101
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Migliorini LB, Brüggemann H, de Sales RO, Koga PCM, de Souza AV, Martino MDV, Galhardo RS, Severino P. Mutagenesis Induced by Sub-Lethal Doses of Ciprofloxacin: Genotypic and Phenotypic Differences Between the Pseudomonas aeruginosa Strain PA14 and Clinical Isolates. Front Microbiol 2019; 10:1553. [PMID: 31354657 PMCID: PMC6636244 DOI: 10.3389/fmicb.2019.01553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/21/2019] [Indexed: 01/16/2023] Open
Abstract
Bacterial resistance is a severe threat to global public health. Exposure to sub-lethal concentrations has been considered a major driver of mutagenesis leading to antibiotic resistance in clinical settings. Ciprofloxacin is broadly used to treat infections caused by Pseudomonas aeruginosa, whereas increased mutagenesis induced by sub-lethal concentrations of ciprofloxacin has been reported for the reference strain, PAO1, in vitro. In this study we report increased mutagenesis induced by sub-lethal concentrations of ciprofloxacin for another reference strain, PA14-UCBPP, and lower mutagenesis for clinical isolates when compared to the reference strain. This unexpected result may be associated with missense mutations in imuB and recX, involved in adaptive responses, and the presence of Pyocin S2, which were found in all clinical isolates but not in the reference strain genome. The genetic differences between clinical isolates of P. aeruginosa and the reference PA14-UCBPP, often used to study P. aeruginosa phenotypes in vitro, may be involved in reduced mutagenesis under sub-lethal concentrations of CIP, a scenario that should be further explored for the understanding of bacterial fitness in hospital environments. Moreover, we highlight the presence of a complete umuDC operon in a P. aeruginosa clinical isolate. Even though the presence of umuDC did not contribute to a significant increase in mutagenesis, it highlights the dynamic exchange of genetic material between bacterial species in the hospital environment.
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Affiliation(s)
- Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | | | - Romario Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | | | - Andrea Vieira de Souza
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | | | - Rodrigo S Galhardo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
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102
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Hay ID, Lithgow T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep 2019; 20:e47427. [PMID: 30952693 PMCID: PMC6549030 DOI: 10.15252/embr.201847427] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.
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Affiliation(s)
- Iain D Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Vic., Australia
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103
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Qi L, Christopher GF. Role of Flagella, Type IV Pili, Biosurfactants, and Extracellular Polymeric Substance Polysaccharides on the Formation of Pellicles by Pseudomonas aeruginosa. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5294-5304. [PMID: 30883129 DOI: 10.1021/acs.langmuir.9b00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microbial biofilms are viscoelastic materials formed by bacteria, which occur on solid surfaces, at liquid interfaces, or in free solution. Although solid surface biofilms have been widely studied, pellicles, biofilms at liquid interfaces, have had significantly less focus. In this work, interfacial shear rheology and scanning electron microscopy imaging are used to characterize how flagella, type IV pili, biosurfactants, and extracellular polymeric substance polysaccharides affect the formation of pellicles by Pseudomonas aeruginosa at an air/water interface. Pellicles still form with the loss of a single biological attachment mechanism, which is hypothesized to be due to surface tension-aided attachment. Changes in the surface structure of the pellicles are observed when changing both the function/structure of type IV pili, removing the flagella, or stopping the expression of biosurfactants. However, these changes do not appear to affect pellicle elasticity in a consistent way. Traits that affect adsorption and growth/spreading appear to affect pellicles in a manner consistent with literature results for solid surface biofilms; small differences are seen in attachment-related mechanisms, which may occur due to surface tension.
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Affiliation(s)
- Lingjuan Qi
- Department of Mechanical Engineering , Texas Tech University , Lubbock 79409 , United States
| | - Gordon F Christopher
- Department of Mechanical Engineering , Texas Tech University , Lubbock 79409 , United States
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104
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Subedi D, Kohli GS, Vijay AK, Willcox M, Rice SA. Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34. PLoS One 2019; 14:e0215038. [PMID: 30986237 PMCID: PMC6464166 DOI: 10.1371/journal.pone.0215038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.
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Affiliation(s)
- Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Gurjeet Singh Kohli
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales, Australia
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105
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Irvine S, Bunk B, Bayes HK, Spröer C, Connolly JPR, Six A, Evans TJ, Roe AJ, Overmann J, Walker D. Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model. Microb Genom 2019; 5:e000262. [PMID: 30920365 PMCID: PMC6521587 DOI: 10.1099/mgen.0.000262] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/10/2019] [Indexed: 01/26/2023] Open
Abstract
Phenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronic Pseudomonas aeruginosa lung infection in patients with cystic fibrosis, well-characterized phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoid P. aeruginosa strain NH57388A. Using a combination of single-molecule real-time (PacBio) and Illumina sequencing we identify a large genomic inversion in the SCV through recombination between homologous regions of two rRNA operons and an associated truncation of one of the 16S rRNA genes and suggest this may be the genetic switch for conversion to the SCV phenotype. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance because the appearance of SCVs during chronic infection is associated with declining lung function.
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Affiliation(s)
- Sharon Irvine
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Boyke Bunk
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhiffenstraße 7B, 38124 Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Hannah K. Bayes
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathrin Spröer
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhiffenstraße 7B, 38124 Braunschweig, Germany
| | - James P. R. Connolly
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Anne Six
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Thomas J. Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Andrew J. Roe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jörg Overmann
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhiffenstraße 7B, 38124 Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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106
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Blazier AS, Papin JA. Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PLoS Comput Biol 2019; 15:e1006507. [PMID: 30973869 PMCID: PMC6478342 DOI: 10.1371/journal.pcbi.1006507] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/23/2019] [Accepted: 03/06/2019] [Indexed: 11/30/2022] Open
Abstract
The identification of genes essential for bacterial growth and survival represents a promising strategy for the discovery of antimicrobial targets. Essential genes can be identified on a genome-scale using transposon mutagenesis approaches; however, variability between screens and challenges with interpretation of essentiality data hinder the identification of both condition-independent and condition-dependent essential genes. To illustrate the scope of these challenges, we perform a large-scale comparison of multiple published Pseudomonas aeruginosa gene essentiality datasets, revealing substantial differences between the screens. We then contextualize essentiality using genome-scale metabolic network reconstructions and demonstrate the utility of this approach in providing functional explanations for essentiality and reconciling differences between screens. Genome-scale metabolic network reconstructions also enable a high-throughput, quantitative analysis to assess the impact of media conditions on the identification of condition-independent essential genes. Our computational model-driven analysis provides mechanistic insight into essentiality and contributes novel insights for design of future gene essentiality screens and the identification of core metabolic processes.
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Affiliation(s)
- Anna S. Blazier
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason A. Papin
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Medicine, Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
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107
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Genomic and Phenotypic Diversity among Ten Laboratory Isolates of Pseudomonas aeruginosa PAO1. J Bacteriol 2019; 201:JB.00595-18. [PMID: 30530517 DOI: 10.1128/jb.00595-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen found ubiquitously in the environment and commonly associated with airway infection in patients with cystic fibrosis. P. aeruginosa strain PAO1 is one of the most commonly used laboratory-adapted research strains and is a standard laboratory-adapted strain in multiple laboratories and strain banks worldwide. Due to potential isolate-to-isolate variability, we investigated the genomic and phenotypic diversity among 10 PAO1 strains (henceforth called sublines) obtained from multiple research laboratories and commercial sources. Genomic analysis predicted a total of 5,682 genes, with 5,434 (95.63%) being identical across all 10 strains. Phenotypic analyses revealed comparable growth phenotypes in rich media and biofilm formation profiles. Limited differences were observed in antibiotic susceptibility profiles and immunostimulatory potential, measured using heat-killed whole-cell preparations in four immortalized cell lines followed by quantification of interleukin-6 (IL-6) and IL-1β secretion. However, variability was observed in the profiles of secreted molecular products, most notably, in rhamnolipid, pyoverdine, pyocyanin, Pseudomonas quinolone signal (PQS), extracellular DNA, exopolysaccharide, and outer membrane vesicle production. Many of the observed phenotypic differences did not correlate with subline-specific genetic changes, suggesting alterations in transcriptional and translational regulation. Taken together, these results suggest that individually maintained sublines of PAO1, even when acquired from the same parent subline, are continuously undergoing microevolution during culture and storage that results in alterations in phenotype, potentially affecting the outcomes of in vitro phenotypic analyses and in vivo pathogenesis studies.IMPORTANCE Laboratory-adapted strains of bacteria are used throughout the world for microbiology research. These prototype strains help keep research data consistent and comparable between laboratories. However, we have observed phenotypic variability when using different strains of Pseudomonas aeruginosa PAO1, one of the major laboratory-adopted research strains. Here, we describe the genomic and phenotypic differences among 10 PAO1 strains acquired from independent sources over 15 years to understand how individual maintenance affects strain characteristics. We observed limited genomic changes but variable phenotypic changes, which may have consequences for cross-comparison of data generated using different PAO1 strains. Our research highlights the importance of limiting practices that may promote the microevolution of model strains and calls for researchers to specify the strain origin to ensure reproducibility.
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108
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Otis G, Bhattacharya S, Malka O, Kolusheva S, Bolel P, Porgador A, Jelinek R. Selective Labeling and Growth Inhibition of Pseudomonas aeruginosa by Aminoguanidine Carbon Dots. ACS Infect Dis 2019; 5:292-302. [PMID: 30589261 DOI: 10.1021/acsinfecdis.8b00270] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pseudomonas aeruginosa is a highly virulent bacterium, particularly associated with the spread of multidrug resistance. Here we show that carbon dots (C-dots), synthesized from aminoguanidine and citric acid precursors, can selectively stain and inhibit the growth of P. aeruginosa strains. The aminoguanidine-C-dots were shown both to target P. aeruginosa bacterial cells and also to inhibit biofilm formation by the bacteria. Mechanistic analysis points to interactions between aminoguanidine residues on the C-dots' surface and P. aeruginosa lipopolysaccharide moieties as the likely determinants for both antibacterial and labeling activities. Indeed, the application of biomimetic membrane assays reveals that LPS-promoted insertion and bilayer permeation constitute the primary factors in the anti- P. aeruginosa effect of the aminoguanidine-C-dots. The aminoguanidine C-dots are easy to prepare in large quantities and are inexpensive and biocompatible and thus may be employed as a useful vehicle for selective staining and antibacterial activity against P. aeruginosa.
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109
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Cafora M, Deflorian G, Forti F, Ferrari L, Binelli G, Briani F, Ghisotti D, Pistocchi A. Phage therapy against Pseudomonas aeruginosa infections in a cystic fibrosis zebrafish model. Sci Rep 2019; 9:1527. [PMID: 30728389 PMCID: PMC6365511 DOI: 10.1038/s41598-018-37636-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) is a hereditary disease due to mutations in the CFTR gene and causes mortality in humans mainly due to respiratory infections caused by Pseudomonas aeruginosa. In a previous work we used phage therapy, which is a treatment with a mix of phages, to actively counteract acute P. aeruginosa infections in mice and Galleria mellonella larvae. In this work we apply phage therapy to the treatment of P. aeruginosa PAO1 infections in a CF zebrafish model. The structure of the CFTR channel is evolutionary conserved between fish and mammals and cftr-loss-of-function zebrafish embryos show a phenotype that recapitulates the human disease, in particular with destruction of the pancreas. We show that phage therapy is able to decrease lethality, bacterial burden, and the pro-inflammatory response caused by PAO1 infection. In addition, phage administration relieves the constitutive inflammatory state of CF embryos. To our knowledge, this is the first time that phage therapy is used to cure P. aeruginosa infections in a CF animal model. We also find that the curative effect against PAO1 infections is improved by combining phages and antibiotic treatments, opening a useful therapeutic approach that could reduce antibiotic doses and time of administration.
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Affiliation(s)
- Marco Cafora
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano - LITA, via Fratelli Cervi 93, 20090, Segrate, MI, Italy
| | - Gianluca Deflorian
- Istituto FIRC di Oncologia Molecolare - IFOM, Via Adamello 16, 20139, Milano, Italy
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Laura Ferrari
- Istituto FIRC di Oncologia Molecolare - IFOM, Via Adamello 16, 20139, Milano, Italy
| | - Giorgio Binelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Via J.H. Dunant 3, Varese, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Daniela Ghisotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano - LITA, via Fratelli Cervi 93, 20090, Segrate, MI, Italy.
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110
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Bushell FML, Tonner PD, Jabbari S, Schmid AK, Lund PA. Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth. Front Microbiol 2019; 9:3196. [PMID: 30671033 PMCID: PMC6331447 DOI: 10.3389/fmicb.2018.03196] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/10/2018] [Indexed: 01/05/2023] Open
Abstract
Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These acids have long been used as bacteriostatic compounds in the food industry, and in some cases are already being used in the clinic. The effects of different organic acids vary with pH, concentration, and the specific organic acid used, but no studies to date on any opportunistic pathogens have examined the detailed interactions between these key variables in a controlled and systematic way. We have therefore comprehensively evaluated the effects of several different weak organic acids on growth of the opportunistic pathogen Pseudomonas aeruginosa. We used a semi-automated plate reader to generate growth profiles for two different strains (model laboratory strain PAO1 and clinical isolate PA1054 from a hospital burns unit) in a range of organic acids at different concentrations and pH, with a high level of replication for a total of 162,960 data points. We then compared two different modeling approaches for the interpretation of this time-resolved dataset: parametric logistic regression (with or without a component to include lag phase) vs. non-parametric Gaussian process (GP) regression. Because GP makes no prior assumptions about the nature of the growth, this method proved to be superior in cases where growth did not follow a standard sigmoid functional form, as is common when bacteria grow under stress. Acetic, propionic and butyric acids were all more detrimental to growth than the other acids tested, and although PA1054 grew better than PAO1 under non-stress conditions, this difference largely disappeared as the levels of stress increased. As expected from knowledge of how organic acids behave, their effect was significantly enhanced in combination with low pH, with this interaction being greatest in the case of propionic acid. Our approach lends itself to the characterization of combinatorial interactions between stressors, especially in cases where their impacts on growth render logistic growth models unsuitable.
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Affiliation(s)
- Francesca M. L. Bushell
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Peter D. Tonner
- Department of Biology, Duke University, Durham, NC, United States
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - Sara Jabbari
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, NC, United States
- Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Peter A. Lund
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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111
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Ackermann M, Kempf H, Hetzel M, Hesse C, Hashtchin AR, Brinkert K, Schott JW, Haake K, Kühnel MP, Glage S, Figueiredo C, Jonigk D, Sewald K, Schambach A, Wronski S, Moritz T, Martin U, Zweigerdt R, Munder A, Lachmann N. Bioreactor-based mass production of human iPSC-derived macrophages enables immunotherapies against bacterial airway infections. Nat Commun 2018; 9:5088. [PMID: 30504915 PMCID: PMC6269475 DOI: 10.1038/s41467-018-07570-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/08/2018] [Indexed: 11/18/2022] Open
Abstract
The increasing number of severe infections with multi-drug-resistant pathogens worldwide highlights the need for alternative treatment options. Given the pivotal role of phagocytes and especially alveolar macrophages in pulmonary immunity, we introduce a new, cell-based treatment strategy to target bacterial airway infections. Here we show that the mass production of therapeutic phagocytes from induced pluripotent stem cells (iPSC) in industry-compatible, stirred-tank bioreactors is feasible. Bioreactor-derived iPSC-macrophages (iPSC-Mac) represent a highly pure population of CD45+CD11b+CD14+CD163+ cells, and share important phenotypic, functional and transcriptional hallmarks with professional phagocytes, however with a distinct transcriptome signature similar to primitive macrophages. Most importantly, bioreactor-derived iPSC-Mac rescue mice from Pseudomonas aeruginosa-mediated acute infections of the lower respiratory tract within 4-8 h post intra-pulmonary transplantation and reduce bacterial load. Generation of specific immune-cells from iPSC-sources in scalable stirred-tank bioreactors can extend the field of immunotherapy towards bacterial infections, and may allow for further innovative cell-based treatment strategies. Pulmonary infections constitute a substantial health problem worldwide. Here the authors show that phagocytes similar to primitive macrophages can be generated from human induced pluripotent stem cells, by the use of industry-compatible, stirred-tank bioreactors, and applied as a cell-based therapy to treat acute bacterial infections in mice.
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Affiliation(s)
- Mania Ackermann
- JRG Translational Hematology of Congenital Diseases, Hannover Medical School, Hannover, Germany.,Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany
| | - Henning Kempf
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.,Department of Stem Cell Biology, Novo Nordisk A/S, 2760, Maaloev, Denmark
| | - Miriam Hetzel
- Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.,RG Reprogramming and Gene Therapy, Hannover Medical School, 30625, Hannover, Germany
| | - Christina Hesse
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), REBIRTH Cluster-of Excellence, 30625, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany
| | - Anna Rafiei Hashtchin
- JRG Translational Hematology of Congenital Diseases, Hannover Medical School, Hannover, Germany.,Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany
| | - Kerstin Brinkert
- Clinical Research Group 'Cystic Fibrosis', Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Juliane Wilhelmine Schott
- Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany
| | - Kathrin Haake
- JRG Translational Hematology of Congenital Diseases, Hannover Medical School, Hannover, Germany.,Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany
| | - Mark Philipp Kühnel
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany.,Institute for Pathology, Hannover Medical School, 30625, Hannover, Germany
| | - Silke Glage
- Institute of Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Constanca Figueiredo
- Institute for Transfusion Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Danny Jonigk
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany.,Institute for Pathology, Hannover Medical School, 30625, Hannover, Germany
| | - Katherina Sewald
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), REBIRTH Cluster-of Excellence, 30625, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02215, USA
| | - Sabine Wronski
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), REBIRTH Cluster-of Excellence, 30625, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany
| | - Thomas Moritz
- Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.,RG Reprogramming and Gene Therapy, Hannover Medical School, 30625, Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany
| | - Antje Munder
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625, Hannover, Germany.,Clinical Research Group 'Cystic Fibrosis', Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Nico Lachmann
- JRG Translational Hematology of Congenital Diseases, Hannover Medical School, Hannover, Germany. .,Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, 30625, Hannover, Germany.
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112
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Raneri M, Pinatel E, Peano C, Rampioni G, Leoni L, Bianconi I, Jousson O, Dalmasio C, Ferrante P, Briani F. Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models. Sci Rep 2018; 8:16912. [PMID: 30442901 PMCID: PMC6237876 DOI: 10.1038/s41598-018-35087-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas spp. are endowed with a complex pathway for glucose uptake that relies on multiple transporters. In this work we report the construction and characterization of Pseudomonas aeruginosa single and multiple mutants with unmarked deletions of genes encoding outer membrane (OM) and inner membrane (IM) proteins involved in glucose uptake. We found that a triple ΔgltKGF ΔgntP ΔkguT mutant lacking all known IM transporters (named GUN for Glucose Uptake Null) is unable to grow on glucose as unique carbon source. More than 500 genes controlling both metabolic functions and virulence traits show differential expression in GUN relative to the parental strain. Consistent with transcriptomic data, the GUN mutant displays a pleiotropic phenotype. Notably, the genome-wide transcriptional profile and most phenotypic traits differ between the GUN mutant and the wild type strain irrespective of the presence of glucose, suggesting that the investigated genes may have additional roles besides glucose transport. Finally, mutants carrying single or multiple deletions in the glucose uptake genes showed attenuated virulence relative to the wild type strain in Galleria mellonella, but not in Caenorhabditis elegans infection model, supporting the notion that metabolic functions may deeply impact P. aeruginosa adaptation to specific environments found inside the host.
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Affiliation(s)
- Matteo Raneri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Eva Pinatel
- Istituto di Tecnologie Biomediche-CNR, Segrate, Italy
| | - Clelia Peano
- Istituto di Tecnologie Biomediche-CNR, Segrate, Italy
- Istituto Clinico Humanitas-CNR, Rozzano, Italy
| | - Giordano Rampioni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Roma, Italy
| | - Livia Leoni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Roma, Italy
| | - Irene Bianconi
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Chiara Dalmasio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Palma Ferrante
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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113
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Nishikawa M, Shen L, Ogawa K. Taurine dioxygenase (tauD)-independent taurine assimilation in Escherichia coli. Microbiology (Reading) 2018; 164:1446-1456. [DOI: 10.1099/mic.0.000723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Masanobu Nishikawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
| | - Lianhua Shen
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
| | - Ken’ichi Ogawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
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114
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Naorem SS, Han J, Zhang SY, Zhang J, Graham LB, Song A, Smith CV, Rashid F, Guo H. Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid. BMC Microbiol 2018; 18:158. [PMID: 30355324 PMCID: PMC6201506 DOI: 10.1186/s12866-018-1319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species. Results We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~ 108, which is ~ 2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported. Conclusion We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research. Electronic supplementary material The online version of this article (10.1186/s12866-018-1319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Stephanie Y Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Junyi Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Lindsey B Graham
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Angelou Song
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Cameron V Smith
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Fariha Rashid
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.
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115
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Abstract
Coordination between chromosome replication and segregation is essential for equal partitioning of genetic material between daughter cells. In bacteria, this is achieved through the proximity of the origin of replication, oriC, and the chromosome partitioning site, parS We report here that in Pseudomonas aeruginosa, segregation but not replication is also controlled at the terminus region of the chromosome. Using the fluorescent repressor operator system (FROS), we investigated chromosome segregation in P. aeruginosa strain PAO1-UW, wherein the chromosome dimer resolution site, dif, is asymmetrically positioned relative to oriC In these cells, segregation proceeded sequentially along the two chromosomal arms and terminated at dif In contrast, chromosome replication terminated elsewhere, opposite from oriC We further found two large domains on the longer arm of the chromosome, wherein DNA segregated simultaneously. Notably, GC-skew, which reflects a bias in nucleotide usage between the leading and lagging strands of the chromosome, switches polarity at the dif locus but not necessarily at the terminus of replication. These data demonstrate that termination of chromosome replication and segregation can be physically separated without adverse effects on bacterial fitness. They also reveal the critical role of the dif region in defining the global layout of the chromosome and the progression of chromosome segregation and suggest that chromosome packing adapts to its subcellular layout.IMPORTANCE Segregation of genetic information is a central event in cellular life. In bacteria, chromosome segregation occurs concurrently with replication, sequentially along the two arms from oriC to dif How the two processes are coordinated is unknown. We explored here chromosome segregation in an opportunistic human pathogen, Pseudomonas aeruginosa, using its strain with markedly unequal chromosomal arms. We found that replication and segregation diverge in this strain and terminate at very different locations, whereas the longer chromosomal arm folds into large domains to align itself with the shorter arm. The significance of this research is in establishing that segregation and replication of bacterial chromosomes are largely uncoupled from each other and that the large-scale structure of the chromosome adapts to its subcellular layout.
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116
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Enhancing extracellular electron transfer between Pseudomonas aeruginosa PAO1 and light driven semiconducting birnessite. Bioelectrochemistry 2018; 123:233-240. [DOI: 10.1016/j.bioelechem.2018.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/24/2018] [Accepted: 06/01/2018] [Indexed: 11/24/2022]
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117
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Parkins MD, Somayaji R, Waters VJ. Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:e00019-18. [PMID: 30158299 PMCID: PMC6148191 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Affiliation(s)
- Michael D Parkins
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ranjani Somayaji
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Valerie J Waters
- Translational Medicine, Research Institute, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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118
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Nilsson I, Prathapam R, Grove K, Lapointe G, Six DA. The sialic acid transporter NanT is necessary and sufficient for uptake of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) and its azido analog in Escherichia coli. Mol Microbiol 2018; 110:204-218. [PMID: 30076772 DOI: 10.1111/mmi.14098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2018] [Indexed: 01/31/2023]
Abstract
3-Deoxy-d-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPS) in the Gram-negative bacterial outer membrane. Metabolic labeling of Escherichia coli LPS with 8-azido-3,8-dideoxy-d-manno-oct-2-ulosonic acid (Kdo-N3 ) has been reported but is inefficient. For optimization, it is important to understand how exogenous Kdo-N3 enters the cytoplasm. Based on similarities between Kdo and sialic acids, we proposed and verified that the sialic acid transporter NanT imports exogenous Kdo-N3 into E. coli. We demonstrated that E. coli ΔnanT were not labeled with Kdo-N3 , while expression of NanT in the ΔnanT mutant restored Kdo-N3 incorporation. Induced NanT expression in a strain lacking Kdo biosynthesis led to higher exogenous Kdo incorporation and restoration of full-length core-LPS, suggesting that NanT also transports Kdo. While Kdo-N3 incorporation was observed in strains having NanT, it was not detected in Pseudomonas aeruginosa and Acinetobacter baumannii, which lack nanT. However, heterologous expression of E. coli NanT in P. aeruginosa enabled Kdo-N3 incorporation and labeling, though this led to abnormal morphology and growth arrest. NanT seems to define which bacteria can be labeled with Kdo-N3 , provides opportunities to enhance Kdo-N3 labeling efficiency and spectrum, and raises the possibility of Kdo biosynthetic bypass where exogenous Kdo is present, perhaps even in vivo.
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Affiliation(s)
- Inga Nilsson
- Department of Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, 94608, USA
| | - Ramadevi Prathapam
- Department of Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, 94608, USA
| | - Kerri Grove
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, 94608, USA
| | - Guillaume Lapointe
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, 94608, USA
| | - David A Six
- Department of Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, 94608, USA
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119
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Kalesinskas L, Cudone E, Fofanov Y, Putonti C. S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences. Evol Bioinform Online 2018; 14:1176934318797354. [PMID: 30245567 PMCID: PMC6144591 DOI: 10.1177/1176934318797354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022] Open
Abstract
With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool proved valuable in identifying genome rearrangements as well as exogenous sequences acquired via LGT in several bacterial species. Herein, we present the next generation of this tool, S-plot2. Similar to its predecessor, S-plot2 creates an interactive, 2-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). This new version, however, includes additional metrics for analysis, new reporting options, and integrated BLAST query functionality for the user to interrogate regions of interest. Furthermore, S-plot2 can evaluate larger sequences, including whole eukaryotic chromosomes. To illustrate some of the applications of the tool, 2 case studies are presented. The first examines strain-specific variation across the Pseudomonas aeruginosa genome and strain-specific LGT events. In the second case study, corresponding human, chimpanzee, and rhesus macaque autosomes were studied and lineage specific contributions to divergence were estimated. S-plot2 provides a means to both visually and quantitatively compare nucleotide sequences, from microbial genomes to eukaryotic chromosomes. The case studies presented illustrate just 2 potential applications of the tool, highlighting its capability to identify and investigate the variation in molecular divergence rates across sequences. S-plot2 is freely available through https://bitbucket.org/lkalesinskas/splot and is supported on the Linux and MS Windows operating systems.
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Affiliation(s)
- Laurynas Kalesinskas
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Evan Cudone
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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120
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Romero M, Silistre H, Lovelock L, Wright VJ, Chan KG, Hong KW, Williams P, Cámara M, Heeb S. Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN. Nucleic Acids Res 2018; 46:6823-6840. [PMID: 29718466 PMCID: PMC6061880 DOI: 10.1093/nar/gky324] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/10/2018] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In Pseudomonas aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues.
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Affiliation(s)
- Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Hazel Silistre
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Lovelock
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Victoria J Wright
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University,Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stephan Heeb
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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121
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Drenkard E, Hibbler RM, Gutu DA, Eaton AD, Silverio AL, Ausubel FM, Hurley BP, Yonker LM. Replication of the Ordered, Nonredundant Library of Pseudomonas aeruginosa strain PA14 Transposon Insertion Mutants. J Vis Exp 2018. [PMID: 29781996 DOI: 10.3791/57298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Pseudomonas aeruginosa is a phenotypically and genotypically diverse and adaptable Gram-negative bacterium ubiquitous in human environments. P. aeruginosa is able to form biofilms, develop antibiotic resistance, produce virulence factors, and rapidly evolve in the course of a chronic infection. Thus P. aeruginosa can cause both acute and chronic, difficult to treat infections, resulting in significant morbidity in certain patient populations. P. aeruginosa strain PA14 is a human clinical isolate with a conserved genome structure that infects a variety of mammalian and nonvertebrate hosts making PA14 an attractive strain for studying this pathogen. In 2006, a nonredundant transposon insertion mutant library containing 5,459 mutants corresponding to 4,596 predicted PA14 genes was generated. Since then, distribution of the PA14 library has allowed the research community to better understand the function of individual genes and complex pathways of P. aeruginosa. Maintenance of library integrity through the replication process requires proper handling and precise techniques. To that end, this manuscript presents protocols that describe in detail the steps involved in library replication, library quality control and proper storage of individual mutants.
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Affiliation(s)
- Eliana Drenkard
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital
| | - Rhianna M Hibbler
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital
| | - D Alina Gutu
- Department of Molecular Biology, Massachusetts General Hospital
| | - Alexander D Eaton
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital
| | - Amy L Silverio
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital
| | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital; Department of Genetics, Harvard Medical School
| | - Bryan P Hurley
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital; Department of Pediatrics, Harvard Medical School
| | - Lael M Yonker
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital; Department of Pediatrics, Harvard Medical School;
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122
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Gill EE, Chan LS, Winsor GL, Dobson N, Lo R, Ho Sui SJ, Dhillon BK, Taylor PK, Shrestha R, Spencer C, Hancock REW, Unrau PJ, Brinkman FSL. High-throughput detection of RNA processing in bacteria. BMC Genomics 2018; 19:223. [PMID: 29587634 PMCID: PMC5870498 DOI: 10.1186/s12864-018-4538-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/12/2018] [Indexed: 01/19/2023] Open
Abstract
Background Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5′-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions. Results The pRNA-Seq library revealed known tRNA, rRNA and transfer-messenger RNA (tmRNA) processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5′ ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to an E. coli RNase E site previously established in vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and were centered on single palindromic TAT(A/T)ATA motifs (likely − 10 promoter elements), suggesting that, consistent with previous in vitro experimentation, these sites can initiate transcription bi-directionally and may thus provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions. Conclusions This study uses pRNA-Seq, a method that provides a genome-wide survey of RNA processing, to study the bacterium Pseudomonas aeruginosa and discover extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation. NOTE: All sequence data has been submitted to the NCBI sequence read archive. Accession numbers are as follows: [NCBI sequence read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse on www.pseudomonas.com. Electronic supplementary material The online version of this article (10.1186/s12864-018-4538-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin E Gill
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Luisa S Chan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Neil Dobson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Raymond Lo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Shannan J Ho Sui
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Bhavjinder K Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Patrick K Taylor
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Raunak Shrestha
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Cory Spencer
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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123
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Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients. mSphere 2018; 3:mSphere00615-17. [PMID: 29564400 PMCID: PMC5853491 DOI: 10.1128/msphere.00615-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/08/2018] [Indexed: 11/22/2022] Open
Abstract
Patients with cystic fibrosis endure “chronic focal infections” with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents—a phenomenon we define as “heterogeneous MICs.” By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair mechanisms, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications. Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P. aeruginosa isolates in comparison to non-CF P. aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P. aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P. aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P. aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P. aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being “locked” inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure “chronic focal infections” with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents—a phenomenon we define as “heterogeneous MICs.” By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.
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Diaz KE, Remold SK, Onyiri O, Bozeman M, Raymond PA, Turner PE. Generalized Growth of Estuarine, Household and Clinical Isolates of Pseudomonas aeruginosa. Front Microbiol 2018; 9:305. [PMID: 29599754 PMCID: PMC5863524 DOI: 10.3389/fmicb.2018.00305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 02/09/2018] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen of particular concern to immune-compromised people, such as cystic fibrosis patients and burn victims. These bacteria grow in built environments including hospitals and households, and in natural environments such as rivers and estuaries. However, there is conflicting evidence whether recent environments like the human lung and open ocean affect P. aeruginosa growth performance in alternate environments. We hypothesized that bacteria recently isolated from dissimilar habitats should grow differently in media containing artificial versus natural resources. To test this idea, we examined growth of P. aeruginosa isolates from three environments (estuary, household, and clinic) in three media types: minimal-glucose lab medium, and media prepared from sugar maple leaves or big bluestem grass. We used automated spectrophotometry to measure high-resolution growth curves for all isolate by media combinations, and studied two fitness parameters: growth rate and maximum population density. Results showed high variability in growth rate among isolates, both overall and in its dependence on assay media, but this variability was not associated with habitat of isolation. In contrast, total growth (change in absorbance over the experiment) differed overall among habitats of isolation, and there were media-specific differences in mean total growth among habitats of isolation, and in among-habitat variability in the media-specific response. This was driven primarily by greater total growth of estuary isolates when compared with those from other habitats of origin, and greater media-specific variability among household isolates than those from other habitats of origin. Taken together, these results suggest that for growth rate P. aeruginosa bacteria appear to be broad generalists without regard to current or recent habitat, whereas for total growth a signature of recent ecological history can be detected.
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Affiliation(s)
- Kelly E Diaz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Susanna K Remold
- Department of Biology, University of Louisville, Louisville, KY, United States
| | - Ogochukwu Onyiri
- Department of Biology, University of Louisville, Louisville, KY, United States
| | - Maura Bozeman
- Yale School of Forestry & Environmental Studies, Yale University, New Haven, CT, United States
| | - Peter A Raymond
- Yale School of Forestry & Environmental Studies, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States.,Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
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125
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Visible Light Enhanced Extracellular Electron Transfer between a Hematite Photoanode and Pseudomonas aeruginosa. MINERALS 2017. [DOI: 10.3390/min7120230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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126
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Latz S, Krüttgen A, Häfner H, Buhl EM, Ritter K, Horz HP. Differential Effect of Newly Isolated Phages Belonging to PB1-Like, phiKZ-Like and LUZ24-Like Viruses against Multi-Drug Resistant Pseudomonas aeruginosa under Varying Growth Conditions. Viruses 2017; 9:v9110315. [PMID: 29077053 PMCID: PMC5707522 DOI: 10.3390/v9110315] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/16/2017] [Accepted: 10/24/2017] [Indexed: 12/19/2022] Open
Abstract
In this study, we characterize three phages (SL1 SL2, and SL4), isolated from hospital sewage with lytic activity against clinical isolates of multi-drug resistant Pseudomonas aeruginosa (MDR-PA). The host spectrum ranged from 41% to 54%, with all three phages together covering 79% of all tested clinical isolates. Genome analysis revealed that SL1 (65,849 bp, 91 open reading frames ORFs) belongs to PB1-like viruses, SL2 (279,696 bp, 354 ORFs) to phiKZ-like viruses and SL4 (44,194 bp, 65 ORFs) to LUZ24-like viruses. Planktonic cells of four of five selected MDR-PA strains were suppressed by at least one phage with multiplicities of infection (MOIs) ranging from 1 to 10−6 for 16 h without apparent regrowth of bacterial populations. While SL2 was most potent in suppressing planktonic cultures the strongest anti-biofilm activity was observed with SL4. Phages were able to rescue bacteria-infected wax moth larvae (Galleria melonella) for 24 h, whereby highest survival rates (90%) were observed with SL1. Except for the biofilm experiments, the effect of a cocktail with all three phages was comparable to the action of the best phage alone; hence, there are no synergistic but also no antagonistic effects among phages. The use of a cocktail with these phages is therefore expedient for increasing host range and minimizing the development of phage resistance.
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Affiliation(s)
- Simone Latz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
| | - Alex Krüttgen
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
| | - Helga Häfner
- Department of Infection Control and Infectious Diseases, RWTH Aachen University Hospital, 52074 Aachen, Germany.
| | - Eva Miriam Buhl
- Electron Microscopy Facility, RWTH Aachen University Hospital, 52074 Aachen, Germany.
| | - Klaus Ritter
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
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Abstract
Chemoreceptors in bacteria detect a variety of signals and feed this information into chemosensory pathways that represent a major mode of signal transduction. The five chemoreceptors from Escherichia coli have served as traditional models in the study of this protein family. Genome analyses revealed that many bacteria contain much larger numbers of chemoreceptors with broader sensory capabilities. Chemoreceptors differ in topology, sensing mode, cellular location, and, above all, the type of ligand binding domain (LBD). Here, we highlight LBD diversity using well-established and emerging model organisms as well as genomic surveys. Nearly a hundred different types of protein domains that are found in chemoreceptor sequences are known or predicted LBDs, but only a few of them are ubiquitous. LBDs of the same class recognize different ligands, and conversely, the same ligand can be recognized by structurally different LBDs; however, recent studies began to reveal common characteristics in signal-LBD relationships. Although signals can stimulate chemoreceptors in a variety of different ways, diverse LBDs appear to employ a universal transmembrane signaling mechanism. Current and future studies aim to establish relationships between LBD types, the nature of signals that they recognize, and the mechanisms of signal recognition and transduction.
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128
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Crespo A, Gavaldà J, Julián E, Torrents E. A single point mutation in class III ribonucleotide reductase promoter renders Pseudomonas aeruginosa PAO1 inefficient for anaerobic growth and infection. Sci Rep 2017; 7:13350. [PMID: 29042684 PMCID: PMC5645315 DOI: 10.1038/s41598-017-14051-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022] Open
Abstract
Pseudomonas aeruginosa strain PAO1 has become the reference strain in many laboratories. One enzyme that is essential for its cell division is the ribonucleotide reductase (RNR) enzyme that supplies the deoxynucleotides required for DNA synthesis and repair. P. aeruginosa is one of the few microorganisms that encodes three different RNR classes (Ia, II and III) in its genome, enabling it to grow and adapt to diverse environmental conditions, including during infection. In this work, we demonstrate that a lack of RNR activity induces cell elongation in P. aeruginosa PAO1. Moreover, RNR gene expression during anaerobiosis differs among P. aeruginosa strains, with class III highly expressed in P. aeruginosa clinical isolates relative to the laboratory P. aeruginosa PAO1 strain. A single point mutation was identified in the P. aeruginosa PAO1 strain class III RNR promoter region that disrupts its anaerobic transcription by the Dnr regulator. An engineered strain that induces the class III RNR expression allows P. aeruginosa PAO1 anaerobic growth and increases its virulence to resemble that of clinical strains. Our results demonstrate that P. aeruginosa PAO1 is adapted to laboratory conditions and is not the best reference strain for anaerobic or infection studies.
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Affiliation(s)
- Anna Crespo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology. Bacterial infections and antimicrobial therapies; Baldiri Reixac 15-21, 08028, Barcelona, Spain
| | - Joan Gavaldà
- Infectious Diseases Research Laboratory, Infectious Diseases Department, Vall d'Hebron Research Institute VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Esther Julián
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Eduard Torrents
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology. Bacterial infections and antimicrobial therapies; Baldiri Reixac 15-21, 08028, Barcelona, Spain.
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17β-Estradiol Dysregulates Innate Immune Responses to Pseudomonas aeruginosa Respiratory Infection and Is Modulated by Estrogen Receptor Antagonism. Infect Immun 2017; 85:IAI.00422-17. [PMID: 28784925 DOI: 10.1128/iai.00422-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/11/2017] [Indexed: 01/22/2023] Open
Abstract
Females have a more severe clinical course than males in terms of several inflammatory lung conditions. Notably, females with cystic fibrosis (CF) suffer worse outcomes, particularly in the setting of Pseudomonas aeruginosa infection. Sex hormones have been implicated in experimental and clinical studies; however, immune mechanisms responsible for this sex-based disparity are unknown and the specific sex hormone target for therapeutic manipulation has not been identified. The objective of this study was to assess mechanisms behind the impact of female sex hormones on host immune responses to P. aeruginosa We used wild-type and CF mice, which we hormone manipulated, inoculated with P. aeruginosa, and then examined for outcomes and inflammatory responses. Neutrophils isolated from mice and human subjects were tested for responses to P. aeruginosa We found that female mice inoculated with P. aeruginosa died earlier and showed slower bacterial clearance than males (P < 0.0001). Ovariectomized females supplemented with 17β-estradiol succumbed to P. aeruginosa challenge earlier than progesterone- or vehicle-supplemented mice (P = 0.0003). 17β-Estradiol-treated ovariectomized female mice demonstrated increased lung levels of inflammatory cytokines, and when rendered neutropenic the mortality difference was abrogated. Neutrophils treated with 17β-estradiol demonstrated an enhanced oxidative burst but decreased P. aeruginosa killing and earlier cell necrosis. The estrogen receptor (ER) antagonist ICI 182,780 improved survival in female mice infected with P. aeruginosa and restored neutrophil function. We concluded that ER antagonism rescues estrogen-mediated neutrophil dysfunction and improves survival in response to P. aeruginosa ER-mediated processes may explain the sex-based mortality gap in CF and other inflammatory lung illnesses, and the ER blockade represents a rational therapeutic strategy.
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Rampioni G, Pillai CR, Longo F, Bondì R, Baldelli V, Messina M, Imperi F, Visca P, Leoni L. Effect of efflux pump inhibition on Pseudomonas aeruginosa transcriptome and virulence. Sci Rep 2017; 7:11392. [PMID: 28900249 PMCID: PMC5596013 DOI: 10.1038/s41598-017-11892-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Efflux pumps of the resistance-nodulation-cell-division (RND) family increase antibiotic resistance in many bacterial pathogens, representing candidate targets for the development of antibiotic adjuvants. RND pumps have also been proposed to contribute to bacterial infection, implying that efflux pump inhibitors (EPIs) could also act as anti-virulence drugs. Nevertheless, EPIs are usually investigated only for their properties as antibiotic adjuvants, while their potential anti-virulence activity is seldom taken into account. In this study it is shown that RND efflux pumps contribute to Pseudomonas aeruginosa PAO1 pathogenicity in an insect model of infection, and that the well-characterized EPI Phe-Arg-β-naphthylamide (PAβN) is able to reduce in vivo virulence of the P. aeruginosa PAO1 laboratory strain, as well as of clinical isolates. The production of quorum sensing (QS) molecules and of QS-dependent virulence phenotypes is differentially affected by PAβN, depending on the strain. Transcriptomic and phenotypic analyses showed that the protection exerted by PAβN from P. aeruginosa PAO1 infection in vivo correlates with the down-regulation of key virulence genes (e.g. genes involved in iron and phosphate starvation). Since PAβN impacts P. aeruginosa virulence, anti-virulence properties of EPIs are worthy to be explored, taking into account possible strain-specificity of their activity.
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Affiliation(s)
| | - Cejoice Ramachandran Pillai
- Department of Science, University Roma Tre, Rome, Italy
- Inter University Centre for Bioscience, Kannur University, Palayad, Kerala, India
| | | | - Roslen Bondì
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Marco Messina
- Department of Science, University Roma Tre, Rome, Italy
| | - Francesco Imperi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy.
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Pseudomonas Endocarditis with an unstable phenotype: the challenges of isolate characterization and Carbapenem stewardship with a partial review of the literature. Antimicrob Resist Infect Control 2017; 6:87. [PMID: 28855980 PMCID: PMC5574246 DOI: 10.1186/s13756-017-0245-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/20/2017] [Indexed: 01/11/2023] Open
Abstract
Background Pseudomonas endocarditis is exceedingly rare, especially in patients without predisposing risks. We present such a case that included unexpected switches in antibacterial resistance profiles in two Pseudomonas aeruginosa (PA) strains with the same whole-genome sequence. The case also involved diagnostic and treatment challenges, such as issues with automated testing platforms, choosing the optimal aminoglycoside, minimizing unnecessary carbapenem exposure, and the need for faster, more informative laboratory tests. Case presentation On hospital day one (HD-1) a cefepime and piperacillin-tazobactam (FEP-TZP)-susceptible P. aeruginosa was isolated from the bloodstream of a 62-year-old man admitted for evaluation of possible endocarditis and treated with gentamicin and cefepime. On HD-2, his antibiotic regimen was changed to tobramycin and cefepime. On HD-11, he underwent aortic valve replacement, and P. aeruginosa was isolated from the explanted valve. Unexpectedly, it was FEP-TZP-resistant, so cefepime was switched to meropenem. On HD-14, in preparation for whole-genome sequencing (WGS), valve and blood isolates were removed from cryo-storage, re-cultured, and simultaneously tested with the same platforms, reagents, and inoculations previously used. Curiously, the valve isolate was now FEP-TZP-susceptible. WGS revealed that both isolates were phylogenetically identical, differing by a single nucleotide in a chemotaxis-encoding gene. They also contained the same resistance genes (blaADC35, aph(3′)-II, blaOXA-50, catB7, fosA). Conclusion Repeated testing on alternate platforms and WGS did not definitively determine the resistance mechanism(s), which in this case, is most likely unstable de-repression of a chromosomal AmpC β-lactamase, porin alterations, or efflux upregulation, with reversion to baseline (non-efflux) transcription. Although sub-culture on specialized media to select for less fit (more resistant) colonies, followed by transcriptome analysis, and multiple sequence alignment, might have revealed the mechanism and better informed the optimal choice of β-lactam, such approaches are neither rapid, nor feasible for hospital laboratories. In this era of escalating drug resistance and dwindling antibiotics, use of the most potent anti-pseudomonals must be balanced with stewardship. Clinicians need access to validated genomic correlates of resistance, and faster, more informative diagnostics. Therefore, we placed these isolates and their sequences in the public domain for inclusion in the Pseudomonas pan-genome and database projects for further countermeasure development.
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Sommerfeld Ross S, Gharse S, Sanchez L, Fiegel J. Dry powder aerosols to co-deliver antibiotics and nutrient dispersion compounds for enhanced bacterial biofilm eradication. Int J Pharm 2017; 531:14-23. [PMID: 28826725 DOI: 10.1016/j.ijpharm.2017.08.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/20/2017] [Accepted: 08/02/2017] [Indexed: 02/01/2023]
Abstract
The purpose of this study was to formulate a dry powder for inhalation containing a combination treatment for eradication of Pseudomonas aeruginosa bacterial biofilms. Dry powders containing an antibiotic (ciprofloxacin hydrochloride, CH) and nutrient dispersion compound (glutamic acid, GA) at a ratio determined to eliminate the biofilms were generated by spray drying. Leucine was added to the spray dried formulation to aid powder flowability. A central composite design of experiments was performed to determine the effects of solution and processing parameters on powder yield and aerodynamic properties. Combinations of CH and GA eradicated bacterial biofilms at lower antibiotic concentrations compared to CH alone. Spray dried powders were produced with yields up to 43% and mass mean aerodynamic diameters (MMAD) in the respirable range. Powder yield was primarily affected by variables that determine cyclone efficiency, i.e. atomizer and solution flow rates and solution concentration; while MMAD was mainly determined by solution concentration. Fine particle fractions (FPF)<4.46μm and <2.82μm of the powders ranged from 56 to 70% and 35 to 46%, respectively. This study demonstrates that dry powder aerosols containing high concentrations of a combination treatment effective against P. aeruginosa biofilms could be developed with high yield, aerodynamic properties appropriate for inhalation, and no loss of potency.
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Affiliation(s)
- S Sommerfeld Ross
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA, 52242, USA
| | - S Gharse
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA, 52242, USA
| | - L Sanchez
- Department of Chemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - J Fiegel
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA, 52242, USA; Department of Chemical and Biochemical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
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Pires DP, Dötsch A, Anderson EM, Hao Y, Khursigara CM, Lam JS, Sillankorva S, Azeredo J. A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors. Front Microbiol 2017; 8:1229. [PMID: 28713356 PMCID: PMC5492357 DOI: 10.3389/fmicb.2017.01229] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/16/2017] [Indexed: 12/19/2022] Open
Abstract
Antibiotic resistance constitutes one of the most serious threats to the global public health and urgently requires new and effective solutions. Bacteriophages are bacterial viruses increasingly recognized as being good alternatives to traditional antibiotic therapies. In this study, the efficacy of phages, targeting different cell receptors, against Pseudomonas aeruginosa PAO1 biofilm and planktonic cell cultures was evaluated over the course of 48 h. Although significant reductions in the number of viable cells were achieved for both cases, the high level of adaptability of the bacteria in response to the selective pressure caused by phage treatment resulted in the emergence of phage-resistant variants. To further investigate the genetic makeup of phage-resistant variants isolated from biofilm infection experiments, some of these bacteria were selected for phenotypic and genotypic characterization. Whole genome sequencing was performed on five phage-resistant variants and all of them carried mutations affecting the galU gene as well as one of pil genes. The sequencing analysis further revealed that three of the P. aeruginosa PAO1 variants carry large deletions (>200 kbp) in their genomes. Complementation of the galU mutants with wild-type galU in trans restored LPS expression on the bacterial cell surface of these bacterial strains and rendered the complemented strains to be sensitive to phages. This provides unequivocal evidence that inactivation of galU function was associated with resistance to the phages that uses LPS as primary receptors. Overall, this work demonstrates that P. aeruginosa biofilms can survive phage attack and develop phage-resistant variants exhibiting defective LPS production and loss of type IV pili that are well adapted to the biofilm mode of growth.
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Affiliation(s)
- Diana P. Pires
- CEB-Centre of Biological Engineering, Universidade do MinhoBraga, Portugal
| | - Andreas Dötsch
- Institute of Functional Interfaces, Karlsruhe Institute of TechnologyEggenstein-Leopoldshafen, Germany
| | - Erin M. Anderson
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, GuelphON, Canada
| | - Youai Hao
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, GuelphON, Canada
| | - Cezar M. Khursigara
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, GuelphON, Canada
| | - Joseph S. Lam
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, GuelphON, Canada
| | - Sanna Sillankorva
- CEB-Centre of Biological Engineering, Universidade do MinhoBraga, Portugal
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, Universidade do MinhoBraga, Portugal
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Sidorenko J, Jatsenko T, Kivisaar M. Ongoing evolution of Pseudomonas aeruginosa PAO1 sublines complicates studies of DNA damage repair and tolerance. Mutat Res 2017; 797-799:26-37. [PMID: 28340408 DOI: 10.1016/j.mrfmmm.2017.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/23/2016] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P. aeruginosa. We found that PAO1 subline PAO1-UT carries a large deletion encompassing the DNA damage inducible imuA-imuB-imuC cassette (PA0669-PA0671), which is implied in mutagenesis in several species. Furthermore, the genetic changes leading to variation in the functionality of the MexEF-OprN efflux system contributed largely to the phenotypic discordance between P. aeruginosa PAO1 sublines. Specifically, we identified multiple mutations in the mexT gene, which encodes a transcriptional regulator of the mexEF-oprN genes, mutations in the mexF, and complete absence of these genes. Of the four tested sublines, MPAO1 was the only subline with the functional MexEF-OprN multidrug efflux system. Active efflux through MexEF-OprN rendered MPAO1 highly resistant to chloramphenicol and ciprofloxacin. Moreover, the functions of specialized DNA polymerase IV and nucleotide excision repair (NER) in 4-NQO-induced DNA damage tolerance appeared to be masked in MPAO1, while were easily detectable in other sublines. Finally, the frequencies of spontaneous and MMS-induced Rifr mutations were also significantly lower in MPAO1 in comparison to the PAO1 sublines with impaired MexEF-OprN efflux system. The MexEF-OprN-attributed differences were also observed between MPAO1 and MPAO1-derived transposon mutants from the two-allele transposon mutant collection. Thus, the accumulating mutations and discordant phenotypes of the PAO1 derivatives challenge the reproducibility and comparability of the results obtained with different PAO1 sublines and also limit the usage of the MPAO1 transposon library in DNA damage tolerance and mutagenesis studies.
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Affiliation(s)
- Julia Sidorenko
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia.
| | - Tatjana Jatsenko
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia
| | - Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia.
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135
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Lightly TJ, Phung RR, Sorensen JL, Cardona ST. Synthetic cystic fibrosis sputum medium diminishes Burkholderia cenocepacia antifungal activity against Aspergillus fumigatus independently of phenylacetic acid production. Can J Microbiol 2017; 63:427-438. [PMID: 28178425 DOI: 10.1139/cjm-2016-0705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phenylacetic acid (PAA), an intermediate of phenylalanine degradation, is emerging as a signal molecule in microbial interactions with the host. In this work, we explore the presence of phenylalanine and PAA catabolism in 3 microbial pathogens of the cystic fibrosis (CF) lung microbiome: Pseudomonas aeruginosa, Burkholderia cenocepacia, and Aspergillus fumigatus. While in silico analysis of B. cenocepacia J2315 and A. fumigatus Af293 genome sequences showed complete pathways from phenylalanine to PAA, the P. aeruginosa PAO1 genome lacked several coding genes for phenylalanine and PAA catabolic enzymes. High-performance liquid chromatography analysis of supernatants from B. cenocepacia K56-2 detected PAA when grown in Luria-Bertani medium but not in synthetic cystic fibrosis sputum medium (SCFM). However, we were unable to identify PAA production by A. fumigatus or P. aeruginosa in any of the conditions tested. The inhibitory effect of B. cenocepacia on A. fumigatus growth was evaluated using agar plate interaction assays. Inhibition of fungal growth by B. cenocepacia was lessened in SCFM but this effect was not dependent on bacterial production of PAA. In summary, while we demonstrated PAA production by B. cenocepacia, we were not able to link this metabolite with the B. cenocepacia - A. fumigatus microbial interaction in CF nutritional conditions.
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Affiliation(s)
- Tasia Joy Lightly
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ryan R Phung
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - John L Sorensen
- b Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Silvia T Cardona
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,c Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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136
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Inter-laboratory evolution of a model organism and its epistatic effects on mutagenesis screens. Sci Rep 2016; 6:38001. [PMID: 27905490 PMCID: PMC5131308 DOI: 10.1038/srep38001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/02/2016] [Indexed: 01/12/2023] Open
Abstract
In theory, a few naturally occurring evolutionary changes in the genome of a model organism may have little or no observable impact on its wild type phenotype, and yet still substantially impact the phenotypes of mutant strains through epistasis. To see if this is happening in a model organism, we obtained nine different laboratories' wild type Myxococcus xanthus DK1622 "sublines" and sequenced each to determine if they had evolved after their physical separation. Under a common garden experiment, each subline satisfied the phenotypic prerequisites for wild type, but many differed to a significant degree in each of the four quantitative phenotypic traits we measured, with some sublines differing by several-fold. Genome resequencing identified 29 variants between the nine sublines, and eight had at least one unique variant within an Open Reading Frame (ORF). By disrupting the ORF MXAN7041 in two different sublines, we demonstrated substantial epistasis from these naturally occurring variants. The impact of such inter-laboratory wild type evolution is important to any genotype-to-phenotype study; an organism's phenotype may be sensitive to small changes in genetic background, so that results from phenotypic screens and other related experiments might not agree with prior published results or the results from other laboratories.
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137
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Fischer S, Greipel L, Klockgether J, Dorda M, Wiehlmann L, Cramer N, Tümmler B. Multilocus amplicon sequencing of Pseudomonas aeruginosa cystic fibrosis airways isolates collected prior to and after early antipseudomonal chemotherapy. J Cyst Fibros 2016; 16:346-352. [PMID: 27836448 DOI: 10.1016/j.jcf.2016.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 01/06/2023]
Abstract
BACKGROUND Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa. METHODS During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa - positive after the first round of antipseudomonal chemotherapy. RESULTS Deep sequencing uncovered coexisting alternative nucleotides at in total 33 of 55,284 examined genome positions including six non-synonymous polymorphisms in the lasR gene, a key regulator of quorum sensing. After early treatment 42 of 50 novel nucleotide substitutions had emerged in exopolysaccharide biosynthesis, efflux pump and porin genes. CONCLUSIONS Early treatment selects pathoadaptive mutations in P. aeruginosa that are typical for chronic infections of CF lungs.
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Affiliation(s)
- Sebastian Fischer
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Leonie Greipel
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Nina Cramer
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany.
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138
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Lagage V, Boccard F, Vallet-Gely I. Regional Control of Chromosome Segregation in Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006428. [PMID: 27820816 PMCID: PMC5098823 DOI: 10.1371/journal.pgen.1006428] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/15/2016] [Indexed: 01/31/2023] Open
Abstract
Chromosome segregation in bacteria occurs concomitantly with DNA replication, and the duplicated regions containing the replication origin oriC are generally the first to separate and migrate to their final specific location inside the cell. In numerous bacterial species, a three-component partition machinery called the ParABS system is crucial for chromosome segregation. This is the case in the gammaproteobacterium Pseudomonas aeruginosa, where impairing the ParABS system is very detrimental for growth, as it increases the generation time and leads to the formation of anucleate cells and to oriC mispositioning inside the cell. In this study, we investigate in vivo the ParABS system in P. aeruginosa. Using chromatin immuno-precipitation coupled with high throughput sequencing, we show that ParB binds to four parS site located within 15 kb of oriC in vivo, and that this binding promotes the formation of a high order nucleoprotein complex. We show that one parS site is enough to prevent anucleate cell formation, therefore for correct chromosome segregation. By displacing the parS site from its native position on the chromosome, we demonstrate that parS is the first chromosomal locus to be separated upon DNA replication, which indicates that it is the site of force exertion of the segregation process. We identify a region of approximatively 650 kb surrounding oriC in which the parS site must be positioned for chromosome segregation to proceed correctly, and we called it “competence zone” of the parS site. Mutant strains that have undergone specific genetic rearrangements allow us to propose that the distance between oriC and parS defines this “competence zone”. Implications for the control of chromosome segregation in P. aeruginosa are discussed. Accurate transmission of the genetic information relies on replication and segregation, two processes essential to all living organisms. In bacteria, these processes occur concomitantly. Replication of the bacterial circular chromosome initiates at a single specific sequence called oriC, and proceed bi-directionally along the chromosome arms. A partition system called ParABS is involved in chromosome segregation in many bacteria. It involves the binding of the ParB protein to parS sequences, which are often found in the close vicinity of oriC. The importance of this system for chromosome segregation varies according to species, ranging from essential to dispensable. In Pseudomonas aeruginosa, an important opportunistic pathogen, the ParABS system plays an important role in chromosome segregation, as mutants affected in this system present a severe growth defect as well as anucleate cells formation, but is not essential. In this study, we characterize the activity of the different determinants of the ParABS system in P. aeruginosa and demonstrate that it is critical for the parS site to be located close to oriC, which suggest that the timing of separation of regions close to oriC after replication is important, and that it could be a function of the ParABS system to keep this timing.
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Affiliation(s)
- Valentine Lagage
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
| | - Frédéric Boccard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail: (IVG); (FB)
| | - Isabelle Vallet-Gely
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail: (IVG); (FB)
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139
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Yang Y, Kitajima M, Pham T, Yu L, Ling R, Gin K, Reinhard M. UsingPseudomonas aeruginosaPAO1 to evaluate hydrogen peroxide as a biofouling control agent in membrane treatment systems. Lett Appl Microbiol 2016; 63:488-494. [DOI: 10.1111/lam.12674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Y. Yang
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
| | - M. Kitajima
- Division of Environmental Engineering; Hokkaido University; Sapporo Japan
| | - T.P.T. Pham
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
| | - L. Yu
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
| | - R. Ling
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
- NUS Environmental Research Institute; National University of Singapore; Singapore Singapore
| | - K.Y.H. Gin
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
- NUS Environmental Research Institute; National University of Singapore; Singapore Singapore
| | - M. Reinhard
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore Singapore
- Department of Civil and Environmental Engineering; Stanford University; Stanford CA USA
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140
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Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep 2016; 6:26717. [PMID: 27225966 PMCID: PMC4880932 DOI: 10.1038/srep26717] [Citation(s) in RCA: 398] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/05/2016] [Indexed: 02/08/2023] Open
Abstract
Increasing prevalence and severity of multi-drug-resistant (MDR) bacterial infections has necessitated novel antibacterial strategies. Ideally, new approaches would target bacterial pathogens while exerting selection for reduced pathogenesis when these bacteria inevitably evolve resistance to therapeutic intervention. As an example of such a management strategy, we isolated a lytic bacteriophage, OMKO1, (family Myoviridae) of Pseudomonas aeruginosa that utilizes the outer membrane porin M (OprM) of the multidrug efflux systems MexAB and MexXY as a receptor-binding site. Results show that phage selection produces an evolutionary trade-off in MDR P. aeruginosa, whereby the evolution of bacterial resistance to phage attack changes the efflux pump mechanism, causing increased sensitivity to drugs from several antibiotic classes. Although modern phage therapy is still in its infancy, we conclude that phages, such as OMKO1, represent a new approach to phage therapy where bacteriophages exert selection for MDR bacteria to become increasingly sensitive to traditional antibiotics. This approach, using phages as targeted antibacterials, could extend the lifetime of our current antibiotics and potentially reduce the incidence of antibiotic resistant infections.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Mark Sistrom
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - John E Wertz
- E. coli Genetic Stock Center, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Kaitlyn E Kortright
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deepak Narayan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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141
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GcsR, a TyrR-Like Enhancer-Binding Protein, Regulates Expression of the Glycine Cleavage System in Pseudomonas aeruginosa PAO1. mSphere 2016; 1:mSphere00020-16. [PMID: 27303730 PMCID: PMC4894688 DOI: 10.1128/msphere.00020-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/06/2016] [Indexed: 02/01/2023] Open
Abstract
Glycine is required for various cellular functions, including cell wall synthesis, protein synthesis, and the biosynthesis of several important metabolites. Regulating levels of glycine metabolism allows P. aeruginosa to maintain the metabolic flux of glycine through several pathways, including the metabolism of glycine to produce other amino acids, entry into the trichloroacetic acid cycle, and the production of virulence factors such as hydrogen cyanide. In this study, we characterized GcsR, a transcriptional regulator that activates the expression of genes involved in P. aeruginosa PAO1 glycine metabolism. Our work reveals that GcsR is the founding member of a novel class of TyrR-like EBPs that likely regulate glycine metabolism in Pseudomonadales. Glycine serves as a major source of single carbon units for biochemical reactions within bacterial cells. Utilization of glycine is tightly regulated and revolves around a key group of proteins known as the glycine cleavage system (GCS). Our lab previously identified the transcriptional regulator GcsR (PA2449) as being required for catabolism of glycine in the opportunistic pathogen Pseudomonas aeruginosa PAO1. In an effort to clarify and have an overall better understanding of the role of GcsR in glycine metabolism, a combination of transcriptome sequencing and electrophoretic mobility shift assays was used to identify target genes of this transcriptional regulator. It was found that GcsR binds to an 18-bp consensus sequence (TGTAACG-N4-CGTTCCG) upstream of the gcs2 operon, consisting of the gcvH2, gcvP2, glyA2, sdaA, and gcvT2 genes. The proteins encoded by these genes, namely, the GCS (GcvH2-GcvP2-GcvT2), serine hydroxymethyltransferase (GlyA2), and serine dehydratase (SdaA), form a metabolic pathway for the conversion of glycine into pyruvate, which can enter the central metabolism. GcsR activates transcription of the gcs2 operon in response to glycine. Interestingly, GcsR belongs to a family of transcriptional regulators known as TyrR-like enhancer-binding proteins (EBPs). Until this study, TyrR-like EBPs were only known to function in regulating aromatic amino acid metabolism. GcsR is the founding member of a new class of TyrR-like EBPs that function in the regulation of glycine metabolism. Indeed, homologs of GcsR and its target genes are present in almost all sequenced genomes of the Pseudomonadales order, suggesting that this genetic regulatory mechanism is a common theme for pseudomonads. IMPORTANCE Glycine is required for various cellular functions, including cell wall synthesis, protein synthesis, and the biosynthesis of several important metabolites. Regulating levels of glycine metabolism allows P. aeruginosa to maintain the metabolic flux of glycine through several pathways, including the metabolism of glycine to produce other amino acids, entry into the trichloroacetic acid cycle, and the production of virulence factors such as hydrogen cyanide. In this study, we characterized GcsR, a transcriptional regulator that activates the expression of genes involved in P. aeruginosa PAO1 glycine metabolism. Our work reveals that GcsR is the founding member of a novel class of TyrR-like EBPs that likely regulate glycine metabolism in Pseudomonadales.
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142
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Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus. J Bacteriol 2016; 198:1401-13. [PMID: 26903416 DOI: 10.1128/jb.00055-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Oxidative phosphorylation using multiple-component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacterium Pseudomonas aeruginosa During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO(3-)→ NO(2-)→ NO → N2O → N2 Genetic experiments suggested that the nitric oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy colocalization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous oxide reductase NosZ is linked via NosR. The nitrate transporter NarK2, the nitrate regulatory system NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins NosFL were also found to be attached. A number of proteins associated with energy generation, including electron-donating dehydrogenases, the complete ATP synthase, almost all enzymes of the tricarboxylic acid (TCA) cycle, and the Sec system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane, and periplasmic proteins to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment. IMPORTANCE The processes of cellular energy generation are catalyzed by large multiprotein enzyme complexes. The molecular basis for the interaction of these complexes is poorly understood. We employed membrane interactomics and electron microscopy to determine the protein-protein interactions involved. The well-investigated enzyme complexes of denitrification of the pathogenic bacterium Pseudomonas aeruginosa served as a model. Denitrification is one essential step of the universal N cycle and provides the bacterium with an effective alternative to oxygen respiration. This process allows the bacterium to form biofilms, which create low-oxygen habitats and which are a key in the infection mechanism. Our results provide new insights into the molecular basis of respiration, as well as opening a new window into the infection strategies of this pathogen.
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143
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Latino L, Midoux C, Hauck Y, Vergnaud G, Pourcel C. Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2016; 162:748-763. [PMID: 26921273 DOI: 10.1099/mic.0.000263] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coevolution between bacteriophages (phages) and their prey is the result of mutualistic interactions. Here, we show that pseudolysogeny is a frequent outcome of infection by virulent phages of Pseudomonas aeruginosa and that selection of resistant bacterial mutants is favoured by continuous production of phages. We investigated the frequency and characteristics of P. aeruginosa strain PAO1 variants resisting infection by different combinations of virulent phages belonging to four genera. The frequency of resistant bacteria was 10- 5 for single phage infection and 10- 6 for infections with combinations of two or four phages. The genome of 27 variants was sequenced and the comparison with the genome of the parental PAO1 strain allowed the identification of point mutations or small indels. Four additional variants were characterized by a candidate gene approach. In total, 27 independent mutations were observed affecting 14 genes and a regulatory region. The mutations affected genes involved in biosynthesis of type IV pilus, alginate, LPS and O-antigen. Half of the variants possessed changes in homopolymer tracts responsible for frameshift mutations and these phase variation mutants were shown to be unstable. Eleven double mutants were detected. The presence of free phage DNA was observed in association with exclusion of superinfection in half of the variants and no chromosomal mutation could be found in three of them. Upon further growth of these pseudolysogens, some variants with new chromosomal mutations were recovered, presumably due to continuous evolutionary pressure.
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Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Yolande Hauck
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
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144
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Pabary R, Singh C, Morales S, Bush A, Alshafi K, Bilton D, Alton EWFW, Smithyman A, Davies JC. Antipseudomonal Bacteriophage Reduces Infective Burden and Inflammatory Response in Murine Lung. Antimicrob Agents Chemother 2016; 60:744-51. [PMID: 26574007 PMCID: PMC4750668 DOI: 10.1128/aac.01426-15] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
As antibiotic resistance increases, there is a need for new therapies to treat infection, particularly in cystic fibrosis (CF), where Pseudomonas aeruginosa is a ubiquitous pathogen associated with increased morbidity and mortality. Bacteriophages are an attractive alternative treatment, as they are specific to the target bacteria and have no documented side effects. The efficacy of phage cocktails was established in vitro. Two P. aeruginosa strains were taken forward into an acute murine infection model with bacteriophage administered either prophylactically, simultaneously, or postinfection. The infective burden and inflammation in bronchoalveolar lavage fluid (BALF) were assessed at various times. With low infective doses, both control mice and those undergoing simultaneous phage treatment cleared P. aeruginosa infection at 48 h, but there were fewer neutrophils in BALF of phage-treated mice (median, 73.2 × 10(4)/ml [range, 35.2 to 102.1 × 10(4)/ml] versus 174 × 10(4)/ml [112.1 to 266.8 × 10(4)/ml], P < 0.01 for the clinical strain; median, 122.1 × 10(4)/ml [105.4 to 187.4 × 10(4)/ml] versus 206 × 10(4)/ml [160.1 to 331.6 × 10(4)/ml], P < 0.01 for PAO1). With higher infective doses of PAO1, all phage-treated mice cleared P. aeruginosa infection at 24 h, whereas infection persisted in all control mice (median, 1,305 CFU/ml [range, 190 to 4,700 CFU/ml], P < 0.01). Bacteriophage also reduced CFU/ml in BALF when administered postinfection (24 h) and both CFU/ml and inflammatory cells in BALF when administered prophylactically. A reduction in soluble inflammatory cytokine levels in BALF was also demonstrated under different conditions. Bacteriophages are efficacious in reducing both the bacterial load and inflammation in a murine model of P. aeruginosa lung infection. This study provides proof of concept for future clinical trials in patients with CF.
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Affiliation(s)
- Rishi Pabary
- National Heart and Lung Institute, Imperial College London, London, United Kingdom Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom
| | - Charanjit Singh
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sandra Morales
- Special Phage Services, Brookvale, New South Wales, Australia
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom
| | - Khalid Alshafi
- Department of Microbiology, Royal Brompton Hospital, London, United Kingdom
| | - Diana Bilton
- Adult Cystic Fibrosis Unit, Royal Brompton Hospital, London, United Kingdom
| | - Eric W F W Alton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom
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Tang L, Liang X, Moore R, Dong TG. Commentary: The icmF3 Locus is Involved in Multiple Adaptation- and Virulence-related Characteristics in Pseudomonas aeruginosa PAO1. Front Cell Infect Microbiol 2015; 5:83. [PMID: 26636045 PMCID: PMC4649053 DOI: 10.3389/fcimb.2015.00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 11/25/2022] Open
Affiliation(s)
- Le Tang
- Ecosystem and Public Health, University of Calgary Calgary, AB, Canada
| | - Xiaoye Liang
- Ecosystem and Public Health, University of Calgary Calgary, AB, Canada
| | - Richard Moore
- Ecosystem and Public Health, University of Calgary Calgary, AB, Canada
| | - Tao G Dong
- Ecosystem and Public Health, University of Calgary Calgary, AB, Canada
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146
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Pseudomonas aeruginosa high-level resistance to polymyxins and other antimicrobial peptides requires cprA, a gene that is disrupted in the PAO1 strain. Antimicrob Agents Chemother 2015; 59:5377-87. [PMID: 26100714 DOI: 10.1128/aac.00904-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/11/2015] [Indexed: 11/20/2022] Open
Abstract
The arn locus, found in many Gram-negative bacterial pathogens, mediates resistance to polymyxins and other cationic antimicrobial peptides through 4-amino-l-arabinose modification of the lipid A moiety of lipopolysaccharide. In Pseudomonas aeruginosa, several two-component regulatory systems (TCSs) control the arn locus, which is necessary but not sufficient for these resistance phenotypes. A previous transposon mutagenesis screen to identify additional polymyxin resistance genes that these systems regulate implicated an open reading frame designated PA1559 in the genome of the P. aeruginosa PAO1 strain. Resequencing of this chromosomal region and bioinformatics analysis for a variety of P. aeruginosa strains revealed that in the sequenced PAO1 strain, a guanine deletion at the end of PA1559 results in a frameshift and truncation of a full-length open reading frame that also encompasses PA1560 in non-PAO1 strains, such as P. aeruginosa PAK. Deletion analysis in the PAK strain showed that this full-length open reading frame, designated cprA, is necessary for polymyxin resistance conferred by activating mutations in the PhoPQ, PmrAB, and CprRS TCSs. The cprA gene was also required for PmrAB-mediated resistance to other cationic antimicrobial peptides in the PAK strain. Repair of the mutated cprA allele in the PAO1 strain restored polymyxin resistance conferred by an activating TCS mutation. The deletion of cprA did not affect the arn-mediated lipid A modification, indicating that the CprA protein is necessary for a different aspect of polymyxin resistance. This protein has a domain structure with a strong similarity to the extended short-chain dehydrogenase/reductase family that comprises isomerases, lyases, and oxidoreductases. These results suggest a new avenue through which to pursue targeted inhibition of polymyxin resistance.
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147
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Knezevic P, Voet M, Lavigne R. Prevalence of Pf1-like (pro)phage genetic elements among Pseudomonas aeruginosa isolates. Virology 2015; 483:64-71. [PMID: 25965796 DOI: 10.1016/j.virol.2015.04.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
Pf1-like bacteriophages (family Inoviridae) of Pseudomonas aeruginosa can contribute to bacterial short term evolution and virulence. Here we examine Pf1-like (pro)phage diversity and prevalence among different P. aeruginosa isolates. Pf1-like prophages in sequenced genomes of P. aeruginosa were analyzed and grouped into four clades: Pf4, Pf5, Pf7 and Pf-LES. P. aeruginosa strains (n=241) were screened for the presence of universal (primers PfUa and PfUb) and specific Pf1-like genetic elements (Pf1, Pf4 and Pf5). More than half of the strains contained at least one Pf1-like genetic element (60%); universal elements were detected in 56% of the strains, Pf4 in 22%, Pf1 in 18% and Pf5 in 7%. Infectivity experiments confirmed that strains yielding PCR products with either universal or Pf4 specific primers can release infective virions. Based on the high prevalence of Pf1-like (pro)phages, it is necessary to further examine their involvement in P. aeruginosa virulence.
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Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000 Novi Sad, Vojvodina, Serbia.
| | - Marleen Voet
- Laboratory of Gene Technology, Department Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
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148
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Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa. Nat Commun 2015; 6:6845. [PMID: 25897488 PMCID: PMC4410645 DOI: 10.1038/ncomms7845] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/04/2015] [Indexed: 12/17/2022] Open
Abstract
Horizontal gene transfer (HGT) plays a key role in bacterial evolution, especially with respect to antibiotic resistance. Fitness costs associated with mobile genetic elements (MGEs) are thought to constrain HGT, but our understanding of these costs remains fragmentary, making it difficult to predict the success of HGT events. Here we use the interaction between P. aeruginosa and a costly plasmid (pNUK73) to investigate the molecular basis of the cost of HGT. Using RNA-Seq, we show that the acquisition of pNUK73 results in a profound alteration of the transcriptional profile of chromosomal genes. Mutations that inactivate two genes encoded on chromosomally integrated MGEs recover these fitness costs and transcriptional changes by decreasing the expression of the pNUK73 replication gene. Our study demonstrates that interactions between MGEs can compromise bacterial fitness via altered gene expression, and we argue that conflicts between mobile elements impose a general constraint on evolution by HGT.
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149
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Mai-Prochnow A, Hui JGK, Kjelleberg S, Rakonjac J, McDougald D, Rice SA. 'Big things in small packages: the genetics of filamentous phage and effects on fitness of their host'. FEMS Microbiol Rev 2015; 39:465-87. [PMID: 25670735 DOI: 10.1093/femsre/fuu007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023] Open
Abstract
This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.
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Affiliation(s)
- Anne Mai-Prochnow
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Janice Gee Kay Hui
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Staffan Kjelleberg
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Diane McDougald
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Scott A Rice
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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150
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Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC. Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene). Indian J Microbiol 2015; 55:140-50. [PMID: 25805900 DOI: 10.1007/s12088-015-0514-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 01/12/2015] [Indexed: 11/26/2022] Open
Abstract
Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho.
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Affiliation(s)
- Ashish Bhushan
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Tanmoy Mukherjee
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Jayadev Joshi
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Pratap Shankar
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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