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PHAGE (New Rochelle, N.Y.) Dec 2020Bacterial soft rot caused by members of the soft rot afflicts plant production of both vegetable and ornamental crops. Recent outbreaks highlight sp. in the etiology...
Bacterial soft rot caused by members of the soft rot afflicts plant production of both vegetable and ornamental crops. Recent outbreaks highlight sp. in the etiology of this disease in potatoes. Since there is a lack of control strategies for these diseases, alternative approaches have been suggested, including the use of biological control mediated by bacteriophages (phages). However, phages infecting many of these members are still undiscovered or poorly described. Two phages targeting subsp. (NCPPB 4097) were isolated from household organic waste and purified. They were then further characterized using whole-genome sequencing and comparative genomics, transmission electron microscopy, latent period and burst size. Dickeya phage Sucellus displayed Siphovirus morphology and had a genome of 39,826 bp with very limited similarity to any previously described phages. Dickeya phage Amaethon had a Podovirus morphology with a genome comprising 41,436 bp and limited similarity to phages in the genus. The phages exhibited burst sizes of app. 94 and 240 virions per cell with latent periods of 91 and 86 minutes for Sucellus and Amaethon, respectively. While both phages had similar adsorption efficiencies and latent periods, the rise periods for the two phages diverged markedly, highlighting an odd growth pattern. Together, the two phages isolated here expand the known diversity of phages infecting the important plant pathogen . As they both share limited similarity to previously described groups of phages, they likely constitute novel genera within their respective groups.
PubMed: 36147281
DOI: 10.1089/phage.2020.0039 -
Microbiology Resource Announcements Jul 2020The plant-pathogenic bacterium causes quick decline in fruit trees (e.g., apple, Japanese pear, and peach). In this study, we report on the draft genome sequences of...
The plant-pathogenic bacterium causes quick decline in fruit trees (e.g., apple, Japanese pear, and peach). In this study, we report on the draft genome sequences of seven strains of that were isolated from fruit trees with typical quick decline symptoms in Japan.
PubMed: 32646907
DOI: 10.1128/MRA.00609-20 -
Frontiers in Plant Science 2020Plant defense stimulators, used in crop protection, are an attractive option to reduce the use of conventional crop protection products and optimize biocontrol...
Plant defense stimulators, used in crop protection, are an attractive option to reduce the use of conventional crop protection products and optimize biocontrol strategies. These products are able to activate plant defenses and thus limit infection by pathogens. However, the effectiveness of these plant defense stimulators remains erratic and is potentially dependent on many agronomic and environmental parameters still unknown or poorly controlled. The developmental stage of the plant as well as its fertilization, and essentially nitrogen nutrition, play major roles in defense establishment in the presence of pathogens or plant defense stimulators. The major nitrogen source used by plants is nitrate. In this study, we investigated the impact of plant developmental stage and nitrate nutrition on its capacity to mount immune reactions in response to two plant defense stimulators triggering two major defense pathways, the salicylic acid and the jasmonic acid pathways. We show that optimal nitrate nutrition is needed for effective defense activation and protection against the pathogenic bacteria and pv. . Using an defense signaling mutant, we showed that nitrate dependent protection against requires a functional gene. Our results indicate that the efficacy of plant defense stimulators is strongly affected by nitrate nutrition and the developmental stage. The nitrate dependent efficacy of plant defense stimulators is not only due to a metabolic effect but also invloves NPR1 mediated defense signaling. Plant defense stimulators may have opposite effects on plant resistance to a pathogen. Together, our results indicate that agronomic use of plant defense stimulators must be optimized according to nitrate fertilization and developmental stage.
PubMed: 32528493
DOI: 10.3389/fpls.2020.00583 -
Frontiers in Microbiology 2020Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry...
Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution is the supplementation of pectinase, an enzyme that degrades pectin within the cell walls of plants, in poultry diets. Therefore, the objective of the current study was to determine the potential role of a pectinase producer, DSM 18020, as a commercially utilized pectinase producer in poultry diets against other known pectinase producers, . In the current study, whole genomes of DSM 18020 (Dd18020), 3937 (Dd3937), IPO 2222 (Ds2222), C-125 (BhC125), and subsp. str. 168 (Bs168) were compared using bioinformatic approaches to compare the chromosomal genome size, GC content, protein coding genes (CDS), total genes, average protein length (a.a.) and determine the predicted metabolic pathways, predicted pectin degrading enzymes, and pectin-degradation pathways across pectinase producers. Due to insufficient information surrounding the genome of Dd18020 (lack of annotation), the genome of Dd3937, a 99% identical genome to Dd18020, was utilized to compare pectinase-associated enzymes and pathways. The results from the current study demonstrated that Dd3937 possessed the most significant proportion of pathways presented and the highest number of pathways related to degradation, assimilation, and utilization of pectin. Also, Dd18020 exhibited a high number of pectinase-related enzymes. Both Dd3937 and Dd2222 shared the pectin degradation I pathway via the EC 3.1.1.11, EC 3.2.1.82, and EC 4.2.2.- enzymes, but did not share this pathway with either species. In conclusion, Dd18020 demonstrated the genetic potential to produce multiple pectinase enzymes that could be beneficial to the degradation of pectin in poultry diets. However, for Dd18020 to become a commercially viable enzyme producer for the poultry industry, further research quantifying the pectinase production and determining the stability of the produced pectinases during feed manufacturing are necessary.
PubMed: 32390987
DOI: 10.3389/fmicb.2020.00751 -
Applied and Environmental Microbiology Mar 2020While rhamnolipids of the type are commercially available, the natural diversity of rhamnolipids and their origin have barely been investigated. Here, we collected...
While rhamnolipids of the type are commercially available, the natural diversity of rhamnolipids and their origin have barely been investigated. Here, we collected known and identified new genes encoding the acyltransferase responsible for the synthesis of the lipophilic rhamnolipid precursor 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA). Generally, all homologs were found in and A likely horizontal gene transfer event into is the only identified exception. The phylogeny of the RhlA homologs from and species is consistent with the organism phylogeny, and genes involved in rhamnolipid synthesis are located in operons. In contrast, RhlA homologs from the do not follow the organisms' phylogeny but form their own branch. Furthermore, in many and from the , an isolated homolog can be found in the genome. The RhlAs from PA01, LMG 05825, LMG 20103, PG1, LMG 19182, sp. strain R57-5, Ech586, and PRI-2C were expressed in and tested for HAA production. Indeed, except for the RhlA, HAAs were produced with the engineered strains. A detailed analysis of the produced HAA congeners by high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) highlights the congener specificity of the RhlA proteins. The congener length varies from 4 to 18 carbon atoms, with the main congeners consisting of different combinations of saturated or monounsaturated C, C, and C fatty acids. The results are discussed in the context of the phylogeny of this unusual enzymatic activity. The RhlA specificity explains the observed differences in 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA) congeners. Whole-cell catalysts can now be designed for the synthesis of different congener mixtures of HAAs and rhamnolipids, thereby contributing to the envisaged synthesis of designer HAAs.
Topics: Acyltransferases; Bacteria; Bacterial Proteins; Carboxylic Acids; Glycolipids
PubMed: 31924623
DOI: 10.1128/AEM.02317-19 -
Molecular Plant-microbe Interactions :... Feb 2020is a plant-pathogenic bacterium that causes soft-rot in a wide range of plants. Although we have previously demonstrated that cyclic bis-(3'-5')-cyclic dimeric...
Tricarboxylic Acid (TCA) Cycle Enzymes and Intermediates Modulate Intracellular Cyclic di-GMP Levels and the Production of Plant Cell Wall-Degrading Enzymes in Soft Rot Pathogen .
is a plant-pathogenic bacterium that causes soft-rot in a wide range of plants. Although we have previously demonstrated that cyclic bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial secondary messenger, plays a central role in virulence regulation in , the upstream signals that modulate c-di-GMP remain enigmatic. Using a genome-wide transposon mutagenesis approach of a Δ mutant strain that has high c-di-GMP and reduced motility, we uncovered transposon mutants that recovered the c-di-GMP-mediated repression on swimming motility. A number of these mutants harbored transposon insertions in genes encoding tricarboxylic acid (TCA) cycle enzymes. Two of these TCA transposon mutants were studied further by generating chromosomal deletions of the gene (encoding fumarase) and the operon (encoding succinate dehydrogenase). Disruption of the TCA cycle in these deletion mutants resulted in reduced intracellular c-di-GMP and enhanced production of pectate lyases (Pels), a major plant cell wall-degrading enzyme (PCWDE) known to be transcriptionally repressed by c-di-GMP. Consistent with this result, addition of TCA cycle intermediates such as citrate also resulted in increased c-di-GMP levels and decreased production of Pels. Additionally, we found that a diguanylate cyclase GcpA was solely responsible for the observed citrate-mediated modulation of c-di-GMP. Finally, we demonstrated that addition of citrate induced not only an overproduction of GcpA protein but also a concomitant repression of the c-di-GMP-degrading phosphodiesterase EGcpB which, together, resulted in an increase in the intracellular concentration of c-di-GMP. In summary, our report demonstrates that bacterial respiration and respiration metabolites serve as signals for the regulation of c-di-GMP signaling.
Topics: Bacterial Proteins; Cell Wall; Cyclic GMP; Dickeya; Gammaproteobacteria; Gene Expression Regulation, Bacterial; Mutation
PubMed: 31851880
DOI: 10.1094/MPMI-07-19-0203-R -
Biomolecules Dec 2019Edible plant fruits are safe raw materials free of toxicants and rich in biomolecules for reducing metal ions and stabilizing nanoparticles. Zinc oxide nanoparticles...
Edible plant fruits are safe raw materials free of toxicants and rich in biomolecules for reducing metal ions and stabilizing nanoparticles. Zinc oxide nanoparticles (ZnONPs) and titanium dioxide nanoparticles (TiONPs) are the most produced consumer nanomaterials and have known antibacterial activities but have rarely been used against phytopathogenic bacteria. Here, we synthesized ZnONPs and TiONPs simply by mixing ZnO or TiO solution with a lemon fruit extract at room temperature and showed their antibacterial activities against Dickeya dadantii, which causes sweet potato stem and root rot disease occurring in major sweet potato planting areas in China. Ultraviolet-visible spectrometry and energy dispersive spectroscopy determined their physiochemical characteristics. Transmission electron microscopy, scanning electron microscopy, and X-ray diffraction spectroscopy revealed the nanoscale size and polymorphic crystalline structures of the ZnONPs and TiONPs. Fourier-transform infrared spectroscopy revealed their surface stabilization groups from the lemon fruit extract. In contrast to ZnO and TiO, which had no antibacterial activity against D. dadantii, ZnONPs and TiONPs showed inhibitions on D. dadantii growth, swimming motility, biofilm formation, and maceration of sweet potato tuber slices. ZnONPs and TiONPs showed similar extents of antibacterial activities, which increased with the increase of nanoparticle concentrations, and inhibited about 60% of activities at the concentration of 50 µg∙mL. The green synthetic ZnONPs and TiONPs can be used to control the sweet potato soft rot disease by control of pathogen contamination of seed tubers.
Topics: Anti-Bacterial Agents; Citrus; Dickeya; Fruit; Gammaproteobacteria; Microbial Sensitivity Tests; Nanoparticles; Plant Extracts; Titanium; Zinc Oxide
PubMed: 31835898
DOI: 10.3390/biom9120863 -
International Journal of Molecular... Nov 2019The prominent antibacterial and quorum sensing (QS) inhibition activity of aromatic plants can be used as a novel intervention strategy for attenuating bacterial...
The prominent antibacterial and quorum sensing (QS) inhibition activity of aromatic plants can be used as a novel intervention strategy for attenuating bacterial pathogenicity. In the present work, a total of 29 chemical components were identified in the essential oil (EO) of leaves by gas chromatography-mass spectrometry (GC-MS). The principal component was methyleugenol, followed by methyl trans-cinnamate, with relative contents of 90.46% and 4.25%, respectively. Meanwhile, the antibacterial activity and the QS inhibitory activity of EO were first evaluated here. Antibacterial activity assay and MIC detection against seven pathogens ( Onc5, ATCC25933, spp., ATCC25922, MG1, PAO1 and ATCC31532) demonstrated that ATCC25933 and MG1 had the higher sensitivity to EO, while PAO1 displayed the strongest resistance to EO. An anti-QS (anti-quorum sensing) assay revealed that at sub-minimal inhibitory concentrations (sub-MICs), EO strongly interfered with the phenotype, including violacein production, biofilm biomass, and swarming motility, as well as -hexanoyl-L-homoserine lactone (C6-HSL) production (i.e., a signaling molecule in ATCC31532) of . Detection of C6-HSL indicated that EO was capable of not only inhibiting C6-HSL production in , but also degrading the C6-HSL. Importantly, changes of exogenous C6-HSL production in CV026 revealed a possible interaction between EO and a regulatory protein (cviR). Additionally, quantitative real-time polymerase chain reaction (RT-qPCR) analysis demonstrated that the expression of QS-related genes (, , , , , , , and ) was significantly suppressed. Conclusively, these results indicated that EO can act as a potential antibacterial agent and QS inhibitor (QSI) against pathogens, preventing and controlling bacterial contamination.
Topics: Anti-Bacterial Agents; Bacteria; Biofilms; Gas Chromatography-Mass Spectrometry; Melaleuca; Microbial Sensitivity Tests; Oils, Volatile; Phenotype; Plant Extracts; Plant Leaves; Quorum Sensing
PubMed: 31739398
DOI: 10.3390/ijms20225696 -
Nature Communications Oct 2019Few secreted proteins involved in plant infection common to necrotrophic bacteria, fungi and oomycetes have been identified except for plant cell wall-degrading enzymes....
Few secreted proteins involved in plant infection common to necrotrophic bacteria, fungi and oomycetes have been identified except for plant cell wall-degrading enzymes. Here we study a family of iron-binding proteins that is present in Gram-negative and Gram-positive bacteria, fungi, oomycetes and some animals. Homolog proteins in the phytopathogenic bacterium Dickeya dadantii (IbpS) and the fungal necrotroph Botrytis cinerea (BcIbp) are involved in plant infection. IbpS is secreted, can bind iron and copper, and protects the bacteria against HO-induced death. Its 1.7 Å crystal structure reveals a classical Venus Fly trap fold that forms dimers in solution and in the crystal. We propose that secreted Ibp proteins binds exogenous metals and thus limit intracellular metal accumulation and ROS formation in the microorganisms.
Topics: Anti-Infective Agents, Local; Arabidopsis; Arabidopsis Proteins; Botrytis; Carrier Proteins; Copper; Defensins; Dickeya; Dimerization; Gammaproteobacteria; Hydrogen Peroxide; Iron; Iron-Binding Proteins; Plant Diseases; Reactive Oxygen Species; Siderophores
PubMed: 31649262
DOI: 10.1038/s41467-019-12826-x -
ACS Chemical Biology Oct 2019Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å,...
Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å, which challenges the high and low measurement limits of conventional nuclear magnetic resonance (NMR) and double electron-electron resonance electron spin resonance spectroscopies. Here, we report the use of F paramagnetic relaxation enhancement (PRE) NMR in combination with F/paramagnetic labeling to equivalent sites in different subunits of a protein complex in micelles to determine intersubunit distances. The feasibility of this strategy was evaluated on a pentameric ligand-gated ion channel, for which we found excellent agreement of the F PRE NMR results with previous structural information. The study suggests that F PRE NMR is a viable tool in extracting distance restraints to define quaternary structures.
Topics: Animals; Bacterial Proteins; Dickeya; Fluorine; Gammaproteobacteria; Ion Channels; Mice; Nuclear Magnetic Resonance, Biomolecular; Protein Structure, Quaternary; Protein Subunits
PubMed: 31525026
DOI: 10.1021/acschembio.9b00692