design, synthesis, and herbicidal activity of novel phenoxypyridine derivatives containing natural product coumarin

BACKGROUND

In recent years, protoporphyrinogen oxidase (PPO, EC 1.3.3.4) inhibitors have been widely studied as important agricultural herbicides. Our research focused on the design and synthesis of novel PPO inhibitor herbicides, through linking of a diphenylether pyridine bioisostere structure to substituted coumarins, which aims to enhance environmental and crop safety while retaining high efficacy.

RESULTS

A total of 21 compounds were synthesized via acylation reactions and all compounds were characterized using infrared, ¹ H NMR, ¹³ C NMR, and high-resolution mass spectra. The respective configurations of compounds IV-6 and IV-12 were also confirmed using single crystal X-ray diffraction. The bioassay results showed that the title compounds displayed notable herbicidal activity, particularly compound IV-6 which displayed better herbicidal activity in greenhouse and field experiments, crop selectivity and safety for cotton and soybean compared with the commercial herbicide oxyfluorfen.

CONCLUSION

The work revealed that compound IV-6 deserves further attention as a candidate structure for a novel and safe herbicide. © 2021 Society of Chemical Industry.

Discovery of N-Phenylaminomethylthioacetylpyrimidine-2,4-diones as Protoporphyrinogen IX Oxidase Inhibitors through a Reaction Intermediate Derivation Approach

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) is an effective target for green herbicide discovery. In this work, we reported the unexpected discovery of a novel series of N-phenylaminomethylthioacetylpyrimidine-2,4-diones (2-6) as promising PPO inhibitors based on investigating the reaction intermediates of our initially designed N-phenyluracil thiazolidinone (1). An efficient one-pot procedure that gave 41 target compounds in good to high yields was developed. Systematic Nicotiana tabacum PPO (NtPPO) inhibitory and herbicidal activity evaluations led to identifying some compounds with improved NtPPO inhibition potency than saflufenacil and good post-emergence herbicidal activity at 37.5-150 g of ai/ha. Among these analogues, ethyl 2-((((2-chloro-4-fluoro-5-(3-methyl-2,6-dioxo-4-(trifluoromethyl)-3,6-dihydropyrimidin-1(2H)-yl)phenyl)amino)methyl)thio)acetate (2c) (Ki = 11 nM), exhibited excellent weed control at 37.5-150 g of ai/ha and was safe for rice at 150 g of ai/ha, indicating that compound 2c has the potential to be developed as a new herbicide for weed management in paddy fields. Additionally, our molecular simulation and metabolism studies showed that the side chains of compound 2c could form a hydrogen-bond-mediated seven-membered ring system; substituting a methyl group at R1 could reinforce the hydrogen bond of the ring system and reduce the metabolic rate of target compounds in planta.

Gene Replacement in Arabidopsis Reveals Manganese Transport as an Ancient Feature of Human, Plant and Cyanobacterial UPF0016 Proteins

The protein family 0016 (UPF0016) is conserved through evolution, and the few members characterized share a function in Mn²⁺ transport. So far, little is known about the history of these proteins in Eukaryotes. In Arabidopsis thaliana five such proteins, comprising four different subcellular localizations including chloroplasts, have been described, whereas non-photosynthetic Eukaryotes have only one. We used a phylogenetic approach to classify the eukaryotic proteins into two subgroups and performed gene-replacement studies to investigate UPF0016 genes of various origins. Replaceability can be scored readily in the Arabidopsis UPF0016 transporter mutant pam71, which exhibits a functional deficiency in photosystem II. The N-terminal region of the Arabidopsis PAM71 was used to direct selected proteins to chloroplast membranes. Transgenic pam71 lines overexpressing the closest plant homolog (CMT1), human TMEM165 or cyanobacterial MNX successfully restored photosystem II efficiency, manganese binding to photosystem II complexes and consequently plant growth rate and biomass production. Thus AtCMT1, HsTMEM165, and SynMNX can operate in the thylakoid membrane and substitute for PAM71 in a non-native environment, indicating that the manganese transport function of UPF0016 proteins is an ancient feature of the family. We propose that the two chloroplast-localized UPF0016 proteins, CMT1 and PAM71, in plants originated from the cyanobacterial endosymbiont that gave rise to the organelle.

Design, Synthesis, and Molecular Mechanism Studies of N-Phenylisoxazoline-thiadiazolo[3,4-a]pyridazine Hybrids as Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) is an important target for green agrochemical discovery. Herein, a novel N-phenylisoxazoline-thiadiazolo[3,4-a]pyridazine herbicidal active scaffold was designed by the scaffold hybridization strategy. Systematic structural optimization enabled the discovery of a series of derivatives with excellent weed control at 9.375-150 g ai/ha by the post-emergent application. Some derivatives exhibited improved Nicotiana tabacum PPO (NtPPO)-inhibitory activity than fluthiacet-methyl. Of these, 2b, with K_i = 21.8 nM, displayed higher weed control than fluthiacet-methyl at the rate of 12-75 g ai/ha, and selective to maize at 75 g ai/ha. In planta, 2b was converted into a bioactive metabolite 5 (K_i = 4.6 nM), which exhibited 4.6-fold more potency than 2b in inhibiting the activity of NtPPO. Molecular dynamics simulation explained that 5 formed stronger π-π interaction with Phe392 than that of 2b. This work not only provides a promising lead compound for weed control in maize fields but is also helpful to understand the molecular mechanism and basis of the designed hybrids.