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Gil-Gil T, Valverde JR, Martínez JL, Corona F. In vivo genetic analysis of Pseudomonas aeruginosa carbon catabolic repression through the study of CrcZ pseudo-revertants shows that Crc-mediated metabolic robustness is needed for proficient bacterial virulence and antibiotic resistance. Microbiol Spectr 2023; 11:e0235023. [PMID: 37902380 PMCID: PMC10714802 DOI: 10.1128/spectrum.02350-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
IIMPORTANCE Hfq and Crc regulate P. aeruginosa carbon catabolic repression at the post-transcriptional level. In vitro work has shown that Hfq binds the target RNAs and Crc stabilizes the complex. A third element in the regulation is the small RNA CrcZ, which sequesters the Crc-Hfq complex under no catabolic repression conditions, allowing the translation of the target mRNAs. A ΔcrcZ mutant was generated and presented fitness defects and alterations in its virulence potential and antibiotic resistance. Eight pseudo-revertants that present different degrees of fitness compensation were selected. Notably, although Hfq is the RNA binding protein, most mutations occurred in Crc. This indicates that Crc is strictly needed for P. aeruginosa efficient carbon catabolic repression in vivo. The compensatory mutations restore in a different degree the alterations in antibiotic susceptibility and virulence of the ΔcrcZ mutant, supporting that Crc plays a fundamental role linking P. aeruginosa metabolic robustness, virulence, and antibiotic resistance.
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Mould DL, Stevanovic M, Ashare A, Schultz D, Hogan DA. Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant. eLife 2022; 11:e76555. [PMID: 35502894 PMCID: PMC9224983 DOI: 10.7554/elife.76555] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/24/2022] [Indexed: 11/21/2022] Open
Abstract
Microbes frequently evolve in reproducible ways. Here, we show that differences in specific metabolic regulation rather than inter-strain interactions explain the frequent presence of lasR loss-of-function (LOF) mutations in the bacterial pathogen Pseudomonas aeruginosa. While LasR contributes to virulence through its role in quorum sensing, lasR mutants have been associated with more severe disease. A model based on the intrinsic growth kinetics for a wild type strain and its LasR- derivative, in combination with an experimental evolution based genetic screen and further genetics analyses, indicated that differences in metabolism were sufficient to explain the rise of these common mutant types. The evolution of LasR- lineages in laboratory and clinical isolates depended on activity of the two-component system CbrAB, which modulates substrate prioritization through the catabolite repression control pathway. LasR- lineages frequently arise in cystic fibrosis lung infections and their detection correlates with disease severity. Our analysis of bronchoalveolar lavage fluid metabolomes identified compounds that negatively correlate with lung function, and we show that these compounds support enhanced growth of LasR- cells in a CbrB-controlled manner. We propose that in vivo metabolomes contribute to pathogen evolution, which may influence the progression of disease and its treatment.
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Affiliation(s)
- Dallas L Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
- Department of Medicine, Dartmouth-Hitchock Medical CenterLebanonUnited States
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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4
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Clamens T, Rosay T, Crépin A, Grandjean T, Kentache T, Hardouin J, Bortolotti P, Neidig A, Mooij M, Hillion M, Vieillard J, Cosette P, Overhage J, O’Gara F, Bouffartigues E, Dufour A, Chevalier S, Guery B, Cornelis P, Feuilloley MGJ, Lesouhaitier O. The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence. Sci Rep 2017; 7:41178. [PMID: 28117457 PMCID: PMC5259723 DOI: 10.1038/srep41178] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022] Open
Abstract
We have previously shown that the eukaryotic C-type natriuretic peptide hormone (CNP) regulates Pseudomonas aeruginosa virulence and biofilm formation after binding on the AmiC sensor, triggering the amiE transcription. Herein, the involvement of the aliphatic amidase AmiE in P. aeruginosa virulence regulation has been investigated. The proteome analysis of an AmiE over-producing strain (AmiE+) revealed an expression change for 138 proteins, including some that are involved in motility, synthesis of quorum sensing compounds and virulence regulation. We observed that the AmiE+ strain produced less biofilm compared to the wild type, and over-produced rhamnolipids. In the same line, AmiE is involved in P. aeruginosa motilities (swarming and twitching) and production of the quorum sensing molecules N-acyl homoserine lactones and Pseudomonas Quinolone Signal (PQS). We observed that AmiE overproduction reduced levels of HCN and pyocyanin causing a decreased virulence in different hosts (i.e. Dictyostelium discoideum and Caenorhabditis elegans). This phenotype was further confirmed in a mouse model of acute lung infection, in which AmiE overproduction resulted in an almost fully virulence decrease. Taken together, our data suggest that, in addition to its role in bacterial secondary metabolism, AmiE is involved in P. aeruginosa virulence regulation by modulating pilus synthesis and cell-to-cell communication.
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Affiliation(s)
- Thomas Clamens
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Thibaut Rosay
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | | | - Teddy Grandjean
- Univ. Lille, CHU Lille, EA 7366 - Recherche Translationnelle: relations hôte pathogènes, Lille, France
| | - Takfarinas Kentache
- Laboratory « Polymères, Biopolymères, Surfaces » (UMR 6270 CNRS), Proteomic Platform PISSARO, Normandie Univ, UNIROUEN, Mont-Saint-Aignan, France
| | - Julie Hardouin
- Laboratory « Polymères, Biopolymères, Surfaces » (UMR 6270 CNRS), Proteomic Platform PISSARO, Normandie Univ, UNIROUEN, Mont-Saint-Aignan, France
| | - Perrine Bortolotti
- Univ. Lille, CHU Lille, EA 7366 - Recherche Translationnelle: relations hôte pathogènes, Lille, France
| | - Anke Neidig
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, PO Box 3640, Karlsruhe, Germany
| | - Marlies Mooij
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
| | - Mélanie Hillion
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Julien Vieillard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Evreux, France
| | - Pascal Cosette
- Laboratory « Polymères, Biopolymères, Surfaces » (UMR 6270 CNRS), Proteomic Platform PISSARO, Normandie Univ, UNIROUEN, Mont-Saint-Aignan, France
| | - Joerg Overhage
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, PO Box 3640, Karlsruhe, Germany
| | - Fergal O’Gara
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Alain Dufour
- Univ. Bretagne-Sud, EA 3884, LBCM, IUEM, Lorient, France
| | - Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Benoit Guery
- Univ. Lille, CHU Lille, EA 7366 - Recherche Translationnelle: relations hôte pathogènes, Lille, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Marc G. J. Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandie Univ, UNIROUEN, Evreux, France
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Matcher GF, Jiwaji M, de la Mare JA, Dorrington RA. Complex pathways for regulation of pyrimidine metabolism by carbon catabolite repression and quorum sensing in Pseudomonas putida RU-KM3S. Appl Microbiol Biotechnol 2013; 97:5993-6007. [DOI: 10.1007/s00253-013-4862-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 03/13/2013] [Indexed: 11/28/2022]
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Bacterial genetics: past achievements, present state of the field, and future challenges. Biotechniques 2008; 44:633-4, 636-41. [PMID: 18474038 DOI: 10.2144/000112807] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genetic tools are required to take full advantage of the wealth of information generated by genome sequencing efforts and ensuing global gene and protein expression analyses. Bacterial genetics was originally developed and refined in Escherichia coli. As a consequence, elegant plasmid, cloning, expression, and mutagenesis systems were developed over the years and a good number of them are commercially available. This is not true for other bacteria. Although the development of genetic tools has generally not kept up with the sequencing pace, substantial progress has been made in this arena with many bacterial species. This short review highlights selected topics and achievements in the field over the past 25 years and presents some strategies that may help address future challenges. BioTechniques has played an integral part in the publication of important technological advances in the field over the first 25 years of its existence and it can be anticipated that it will continue to do so in the future.
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del Castillo T, Ramos JL. Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 2007; 189:6602-10. [PMID: 17616587 PMCID: PMC2045187 DOI: 10.1128/jb.00679-07] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440(pWW0) can use toluene via the TOL plasmid-encoded catabolic pathways and can use glucose via a series of three peripheral chromosome-encoded routes that convert glucose into 6-phosphogluconate (6PG), namely, the glucokinase pathway, in which glucose is transformed to 6PG through the action of glucokinase and glucose-6-phosphate dehydrogenase. Alternatively, glucose can be oxidized to gluconate, which can be phosphorylated by gluconokinase to 6PG or oxidized to 2-ketogluconate, which, in turn, is converted into 6PG. Our results show that KT2440 metabolizes glucose and toluene simultaneously, as revealed by net flux analysis of [(13)C]glucose. Determination of glucokinase and gluconokinase activities in glucose metabolism, gene expression assays using a fusion of the promoter of the Pu TOL upper pathway to 'lacZ, and global transcriptomic assays revealed simultaneous catabolite repression in the use of these two carbon sources. The effect of toluene on glucose metabolism was directed to the glucokinase branch and did not affect gluconate metabolism. Catabolite repression of the glucokinase pathway and the TOL pathway was triggered by two different catabolite repression systems. Expression from Pu was repressed mainly via PtsN in response to high levels of 2-dehydro-3-deoxygluconate-6-phosphate, whereas repression of the glucokinase pathway was channeled through Crc.
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Aranda-Olmedo I, Ramos JL, Marqués S. Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl Environ Microbiol 2005; 71:4191-8. [PMID: 16085802 PMCID: PMC1183334 DOI: 10.1128/aem.71.8.4191-4198.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toluene degradation in Pseudomonas putida KT2440 pWW0 plasmid is subjected to catabolite repression. Pu and P(S1) promoters of the pWW0 TOL plasmid are down-regulated in vivo during exponential growth in rich medium. In cells growing on minimal medium, yeast extract (YE) addition mimics exponential-phase rich medium repression of these promoters. We have constructed and tested mutants in a series of global regulators described in Pseudomonas. We describe that a mutant in crc (catabolite repression control) partially relieves YE repression. Macroarray experiments show that crc transcription is strongly increased in the presence of YE, inversely correlated with TOL pathway expression. On the other hand, we have found that induced levels of expression from Pu and P(S) in the presence of YE are partially derepressed in a ptsN mutant of P. putida. PtsN but not Crc seems to directly interfere with XylR activation at target promoters. The effect of the double mutation in ptsN and crc is not the sum of the effects of each independent mutation and suggests that both regulators are elements of a common regulatory pathway. Basal expression levels from these promoters in the absence of inducer are still XylR dependent and are also repressed in the presence of yeast extract. Neither crc nor ptsN could relieve this repression.
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Affiliation(s)
- Isabel Aranda-Olmedo
- Department of Biochemistry and Molecular and Cellular Biology of Plants, EEZ-CSIC, Apdo. de Correos 419, E-18080 Granada, Spain
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Velázquez F, di Bartolo I, de Lorenzo V. Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma54 Pu promoter of Pseudomonas putida. J Bacteriol 2005; 186:8267-75. [PMID: 15576775 PMCID: PMC532441 DOI: 10.1128/jb.186.24.8267-8275.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucose and other C sources exert an atypical form of catabolic repression on the sigma54-dependent promoter Pu, which drives transcription of an operon for m-xylene degradation encoded by the TOL plasmid pWW0 in Pseudomonas putida. We have used a genetic approach to identify the catabolite(s) shared by all known repressive C sources that appears to act as the intracellular signal that triggers downregulation of Pu. To this end, we reconstructed from genomic data the pathways for metabolism of repressor (glucose, gluconate) and nonrepressor (fructose) C sources. Since P. putida lacks fructose-6-phosphate kinase, glucose and gluconate appear to be metabolized exclusively by the Entner-Doudoroff (ED) pathway, while fructose can be channeled through the Embden-Meyerhof (EM) route. An insertion in the gene fda (encoding fructose-1,6-bisphosphatase) that forces fructose metabolism to be routed exclusively to the ED pathway makes this sugar inhibitory for Pu. On the contrary, a crc mutation known to stimulate expression of the ED enzymes causes the promoter to be less sensitive to glucose. Interrupting the ED pathway by knocking out eda (encoding 2-dehydro-3-deoxyphosphogluconate aldolase) exacerbates the inhibitory effect of glucose in Pu. These observations pinpoint the key catabolites of the ED route, 6-phosphogluconate and/or 2-dehydro-3-deoxyphosphogluconate, as the intermediates that signal Pu repression. This notion is strengthened by the observation that 2-ketogluconate, which enters the ED pathway by conversion into these compounds, is a strong repressor of the Pu promoter.
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O'Toole GA, Gibbs KA, Hager PW, Phibbs PV, Kolter R. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J Bacteriol 2000; 182:425-31. [PMID: 10629189 PMCID: PMC94292 DOI: 10.1128/jb.182.2.425-431.2000] [Citation(s) in RCA: 238] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transition from a planktonic (free-swimming) existence to growth attached to a surface in a biofilm occurs in response to environmental factors, including the availability of nutrients. We show that the catabolite repression control (Crc) protein, which plays a role in the regulation of carbon metabolism, is necessary for biofilm formation in Pseudomonas aeruginosa. Using phase-contrast microscopy, we found that a crc mutant only makes a dispersed monolayer of cells on a plastic surface but does not develop the dense monolayer punctuated by microcolonies typical of the wild-type strain. This is a phenotype identical to that observed in mutants defective in type IV pilus biogenesis. Consistent with this observation, crc mutants are defective in type IV pilus-mediated twitching motility. We show that this defect in type IV pilus function is due (at least in part) to a decrease in pilA (pilin) transcription. We propose that nutritional cues are integrated by Crc as part of a signal transduction pathway that regulates biofilm development.
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Affiliation(s)
- G A O'Toole
- Department of Microbiology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA. George.O'
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