Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds

Se-Pair Search for Deciphering Selenium-Encoded Peptide and a Pyrolysis-Thermolysis Dietary Model for Minimizing Loss of "KKSe(M)R" during Processing

Dietary deficiency of selenium is a global health hazard. Supplementation of organic selenopeptides via food crops is a relatively safe approach. Selenopeptides with heterogeneous selenium-encoded isotopes or a poorly fragmented peptide backbone remain unidentified in site-specific selenoproteomic analysis. Herein, we developed the Se-Pair Search, a UniProtKB-FASTA-independent peptide-matching strategy, exploiting the fragmentation patterns of shared peptide backbones in selenopeptides to optimize spectral interpretation, along with developing new selenosite assignment schemes (steps 1-3) to standardize selenium-localization data reporting for the selenoproteome community and thereby facilitating the discovery of unexpected selenopeptides. Using selenium-biofortified rice under cooking, fermentation, and high-temperature and high-pressure processing conditions as a pyrolysis-thermolysis dietary model, we probed the single-molecule-level kinetic evolution of the novel selenopeptide "KKSe(M)R" with qual-quantitative information on graph-theory-oriented localization calculations, abundance patterns, activation energy, and rate constants at a selenoproteome-wide scale. We ground-truth-annotated thirteen pyrolysis-thermolysis products and inferred four pyrolysis-thermolysis pathways to characterize the formation reactivity of the main intermediate variables of KKSe(M)R and constructed an advanced probe-type ultrasound technique prior to pyrolysis-thermolysis conditions for minimizing loss of KKSe(M)R during processing. Importantly, we reveal the unappreciated pyro-excitation diversion of KKSe(M)R at pyrolysis-thermolysis time and temperature matrices. These findings provide pioneering theoretical guidance for controlling dietary selenium supplementation within the safety thresholds.

Inhibitory role of copper and silver nanocomposite on important bacterial and fungal pathogens in rice (Oryza sativa)

Rice (Oryza sativa) being among the most important food crops in the world is also susceptible to various bacterial and fungal diseases that are the major stumbling blocks in the way of increased production and productivity. The bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae and the sheath blight disease caused by Rhizoctonia solani are among the most devastating diseases of the rice crop. In spite of the availability of array of chemical control, there are chances of development of resistance. Thus, there is a need for the nanotechnological intervention for management of disease in the form of copper and silver nano-composites. The copper (CuNPs) and silver nanoparticles (AgNPs) were synthesized using green route and characterized using different high throughput techniques, i.e., UV-Vis, FT-IR, DLS, XRD, FE-SEM, TEM. The particle size and zeta potential of synthesized CuNPs and AgNPs were found 273 nm and - 24.2 mV; 95.19 nm and - 25.5 mV respectively. The nanocomposite of CuNPs and AgNPs were prepared having particle size in the range of 375-306 nm with improved stability (zeta potential - 54.7 to - 39.4 mV). The copper and silver nanoparticle composites evaluated against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani were found to have higher antibacterial (inhibition zone 13 mm) and antifungal activities (77%) compared to only the copper nanoparticle (8 mm; 62% respectively). Net house trials of nano-composite formulations against the bacterial blight of rice also corroborated the potential of nanocomposite formulation. In silico studies were carried out selecting two disease-causing proteins, peptide deformylase (Xanthomonas oryzae) and pectate lyase (Rhizoctonia solani) to perform the molecular docking. Interaction studies indicatedthat both of these proteins generated better complex with CuNPs than AgNPs. The study suggested that the copper and silver nano-composites could be used for developing formulations to control these devastating rice diseases.

Investigating the bioaccumulation potential of anionic organic compounds using a permanent rainbow trout liver cell line

Permanent rainbow trout (Oncorhynchus mykiss) cell lines represent potential in vitro alternatives to experiments with fish. We here developed a method to assess the bioaccumulation potential of anionic organic compounds in fish, using the rainbow trout liver-derived RTL-W1 cell line. Based on the availability of high quality in vivo bioconcentration (BCF) and biomagnification (BMF) data and the substances' charge state at physiological pH, four anionic compounds were selected: pentachlorophenol (PCP), diclofenac (DCF), tecloftalam (TT) and benzotriazol-tert-butyl-hydroxyl-phenyl propanoic acid (BHPP). The fish cell line acute toxicity assay (OECD TG249) was used to derive effective concentrations 50 % and non-toxic exposure concentrations to determine exposure concentrations for bioaccumulation experiments. Bioaccumulation experiments were performed over 48 h with a total of six time points, at which cell, medium and plastic fractions were sampled and measured using high resolution tandem mass spectrometry after online solid phase extraction. Observed cell internal concentrations were over-predicted by KOW-derived predictions while pH-dependent octanol-water partitioning (DOW) and membrane lipid-water partitioning (DMLW) gave better predictions of cell internal concentrations. Measured medium and cell internal concentrations at steady state were used to calculate RTL-W1-based BCF, which were compared to DOW- or DMLW-based model approaches and in vivo data. With the exception of PCP, the cell-derived BCF best compared to DOW-based model predictions, which were higher than predictions based on DMLW. All methods predicted the in vivo BCF for diclofenac well. For PCP, the cell-derived BCF was lowest although all BCF predictions underestimated the in vivo BCF by ≥ 1 order of magnitude. The RTL-W1 cells, and all other prediction methods, largely overestimated in vivo BMF, which were available for PCP, TT and BHPP. We conclude that the RTL-W1 cell line can supplement BCF predictions for anionic compounds. For BMF estimations, however, in vitro-in vivo extrapolations need adaptation or a multiple cell line approach.

Isolation, purification, and structural elucidation of Mellein from endophytic fungus Lasiodiplodia theobromae strain (SJF-1) and its broad-spectrum antimicrobial and pharmacological properties

In an ongoing investigation of bioactive metabolites producing potential endophytic fungi, the strain Lasiodiplodia theobromae (SJF-1) was isolated from a medicinal plant Syzygium cumini. The cultural, morphological, and molecular identification was done with the SJF-1 strain. The obtained gene sequence was deposited in NCBI with accession number MG 938644. The methanolic extract of SJF-1 strain possessed one major bioactive fraction and it was purified by column chromatography. Further, it was identified as Mellein by various spectroscopic studies (¹ H, ¹³ C, DEPT-135°, FT-IR, ESI-HR-MS, and 2D NMR). Biologically, Mellein showed potent anti-Xanthomonas activity with MIC values ranging from 1.9-62.5 μgml^-1 against eleven Xanthomonas strains; a broad-spectrum antimicrobial activity with MIC 7.8-31.25 μgml^-1 and 1.9-31.25 μgml^-1 towards both bacterial and fungal strains respectively. The SEM analysis proved the anti-microbial efficacy of a Mellein by rupturing the cell walls of Xanthomonas sp. Molecular docking studies further supported that the Mellein showed good binding interactions with the proteins of Xanthomonas sp. to reduce pathogenicity. Further, in silico pharmacological studies showed that this metabolite exhibited high gastrointestinal absorption properties and promising oral drug bioavailability. We report, anti-Xanthomonas, in silico docking, and pharmacological studies of Mellein from (SJF-1) strain for the first time.

Synthesis of N-Methylmorpholinium Derivatives Possessing a 1,3,4-Oxadiazole Core as Feasible Antibacterial Agents against Plant Bacterial Diseases

To develop a kind of quaternary ammonium compounds that can safely apply in agriculture for managing the plant bacterial diseases, herein, a series of N-methylmorpholinium derivatives possessing a classical 1,3,4-oxadiazole core were prepared and the antibacterial activities both in vitro and in vivo were screened. Bioassay results revealed that compounds 3l and 3i showed the strongest antibacterial activity toward pathogens Xanthomonas oryzae pv. oryzae and X. axonopodis pv. citri with the lowest EC50 values of 1.40 and 0.90 μg/mL, respectively. Phytotoxicity test trials indicated that target compounds bearing a bulky N-methylmorpholinium pendant are safe for plants. The following in vivo bioassays showed that compound 3l could control the rice bacterial blight disease, thereby affording good control efficiencies of 55.95% (curative activity) and 53.09% (protective activity) at the dose of 200 μg/mL. Preliminary antibacterial mechanism studies suggested that target compounds had strong interactions with the cell membrane of bacteria via scanning electron microscopy imaging. Additionally, this kind of framework also displayed certain antifungal activity toward Fusarium oxysporum and Phytophthora cinnamomi. Given the above privileged characteristics, this kind of 1,3,4-oxadiazole-tailored N-methylmorpholinium derivatives could stimulate the design of safe quaternary ammonium bactericides for controlling plant bacterial diseases.

Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase

Xanthomonas oryzae pv. Oryzae (Xoo) causes bacterial leaf blight (BLB) of rice which results in a huge loss in production. Many chemicals are used to control BLB disease. However, these chemicals are toxic to the environments, animals and human beings. Thus, there is a demand to discover potential and safe natural pesticides to manage BLB disease successfully. Therefore, we screened a library of phytochemicals of different plants having antibacterial activity by targeting Peptide Deformylase (PDF) of Xoo using in silico techniques. A library of 318 phytochemicals was prepared and subjected to rigid and flexible molecular docking against PDF followed by molecular dynamics simulation and free energy analysis of protein-ligand complexes. The results of virtual screening showed that 14 compounds from different plants have good binding energy as compare to reference molecule (3 R)-2,3-dihydro[1,3] thiazolo [3,2 a]benzimidazol-3-ol) (-7.7 kcal mol^-1). Out of 14 hit compounds, eight compounds that were selected based on binding energy were analyzed by Molecular dynamic (MD) simulation. Analysis of MD simulation revealed that eight compounds namely; Bisdemethoxycurcumin, Rosmarinic acid, Piperanine, Dihydropiperlonguminine, Piperdardine, Dihydrocurcumin and Lonhumosides B achieved good stability during the 80 ns MD simulation at 300 K in term of the RMSD. Further, we calculated RMSF, RG, SASA, and interaction energy after 40 ns due to showing the stability of complexes. From our results, we conclude that these natural compounds could inhibit Xoo by targeting PDF receptor and can be used as potential bactericidal candidates against BLB disease of rice against Xoo and other bacteria. Communicated by Ramaswamy H. Sarma.

Antibiotic activities of propanolamine containing 1,4-benzoxazin-3-ones against phytopathogenic bacteria

Various 1,4-benzoxazin-3-one derivatives containing propanolamine groups have been shown to exhibit good antibacterial activity against Pseudomonas syringae pv actinidiae (Psa), X. axonopodis pv citri (Xac) and Xanthomonas oryzae pv oryzae (Xoo). 1,4-benzoxazin-3-one 4n showed the best inhibitory effects against Psa, Xac and Xoo, exhibiting in vitro EC₅₀ values of 4.95, 4.71 and 8.50 μg mL⁻¹, respectively. These potencies were superior to the corresponding EC₅₀ values of the commercial antibiotics bismerthiazol (BT, 89.10, and 116.90 μg mL⁻¹) and thiodiazole copper (TC, 127.30, 82.73 and 87.50 μg mL⁻¹). Treatment on the bacterial leaf blight of rice revealed that compound 4n displayed better curative (51%) and protective (48%) activities for reducing rice BLB than either BT (41%, 39%) or TC (43%, 41%). Scanning electron microscopy (SEM) imaging of Xoo that had been treated with 1,4-benzoxazin-3-one 4n (50–100 μg mL⁻¹) revealed that the bacterial cells had experienced extensive cell wall damage, which is the likely cause of its antimicrobial activity and bacterial death.

Various 1,4-benzoxazin-3-one derivatives containing propanolamine groups have been shown to exhibit good antibacterial activity against Pseudomonas syringae pv actinidiae (Psa), X. axonopodis pv citri (Xac) and Xanthomonas oryzae pv oryzae (Xoo).

Synthesis and In Vitro and In Vivo Biological Activity Evaluation and Quantitative Proteome Profiling of Oxadiazoles Bearing Flexible Heterocyclic Patterns

A novel series of simple 1,3,4-oxadiazoles that bear flexible heterocyclic patterns was prepared, and their biological activities in plant pathogenic bacteria, fungi, oomycetes, and Meloidogyne incognita in vitro and in vivo were screened to explore low-cost and versatile antimicrobial agents. Screening results showed that compounds, such as A₀, B₀, and C₄, were bioactive against Xanthomonas oryzae pv oryzae in vitro and in vivo, and such bioactivities were superior to those of commercial agents bismerthiazol and thiodiazole copper. Their antibacterial mechanisms were further investigated by quantitative proteomics and concentration-dependent scanning electron microscopy images. Antifungal results indicated that compound A₀ displayed a selective and better antifungal effect on Botrytis cinerea with inhibition rate of 96.8% at 50 μg/mL. Nematocidal bioassays suggested that compound D₁ had good in vitro nematocidal activity toward M. incognita at 24, 48, and 72 h, with the corresponding insecticidal efficiency of 48.7%, 64.1%, and 87.2% at 40 μg/mL. In vivo study further confirmed that compounds D₁ and F₂ showed nematocidal actions at 80 μg/mL with a disease index of 1.5. Given these advantages, this kind of molecular frameworks could be a suitable platform for exploring highly efficient agrochemicals.

Identification of Racemic and Chiral Carbazole Derivatives Containing an Isopropanolamine Linker as Prospective Surrogates against Plant Pathogenic Bacteria: In Vitro and In Vivo Assays and Quantitative Proteomics

Recent observations on the emergence of drug-resistant plant pathogenic bacteria have highlighted and elicited an acute campaign to develop novel, highly efficient antibiotic surrogates for managing bacterial diseases in agriculture. Thus, a type of racemic and chiral carbazole derivative containing an isopropanolamine pattern was systematically synthesized to discover low-cost and efficient antibacterial candidates. Screening results showed that compounds 2f, 6c, and 2j could significantly suppress the growth of tested plant pathogens, namely Xanthomonas oryzae pv oryzae, X. axonopodis pv citri, and Pseudomonas syringae pv actinidiae, and provided the corresponding EC₅₀ values of 1.27, 0.993, and 0.603 μg/mL, which were significantly better than those of existing commercial drugs. In vivo studies confirmed their prospective applications for controlling plant bacterial diseases. Label-free quantitative proteomics analysis indicated that compound 2f could dramatically induce the up- and down-regulation of a total of 247 differentially expressed proteins, which was further validated by the parallel reaction monitoring technique. Moreover, fluorescence spectra and SEM images were obtained to further explore the antibacterial mechanism.

Rational Optimization and Action Mechanism of Novel Imidazole (or Imidazolium)-Labeled 1,3,4-Oxadiazole Thioethers as Promising Antibacterial Agents against Plant Bacterial Diseases

The emergence and widespread occurrence of plant bacterial diseases that cause global production constraints have become major challenges to agriculture worldwide. To promote the discovery and development of new bactericides, imidazole-labeled 1,3,4-oxadiazole thioethers were first fabricated by integrating the crucially bioactive scaffolds of the imidazole motif and 1,3,4-oxadiazole skeleton in a single molecular architecture. Subsequently, a superior antibacterial compound A₆ was gradually discovered possessing excellent competence against plant pathogens Xanthomonas oryzae pv oryzae and Xanthomonas axonopodis pv citri with EC₅₀ values of 0.734 and 1.79 μg/mL, respectively. These values were better than those of commercial agents bismerthiazol (92.6 μg/mL) and thiodiazole copper (77.0 μg/mL). Further modifying the imidazole moiety into the imidazolium scaffold led to the discovery of an array of potent antibacterial compounds providing the corresponding minimum EC₅₀ values of 0.295 and 0.607 μg/mL against the two strains. Moreover, a plausible action mechanism for attacking pathogens was proposed based on the concentration dependence of scanning electron microscopy, transmission electron microscopy, and fluorescence microscopy images. Given the simple molecular structures, easy synthetic procedure, and highly efficient bioactivity, imidazole (or imidazolium)-labeled 1,3,4-oxadiazole thioethers can be further explored and developed as promising indicators for the development of commercial drugs.

Identification, Characteristics and Mechanism of 1-Deoxy-N-acetylglucosamine from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493

Xanthomonas oryzae pv. oryzae, which causes rice bacterial blight, is one of the most destructive pathogenic bacteria. Biological control against plant pathogens has recently received increasing interest. 1-Deoxy-N-acetylglucosamine (1-DGlcNAc) was extracted from the supernatant of Virgibacillus dokdonensis MCCC 1A00493 fermentation through antibacterial bioassay-guided isolation. Its structure was elucidated by LC/MS, NMR, chemical synthesis and time-dependent density functional theory (TD-DFT) calculations. 1-DGlcNAc specifically suppressed X. oryzae pv. oryzae PXO99A (MIC was 23.90 μg/mL), but not other common pathogens including Xanthomonas campestris pv. campestris str.8004 and Xanthomonas oryzae pv. oryzicola RS105. However, its diastereomer (2-acetamido-1,5-anhydro-2-deoxy-d-mannitol) also has no activity to X. oryzae pv. oryzae. This result suggested that activity of 1-DGlcNAc was related to the difference in the spatial conformation of the 2-acetamido moiety, which might be attributed to their different interactions with a receptor. Eighty-four unique proteins were found in X. oryzae pv. oryzae PXO99A compared with the genome of strains8004 and RS105 by blastp. There may be unique interactions between 1-DGlcNAc and one or more of these unique proteins in X. oryzae pv. oryzae. Quantitative real-time PCR and the pharmMapper server indicated that proteins involved in cell division could be the targets in PXO99A. This research suggested that specificity of active substance was based on the active group and spatial conformation selection, and these unique proteins could help to reveal the specific mechanism of action of 1-DGlcNAc against PXO99A.