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  1. Article ; Online: A bumpy road ahead for genetic biocontainment.

    George, Dalton R / Danciu, Mark / Davenport, Peter W / Lakin, Matthew R / Chappell, James / Frow, Emma K

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 650

    Language English
    Publishing date 2024-01-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44531-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Quorum Sensing Is Accompanied by Global Metabolic Changes in the Opportunistic Human Pathogen Pseudomonas aeruginosa.

    Davenport, Peter W / Griffin, Julian L / Welch, Martin

    Journal of bacteriology

    2015  Volume 197, Issue 12, Page(s) 2072–2082

    Abstract: Unlabelled: Pseudomonas aeruginosa uses N-acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in ... ...

    Abstract Unlabelled: Pseudomonas aeruginosa uses N-acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in nutrient acquisition, microbial competition, and virulence. In this study, we investigated the metabolic consequences of AHL-dependent QS by monitoring the metabolic profile(s) of a lasI rhlI double mutant (unable to make QS signaling molecules) and its wild-type progenitor as they progressed through the growth curve. Analysis of culture supernatants by (1)H-nuclear magnetic resonance ((1)H-NMR) spectroscopy revealed that at the point where AHL concentrations peaked in the wild type, the metabolic footprints (i.e., extracellular metabolites) of the wild-type and lasI rhlI mutant diverged. Subsequent gas chromatography-mass spectrometry (GC-MS)-based analysis of the intracellular metabolome revealed QS-dependent perturbations in around one-third of all identified metabolites, including altered concentrations of tricarboxylic acid (TCA) cycle intermediates, amino acids, and fatty acids. Further targeted fatty acid methyl ester (FAME) GC-MS-based profiling of the cellular total fatty acid pools revealed that QS leads to changes associated with decreased membrane fluidity and higher chemical stability. However, not all of the changes we observed were necessarily a direct consequence of QS; liquid chromatography (LC)-MS analyses revealed that polyamine levels were elevated in the lasI rhlI mutant, perhaps a response to the absence of QS-dependent adaptations. Our data suggest that QS leads to a global readjustment in central metabolism and provide new insight into the metabolic changes associated with QS during stationary-phase adaptation.
    Importance: Quorum sensing (QS) is a transcriptional regulatory mechanism that allows bacteria to coordinate their gene expression profile with the population cell density. The opportunistic human pathogen Pseudomonas aeruginosa uses QS to control the production of secreted virulence factors. In this study, we show that QS elicits a global "metabolic rewiring" in P. aeruginosa. This metabolic rerouting of fluxes is consistent with a variety of drivers, ranging from altered QS-dependent transcription of "metabolic genes" through to the effect(s) of global "metabolic readjustment" as a consequence of QS-dependent exoproduct synthesis, as well as a general stress response, among others. To our knowledge, this is the first study of its kind to assess the global impact of QS on the metabolome.
    MeSH term(s) Acyl-Butyrolactones/metabolism ; Alanine/metabolism ; Amino Acids/metabolism ; Energy Metabolism/physiology ; Fatty Acids/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Mutation ; Polyamines/metabolism ; Principal Component Analysis ; Pseudomonas aeruginosa/metabolism ; Pseudomonas aeruginosa/physiology ; Quorum Sensing/physiology
    Chemical Substances Acyl-Butyrolactones ; Amino Acids ; Fatty Acids ; Polyamines ; Alanine (OF5P57N2ZX)
    Language English
    Publishing date 2015-04-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.02557-14
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Quorum Sensing Is Accompanied by Global Metabolic Changes in the Opportunistic Human Pathogen Pseudomonas aeruginosa

    Davenport, Peter W / Griffin, Julian L / Welch, Martin

    Journal of bacteriology. 2015 June 15, v. 197, no. 12

    2015  

    Abstract: Pseudomonas aeruginosa uses N -acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in nutrient ... ...

    Abstract Pseudomonas aeruginosa uses N -acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in nutrient acquisition, microbial competition, and virulence. In this study, we investigated the metabolic consequences of AHL-dependent QS by monitoring the metabolic profile(s) of a lasI rhlI double mutant (unable to make QS signaling molecules) and its wild-type progenitor as they progressed through the growth curve. Analysis of culture supernatants by ¹H-nuclear magnetic resonance (¹H-NMR) spectroscopy revealed that at the point where AHL concentrations peaked in the wild type, the metabolic footprints (i.e., extracellular metabolites) of the wild-type and lasI rhlI mutant diverged. Subsequent gas chromatography-mass spectrometry (GC-MS)-based analysis of the intracellular metabolome revealed QS-dependent perturbations in around one-third of all identified metabolites, including altered concentrations of tricarboxylic acid (TCA) cycle intermediates, amino acids, and fatty acids. Further targeted fatty acid methyl ester (FAME) GC-MS-based profiling of the cellular total fatty acid pools revealed that QS leads to changes associated with decreased membrane fluidity and higher chemical stability. However, not all of the changes we observed were necessarily a direct consequence of QS; liquid chromatography (LC)-MS analyses revealed that polyamine levels were elevated in the lasI rhlI mutant, perhaps a response to the absence of QS-dependent adaptations. Our data suggest that QS leads to a global readjustment in central metabolism and provide new insight into the metabolic changes associated with QS during stationary-phase adaptation. IMPORTANCE Quorum sensing (QS) is a transcriptional regulatory mechanism that allows bacteria to coordinate their gene expression profile with the population cell density. The opportunistic human pathogen Pseudomonas aeruginosa uses QS to control the production of secreted virulence factors. In this study, we show that QS elicits a global “metabolic rewiring” in P. aeruginosa . This metabolic rerouting of fluxes is consistent with a variety of drivers, ranging from altered QS-dependent transcription of “metabolic genes” through to the effect(s) of global “metabolic readjustment” as a consequence of QS-dependent exoproduct synthesis, as well as a general stress response, among others. To our knowledge, this is the first study of its kind to assess the global impact of QS on the metabolome.
    Keywords Pseudomonas aeruginosa ; amino acids ; bacteria ; fatty acid methyl esters ; fatty acids ; gas chromatography-mass spectrometry ; gene expression ; genes ; humans ; liquid chromatography ; membrane fluidity ; metabolism ; metabolites ; metabolome ; microbial competition ; monitoring ; mutants ; nuclear magnetic resonance spectroscopy ; pathogens ; polyamines ; quorum sensing ; stress response ; transcription (genetics) ; virulence
    Language English
    Dates of publication 2015-0615
    Size p. 2072-2082.
    Publishing place American Society for Microbiology
    Document type Article
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.02557-14
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Analysis of chloroformate-derivatised amino acids, dipeptides and polyamines by LC-MS/MS.

    Ubhi, Baljit K / Davenport, Peter W / Welch, Martin / Riley, John / Griffin, Julian L / Connor, Susan C

    Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

    2013  Volume 934, Page(s) 79–88

    Abstract: A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed which, with sample preparation using a commercially available kit, allows rapid quantitation of 39 chloroformate-derivatised amino acids (AAs), polyamines (PAs) and ... ...

    Abstract A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed which, with sample preparation using a commercially available kit, allows rapid quantitation of 39 chloroformate-derivatised amino acids (AAs), polyamines (PAs) and dipeptides (DPs) in complex biological matrices. Lower limits of quantitation (LOQ) were 20-150nM for putrescine, spermine, spermidine, cadaverine, agmatine, and below 5μM for all analytes. Responses were linear for all analytes between 0.5 and 50μM. Quantitative measurements of all 39 metabolites were achieved within a 15min runtime. The method was evaluated with a Pseudomonas aeruginosa cell extract study (n=24) and a larger human urine study (n=308). Batch effects were observed in the urine study and an investigation of instrument and sample stability showed a wave-like pattern in the MS responses. Both the run order and inter-batch variation were successfully corrected by normalising to pooled urine quality control data. Thus, this method should be suitable for diverse biological matrices and for large as well as small sample sets.
    MeSH term(s) Amino Acids/chemistry ; Amino Acids/urine ; Chromatography, Liquid/methods ; Dipeptides/chemistry ; Dipeptides/urine ; Formates/chemistry ; Humans ; Polyamines/chemistry ; Polyamines/urine ; Pseudomonas aeruginosa/chemistry ; Pseudomonas aeruginosa/metabolism ; Tandem Mass Spectrometry/methods
    Chemical Substances Amino Acids ; Dipeptides ; Formates ; Polyamines ; chlorocarbonic acid (463-73-0)
    Language English
    Publishing date 2013-06-29
    Publishing country Netherlands
    Document type Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180823-8
    ISSN 1873-376X ; 0378-4347 ; 1570-0232 ; 1387-2273
    ISSN (online) 1873-376X
    ISSN 0378-4347 ; 1570-0232 ; 1387-2273
    DOI 10.1016/j.jchromb.2013.06.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Escherichia coli flagellar genes as target sites for integration and expression of genetic circuits.

    Juhas, Mario / Evans, Lewis D B / Frost, Joe / Davenport, Peter W / Yarkoni, Orr / Fraser, Gillian M / Ajioka, James W

    PloS one

    2014  Volume 9, Issue 10, Page(s) e111451

    Abstract: E. coli is a model platform for engineering microbes, so genetic circuit design and analysis will be greatly facilitated by simple and effective approaches to introduce genetic constructs into the E. coli chromosome at well-characterised loci. We ... ...

    Abstract E. coli is a model platform for engineering microbes, so genetic circuit design and analysis will be greatly facilitated by simple and effective approaches to introduce genetic constructs into the E. coli chromosome at well-characterised loci. We combined the Red recombinase system of bacteriophage λ and Isothermal Gibson Assembly for rapid integration of novel DNA constructs into the E. coli chromosome. We identified the flagellar region as a promising region for integration and expression of genetic circuits. We characterised integration and expression at four candidate loci, fliD, fliS, fliT, and fliY, of the E. coli flagellar region 3a. The integration efficiency and expression from the four integrations varied considerably. Integration into fliD and fliS significantly decreased motility, while integration into fliT and fliY had only a minor effect on the motility. None of the integrations had negative effects on the growth of the bacteria. Overall, we found that fliT was the most suitable integration site.
    MeSH term(s) Bacterial Proteins/genetics ; Bacteriophage lambda/metabolism ; Chromosomes, Bacterial ; DNA, Bacterial/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Flagella/metabolism ; Flagellin/genetics ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Green Fluorescent Proteins/metabolism ; Membrane Proteins/genetics ; Molecular Chaperones/genetics ; Mutation ; Open Reading Frames ; Polymerase Chain Reaction ; Recombinases/metabolism ; Synthetic Biology
    Chemical Substances Bacterial Proteins ; DNA, Bacterial ; Escherichia coli Proteins ; Membrane Proteins ; Molecular Chaperones ; Recombinases ; Flagellin (12777-81-0) ; Green Fluorescent Proteins (147336-22-9) ; FlaD protein, Bacteria (147757-14-0) ; FliS protein, Bacteria (147757-15-1) ; fliT protein, Bacteria (147757-16-2) ; FliY protein, Bacteria (148997-36-8)
    Language English
    Publishing date 2014-10-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0111451
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Mutation of nfxB causes global changes in the physiology and metabolism of Pseudomonas aeruginosa.

    Stickland, Hannah G / Davenport, Peter W / Lilley, Kathryn S / Griffin, Julian L / Welch, Martin

    Journal of proteome research

    2010  Volume 9, Issue 6, Page(s) 2957–2967

    Abstract: Loss-of-function mutations in nfxB lead to up-regulation of mexCD-oprJ expression and, consequently, increased resistance to fluoroquinolone antibiotics. Such nfxB mutants have also been reported to exhibit altered virulence profiles, diminished type III ...

    Abstract Loss-of-function mutations in nfxB lead to up-regulation of mexCD-oprJ expression and, consequently, increased resistance to fluoroquinolone antibiotics. Such nfxB mutants have also been reported to exhibit altered virulence profiles, diminished type III secretion system-dependent cytotoxicity, and impaired fitness. However, it is not clear whether these phenotypes are directly linked to NfxB activity or whether inappropriate expression of the MexCD-OprJ pump has pleiotropic effects, thereby impacting indirectly on the phenotype of the cells. The aim of the current work is to investigate which of these possibilities is correct. We isolated a novel type of nfxB mutant generated by a spontaneous polygenic deletion and show that this mutant is rapidly out-competed when grown in a mixed culture with the wild-type progenitor. This competitive fitness defect only manifested itself during the stationary phase of growth. The endoproteome of the nfxB mutant, assessed using 2D-DiGE (difference gel electrophoresis), showed major alterations compared with the wild-type. Consistent with this, we found that the nfxB mutant was impaired in all forms of motility (swimming, swarming, and twitching) as well as in the production of siderophores, rhamnolipid, secreted protease, and pyocyanin. Further investigation showed that the exoproteome, endometabolome, and exometabolome of the nfxB mutant were all globally different compared with the wild-type. The exometabolome of the nfxB mutant was enriched in a selection of long chain fatty acids raising the possibility that these might be substrates for the MexCD-OprJ pump. The nfxB mutant metabotype could be complemented by expression of nfxB in trans and was abolished in an nfxB mexD double mutant, suggesting that inappropriate overexpression of a functional MexCD-OprJ efflux pump causes pleiotropic changes. Taken together, our data suggest that many of the nfxB mutant phenotypes are not caused by the direct effects of the NfxB regulator, but instead by inappropriate mexCD-oprJ expression. Furthermore, the pleiotropic nature of the phenotypes indicate that these may simply reflect the globally dysregulated physiology of the strain.
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacterial Proteins/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/physiology ; Electrophoresis, Gel, Two-Dimensional ; Membrane Transport Proteins/metabolism ; Metabolome ; Mutation ; Phenotype ; Principal Component Analysis ; Proteome ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Pseudomonas aeruginosa/physiology ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription Factors/physiology
    Chemical Substances Bacterial Proteins ; DNA-Binding Proteins ; Membrane Transport Proteins ; NfxB protein, Pseudomonas aeruginosa ; Proteome ; Transcription Factors
    Language English
    Publishing date 2010-04-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/pr9011415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Quorum Sensing Is Accompanied by Global Metabolic Changes in the Opportunistic Human Pathogen Pseudomonas aeruginosa

    Davenport, Peter W. / Griffin, Julian L. / Welch, Martin

    Journal of bacteriology

    Volume v. 197,, Issue no. 1

    Abstract: Pseudomonas aeruginosa uses N -acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in nutrient ... ...

    Abstract Pseudomonas aeruginosa uses N -acyl-homoserine lactone (AHL)-dependent quorum sensing (QS) systems to control the expression of secreted effectors. These effectors can be crucial to the ecological fitness of the bacterium, playing roles in nutrient acquisition, microbial competition, and virulence. In this study, we investigated the metabolic consequences of AHL-dependent QS by monitoring the metabolic profile(s) of a lasI rhlI double mutant (unable to make QS signaling molecules) and its wild-type progenitor as they progressed through the growth curve. Analysis of culture supernatants by ¹H-nuclear magnetic resonance (¹H-NMR) spectroscopy revealed that at the point where AHL concentrations peaked in the wild type, the metabolic footprints (i.e., extracellular metabolites) of the wild-type and lasI rhlI mutant diverged. Subsequent gas chromatography-mass spectrometry (GC-MS)-based analysis of the intracellular metabolome revealed QS-dependent perturbations in around one-third of all identified metabolites, including altered concentrations of tricarboxylic acid (TCA) cycle intermediates, amino acids, and fatty acids. Further targeted fatty acid methyl ester (FAME) GC-MS-based profiling of the cellular total fatty acid pools revealed that QS leads to changes associated with decreased membrane fluidity and higher chemical stability. However, not all of the changes we observed were necessarily a direct consequence of QS; liquid chromatography (LC)-MS analyses revealed that polyamine levels were elevated in the lasI rhlI mutant, perhaps a response to the absence of QS-dependent adaptations. Our data suggest that QS leads to a global readjustment in central metabolism and provide new insight into the metabolic changes associated with QS during stationary-phase adaptation. IMPORTANCE Quorum sensing (QS) is a transcriptional regulatory mechanism that allows bacteria to coordinate their gene expression profile with the population cell density. The opportunistic human pathogen Pseudomonas aeruginosa uses QS to control the production of secreted virulence factors. In this study, we show that QS elicits a global “metabolic rewiring” in P. aeruginosa . This metabolic rerouting of fluxes is consistent with a variety of drivers, ranging from altered QS-dependent transcription of “metabolic genes” through to the effect(s) of global “metabolic readjustment” as a consequence of QS-dependent exoproduct synthesis, as well as a general stress response, among others. To our knowledge, this is the first study of its kind to assess the global impact of QS on the metabolome.
    Keywords liquid chromatography ; metabolites ; monitoring ; fatty acids ; quorum sensing ; genes ; metabolism ; gas chromatography-mass spectrometry ; humans ; pathogens ; transcription (genetics) ; stress response ; mutants ; metabolome ; microbial competition ; polyamines ; amino acids ; bacteria ; fatty acid methyl esters ; virulence ; membrane fluidity ; gene expression ; Pseudomonas aeruginosa ; nuclear magnetic resonance spectroscopy
    Language English
    Document type Article
    ISSN 0021-9193
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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  8. Article: Analysis of chloroformate-derivatised amino acids, dipeptides and polyamines by LC–MS/MS

    Ubhi, Baljit K. / Davenport, Peter W. / Welch, Martin / Riley, John / Griffin, Julian L. / Connor, Susan C.

    Journal of chromatography

    Volume v. 934

    Abstract: A liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed which, with sample preparation using a commercially available kit, allows rapid quantitation of 39 chloroformate-derivatised amino acids (AAs), polyamines (PAs) and ... ...

    Abstract A liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed which, with sample preparation using a commercially available kit, allows rapid quantitation of 39 chloroformate-derivatised amino acids (AAs), polyamines (PAs) and dipeptides (DPs) in complex biological matrices. Lower limits of quantitation (LOQ) were 20–150nM for putrescine, spermine, spermidine, cadaverine, agmatine, and below 5μM for all analytes. Responses were linear for all analytes between 0.5 and 50μM. Quantitative measurements of all 39 metabolites were achieved within a 15min runtime. The method was evaluated with a Pseudomonas aeruginosa cell extract study (n=24) and a larger human urine study (n=308). Batch effects were observed in the urine study and an investigation of instrument and sample stability showed a wave-like pattern in the MS responses. Both the run order and inter-batch variation were successfully corrected by normalising to pooled urine quality control data. Thus, this method should be suitable for diverse biological matrices and for large as well as small sample sets.
    Keywords liquid chromatography ; metabolites ; cadaverine ; spermidine ; dipeptides ; spermine ; humans ; urine ; putrescine ; tandem mass spectrometry ; quantitative analysis ; amino acids ; quality control ; Pseudomonas aeruginosa ; agmatine
    Language English
    Document type Article
    ISSN 1570-0232
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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