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Nucleic Acids Research Jan 2021Bacterial pathogenic growth requires a swift coordination of pathogenicity function with various kinds of environmental stress encountered in the course of host...
Bacterial pathogenic growth requires a swift coordination of pathogenicity function with various kinds of environmental stress encountered in the course of host infection. Among the factors critical for bacterial adaptation are changes of DNA topology and binding effects of nucleoid-associated proteins transducing the environmental signals to the chromosome and coordinating the global transcriptional response to stress. In this study, we use the model phytopathogen Dickeya dadantii to analyse the organisation of transcription by the nucleoid-associated heterodimeric protein IHF. We inactivated the IHFα subunit of IHF thus precluding the IHFαβ heterodimer formation and determined both phenotypic effects of ihfA mutation on D. dadantii virulence and the transcriptional response under various conditions of growth. We show that ihfA mutation reorganises the genomic expression by modulating the distribution of chromosomal DNA supercoils at different length scales, thus affecting many virulence genes involved in both symptomatic and asymptomatic phases of infection, including those required for pectin catabolism. Altogether, we propose that IHF heterodimer is a 'transcriptional domainin' protein, the lack of which impairs the spatiotemporal organisation of transcriptional stress-response domains harbouring various virulence traits, thus abrogating the pathogenicity of D. dadantii.
Topics: Bacterial Proteins; Binding Sites; Cellulase; Cichorium intybus; DNA, Bacterial; DNA, Superhelical; Dickeya; Dimerization; Gene Expression Regulation, Bacterial; Genetic Association Studies; Integration Host Factors; Motion; Peptide Hydrolases; Plasmids; Polygalacturonase; Promoter Regions, Genetic; Recombinant Proteins; Siderophores; Transcription, Genetic; Transcriptome; Virulence
PubMed: 33337488
DOI: 10.1093/nar/gkaa1227 -
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 Microbiology 2022, a plant soft-rot pathogen, possesses a type III secretion system (T3SS) as one of the major virulence factors, infecting a wide variety of monocotyledonous and...
, a plant soft-rot pathogen, possesses a type III secretion system (T3SS) as one of the major virulence factors, infecting a wide variety of monocotyledonous and dicotyledonous plants and causing serious losses to the production of economic crops. In order to alleviate the problem of pesticide resistance during bacterial disease treatment, compounds targeting at T3SS have been screened using a bioreporter. After screening by Multifunctional Microplate Reader and determining by flow cytometer, five compounds including salicylic acid (SA), p-hydroxybenzoic acid (PHBA), cinnamyl alcohol (CA), p-coumaric acid (PCA), and hydrocinnamic acid (HA) significantly inhibiting promoter activity without affecting bacterial growth have been screened out. All the five compounds reduced hypersensitive response (HR) on non-host tobacco leaves and downregulated the expression of T3SS, especially the master regulator encoding gene . Inhibition efficacy of the five compounds against soft rot were also evaluated and results confirmed that the above compounds significantly lessened the soft-rot symptoms caused by 3937 on potato, CL3 on taro, EC1 on rice, and MS2 on banana seedlings. Findings in this study provide potential biocontrol agents for prevention of soft-rot disease caused by spp.
PubMed: 35273588
DOI: 10.3389/fmicb.2022.839025 -
The Journal of Biological Chemistry 2021The type II secretion system (T2SS) transports fully folded proteins of various functions and structures through the outer membrane of Gram-negative bacteria. The...
The type II secretion system (T2SS) transports fully folded proteins of various functions and structures through the outer membrane of Gram-negative bacteria. The molecular mechanisms of substrate recruitment by T2SS remain elusive but a prevailing view is that the secretion determinants could be of a structural nature. The phytopathogenic γ-proteobacteria, Pectobacterium carotovorum and Dickeya dadantii, secrete similar sets of homologous plant cell wall degrading enzymes, mainly pectinases, by similar T2SSs, called Out. However, the orthologous pectate lyases Pel3 and PelI from these bacteria, which share 67% of sequence identity, are not secreted by the counterpart T2SS of each bacterium, indicating a fine-tuned control of protein recruitment. To identify the related secretion determinants, we first performed a structural characterization and comparison of Pel3 with PelI using X-ray crystallography. Then, to assess the biological relevance of the observed structural variations, we conducted a loop-substitution analysis of Pel3 combined with secretion assays. We showed that there is not one element with a definite secondary structure but several distant and structurally flexible loop regions that are essential for the secretion of Pel3 and that these loop regions act together as a composite secretion signal. Interestingly, depending on the crystal contacts, one of these key secretion determinants undergoes disorder-to-order transitions that could reflect its transient structuration upon the contact with the appropriate T2SS components. We hypothesize that such T2SS-induced structuration of some intrinsically disordered zones of secretion substrates could be part of the recruitment mechanism used by T2SS.
Topics: Amino Acid Sequence; Bacterial Proteins; Binding Sites; Cell Wall; Cloning, Molecular; Crystallography, X-Ray; Dickeya; Escherichia coli; Gene Expression; Genetic Vectors; Isoenzymes; Models, Molecular; Pectobacterium carotovorum; Phylogeny; Plant Cells; Plants; Polysaccharide-Lyases; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Recombinant Proteins; Sequence Alignment; Sequence Homology, Amino Acid; Type II Secretion Systems
PubMed: 33465378
DOI: 10.1016/j.jbc.2021.100305 -
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 -
An uncommon [K(Mg)] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.RNA (New York, N.Y.) Oct 2021The widespread -I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the...
The widespread -I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the -I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from and , our structure reveals a chelated K ion adjacent to two Mg ions in the guanidine-binding pocket. Thermal melting analysis shows that K chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K(Mg)] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of -I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K chelation in the Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg ion binding in place of the K ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among -I riboswitches.
Topics: Aptamers, Nucleotide; Base Pairing; Base Sequence; Biological Evolution; Burkholderia; Chelating Agents; Clostridiales; Crystallography, X-Ray; Dickeya; Guanidines; Magnesium; Models, Molecular; Mutation; Nucleic Acid Conformation; Potassium; Ribosomes; Riboswitch; Water
PubMed: 34257148
DOI: 10.1261/rna.078824.121 -
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 -
Microbiology Resource Announcements Sep 2021Erwinia chrysanthemi S3-1 is a bacterial soft rot pathogen of the white-flowered calla lily. The complete genome sequence of the strain was determined and used to...
Erwinia chrysanthemi S3-1 is a bacterial soft rot pathogen of the white-flowered calla lily. The complete genome sequence of the strain was determined and used to reclassify the strain as Dickeya dadantii subsp. . The sequence will be useful to study plant host-driven speciation in strains of D. dadantii.
PubMed: 34528816
DOI: 10.1128/MRA.00620-21 -
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 2023For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins...
For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins sigma factors and modulation of DNA topology. In this study, we investigate replication-induced gene copy numbers - a regulatory concept that is unlike the others not based on modulation of promoter activity but on replication dynamics. We show that a large fraction of genes are predominantly affected by transient copy numbers and identify cellular functions and central pathways governed by this mechanism in . Furthermore, we show quantitatively that the previously observed spatio-temporal expression pattern between different growth phases mainly emerges from transient chromosomal copy numbers. We extend the analysis to the plant pathogen and the biotechnologically relevant organism . The analysis reveals a connection between growth phase dependent gene expression and evolutionary gene migration in these species. A further extension to the bacterial kingdom indicates that chromosome evolution is governed by growth rate related transient copy numbers.
PubMed: 37152747
DOI: 10.3389/fmicb.2023.1119878