-
PLoS Pathogens Aug 2019Necrotrophic plant pathogens acquire nutrients from dead plant cells, which requires the disintegration of the plant cell wall and tissue structures by the pathogen....
Necrotrophic plant pathogens acquire nutrients from dead plant cells, which requires the disintegration of the plant cell wall and tissue structures by the pathogen. Infected plants lose tissue integrity and functional immunity as a result, exposing the nutrient rich, decayed tissues to the environment. One challenge for the necrotrophs to successfully cause secondary infection (infection spread from an initially infected plant to the nearby uninfected plants) is to effectively utilize nutrients released from hosts towards building up a large population before other saprophytes come. In this study, we observed that the necrotrophic pathogen Dickeya dadantii exhibited heterogeneity in bacterial cell length in an isogenic population during infection of potato tuber. While some cells were regular rod-shape (<10μm), the rest elongated into filamentous cells (>10μm). Short cells tended to occur at the interface of healthy and diseased tissues, during the early stage of infection when active attacking and killing is occurring, while filamentous cells tended to form at a later stage of infection. Short cells expressed all necessary virulence factors and motility, whereas filamentous cells did not engage in virulence, were non-mobile and more sensitive to environmental stress. However, compared to the short cells, the filamentous cells displayed upregulated metabolic genes and increased growth, which may benefit the pathogens to build up a large population necessary for the secondary infection. The segregation of the two subpopulations was dependent on differential production of the alarmone guanosine tetraphosphate (ppGpp). When exposed to fresh tuber tissues or freestanding water, filamentous cells quickly transformed to short virulent cells. The pathogen adaptation of cell length heterogeneity identified in this study presents a model for how some necrotrophs balance virulence and vegetative growth to maximize fitness during infection.
Topics: Bacterial Proteins; Cell Wall; Enterobacteriaceae; Gene Expression Regulation, Bacterial; Guanosine Tetraphosphate; Host-Pathogen Interactions; Plant Diseases; Solanum tuberosum; Virulence; Virulence Factors
PubMed: 31381590
DOI: 10.1371/journal.ppat.1007703 -
Mobile DNA Aug 2022ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal...
BACKGROUND
ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.
RESULTS
Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.
CONCLUSIONS
Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.
PubMed: 35962419
DOI: 10.1186/s13100-022-00275-1 -
Molecules (Basel, Switzerland) Mar 2023Essential oils (EOs) obtained by hydro-distillation from different parts of twigs (EOT), leaves (EOL), and fruits (EOF) of Hook. f. were screened for their chemical...
Essential oils (EOs) obtained by hydro-distillation from different parts of twigs (EOT), leaves (EOL), and fruits (EOF) of Hook. f. were screened for their chemical composition, insecticidal, repellence, and antibacterial properties. Based on GC and GC/MS analysis, 23 constituents were identified across the twigs, leaves, and fruits, with 23, 23, and 21 components, respectively. The primary significant class was oxygenated monoterpenes (82.2-95.5%). The main components were 1,8-cineole (65.6-86.1%), α-terpinyl acetate (2.5-7.6%), o-cymene (3.3-7.5%), and α-terpineol (3.3-3.5%). All three EOs exhibited moderate antibacterial activities. EOL was found to have higher antibacterial activity against all tested strains except (CFBP 8199), for which EOT showed more potency. Globally, (CFBP 8199) was the most sensitive (MIC ≤ 2 mg/mL), while the most resistant bacteria were (CFBP 3855) and subsp. (CFBP 5387). Fumigant, contact toxicity, and repellent bioassays showed different potential depending on plant extracts, particularly EOT and EOL as moderate repellents and EOT as a medium toxicant.
Topics: Oils, Volatile; Eucalyptus; Myrtaceae; Plant Leaves; Insect Repellents; Anti-Bacterial Agents; Plant Oils
PubMed: 36985610
DOI: 10.3390/molecules28062638 -
Nucleic Acids Research Sep 2019Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data,...
Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5' and 3' ends of all transcripts. Since sRNAs are about the same size as individual fragments (50-350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5' UTR or 3' UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO.
Topics: Algorithms; Datasets as Topic; Enterobacteriaceae; Escherichia coli; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Internet; RNA, Antisense; RNA, Bacterial; RNA, Messenger; RNA, Small Untranslated; Salmonella enterica; Sequence Analysis, RNA; Software
PubMed: 31147705
DOI: 10.1093/nar/gkz485 -
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 -
Natural Product Research Dec 2023The GC and GC/MS analysis of the essential oil samples obtained separately from whole aerial parts and the roots of resulted in the identification of a total of 40...
A comparative study on chemical composition and antibacterial activity of essential oils from the aerial parts and roots of (Siebold & Zucc.) Wedd. growing in the Central Himalayan region.
The GC and GC/MS analysis of the essential oil samples obtained separately from whole aerial parts and the roots of resulted in the identification of a total of 40 compounds from the whole aerial parts and 45 compounds from the roots representing 89.7% and 82.9%, respectively, of the total essential oil composition. The essential oil from aerial parts is dominated by oxygenated sesquiterpenes (66.4%) with elemol (55.1%), germacrene D-4-ol (4.2%), linalool (3.5%) and phytol (3.4%) as the major constituents while the root essential oil is dominated by oxygenated monoterpenes (30.4%) with -myrtanol (16.3%), -myrtanol (11.6%), nopinone (7.8%), cadin-4-en-10-ol (4.7%), and -elemol (3.4%) as major constituents. The essential oil from whole aerial parts showed bactericidal effect at 250 µL/mL concentration (MBC) against and while the root essential oil exhibited bactericidal effect at 125 µL/mL against , and .
PubMed: 38073501
DOI: 10.1080/14786419.2023.2289187 -
Carbohydrate Research Nov 2020The species Dickeya aquatica was established in 2014 after the genomic characterization of the pectinolytic bacteria isolated from water. It was demonstrated that D....
The structure of the O-polysaccharide isolated from pectinolytic gram-negative bacterium Dickeya aquatica IFB0154 is different from the O-polysaccharides of other Dickeya species.
The species Dickeya aquatica was established in 2014 after the genomic characterization of the pectinolytic bacteria isolated from water. It was demonstrated that D. aquatica was able to cause symptoms of soft rot on the fruit of tomato and cucumber. According to earlier works, lipopolysaccharides are regarded as an important virulence factor of Pectobacteriaceae. An O-specific polysaccharide containing d-Fuc and l-Rha was obtained by mild acid hydrolysis of the lipopolysaccharide of D. aquatica IFB0154 (strain Dw044 isolated in Finland). By means of compositional analyses and NMR spectroscopy, the chemical repeating unit of the polymer was identified as a linear disaccharide of the structure shown below. The rhamnose residue was partially acetylated at O-2 or O-3. OAc (~40%) ↓ →3)-α-d-Fucp-(1 → 4)-α-l-Rhap-(1→ ↑ OAc (~30%) The O-polysaccharides isolated from Dickeya dianthicola IFB0485 and Dickeya zeae IPO946 have a different structure, identical to that previously described for several strains of Dickeya solani and Dickeya dadantii 3937.
Topics: Carbohydrate Sequence; Dickeya; O Antigens; Species Specificity
PubMed: 32911204
DOI: 10.1016/j.carres.2020.108135 -
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