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Naughton S, Parker D, Seemann T, Thomas T, Turnbull L, Rose B, Bye P, Cordwell S, Whitchurch C, Manos J. Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung. PLoS One 2011; 6:e24526. [PMID: 21935417 PMCID: PMC3174184 DOI: 10.1371/journal.pone.0024526] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/12/2011] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients.
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Affiliation(s)
- Sharna Naughton
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
| | - Dane Parker
- Department of Microbiology, Monash University, Melbourne, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Melbourne, Australia
| | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney, Australia
| | - Lynne Turnbull
- Department of Microbiology, Monash University, Melbourne, Australia
- The ithree institute, University of Technology, Sydney, Australia
| | - Barbara Rose
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
| | - Peter Bye
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Stuart Cordwell
- School of Molecular Biosciences, University of Sydney, Sydney, Australia
| | - Cynthia Whitchurch
- Department of Microbiology, Monash University, Melbourne, Australia
- The ithree institute, University of Technology, Sydney, Australia
| | - Jim Manos
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
- * E-mail:
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Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. BMC Genomics 2011; 12:373. [PMID: 21781329 PMCID: PMC3155924 DOI: 10.1186/1471-2164-12-373] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 07/22/2011] [Indexed: 11/29/2022] Open
Abstract
Background Burkholderia cenocepacia is a member of the Burkholderia cepacia complex group of bacteria that cause infections in individuals with cystic fibrosis. B. cenocepacia isolate J2315 has been genome sequenced and is representative of a virulent, epidemic CF strain (ET12). Its genome encodes multiple antimicrobial resistance pathways and it is not known which of these is important for intrinsic or spontaneous resistance. To map these pathways, transcriptomic analysis was performed on: (i) strain J2315 exposed to sub-inhibitory concentrations of antibiotics and the antibiotic potentiator chlorpromazine, and (ii) on spontaneous mutants derived from J2315 and with increased resistance to the antibiotics amikacin, meropenem and trimethoprim-sulfamethoxazole. Two pan-resistant ET12 outbreak isolates recovered two decades after J2315 were also compared to identify naturally evolved gene expression changes. Results Spontaneous resistance in B. cenocepacia involved more gene expression changes and different subsets of genes than those provoked by exposure to sub inhibitory concentrations of each antibiotic. The phenotype and altered gene expression in the resistant mutants was also stable irrespective of the presence of the priming antibiotic. Both known and novel genes involved in efflux, antibiotic degradation/modification, membrane function, regulation and unknown functions were mapped. A novel role for the phenylacetic acid (PA) degradation pathway genes was identified in relation to spontaneous resistance to meropenem and glucose was found to repress their expression. Subsequently, 20 mM glucose was found to produce greater that 2-fold reductions in the MIC of multiple antibiotics against B. cenocepacia J2315. Mutation of an RND multidrug efflux pump locus (BCAM0925-27) and squalene-hopene cyclase gene (BCAS0167), both upregulated after chlorpromazine exposure, confirmed their role in resistance. The recently isolated outbreak isolates had altered the expression of multiple genes which mirrored changes seen in the antibiotic resistant mutants, corroborating the strategy used to model resistance. Mutation of an ABC transporter gene (BCAS0081) upregulated in both outbreak strains, confirmed its role in B. cenocepacia resistance. Conclusions Global mapping of the genetic pathways which mediate antibiotic resistance in B. cenocepacia has revealed that they are multifactorial, identified potential therapeutic targets and also demonstrated that putative catabolite repression of genes by glucose can improve antibiotic efficacy.
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103
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Méndez V, Agulló L, González M, Seeger M. The homogentisate and homoprotocatechuate central pathways are involved in 3- and 4-hydroxyphenylacetate degradation by Burkholderia xenovorans LB400. PLoS One 2011; 6:e17583. [PMID: 21423751 PMCID: PMC3053370 DOI: 10.1371/journal.pone.0017583] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/05/2011] [Indexed: 11/24/2022] Open
Abstract
Background Genome characterization of the model PCB-degrading bacterium Burkholderia xenovorans LB400 revealed the presence of eleven central pathways for aromatic compounds degradation, among them, the homogentisate and the homoprotocatechuate pathways. However, the functionality of these central pathways in strain LB400 has not been assessed and related peripheral pathways has not been described. Methodology/Principal Findings The aims of this study were to determine the functionality of the homogentisate and homoprotocatechuate central pathways in B. xenovorans LB400 and to establish their role in 3-hydroxyphenylacetate (3-HPA) and 4-hydroxyphenylacetate (4-HPA) catabolism. Strain LB400 was able to grow using 3-HPA and 4-HPA as sole carbon source. A genomic search in LB400 suggested the presence of mhaAB and hpaBC genes clusters encoding proteins of the 3-hydroxyphenylacetate and 4-hydroxyphenylacetate peripheral pathways. LB400 cells grown with 3-HPA and 4-HPA degraded homogentisate and homoprotocatechuate and showed homogentisate 1,2-dioxygenase and homoprotocatechuate 2,3-dioxygenase activities. Transcriptional analyses by RT-PCR showed the expression of two chromosomally-encoded homogentisate dioxygenases (BxeA2725 and BxeA3900) and the hpaD gene encoding the homoprotocatechuate 2,3-dioxygenase during 3-HPA and 4-HPA degradation. The proteome analyses by two-dimensional polyacrilamide gel electrophoresis of B. xenovorans LB400 grown in 3-HPA and 4-HPA showed the induction of fumarylacetoacetate hydrolase HmgB (BxeA3899). Conclusions/Significance This study revealed that strain LB400 used both homogentisate and homoprotocatechuate ring-cleavage pathways for 3- hydroxyphenylacetate and 4-hydroxyphenylacetate catabolism and that these four catabolic routes are functional, confirming the metabolic versatility of B. xenovorans LB400.
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Affiliation(s)
- Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Loreine Agulló
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Myriam González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
- * E-mail:
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104
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A putative ABC transporter, hatABCDE, is among molecular determinants of pyomelanin production in Pseudomonas aeruginosa. J Bacteriol 2010; 192:5962-71. [PMID: 20870774 DOI: 10.1128/jb.01021-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyomelanin overproduction is a common phenotype among Pseudomonas aeruginosa isolates recovered from cystic fibrosis and urinary tract infections. Its prevalence suggests that it contributes to the persistence of the producing microbial community, yet little is known about the mechanisms of its production. Using transposon mutagenesis, we identified factors that contribute to melanogenesis in a clinical isolate of P. aeruginosa. In addition to two enzymes already known to be involved in its biosynthesis (homogentisate dioxygenase and hydroxyphenylpyruvate dioxygenase), we identified 26 genes that encode regulatory, metabolic, transport, and hypothetical proteins that contribute to the production of homogentisic acid (HGA), the monomeric precursor of pyomelanin. One of these, PA14_57880, was independently identified four times and is predicted to encode the ATP-binding cassette of an ABC transporter homologous to proteins in Pseudomonas putida responsible for the extrusion of organic solvents from the cytosol. Quantification of HGA production by P. aeruginosa PA14 strains missing the predicted subcomponents of this transporter confirmed its role in HGA production: mutants unable to produce the ATP-binding cassette (PA14_57880) or the permease (PA14_57870) produced substantially less extracellular HGA after growth for 20 h than the parental strain. In these mutants, concurrent accumulation of intracellular HGA was observed. In addition, quantitative real-time PCR revealed that intracellular accumulation of HGA elicits upregulation of these transport genes. Based on their involvement in homogentisic acid transport, we rename the genes of this operon hatABCDE.
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Liang H, Duan J, Sibley CD, Surette MG, Duan K. Identification of mutants with altered phenazine production in Pseudomonas aeruginosa. J Med Microbiol 2010; 60:22-34. [PMID: 20705730 DOI: 10.1099/jmm.0.022350-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that causes serious and chronic infections. Many secondary metabolites are secreted throughout its growth, among which phenazine is a known virulence factor and signalling molecule. Phenazine is coordinately controlled by the global regulatory quorum-sensing (QS) systems. Despite the detailed understanding of phenazine biosynthesis pathways in P. aeruginosa, the regulatory networks are still not fully clear. In the present study, the regulation of the phzA1B1C1D1E1F1G1 operon (phzA1) has been investigated. Screening of 5000 transposon mutants revealed 14 interrupted genes with altered phzA1 expression, including PA2593 (QteE), which has been identified as a novel regulator of the QS system. Overexpression of qteE in P. aeruginosa significantly reduced the accumulation of homoserine lactone signals and affected the QS-controlled phenotypes such as the production of pyocyanin, rhamnolipids and LasA protease and swarming motility. Indeed, overexpression of qteE in P. aeruginosa attenuated its pathogenicity in the potato and fruit fly infection models. These findings suggest that qteE plays an important role in P. aeruginosa pathogenicity and is part of the regulatory networks controlling phenazine production.
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Affiliation(s)
- Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, PR China
| | - Jiali Duan
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, PR China
| | - Christopher D Sibley
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada
| | - Michael G Surette
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada
| | - Kangmin Duan
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, PR China
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106
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Lan L, Murray TS, Kazmierczak BI, He C. Pseudomonas aeruginosa OspR is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection. Mol Microbiol 2009; 75:76-91. [PMID: 19943895 DOI: 10.1111/j.1365-2958.2009.06955.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oxidative stress is one of the main challenges bacteria must cope with during infection. Here, we identify a new oxidative stress sensing and response ospR (oxidative stress response and pigment production Regulator) gene in Pseudomonas aeruginosa. Deletion of ospR leads to a significant induction in H(2)O(2) resistance. This effect is mediated by de-repression of PA2826, which lies immediately upstream of ospR and encodes a glutathione peroxidase. Constitutive expression of ospR alters pigment production and beta-lactam resistance in P. aeruginosa via a PA2826-independent manner. We further discovered that OspR regulates additional genes involved in quorum sensing and tyrosine metabolism. These regulatory effects are redox-mediated as addition of H(2)O(2) or cumene hydroperoxide leads to the dissociation of OspR from promoter DNA. A conserved Cys residue, Cys-24, plays the major role of oxidative stress sensing in OspR. The serine substitution mutant of Cys-24 is less susceptible to oxidation in vitro and exhibits altered pigmentation and beta-lactam resistance. Lastly, we show that an ospR null mutant strain displays a greater capacity for dissemination than wild-type MPAO1 strain in a murine model of acute pneumonia. Thus, OspR is a global regulator that senses oxidative stress and regulates multiple pathways to enhance the survival of P. aeruginosa inside host.
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Affiliation(s)
- Lefu Lan
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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