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David A, Tahrioui A, Duchesne R, Tareau AS, Maillot O, Barreau M, Feuilloley MGJ, Lesouhaitier O, Cornelis P, Bouffartigues E, Chevalier S. Membrane fluidity homeostasis is required for tobramycin-enhanced biofilm in Pseudomonas aeruginosa. Microbiol Spectr 2024; 12:e0230323. [PMID: 38411953 PMCID: PMC10986583 DOI: 10.1128/spectrum.02303-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen, which causes chronic infections, especially in cystic fibrosis (CF) patients where it colonizes the lungs via the build-up of biofilms. Tobramycin, an aminoglycoside, is often used to treat P. aeruginosa infections in CF patients. Tobramycin at sub-minimal inhibitory concentrations enhances both biofilm biomass and thickness in vitro; however, the mechanism(s) involved are still unknown. Herein, we show that tobramycin increases the expression and activity of SigX, an extracytoplasmic sigma factor known to be involved in the biosynthesis of membrane lipids and membrane fluidity homeostasis. The biofilm enhancement by tobramycin is not observed in a sigX mutant, and the sigX mutant displays increased membrane stiffness. Remarkably, the addition of polysorbate 80 increases membrane fluidity of sigX-mutant cells in biofilm, restoring the tobramycin-enhanced biofilm formation. Our results suggest the involvement of membrane fluidity homeostasis in biofilm development upon tobramycin exposure.IMPORTANCEPrevious studies have shown that sub-lethal concentrations of tobramycin led to an increase biofilm formation in the case of infections with the opportunistic pathogen Pseudomonas aeruginosa. We show that the mechanism involved in this phenotype relies on the cell envelope stress response, triggered by the extracytoplasmic sigma factor SigX. This phenotype was abolished in a sigX-mutant strain. Remarkably, we show that increasing the membrane fluidity of the mutant strain is sufficient to restore the effect of tobramycin. Altogether, our data suggest the involvement of membrane fluidity homeostasis in biofilm development upon tobramycin exposure.
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Affiliation(s)
- Audrey David
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Ali Tahrioui
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Rachel Duchesne
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Anne-Sophie Tareau
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Olivier Maillot
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Magalie Barreau
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Marc G. J. Feuilloley
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Olivier Lesouhaitier
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Pierre Cornelis
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Emeline Bouffartigues
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
| | - Sylvie Chevalier
- Unité de recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Université de Rouen Normandie, Normandie Université, Evreux, France
- Fédération de Recherche Normande Sécurité Sanitaire, bien être, Aliment Durable (SéSAD), Evreux, France
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2
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Sánchez-Jiménez A, Llamas MA, Marcos-Torres FJ. Transcriptional Regulators Controlling Virulence in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11895. [PMID: 37569271 PMCID: PMC10418997 DOI: 10.3390/ijms241511895] [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: 07/04/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is a pathogen capable of colonizing virtually every human tissue. The host colonization competence and versatility of this pathogen are powered by a wide array of virulence factors necessary in different steps of the infection process. This includes factors involved in bacterial motility and attachment, biofilm formation, the production and secretion of extracellular invasive enzymes and exotoxins, the production of toxic secondary metabolites, and the acquisition of iron. Expression of these virulence factors during infection is tightly regulated, which allows their production only when they are needed. This process optimizes host colonization and virulence. In this work, we review the intricate network of transcriptional regulators that control the expression of virulence factors in P. aeruginosa, including one- and two-component systems and σ factors. Because inhibition of virulence holds promise as a target for new antimicrobials, blocking the regulators that trigger the production of virulence determinants in P. aeruginosa is a promising strategy to fight this clinically relevant pathogen.
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Affiliation(s)
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Francisco Javier Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
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3
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Cornelis P, Tahrioui A, Lesouhaitier O, Bouffartigues E, Feuilloley M, Baysse C, Chevalier S. High affinity iron uptake by pyoverdine in Pseudomonas aeruginosa involves multiple regulators besides Fur, PvdS, and FpvI. Biometals 2023; 36:255-261. [PMID: 35171432 DOI: 10.1007/s10534-022-00369-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/03/2022] [Indexed: 11/02/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium which can cause serious infections among immune-depressed people including cystic fibrosis patients where it can colonize the lungs causing chronic infections. Iron is essential for P. aeruginosa and can be provided via three sources under aerobic conditions: its own siderophores pyochelin (PCH) and pyoverdine (PVD), xenosiderophores, or heme, respectively. Pyoverdine is the high affinity siderophore and its synthesis and uptake involve more than 30 genes organized in different operons. Its synthesis and uptake are triggered by iron scarcity via the Fur regulator and involves two extra cytoplasmic sigma factors (ECF), PvdS for the biosynthesis of PVD and FpvI for the uptake via the TonB-dependent FpvA outer membrane transporter and other periplasmic and inner membrane proteins. It appeared recently that the regulation of PVD biosynthesis and uptake involves other regulators, including other ECF factors, and LysR regulators. This is the case especially for the genes coding for periplasmic and inner membrane proteins involved in the reduction of Fe3+ to Fe2+ and the transport of ferrous iron to the cytoplasm that appears to represent a crucial step in the uptake process.
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Affiliation(s)
- Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France.
- Laboratorium Microbiologie, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Ali Tahrioui
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France
| | - Marc Feuilloley
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France
| | - Christine Baysse
- CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Université de Rennes, Rennes, France
| | - Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironnements (LMSM) EA 4312, University of Rouen Normandy, 27000, Evreux, France
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4
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Sauvage S, Gaviard C, Tahrioui A, Coquet L, Le H, Alexandre S, Ben Abdelkrim A, Bouffartigues E, Lesouhaitier O, Chevalier S, Jouenne T, Hardouin J. Impact of Carbon Source Supplementations on Pseudomonas aeruginosa Physiology. J Proteome Res 2022; 21:1392-1407. [PMID: 35482949 DOI: 10.1021/acs.jproteome.1c00936] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen highly resistant to a wide range of antimicrobial agents, making its infections very difficult to treat. Since microorganisms need to perpetually adapt to their surrounding environment, understanding the effect of carbon sources on P. aeruginosa physiology is therefore essential to avoid increasing drug-resistance and better fight this pathogen. By a global proteomic approach and phenotypic assays, we investigated the impact of various carbon source supplementations (glucose, glutamate, succinate, and citrate) on the physiology of the P. aeruginosa PA14 strain. A total of 581 proteins were identified as differentially expressed in the 4 conditions. Most of them were more abundant in citrate supplementation and were involved in virulence, motility, biofilm development, and antibiotic resistance. Phenotypic assays were performed to check these hypotheses. By coupling all this data, we highlight the importance of the environment in which the bacterium evolves on its metabolism, and thus the necessity to better understand the metabolic pathways implied in its adaptative response according to the nutrient availability.
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Affiliation(s)
- Salomé Sauvage
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Charlotte Gaviard
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Ali Tahrioui
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Laurent Coquet
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Hung Le
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Stéphane Alexandre
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Ahmed Ben Abdelkrim
- Lactanet, Valacta, 555 Boul des Anciens-Combattants, Sainte-Anne-de-Bellevue, Québec H9X 3R4, Canada
| | - Emeline Bouffartigues
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Sylvie Chevalier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Thierry Jouenne
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
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5
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Monteagudo-Cascales E, Santero E, Canosa I. The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions. Genes (Basel) 2022; 13:genes13020375. [PMID: 35205417 PMCID: PMC8871633 DOI: 10.3390/genes13020375] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.
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Affiliation(s)
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
| | - Inés Canosa
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
- Correspondence: ; Tel.: +34-954349052
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6
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Ramsay KA, McTavish SM, Wardell SJT, Lamont IL. The Effects of Sub-inhibitory Antibiotic Concentrations on Pseudomonas aeruginosa: Reduced Susceptibility Due to Mutations. Front Microbiol 2021; 12:789550. [PMID: 34987489 PMCID: PMC8721600 DOI: 10.3389/fmicb.2021.789550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa chronically infects in the lungs of people with cystic fibrosis and other forms of lung disease. Infections are treated with antibiotics, but over time, the bacteria acquire mutations that reduce their antibiotic susceptibility. The effects of inhibitory amounts of antibiotics in selecting for antibiotic-resistant mutants have been well studied. However, the concentrations of antibiotics that reach infecting bacteria can be sub-inhibitory and but may nonetheless promote emergence of antibiotic-resistant bacteria. Therefore, the aim of this research was to investigate the effects of sub-inhibitory concentrations of antibiotics on the antibiotic susceptibility of P. aeruginosa. Two P. aeruginosa reference strains, PAO1 and PA14, and six isolates from individuals with cystic fibrosis were studied. The bacteria were passaged in the presence of antibiotics (ceftazidime, ciprofloxacin, meropenem or tobramycin) at sub-inhibitory amounts. Fifteen populations of bacteria (up to five per strain) were exposed to each of the four antibiotics. Antibiotic susceptibility was determined following 10 passages on agar supplemented with antibiotic and compared with susceptibility prior to antibiotic exposure. Antibiotic exposure resulted in susceptibility being significantly (>2-fold) reduced for 13 of the 60 populations. Seven samples had reduced susceptibility to ciprofloxacin, three to tobramycin, two to ceftazidime and one to meropenem. Whole-genome sequencing revealed the mutations arising following antibiotic exposure. Mutants with reduced antibiotic susceptibility had mutations in genes known to affect antibiotic resistance, including regulators of efflux pumps (mexR, mexS, mexZ and nalC) and the fusA1 gene that is associated with aminoglycoside resistance. Genes not previously associated with resistance, including gacS, sigX and crfX and two genes with no known function, were also mutated in some isolates with reduced antibiotic susceptibility. Our results show that exposure to sub-inhibitory amounts of antibiotics can select for mutations that reduce the susceptibility of P. aeruginosa to antibiotics and that the profile of mutations is different from that arising during selection with inhibitory antibiotic concentrations. It is likely that exposure to sub-inhibitory amounts of antibiotics during infection contributes to P. aeruginosa becoming antibiotic-resistant.
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Affiliation(s)
| | | | | | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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8
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Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA. Rewiring the specificity of extracytoplasmic function sigma factors. Proc Natl Acad Sci U S A 2020; 117:33496-33506. [PMID: 33318184 PMCID: PMC7776599 DOI: 10.1073/pnas.2020204117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Kevin S Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Hao Li
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Timothy J Donohue
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158
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9
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Azuama OC, Ortiz S, Quirós-Guerrero L, Bouffartigues E, Tortuel D, Maillot O, Feuilloley M, Cornelis P, Lesouhaitier O, Grougnet R, Boutefnouchet S, Wolfender JL, Chevalier S, Tahrioui A. Tackling Pseudomonas aeruginosa Virulence by Mulinane-Like Diterpenoids from Azorella atacamensis. Biomolecules 2020; 10:E1626. [PMID: 33276611 PMCID: PMC7761567 DOI: 10.3390/biom10121626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is an important multidrug-resistant human pathogen by dint of its high intrinsic, acquired, and adaptive resistance mechanisms, causing great concern for immune-compromised individuals and public health. Additionally, P. aeruginosa resilience lies in the production of a myriad of virulence factors, which are known to be tightly regulated by the quorum sensing (QS) system. Anti-virulence therapy has been adopted as an innovative alternative approach to circumvent bacterial antibiotic resistance. Since plants are known repositories of natural phytochemicals, herein, we explored the anti-virulence potential of Azorella atacamensis, a medicinal plant from the Taira Atacama community (Calama, Chile), against P. aeruginosa. Interestingly, A. atacamensis extract (AaE) conferred a significant protection for human lung cells and Caenorhabditis elegans nematodes towards P. aeruginosa pathogenicity. The production of key virulence factors was decreased upon AaE exposure without affecting P. aeruginosa growth. In addition, AaE was able to decrease QS-molecules production. Furthermore, metabolite profiling of AaE and its derived fractions achieved by combination of a molecular network and in silico annotation allowed the putative identification of fourteen diterpenoids bearing a mulinane-like skeleton. Remarkably, this unique interesting group of diterpenoids seems to be responsible for the interference with virulence factors as well as on the perturbation of membrane homeostasis of P. aeruginosa. Hence, there was a significant increase in membrane stiffness, which appears to be modulated by the cell wall stress response ECFσ SigX, an extracytoplasmic function sigma factor involved in membrane homeostasis as well as P. aeruginosa virulence.
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Affiliation(s)
- Onyedikachi Cecil Azuama
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
- Department of Biological Sciences, Alex-Ekwueme Federal University, Ndufu Alike Ikwo PMB1010, Nigeria
| | - Sergio Ortiz
- Équipe Produits Naturels, Analyses et Synthèses (PNAS), CiTCoM UMR 8038 CNRS, Faculté de Pharmacie, Université de Paris, 75006 Paris, France; (S.O.); (R.G.); (S.B.)
| | - Luis Quirós-Guerrero
- Phytochemistry and Bioactive Natural Products, School of Pharmaceutical Science, University of Geneva, 1211 Geneva, Switzerland; (L.Q.-G.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSW), University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Emeline Bouffartigues
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Damien Tortuel
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Olivier Maillot
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Pierre Cornelis
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Raphaël Grougnet
- Équipe Produits Naturels, Analyses et Synthèses (PNAS), CiTCoM UMR 8038 CNRS, Faculté de Pharmacie, Université de Paris, 75006 Paris, France; (S.O.); (R.G.); (S.B.)
| | - Sabrina Boutefnouchet
- Équipe Produits Naturels, Analyses et Synthèses (PNAS), CiTCoM UMR 8038 CNRS, Faculté de Pharmacie, Université de Paris, 75006 Paris, France; (S.O.); (R.G.); (S.B.)
| | - Jean-Luc Wolfender
- Phytochemistry and Bioactive Natural Products, School of Pharmaceutical Science, University of Geneva, 1211 Geneva, Switzerland; (L.Q.-G.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSW), University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Sylvie Chevalier
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
| | - Ali Tahrioui
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, Université de Rouen Normandie, LMSM EA4312, 27000 Évreux, France; (O.C.A.); (E.B.); (D.T.); (O.M.); (M.F.); (P.C.); (O.L.); (S.C.)
- Fédération de Recherche Sécurité Sanitaire, Bien-Être, Aliments Durables (SéSAD), Normandie Université, Université de Rouen Normandie, 27000 Évreux, France
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10
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Schinner S, Preusse M, Kesthely C, Häussler S. Analysis of the organization and expression patterns of the convergent Pseudomonas aeruginosa lasR/rsaL gene pair uncovers mutual influence. Mol Microbiol 2020; 115:643-657. [PMID: 33073409 DOI: 10.1111/mmi.14628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 11/30/2022]
Abstract
The two adjacent genes encoding the major Pseudomonas aeruginosa quorum-sensing regulator, LasR, and its opponent, RsaL, overlap in their coding 3' ends and produce mRNA transcripts with long untranslated 3' ends that overlap with the sense transcripts of the gene on the opposing DNA strand. In this study, we evaluated whether the overlapping genes are involved in mutual regulatory events and studied interference by natural antisense transcripts. We introduced various gene expression constructs into a P. aeruginosa PA14 lasR/rsaL double deletion mutant, and found that although complementary RNA is produced, this does not interfere with the sense gene expression levels of lasR and rsaL and does not have functional consequences on down-stream gene regulation. Nevertheless, expression of lasR, but not of rsaL, was shown to be enhanced if transcription was terminated at the end of the respective gene so that no overlapping transcription was allowed. Our data indicate that the natural organization with a partial overlap at the 3' ends of the lasR/rsaL genes gives rise to a system of checks and balances to prevent dominant and unilateral control by LasR over the RsaL transcriptional regulator of opposing function.
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Affiliation(s)
- Silvia Schinner
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Christopher Kesthely
- Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital -Rigshospitalet, Copenhagen, Denmark.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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11
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Activation of the Cell Wall Stress Response in Pseudomonas aeruginosa Infected by a Pf4 Phage Variant. Microorganisms 2020; 8:microorganisms8111700. [PMID: 33143386 PMCID: PMC7693463 DOI: 10.3390/microorganisms8111700] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa PAO1 has an integrated Pf4 prophage in its genome, encoding a relatively well-characterized filamentous phage, which contributes to the bacterial biofilm organization and maturation. Pf4 variants are considered as superinfectives when they can re-infect and kill the prophage-carrying host. Herein, the response of P. aeruginosa H103 to Pf4 variant infection was investigated. This phage variant caused partial lysis of the bacterial population and modulated H103 physiology. We show by confocal laser scanning microscopy that a Pf4 variant-infection altered P. aeruginosa H103 biofilm architecture either in static or dynamic conditions. Interestingly, in the latter condition, numerous cells displayed a filamentous morphology, suggesting a link between this phenotype and flow-related forces. In addition, Pf4 variant-infection resulted in cell envelope stress response, mostly mediated by the AlgU and SigX extracytoplasmic function sigma factors (ECFσ). AlgU and SigX involvement may account, at least partly, for the enhanced expression level of genes involved in the biosynthesis pathways of two matrix exopolysaccharides (Pel and alginates) and bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) metabolism.
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12
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Bouffartigues E, Si Hadj Mohand I, Maillot O, Tortuel D, Omnes J, David A, Tahrioui A, Duchesne R, Azuama CO, Nusser M, Brenner-Weiss G, Bazire A, Connil N, Orange N, Feuilloley MGJ, Lesouhaitier O, Dufour A, Cornelis P, Chevalier S. The Temperature-Regulation of Pseudomonas aeruginosa cmaX-cfrX-cmpX Operon Reveals an Intriguing Molecular Network Involving the Sigma Factors AlgU and SigX. Front Microbiol 2020; 11:579495. [PMID: 33193206 PMCID: PMC7641640 DOI: 10.3389/fmicb.2020.579495] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a highly adaptable Gram-negative opportunistic pathogen, notably due to its large number of transcription regulators. The extracytoplasmic sigma factor (ECFσ) AlgU, responsible for alginate biosynthesis, is also involved in responses to cell wall stress and heat shock via the RpoH alternative σ factor. The SigX ECFσ emerged as a major regulator involved in the envelope stress response via membrane remodeling, virulence and biofilm formation. However, their functional interactions to coordinate the envelope homeostasis in response to environmental variations remain to be determined. The regulation of the putative cmaX-cfrX-cmpX operon located directly upstream sigX was investigated by applying sudden temperature shifts from 37°C. We identified a SigX- and an AlgU- dependent promoter region upstream of cfrX and cmaX, respectively. We show that cmaX expression is increased upon heat shock through an AlgU-dependent but RpoH independent mechanism. In addition, the ECFσ SigX is activated in response to valinomycin, an agent altering the membrane structure, and up-regulates cfrX-cmpX transcription in response to cold shock. Altogether, these data provide new insights into the regulation exerted by SigX and networks that are involved in maintaining envelope homeostasis.
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Affiliation(s)
- Emeline Bouffartigues
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Ishac Si Hadj Mohand
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Olivier Maillot
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Damien Tortuel
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Jordane Omnes
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Audrey David
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Ali Tahrioui
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Rachel Duchesne
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Cecil Onyedikachi Azuama
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Michael Nusser
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gerald Brenner-Weiss
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines (LBCM) EA3884, IUEM, Université de Bretagne-Sud, Lorient, France
| | - Nathalie Connil
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Nicole Orange
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Marc G J Feuilloley
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines (LBCM) EA3884, IUEM, Université de Bretagne-Sud, Lorient, France
| | - Pierre Cornelis
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
| | - Sylvie Chevalier
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Normandie Université, Université de Rouen Normandie, Centre de Sécurité Sanitaire de Normandie, Evreux, France
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13
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Tahrioui A, Ortiz S, Azuama OC, Bouffartigues E, Benalia N, Tortuel D, Maillot O, Chemat S, Kritsanida M, Feuilloley M, Orange N, Michel S, Lesouhaitier O, Cornelis P, Grougnet R, Boutefnouchet S, Chevalier S. Membrane-Interactive Compounds From Pistacia lentiscus L. Thwart Pseudomonas aeruginosa Virulence. Front Microbiol 2020; 11:1068. [PMID: 32528451 PMCID: PMC7264755 DOI: 10.3389/fmicb.2020.01068] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/29/2020] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa is capable to deploy a collection of virulence factors that are not only essential for host infection and persistence, but also to escape from the host immune system and to become more resistant to drug therapies. Thus, developing anti-virulence agents that may directly counteract with specific virulence factors or disturb higher regulatory pathways controlling the production of virulence armories are urgently needed. In this regard, this study reports that Pistacia lentiscus L. fruit cyclohexane extract (PLFE1) thwarts P. aeruginosa virulence by targeting mainly the pyocyanin pigment production by interfering with 4-hydroxy-2-alkylquinolines molecules production. Importantly, the anti-virulence activity of PLFE1 appears to be associated with membrane homeostasis alteration through the modulation of SigX, an extracytoplasmic function sigma factor involved in cell wall stress response. A thorough chemical analysis of PLFE1 allowed us to identify the ginkgolic acid (C17:1) and hydroginkgolic acid (C15:0) as the main bioactive membrane-interactive compounds responsible for the observed increased membrane stiffness and anti-virulence activity against P. aeruginosa. This study delivers a promising perspective for the potential future use of PLFE1 or ginkgolic acid molecules as an adjuvant therapy to fight against P. aeruginosa infections.
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Affiliation(s)
- Ali Tahrioui
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Sergio Ortiz
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Onyedikachi Cecil Azuama
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Emeline Bouffartigues
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Nabiha Benalia
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Damien Tortuel
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Olivier Maillot
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Smain Chemat
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques, CRAPC, Bou Ismaïl, Algeria
| | - Marina Kritsanida
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Nicole Orange
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Sylvie Michel
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Pierre Cornelis
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
| | - Raphaël Grougnet
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Sabrina Boutefnouchet
- CiTCoM UMR 8038 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Équipe Produits Naturels, Analyses et Synthèses (PNAS), Université Paris Descartes, Paris, France
| | - Sylvie Chevalier
- Laboratoire de Microbiologie Signaux et Microenvironnement, LMSM EA4312, Université de Rouen Normandie, Normandie Université, Évreux, France
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14
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Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells. Antimicrob Agents Chemother 2020; 64:AAC.01999-19. [PMID: 31844008 DOI: 10.1128/aac.01999-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/10/2019] [Indexed: 01/25/2023] Open
Abstract
Swarming surface motility is a complex adaptation leading to multidrug antibiotic resistance and virulence factor production in Pseudomonas aeruginosa Here, we expanded previous studies to demonstrate that under swarming conditions, P. aeruginosa PA14 is more resistant to multiple antibiotics, including aminoglycosides, β-lactams, chloramphenicol, ciprofloxacin, tetracycline, trimethoprim, and macrolides, than swimming cells, but is not more resistant to polymyxin B. We investigated the mechanism(s) of swarming-mediated antibiotic resistance by examining the transcriptomes of swarming cells and swarming cells treated with tobramycin by transcriptomics (RNA-Seq) and reverse transcriptase quantitative PCR (qRT-PCR). RNA-Seq of swarming cells (versus swimming) revealed 1,581 dysregulated genes, including 104 transcriptional regulators, two-component systems, and sigma factors, numerous upregulated virulence and iron acquisition factors, and downregulated ribosomal genes. Strain PA14 mutants in resistome genes that were dysregulated under swarming conditions were tested for their ability to swarm in the presence of tobramycin. In total, 41 mutants in genes dysregulated under swarming conditions were shown to be more resistant to tobramycin under swarming conditions, indicating that swarming-mediated tobramycin resistance was multideterminant. Focusing on two genes downregulated under swarming conditions, both prtN and wbpW mutants were more resistant to tobramycin, while the prtN mutant was additionally resistant to trimethoprim under swarming conditions; complementation of these mutants restored susceptibility. RNA-Seq of swarming cells treated with subinhibitory concentrations of tobramycin revealed the upregulation of the multidrug efflux pump MexXY and downregulation of virulence factors.
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15
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Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes 2020; 6:2. [PMID: 31934344 PMCID: PMC6954232 DOI: 10.1038/s41522-019-0113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/16/2019] [Indexed: 01/28/2023] Open
Abstract
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
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Affiliation(s)
- Janne G. Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nora Grahl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven D. Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Mathias Müsken
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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16
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Otero-Asman JR, Wettstadt S, Bernal P, Llamas MA. Diversity of extracytoplasmic function sigma (σ ECF ) factor-dependent signaling in Pseudomonas. Mol Microbiol 2019; 112:356-373. [PMID: 31206859 DOI: 10.1111/mmi.14331] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/23/2022]
Abstract
Pseudomonas bacteria are widespread and are found in soil and water, as well as pathogens of both plants and animals. The ability of Pseudomonas to colonize many different environments is facilitated by the multiple signaling systems these bacteria contain that allow Pseudomonas to adapt to changing circumstances by generating specific responses. Among others, signaling through extracytoplasmic function σ (σECF ) factors is extensively present in Pseudomonas. σECF factors trigger expression of functions required under particular conditions in response to specific signals. This manuscript reviews the phylogeny and biological roles of σECF factors in Pseudomonas, and highlights the diversity of σECF -signaling pathways of this genus in terms of function and activation. We show that Pseudomonas σECF factors belong to 16 different phylogenetic groups. Most of them are included within the iron starvation group and are mainly involved in iron acquisition. The second most abundant group is formed by RpoE-like σECF factors, which regulate the responses to cell envelope stress. Other groups controlling solvent tolerance, biofilm formation and the response to oxidative stress, among other functions, are present in lower frequency. The role of σECF factors in the virulence of Pseudomonas pathogenic species is described.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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17
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Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism. mBio 2019; 10:mBio.02577-18. [PMID: 31064836 PMCID: PMC6509195 DOI: 10.1128/mbio.02577-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
P. putida lysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, the connection of lysine catabolism to central metabolism in P. putida remained undefined. Here, we used random barcode transposon sequencing to fill the gaps of lysine metabolism in P. putida. We describe a route of 2-oxoadipate (2OA) catabolism, which utilizes DUF1338-containing protein P. putida 5260 (PP_5260) in bacteria. Despite its prevalence in many domains of life, DUF1338-containing proteins have had no known biochemical function. We demonstrate that PP_5260 is a metalloenzyme which catalyzes an unusual route of decarboxylation of 2OA to d-2-hydroxyglutarate (d-2HG). Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results and expand the understanding of glutarate hydroxylase CsiD by showing that can it use either 2OA or 2KG as a cosubstrate. Our work demonstrated that biological novelty can be rapidly identified using unbiased experimental genetics and that RB-TnSeq can be used to rapidly validate previous results. Despite intensive study for 50 years, the biochemical and genetic links between lysine metabolism and central metabolism in Pseudomonas putida remain unresolved. To establish these biochemical links, we leveraged random barcode transposon sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both l- and d-lysine metabolism. We first describe three pathway enzymes that catabolize l-2-aminoadipate (l-2AA) to 2-ketoglutarate (2KG), connecting d-lysine to the TCA cycle. One of these enzymes, P. putida 5260 (PP_5260), contains a DUF1338 domain, representing a family with no previously described biological function. Our work also identified the recently described coenzyme A (CoA)-independent route of l-lysine degradation that results in metabolization to succinate. We expanded on previous findings by demonstrating that glutarate hydroxylase CsiD is promiscuous in its 2-oxoacid selectivity. Proteomics of selected pathway enzymes revealed that expression of catabolic genes is highly sensitive to the presence of particular pathway metabolites, implying intensive local and global regulation. This work demonstrated the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria, as well as its utility a powerful tool for validating previous research.
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18
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Fléchard M, Duchesne R, Tahrioui A, Bouffartigues E, Depayras S, Hardouin J, Lagy C, Maillot O, Tortuel D, Azuama CO, Clamens T, Duclairoir-Poc C, Catel-Ferreira M, Gicquel G, Feuilloley MGJ, Lesouhaitier O, Heipieper HJ, Groleau MC, Déziel É, Cornelis P, Chevalier S. The absence of SigX results in impaired carbon metabolism and membrane fluidity in Pseudomonas aeruginosa. Sci Rep 2018; 8:17212. [PMID: 30464317 PMCID: PMC6249292 DOI: 10.1038/s41598-018-35503-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
In Pseudomonas aeruginosa, SigX is an extra-cytoplasmic function σ factor that belongs to the cell wall stress response network. In previous studies, we made the puzzling observation that sigX mutant growth was severely affected in rich lysogeny broth (LB) but not in minimal medium. Here, through comparative transcriptomic and proteomic analysis, we show that the absence of SigX results in dysregulation of genes, whose products are mainly involved in transport, carbon and energy metabolisms. Production of most of these genes is controlled by carbon catabolite repression (CCR), a key regulatory system than ensures preferential carbon source uptake and utilization, substrate prioritization and metabolism. The strong CCR response elicited in LB was lowered in a sigX mutant, suggesting altered nutrient uptake. Since the absence of SigX affects membrane composition and fluidity, we suspected membrane changes to cause such phenotype. The detergent polysorbate 80 (PS80) can moderately destabilize the envelope resulting in non-specific increased nutrient intake. Remarkably, growth, membrane fluidity and expression of dysregulated genes in the sigX mutant strain were restored in LB supplemented with PS80. Altogether, these data suggest that SigX is indirectly involved in CCR regulation, possibly via its effects on membrane integrity and fluidity.
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Affiliation(s)
- Maud Fléchard
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Rachel Duchesne
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ali Tahrioui
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Emeline Bouffartigues
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ségolène Depayras
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Julie Hardouin
- Normandie Université, Université de Rouen Normandie, Laboratoire Polymères Biopolymères Surfaces, PBS, UMR, 6270 CNRS, Mont-Saint-Aignan, France
| | - Coralie Lagy
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Maillot
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Damien Tortuel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cecil Onyedikachi Azuama
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Thomas Clamens
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cécile Duclairoir-Poc
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Manuella Catel-Ferreira
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Gwendoline Gicquel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Marc G J Feuilloley
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Lesouhaitier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, UFZ Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Éric Déziel
- INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | - Pierre Cornelis
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Sylvie Chevalier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France.
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19
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Sun Y, Luo G, Zhao L, Huang L, Qin Y, Su Y, Yan Q. Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida. Front Immunol 2018; 9:1624. [PMID: 30061893 PMCID: PMC6054955 DOI: 10.3389/fimmu.2018.01624] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/02/2018] [Indexed: 11/15/2022] Open
Abstract
Pseudomonas plecoglossicida is an important pathogen for aquaculture and causes high mortality in various marine fishes. Expression of sigX was found significantly up-regulated at 18°C than at 28°C, which was verified by quantitative real-time PCR (qRT-PCR). RNAi significantly reduced the content of sigX mRNA of P. plecoglossicida, whether in in vitro or in the spleen at all sampling time points. Compared with the wild-type strain, the infection of sigX-RNAi strain resulted in the onset time delay, and 20% reduction in mortality of Epinephelus coioides, as well as alleviates in the symptoms of E. coioides spleen. Compared with wild-type strain, the gene silence of sigX in P. plecoglossicida resulted in a significant change in transcriptome of infected E. coioides. The result of gene ontology and KEGG analysis on E. coioides showed that genes of serine-type endopeptidase and chemokine signaling pathway, coagulation and complement system, and intestinal immune network for IgA production pathway were mostly affected by sigX of P. plecoglossicida. Meanwhile, the immune genes were associated with different number of miRNA and lncRNA, and some miRNAs were associated with more than one gene at the same time. The results indicated that sigX was a virulent gene of P. plecoglossicida. The up-regulation of the immune pathways made E. coioides more likely to kill sigX-RNAi strain than the wild-type strain of P. plecoglossicida, while the immune genes were regulated by miRNA and lncRNA by a complex mode.
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Affiliation(s)
- Yujia Sun
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Gang Luo
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yingxue Qin
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China
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20
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Abstract
A large number of antisense transcripts have been detected in diverse microbial genomes and considerable effort has been devoted to elucidating the functional role of antisense transcription. In this study, we reanalysed extensive RNA sequencing data from the opportunistic pathogen Pseudomonas aeruginosa and found that the majority of genes have a propensity for antisense transcription. Although antisense transcripts were found in more than 80 % of the genes of the P. aeruginosa genome, the majority of sequencing reads were mapping sense and only a minority (<2 %) were mapping antisense to genes. Similarly to the sense expression levels, the antisense expression levels varied under different environmental conditions, with the sense and antisense expression levels often being inversely regulated and modulated by the activity of alternative sigma factors. Environment-modulated antisense transcription showed a bias towards being antisense to genes within regions of genomic plasticity and to those encoding small regulatory RNAs. In the future, the validation and functional characterization of antisense transcripts, and novel transcripts that are antisense to small regulatory RNAs in particular, have the potential to contribute to our understanding of the various levels of transcriptional regulation and its dynamics in the bacterial pathogen P. aeruginosa.
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Affiliation(s)
- Denitsa Eckweiler
- Present address: Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE, Centre of Experimental and Clinical Infection Research, Hannover, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute of Molecular Bacteriology, TWINCORE, Centre of Experimental and Clinical Infection Research, Hannover, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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21
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Chevalier S, Bouffartigues E, Bazire A, Tahrioui A, Duchesne R, Tortuel D, Maillot O, Clamens T, Orange N, Feuilloley MGJ, Lesouhaitier O, Dufour A, Cornelis P. Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:706-721. [PMID: 29729420 DOI: 10.1016/j.bbagrm.2018.04.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/06/2018] [Accepted: 04/30/2018] [Indexed: 01/26/2023]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, like all members of the genus Pseudomonas, has the capacity to thrive in very different environments, ranging from water, plant roots, to animals, including humans to whom it can cause severe infections. This remarkable adaptability is reflected in the number of transcriptional regulators, including sigma factors in this bacterium. Among those, the 19 to 21 extracytoplasmic sigma factors (ECFσ) are endowed with different regulons and functions, including the iron starvation σ (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFσ AlgU, SigX and SbrI, and the unorthodox σVreI involved in the expression of virulence. Recently published data show that these ECFσ have separate regulons although presenting some cross-talk. We will present evidence that these different ECFσ are involved in the expression of different phenotypes, ranging from cell-wall stress response, production of extracellular polysaccharides, formation of biofilms, to iron acquisition.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France.
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alexis Bazire
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Ali Tahrioui
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Rachel Duchesne
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Damien Tortuel
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Thomas Clamens
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
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22
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Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley MGJ, Orange N, Dufour A, Cornelis P. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev 2017; 41:698-722. [PMID: 28981745 DOI: 10.1093/femsre/fux020] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Josselin Bodilis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Laboratoire de Biotechnologie et Chimie Marines EA 3884, Université de Bretagne-Sud (UEB), 56321 Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
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23
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Li X, Gu GQ, Chen W, Gao LJ, Wu XH, Zhang LQ. The outer membrane protein OprF and the sigma factor SigX regulate antibiotic production in Pseudomonas fluorescens 2P24. Microbiol Res 2017; 206:159-167. [PMID: 29146252 DOI: 10.1016/j.micres.2017.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/09/2017] [Accepted: 10/15/2017] [Indexed: 10/18/2022]
Abstract
Pseudomonas fluorescens 2P24 produces 2,4-diacetylphloroglucinol (2,4-DAPG) as the major antibiotic compound that protects plants from soil-borne diseases. Expression of the 2,4-DAPG biosynthesis enzymes, which are encoded by the phlACBD locus, is under the control of a delicate regulatory network. In this study, we identified a novel role for the outer membrane protein gene oprF, in negatively regulating the 2,4-DAPG production by using random mini-Tn5 mutagentsis. A sigma factor gene sigX was located immediately upstream of the oprF gene and shown to be a positive regulator for oprF transcription and 2,4-DAPG production. Genetic analysis of an oprF and sigX double-mutant indicated that the 2,4-DAPG regulation by oprF was dependent on SigX. The sigX gene did not affect PhlA and PhlD expression, but positively regulated the level of malonyl-CoA, the substrate of 2,4-DAPG synthesis, by influencing the expression of acetyl-CoA carboxylases. Further investigations revealed that sigX transcription was induced under conditions of salt starvation or glycine addition. All these findings indicate that SigX is a novel regulator of substrate supplements for 2,4-DAPG production.
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Affiliation(s)
- Xu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Gao-Qi Gu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Wei Chen
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Li-Juan Gao
- Beijing Centre for Physical and Chemical Analysis, Beijing, 100089, China
| | - Xue-Hong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China; Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Beijing, China
| | - Li-Qun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China; Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Beijing, China.
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24
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Ebert M, Laaß S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E, Jahn D. FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae. Front Microbiol 2017; 8:642. [PMID: 28473807 PMCID: PMC5398030 DOI: 10.3389/fmicb.2017.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/29/2017] [Indexed: 11/14/2022] Open
Abstract
The heterotrophic marine bacterium Dinoroseobacter shibae utilizes aerobic respiration and anaerobic denitrification supplemented with aerobic anoxygenic photosynthesis for energy generation. The aerobic to anaerobic transition is controlled by four Fnr/Crp family regulators in a unique cascade-type regulatory network. FnrL is utilizing an oxygen-sensitive Fe-S cluster for oxygen sensing. Active FnrL is inducing most operons encoding the denitrification machinery and the corresponding heme biosynthesis. Activation of gene expression of the high oxygen affinity cbb3-type and repression of the low affinity aa3-type cytochrome c oxidase is mediated by FnrL. Five regulator genes including dnrE and dnrF are directly controlled by FnrL. Multiple genes of the universal stress protein (USP) and cold shock response are further FnrL targets. DnrD, most likely sensing NO via a heme cofactor, co-induces genes of denitrification, heme biosynthesis, and the regulator genes dnrE and dnrF. DnrE is controlling genes for a putative Na+/H+ antiporter, indicating a potential role of a Na+ gradient under anaerobic conditions. The formation of the electron donating primary dehydrogenases is coordinated by FnrL and DnrE. Many plasmid encoded genes were DnrE regulated. DnrF is controlling directly two regulator genes including the Fe-S cluster biosynthesis regulator iscR, genes of the electron transport chain and the glutathione metabolism. The genes for nitrate reductase and CO dehydrogenase are repressed by DnrD and DnrF. Both regulators in concert with FnrL are inducing the photosynthesis genes. One of the major denitrification operon control regions, the intergenic region between nirS and nosR2, contains one Fnr/Dnr binding site. Using regulator gene mutant strains, lacZ-reporter gene fusions in combination with promoter mutagenesis, the function of the single Fnr/Dnr binding site for FnrL-, DnrD-, and partly DnrF-dependent nirS and nosR2 transcriptional activation was shown. Overall, the unique regulatory network of the marine bacterium D. shibae for the transition from aerobic to anaerobic growth composed of four Crp/Fnr family regulators was elucidated.
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Affiliation(s)
- Matthias Ebert
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Sebastian Laaß
- Institute for Molecular Biosciences, Goethe-University FrankfurtFrankfurt, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Louisa Roselius
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
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25
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Binder SC, Eckweiler D, Schulz S, Bielecka A, Nicolai T, Franke R, Häussler S, Meyer-Hermann M. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Sci Rep 2016; 6:22212. [PMID: 26915971 PMCID: PMC4768184 DOI: 10.1038/srep22212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/10/2016] [Indexed: 01/30/2023] Open
Abstract
The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability.
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Affiliation(s)
- Sebastian C Binder
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38124 Braunschweig, Germany
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26
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The LasB Elastase of Pseudomonas aeruginosa Acts in Concert with Alkaline Protease AprA To Prevent Flagellin-Mediated Immune Recognition. Infect Immun 2015; 84:162-71. [PMID: 26502908 DOI: 10.1128/iai.00939-15] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/16/2015] [Indexed: 01/02/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is capable of establishing severe and persistent infections in various eukaryotic hosts. It encodes a wide array of virulence factors and employs several strategies to evade immune detection. In the present study, we screened the Harvard Medical School transposon mutant library of P. aeruginosa PA14 for bacterial factors that modulate interleukin-8 responses in A549 human airway epithelial cells. We found that in addition to the previously identified alkaline protease AprA, the elastase LasB is capable of degrading exogenous flagellin under calcium-replete conditions and prevents flagellin-mediated immune recognition. Our results indicate that the production of two proteases with anti-flagellin activity provides a failsafe mechanism for P. aeruginosa to ensure the maintenance of protease-dependent immune-modulating functions.
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27
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Abstract
Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knock-ins, as well as single-nucleotide insertions, deletions and substitutions, in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selections are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic-resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ∼2 weeks.
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Bonocora RP, Smith C, Lapierre P, Wade JT. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. PLoS Genet 2015; 11:e1005552. [PMID: 26425847 PMCID: PMC4591121 DOI: 10.1371/journal.pgen.1005552] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription. There are two families of σ factor: σ70 and σ54. Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences, in association with RNA polymerase, in a transcriptionally inactive state. We have determined positions in the Escherichia coli genome that are bound by σ54, the archetypal member of the σ54 family. Surprisingly, we identified 135 binding sites for σ54, a huge increase over the number of previously described sites. Our data suggest that there are more than 250 σ54 sites in total. Strikingly, most σ54 binding sites are located inside genes, whereas only one intragenic σ54 binding site has previously been described. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved in other bacterial species. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this notion, we identify three σ54 promoters in E. coli that are located inside genes but drive transcription of unusual mRNAs for the neighboring genes.
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Affiliation(s)
- Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail:
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The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation. mBio 2015; 6:e00749. [PMID: 26126853 PMCID: PMC4488947 DOI: 10.1128/mbio.00749-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phenotypic variability among bacteria depends on gene expression in response to different environments, and it also reflects differences in genomic structure. In this study, we analyzed transcriptome sequencing (RNA-seq) profiles of 151 Pseudomonas aeruginosa clinical isolates under standard laboratory conditions and of one P. aeruginosa type strain under 14 different environmental conditions. Our approach allowed dissection of the impact of the genetic background versus environmental cues on P. aeruginosa gene expression profiles and revealed that phenotypic variation was larger in response to changing environments than between genomically different isolates. We demonstrate that mutations within the global regulator LasR affect more than one trait (pleiotropy) and that the interaction between mutations (epistasis) shapes the P. aeruginosa phenotypic plasticity landscape. Because of pleiotropic and epistatic effects, average genotype and phenotype measures appeared to be uncorrelated in P. aeruginosa. This work links experimental data of unprecedented complexity with evolution theory and delineates the transcriptional landscape of the opportunistic pathogen Pseudomonas aeruginosa. We found that gene expression profiles are most strongly influenced by environmental cues, while at the same time the transcriptional profiles were also shaped considerably by genetic variation within global regulators. The comprehensive set of transcriptomic and genomic data of more than 150 clinical P. aeruginosa isolates will be made publically accessible to all researchers via a dedicated web interface. Both Pseudomonas specialists interested in expression and regulation of specific genes and researchers from other fields with more global interest in the phenotypic and genotypic variation of this important model species can access all information on various levels of detail.
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Bouffartigues E, Moscoso JA, Duchesne R, Rosay T, Fito-Boncompte L, Gicquel G, Maillot O, Bénard M, Bazire A, Brenner-Weiss G, Lesouhaitier O, Lerouge P, Dufour A, Orange N, Feuilloley MGJ, Overhage J, Filloux A, Chevalier S. The absence of the Pseudomonas aeruginosa OprF protein leads to increased biofilm formation through variation in c-di-GMP level. Front Microbiol 2015; 6:630. [PMID: 26157434 PMCID: PMC4477172 DOI: 10.3389/fmicb.2015.00630] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/09/2015] [Indexed: 11/13/2022] Open
Abstract
OprF is the major outer membrane porin in bacteria belonging to the Pseudomonas genus. In previous studies, we have shown that OprF is required for full virulence expression of the opportunistic pathogen Pseudomonas aeruginosa. Here, we describe molecular insights on the nature of this relationship and report that the absence of OprF leads to increased biofilm formation and production of the Pel exopolysaccharide. Accordingly, the level of c-di-GMP, a key second messenger in biofilm control, is elevated in an oprF mutant. By decreasing c-di-GMP levels in this mutant, both biofilm formation and pel gene expression phenotypes were restored to wild-type levels. We further investigated the impact on two small RNAs, which are associated with the biofilm lifestyle, and found that expression of rsmZ but not of rsmY was increased in the oprF mutant and this occurs in a c-di-GMP-dependent manner. Finally, the extracytoplasmic function (ECF) sigma factors AlgU and SigX displayed higher activity levels in the oprF mutant. Two genes of the SigX regulon involved in c-di-GMP metabolism, PA1181 and adcA (PA4843), were up-regulated in the oprF mutant, partly explaining the increased c-di-GMP level. We hypothesized that the absence of OprF leads to a cell envelope stress that activates SigX and results in a c-di-GMP elevated level due to higher expression of adcA and PA1181. The c-di-GMP level can in turn stimulate Pel synthesis via increased rsmZ sRNA levels and pel mRNA, thus affecting Pel-dependent phenotypes such as cell aggregation and biofilm formation. This work highlights the connection between OprF and c-di-GMP regulatory networks, likely via SigX (ECF), on the regulation of biofilm phenotypes.
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Affiliation(s)
- Emeline Bouffartigues
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Joana A Moscoso
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London London, UK
| | - Rachel Duchesne
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Thibaut Rosay
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Laurène Fito-Boncompte
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Gwendoline Gicquel
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Olivier Maillot
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Magalie Bénard
- Cell Imaging Platform of Normandy (PRIMACEN), Institute for Research and Innovation in Biomedicine, University of Rouen Mont-Saint-Aignan, France
| | - Alexis Bazire
- EA 3884-Laboratoire de Biotechnologie et Chimie Marines, Institut Universitaire Européen de la Mer, Université de Bretagne-Sud Lorient, France
| | - Gerald Brenner-Weiss
- Institute of Functional Interfaces, Karlsruhe Institute of Technology Karlsruhe, Germany
| | - Olivier Lesouhaitier
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Patrice Lerouge
- Glyco-MeV Laboratory, University of Rouen, Normandy University Mont-Saint-Aignan, France
| | - Alain Dufour
- EA 3884-Laboratoire de Biotechnologie et Chimie Marines, Institut Universitaire Européen de la Mer, Université de Bretagne-Sud Lorient, France
| | - Nicole Orange
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Marc G J Feuilloley
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
| | - Joerg Overhage
- Institute of Functional Interfaces, Karlsruhe Institute of Technology Karlsruhe, Germany
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London London, UK
| | - Sylvie Chevalier
- EA 4312-Laboratory of Microbiology Signals and Microenvironment, University of Rouen - Normandy University Evreux, France
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Bielecki P, Jensen V, Schulze W, Gödeke J, Strehmel J, Eckweiler D, Nicolai T, Bielecka A, Wille T, Gerlach RG, Häussler S. Cross talk between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa. Nucleic Acids Res 2015; 43:6413-25. [PMID: 26082498 PMCID: PMC4513871 DOI: 10.1093/nar/gkv599] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/25/2015] [Indexed: 01/08/2023] Open
Abstract
Two-component systems (TCS) serve as stimulus-response coupling mechanisms to allow organisms to adapt to a variety of environmental conditions. The opportunistic pathogen Pseudomonas aeruginosa encodes for more than 100 TCS components. To avoid unwanted cross-talk, signaling cascades are very specific, with one sensor talking to its cognate response regulator (RR). However, cross-regulation may provide means to integrate different environmental stimuli into a harmonized output response. By applying a split luciferase complementation assay, we identified a functional interaction of two RRs of the OmpR/PhoB subfamily, namely PhoB and TctD in P. aeruginosa. Transcriptional profiling, ChIP-seq analysis and a global motif scan uncovered the regulons of the two RRs as well as a quadripartite binding motif in six promoter regions. Phosphate limitation resulted in PhoB-dependent expression of the downstream genes, whereas the presence of TctD counteracted this activation. Thus, the integration of two important environmental signals e.g. phosphate availability and the carbon source are achieved by a titration of the relative amounts of two phosphorylated RRs that inversely regulate a common subset of genes. In conclusion, our results on the PhoB and TctD mediated two-component signal transduction pathways exemplify how P. aeruginosa may exploit cross-regulation to adapt bacterial behavior to complex environments.
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Affiliation(s)
- Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Vanessa Jensen
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Wiebke Schulze
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Julia Gödeke
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Janine Strehmel
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Denitsa Eckweiler
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany Department of Molecular Bacteriology; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Agata Bielecka
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany Department of Molecular Bacteriology; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Thorsten Wille
- Junior Research Group 3, Robert Koch-Institute, Wernigerode Branch, Burgstrasse 37, 38855 Wernigerode, Germany
| | - Roman G Gerlach
- Junior Research Group 3, Robert Koch-Institute, Wernigerode Branch, Burgstrasse 37, 38855 Wernigerode, Germany
| | - Susanne Häussler
- Institute of Molecular Bacteriology, TWINCORE GmbH, Centre for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany Department of Molecular Bacteriology; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
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Blanka A, Düvel J, Dötsch A, Klinkert B, Abraham WR, Kaever V, Ritter C, Narberhaus F, Häussler S. Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition. Sci Signal 2015; 8:ra36. [PMID: 25872871 DOI: 10.1126/scisignal.2005943] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Most bacteria can form multicellular communities called biofilms on biotic and abiotic surfaces. This multicellular response to surface contact correlates with an increased resistance to various adverse environmental conditions, including those encountered during infections of the human host and exposure to antimicrobial compounds. Biofilm formation occurs when freely swimming (planktonic) cells encounter a surface, which stimulates the chemosensory-like, surface-sensing system Wsp and leads to generation of the intracellular second messenger 3',5'-cyclic-di-guanosine monophosphate (c-di-GMP). We identified adaptive mutations in a clinical small colony variant (SCV) of Pseudomonas aeruginosa and correlated their presence with self-aggregating growth behavior and an enhanced capacity to form biofilms. We present evidence that a point mutation in the 5' untranslated region of the accBC gene cluster, which encodes components of an enzyme responsible for fatty acid biosynthesis, was responsible for a stabilized mRNA structure that resulted in reduced translational efficiency and an increase in the proportion of short-chain fatty acids in the plasma membrane. We propose a model in which these changes in P. aeruginosa serve as a signal for the Wsp system to constitutively produce increased amounts of c-di-GMP and thus play a role in the regulation of adhesion-stimulated bacterial responses.
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Affiliation(s)
- Andrea Blanka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30625 Hannover, Germany
| | - Juliane Düvel
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30625 Hannover, Germany. Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Andreas Dötsch
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30625 Hannover, Germany. Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Birgit Klinkert
- Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wolf-Rainer Abraham
- Department of Chemical Microbiology, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, 30625 Hannover, Germany
| | - Christiane Ritter
- Department of Macromolecular Interactions, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30625 Hannover, Germany. Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.
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Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S. Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk. PLoS Pathog 2015; 11:e1004744. [PMID: 25780925 PMCID: PMC4362757 DOI: 10.1371/journal.ppat.1004744] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/11/2015] [Indexed: 12/31/2022] Open
Abstract
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN. Pseudomonas aeruginosa is well known for its high adaptability to a large range of environmental conditions, including those encountered within the human host. Transcription initiation represents a major regulatory target which drives versatility, and enables bacterial adaptation to challenging conditions and expression of virulence and pathogenicity. In bacteria, this process is largely orchestrated by sigma factors. Here, we performed an integrative approach, and by the combined use of three global profiling technologies uncovered the networks of 10 alternative sigma factors in the opportunistic pathogen P. aeruginosa. We demonstrate that these networks largely represent self-contained functional modules which exhibit a limited but highly specific crosstalk to build up higher-level functions. Our results do not only give extensive information on sigma factor binding sites throughout the P. aeruginosa genome, but also advance the understanding of sigma factor network architecture which provides bacteria with a framework to function adequately in their environment.
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Affiliation(s)
- Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Dötsch
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Hornischer
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian Bruchmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Juliane Düvel
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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Mirouze N, Bidnenko E, Noirot P, Auger S. Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis. Microbiologyopen 2015; 4:423-35. [PMID: 25755103 PMCID: PMC4475385 DOI: 10.1002/mbo3.249] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/22/2015] [Accepted: 02/02/2015] [Indexed: 01/13/2023] Open
Abstract
Under nitrogen limitation conditions, Bacillus subtilis induces a sophisticated network of adaptation responses. More precisely, the B. subtilis TnrA regulator represses or activates directly or indirectly the expression of a hundred genes in response to nitrogen availability. The global TnrA regulon have already been identified among which some directly TnrA-regulated genes have been characterized. However, a genome-wide mapping of in vivo TnrA-binding sites was still needed to clearly define the set of genes directly regulated by TnrA. Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we now provide in vivo evidence that TnrA reproducibly binds to 42 regions on the chromosome. Further analysis with real-time in vivo transcriptional profiling, combined with results from previous reports, allowed us to define the TnrA primary regulon. We identified 35 promoter regions fulfilling three criteria necessary to be part of this primary regulon: (i) TnrA binding in ChIP-on-chip experiments and/or in previous in vitro studies; (ii) the presence of a TnrA box; (iii) TnrA-dependent expression regulation. In addition, the TnrA primary regulon delimitation allowed us to improve the TnrA box consensus. Finally, our results reveal new interconnections between the nitrogen regulatory network and other cellular processes.
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Affiliation(s)
- Nicolas Mirouze
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Elena Bidnenko
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Philippe Noirot
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Sandrine Auger
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
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Fitzgerald DM, Bonocora RP, Wade JT. Comprehensive mapping of the Escherichia coli flagellar regulatory network. PLoS Genet 2014; 10:e1004649. [PMID: 25275371 PMCID: PMC4183435 DOI: 10.1371/journal.pgen.1004649] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 08/03/2014] [Indexed: 12/14/2022] Open
Abstract
Flagellar synthesis is a highly regulated process in all motile bacteria. In Escherichia coli and related species, the transcription factor FlhDC is the master regulator of a multi-tiered transcription network. FlhDC activates transcription of a number of genes, including some flagellar genes and the gene encoding the alternative Sigma factor FliA. Genes whose expression is required late in flagellar assembly are primarily transcribed by FliA, imparting temporal regulation of transcription and coupling expression to flagellar assembly. In this study, we use ChIP-seq and RNA-seq to comprehensively map the E. coli FlhDC and FliA regulons. We define a surprisingly restricted FlhDC regulon, including two novel regulated targets and two binding sites not associated with detectable regulation of surrounding genes. In contrast, we greatly expand the known FliA regulon. Surprisingly, 30 of the 52 FliA binding sites are located inside genes. Two of these intragenic promoters are associated with detectable noncoding RNAs, while the others either produce highly unstable RNAs or are inactive under these conditions. Together, our data redefine the E. coli flagellar regulatory network, and provide new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process. Flagella are surface-associated appendages that propel bacteria and are involved in diverse functions such as chemotaxis, surface attachment, and host cell invasion. Flagella are incredibly complex macromolecular machines that are energetically costly to produce, assemble, and power. Flagellar production is tightly regulated and flagellar components are only synthesized when flagellar motility is advantageous. Regulation also ensures that flagellar components are produced in roughly the same order in which they are needed, increasing efficiency of the assembly process. The transcriptional regulation of flagellar genes has been studied extensively in the model organism Escherichia coli; however, many questions remain. We have used an unbiased, genome-wide approach to comprehensively identify all of the binding sites and regulatory targets for the two key regulators of flagellar synthesis, FlhDC and FliA. Our results redefine the flagellar regulatory network, and suggest that FliA binds many sites that are not associated with productive transcription. This work is important because it suggests possible new functions for FliA outside of the transcription of canonical mRNAs, and it provides new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
| | - Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail:
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The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms. J Bacteriol 2014; 196:4163-71. [PMID: 25225275 DOI: 10.1128/jb.02000-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Regulation of gene expression plays a key role in bacterial adaptability to changes in the environment. An integral part of this gene regulatory network is achieved via quorum sensing (QS) systems that coordinate bacterial responses under high cellular densities. In the nosocomial pathogen Pseudomonas aeruginosa, the 2-alkyl-4-quinolone (pqs) signaling pathway is crucial for bacterial survival under stressful conditions. Biosynthesis of the Pseudomonas quinolone signal (PQS) is dependent on the pqsABCDE operon, which is positively regulated by the LysR family regulator PqsR and repressed by the transcriptional regulator protein RhlR. However, the molecular mechanisms underlying this inhibition have remained elusive. Here, we demonstrate that not only PqsR but also RhlR activates transcription of pqsA. The latter uses an alternative transcriptional start site and induces expression of a longer transcript that forms a secondary structure in the 5' untranslated leader region. As a consequence, access of the ribosome to the Shine-Dalgarno sequence is restricted and translation efficiency reduced. We propose a model of a novel posttranscriptional regulation mechanism that fine-tunes PQS biosynthesis, thus highlighting the complexity of quorum sensing in P. aeruginosa.
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Llamas MA, Imperi F, Visca P, Lamont IL. Cell-surface signaling inPseudomonas: stress responses, iron transport, and pathogenicity. FEMS Microbiol Rev 2014; 38:569-97. [DOI: 10.1111/1574-6976.12078] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/20/2014] [Accepted: 05/27/2014] [Indexed: 01/06/2023] Open
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Bouffartigues E, Duchesne R, Bazire A, Simon M, Maillot O, Dufour A, Feuilloley M, Orange N, Chevalier S. Sucrose favors Pseudomonas aeruginosa pellicle production through the extracytoplasmic function sigma factor SigX. FEMS Microbiol Lett 2014; 356:193-200. [PMID: 24861220 DOI: 10.1111/1574-6968.12482] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/16/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022] Open
Abstract
Pseudomonas aeruginosa biofilm formation was increased by addition of sucrose to Luria-Bertani medium, whereas addition of NaCl to a final similar osmolarity and use of maltose instead of sucrose, were ineffective. In a previous study, we showed that the extracytoplasmic sigma factor SigX is activated in the presence of sucrose. The sucrose-mediated pellicle increase was abolished in a sigX mutant strain. Sucrose addition led to an increase in pel expression and cyclic-diguanylate (c-di-GMP) pool level production. Interestingly, these two phenotypes were strongly decreased in a sigX mutant. Since pel is not known as a SigX-target, we suspect SigX to be involved in the c-di-GMP production. We found that expression of the diguanylate cyclase PA4843 gene was increased in the presence of sucrose at least partly through SigX activity. Our study shows that sucrose itself rather than osmolarity favours the biofilm mode of P. aeruginosa through the activation of SigX.
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Affiliation(s)
- Emeline Bouffartigues
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), EA 4312, Normandie Université, Université de Rouen, Rouen, France
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Nicastro GG, Kaihami GH, Pereira TO, Meireles DA, Groleau MC, Déziel E, Baldini RL. Cyclic-di-GMP levels affect Pseudomonas aeruginosa fitness in the presence of imipenem. Environ Microbiol 2014; 16:1321-33. [PMID: 24975931 DOI: 10.1111/1462-2920.12422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 11/26/2022]
Abstract
A large number of genes coding for enzymes predicted to synthesize and degrade 3'-5'-cyclic diguanylic acid (c-di-GMP) is found in most bacterial genomes and this dinucleotide emerged as an intracellular signal-controlling bacterial behaviour. An association between high levels of c-di-GMP and antibiotic resistance may be expected because c-di-GMP regulates biofilm formation and this mode of growth leads to enhanced antibiotic resistance. However, a clear understanding of this correlation has not been established. We found that increased levels of c-di-GMP in Pseudomonas aeruginosa improve fitness in the presence of imipenem, even when grown as planktonic cells. P. aeruginosa post-transcriptionally regulates the amounts of five porins in response to c-di-GMP, including OprD, responsible for imipenem uptake. Cells with low c-di-GMP levels are consequently more sensitive to this antibiotic. Main efflux pumps or β-lactamase genes did not show altered mRNA levels in P. aeruginosa strains with modified different c-di-GMP concentrations. Together, our findings show that c-di-GMP levels modulate fitness of planktonic cultures in the presence of imipenem.
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Affiliation(s)
- Gianlucca G Nicastro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Tümmler B, Wiehlmann L, Klockgether J, Cramer N. Advances in understanding Pseudomonas. F1000PRIME REPORTS 2014; 6:9. [PMID: 24592321 PMCID: PMC3913036 DOI: 10.12703/p6-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa, the type species of pseudomonads, is an opportunistic pathogen that colonizes a wide range of niches. Current genome sequencing projects are producing previously inconceivable detail about the population biology and evolution of P. aeruginosa. Its pan-genome has a larger genetic repertoire than the human genome, which explains the broad metabolic capabilities of P. aeruginosa and its ubiquitous distribution in aquatic habitats. P. aeruginosa may persist in the airways of individuals with cystic fibrosis for decades. The ongoing whole-genome analyses of serial isolates from cystic fibrosis patients provide the so far singular opportunity to monitor the microevolution of a bacterial pathogen during chronic infection over thousands of generations. Although the evolution in cystic fibrosis lungs is neutral overall, some pathoadaptive mutations are selected during the within-host evolutionary process. Even a single mutation may be sufficient to generate novel complex traits provided that predisposing mutational events have previously occurred in the clonal lineage.
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