Sequencing of environmental pseudomonas isolates
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ABSTRACT:
PROVIDER: PRJEB21289 | ENA |
REPOSITORIES: ENA
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Project description:Most habitats on earth are colonized by diverse bacterial communities, offering ample opportunities for inter-species interactions. While competition for space and nutrients might often dominate such interactions, little is known about whether bacteria can sense competitors and mount specific responses to withstand their attacks. The competition-sensing hypothesis proposes that bacteria can do so through nutrient stress and cell damage cues. Here, we conducted a replicated RNAseq-transcriptomic study to test this hypothesis. We exposed Pseudomonas aeruginosa to either its own spent medium or to the supernatant of its competitor Burkholderia cenocepacia. Compared to controls, we detected significant changes in the transcriptome of P. aeruginosa that entail both general responses to spent medium and specific responses to the competitor. Specifically, genes encoding various competitive traits, including the type-VI secretion system, the siderophore pyoverdine, and the toxins phenazines and hydrogen cyanide, were upregulated when exposed to the competitor supernatant. Similarly, several stress response and quorum-sensing regulators were overexpressed. Moreover, we found transcriptional responses to vary as a function of iron availability, whereby metabolically more costly responses were launched under iron rich conditions. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when exposed to B. cenocepacia supernatant, integrating both environmental and social cues.
2023-12-31 | GSE224821 | GEO
Project description:Bacteria access iron, a key nutrient, by producing siderophores or using siderophores produced by other microorganisms. The pathogen Pseudomonas aeruginosa produces two siderophores but is also able to pirate enterobactin (ENT), the siderophore produced by Escherichia coli. ENT-Fe complexes are imported across the outer membranes of P. aeruginosa by the two-outer membrane transporters PfeA and PirA. Iron is released from ENT in the P. aeruginosa periplasm by hydrolysis of ENT by the esterase PfeE. We show here that pfeE gene deletion renders P. aeruginosa unable to grow in the presence of ENT because it is unable to access iron via this siderophore. Two-species co-culture under iron-restricted conditions show that P. aeruginosa strongly represses the growth of E. coli as long it is able to produce its own siderophores. Both strains are present in similar proportions in the culture as long as the siderophore-deficient P. aeruginosa strain is able to use ENT produced by E. coli to access iron. If pfeE is deleted, E. coli has the upper hand in the culture and P. aeruginosa growth is repressed. Overall, these data show that PfeE is the Achilles heel of P. aeruginosa in communities with bacteria producing ENT.
2021-04-29 | PXD023712 | Pride
Project description:The development of new antibiotics against Gram-negative bacteria has to deal with the low permeability of the outer membrane. This obstacle can be overcome by utilizing siderophore-dependent iron uptake pathways as gates for antibiotic uptake. Iron-chelating siderophores are actively imported by bacteria, and their conjugation to antibiotics allows smuggling the latter into bacterial cells. Synthetic siderophore mimetics based on MECAM and DOTAM cores, both chelating iron via catechol groups, have been recently applied as versatile carriers of functional cargo. In the present study, we show that MECAM and the MECAM-ampicillin conjugate 3 transport iron into Pseudomonas aeruginosa cells via the catechol-type outer membrane transporters PfeA and PirA, and DOTAM solely via PirA. Differential proteomics and RTqPCR showed that MECAM import induced the expression of pfeA, whereas 3 led to an increase in the expression of pfeA and ampc, a gene conferring ampicillin resistance. The presence of DOTAM did not induce the expression of pirA, but upregulated the expression two zinc transporters (cntO and PA0781), pointing out that bacteria become zinc starved in the presence of this compound. Kinetic experiments with radioactive 55Fe demonstrated that iron uptake was as efficient as with the natural prototype siderophore enterobactin. The study provides a mechanistic and functional validation for DOTAM- and MECAM-based artificial siderophore mimetics as vehicles for the delivery of cargo into Gram-negative bacteria.
2022-10-28 | PXD031065 | Pride
Project description:A special immune system exists at distinct respiratory epithelium to combat invasion by Pseudomonas aeruginosa (PAO1). This study aimes to determine if interleukin-17C (IL-17C) is correlated with acute PAO1 infection in human nasal epithelium and to prove the role of IL-17C on iron sequestration during PAO1 infection. IL-17C has antipseudomonal effect by lowering iron sequestration and reducing siderophore activity. IL-17C could be efficient mediator to control PAO1 infection in human nasal epithelium.
2018-01-12 | GSE109118 | GEO
Project description:In the arms race of bacterial pathogenesis, bacteria produce an array of toxins and virulence factors that disrupt host processes while hosts respond with immune countermeasures. One key virulence mediator of the ubiquitous, opportunistic, extracellular pathogen Pseudomonas aeruginosa is the iron-binding siderophore pyoverdin (PMID:10722571;PMID: 8550201). The mechanisms used by pyoverdin to acquire iron from the host remain incompletely elucidated. Here we demonstrate that mitochondria represent an important target for iron acquisition and that exposure to this toxin results in loss of mitochondrial membrane potential, altered mitochondrial dynamics, and mitophagy in both Caenorhabditis elegans and mammalian cells. We also show that animal mitophagy protects the consequences of siderophore activity, conferring resistance to pyoverdin-mediated host killing. In C. elegans, the conserved autophagic genes bec-1/BECN1 and lgg-1/LC3, and the mitophagic regulator pink-1/PINK1 are required for iron chelator-elicited mitochondrial turnover and provide protection against iron sequestration by P. aeruginosa, likely by ameliorating the mitochondrial damage. While autophagic mechanisms have been implicated in the destruction of intracellular bacteria via a process called “xenophagy” (PMID: 24005326), our findings represent the first report of resistance to an extracellular pathogen being conferred by authentic autophagic activity that targets host organelles.
2017-06-20 | GSE55422 | GEO
Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of M-NM-^ThapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals. Iron dependent gene expression in Fusarium oxysporum wt and M-NM-^ThapX mutant was measured 1 hour after shifting the mycelia to minimal medium with or without 50 M-NM-<M Fe2(SO4)3. Three independent experiments were performed.
2012-07-13 | E-GEOD-39325 | biostudies-arrayexpress
Project description:Pseudomonas and other environmental microorganisms have been proven capable of synthesizing siderophores, which are instrumental in the removal of iron and other metal ions from a variety of waste materials. We have elucidated the molecular mechanisms by which the BfmRS two-component system (TCS) mediates environmental stress signals to regulate siderophore production in Pseudomonas aeruginosa. In this study, we further confirm the pivotal role of the BfmRS system in bacterial iron metabolism, demonstrating its regulatory influence on key genes involved in siderophore synthesis. Moreover, overexpression of BfmR led to a marked increase in mRNA levels of siderophore-related genes, with a 2.4- to 6.7-fold elevation, which in turn significantly enhanced siderophore production and consequently improved iron utilization efficiency when compared to the wild type (WT). The heightened efficiency of the genetically modified strain to extract iron from coal fly ash (CFA) suggests the feasibility of engineered bacterial system in bioremediation. This work not only validate the intricate TCSs involved in siderophore regulation within P. aeruginosa, but also provides a compelling strategy in heavy metal recovery and hazardous waste detoxification.
2023-12-25 | PXD048123 | iProX
Project description:Pseudomonas chlororaphis strain 30-84 is an effective biological control agent against take-all disease of wheat. Phenazines, bacterial secondary metabolites produced by 30-84, are essential for 30-84 to inhibit fungal pathogens, form biofilms, and effectively colonize the rhizosphere. However, how the bacteria themselves respond to phenazines remains unknown. In this study, we conducted an RNA-seq analysis by comparing the wild type strain with a phenazine deficient mutant. RNA-seq analysis identified over 200 genes differentially regulated by phenazines. Consistent with previous findings in Pseudomonas aeruginosa PAO1, phenazines positively contribute to the expression of their own biosynthetic genes. Moreover, phenazine regulatory genes including the phzI/phzR quorum sensing system and the rpeB response regulatory were also expressed at high levels in the presence of phenazines. Besides phenazine biosynthesis and regulatory genes, genes involved in secondary metabolism, exopoysaccharide production and iron uptake as well as amino acid transport were identified as the major components under phenazine control, including many novel genes. We have also demonstrated that mutation of the primary siderophore gene pvdA resulted in up-regulation of phenazine genes when grown in iron-limiting media. These findings implicate phenazines as signaling molecules to regulate gene expression and hence alter metabolism in P. chlororaphis strain 30-84. A total of 4 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (2 replicates); Pseudomonas chlororaphis ZN mutant (2 replicates).
2014-11-25 | E-GEOD-45247 | biostudies-arrayexpress
Project description:Pseudomonas aeruginosa is a common nosocomial pathogen which produces siderophores to solubilize and transport chelated Fe3+ to aid its survival in both the environment and the host. However, there is a lack of comprehensive understanding regarding the molecular mechanisms underlying siderophore synthesis, uptake, and regulation within various ecological niches. In this study, we demonstrated that the BfmRS two-component system, part of the core genome of P. aeruginosa, plays a crucial role in siderophore metabolism. We have identified BfmS as an osmosensing histidine kinase that responds to external osmolytes, then modulates the activation of the response regulator BfmR. Under high osmolality, BfmR could directly bind to the promoters of pvd, fpv, and femARI gene clusters, thereby enhancing their expression and promoting siderophore metabolism. The proteomic and phenotypic analyses confirmed that deletion of bfmRS results in reduced expression levels of siderophore-related proteins as well as siderophore production. Importantly, loss of bfmR or bfmS significantly impaired bacterial survival in both iron deficiency medium and mouse lung infection models. Furthermore, phylogenetic analysis revealed that BfmRS is highly conserved and widely distributed across Pseudomonas species, evidences also proved that the BfmR of P. putida KT2440 and P. sp. MRSN12121 activated siderophore genes in response to high osmolality. Overall, this study sheds light on the previously unexplored signal transduction pathway, BfmRS, which governs the siderophore regulation in Pseudomonas species through perceiving an osmotic upshift. Considering that siderophores serve as unique social mediators, our findings contribute to a better understanding of how siderophores facilitate bacterial interactions with their eukaryotic hosts and contribute to the establishment of stable communities.
2023-10-30 | PXD046481 | iProX
Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of ΔhapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals.
2012-07-14 | GSE39325 | GEO