1
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Rodríguez-Urretavizcaya B, Vilaplana L, Marco MP. Strategies for Quorum Sensing inhibition as a tool for controlling Pseudomonas aeruginosa infections. Int J Antimicrob Agents 2024; 64:107323. [PMID: 39242051 DOI: 10.1016/j.ijantimicag.2024.107323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/06/2024] [Accepted: 08/29/2024] [Indexed: 09/09/2024]
Abstract
Antibiotic resistance is one of the most important concerns in global health today. A growing number of infections are becoming harder to treat with conventional drugs and fewer new antibiotics are being developed. In this context, strategies based on blocking or attenuating virulence pathways that do not focus on eradication of bacteria are potential therapeutic approaches that should reduce the selective pressure exerted on the pathogen. This virulence depletion can be achieved by inhibiting the conserved quorum sensing (QS) system, a mechanism that enables bacteria to communicate with one another in a density-dependent manner. QS regulates gene expression, leading to the activation of important processes such as virulence and biofilm formation. This review highlights the approaches reported so far for disrupting different steps of the QS system of the multiresistant pathogen Pseudomonas aeruginosa. The authors describe different types of molecules (including enzymes, natural and synthetic small molecules, and antibodies) already identified as P. aeruginosa quorum quenchers (QQs) or QS inhibitors (QSIs), grouped according to the QS circuit that they block (Las, Rhl, Pqs and some examples from the controversial pathway Iqs). The discovery of new QQs and QSIs is expected to help reduce antibiotic doses, or at least to provide options that act as adjuvants to enhance the effect of antibiotic treatment. Moreover, this article outlines the advantages and possible drawbacks of each strategy and provides perspectives on the potential developments in this field in the future.
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Affiliation(s)
- Bárbara Rodríguez-Urretavizcaya
- Nanobiotechnology for diagnostics group (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Lluïsa Vilaplana
- Nanobiotechnology for diagnostics group (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - M-Pilar Marco
- Nanobiotechnology for diagnostics group (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
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2
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Juszczuk-Kubiak E. Molecular Aspects of the Functioning of Pathogenic Bacteria Biofilm Based on Quorum Sensing (QS) Signal-Response System and Innovative Non-Antibiotic Strategies for Their Elimination. Int J Mol Sci 2024; 25:2655. [PMID: 38473900 DOI: 10.3390/ijms25052655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
One of the key mechanisms enabling bacterial cells to create biofilms and regulate crucial life functions in a global and highly synchronized way is a bacterial communication system called quorum sensing (QS). QS is a bacterial cell-to-cell communication process that depends on the bacterial population density and is mediated by small signalling molecules called autoinducers (AIs). In bacteria, QS controls the biofilm formation through the global regulation of gene expression involved in the extracellular polymeric matrix (EPS) synthesis, virulence factor production, stress tolerance and metabolic adaptation. Forming biofilm is one of the crucial mechanisms of bacterial antimicrobial resistance (AMR). A common feature of human pathogens is the ability to form biofilm, which poses a serious medical issue due to their high susceptibility to traditional antibiotics. Because QS is associated with virulence and biofilm formation, there is a belief that inhibition of QS activity called quorum quenching (QQ) may provide alternative therapeutic methods for treating microbial infections. This review summarises recent progress in biofilm research, focusing on the mechanisms by which biofilms, especially those formed by pathogenic bacteria, become resistant to antibiotic treatment. Subsequently, a potential alternative approach to QS inhibition highlighting innovative non-antibiotic strategies to control AMR and biofilm formation of pathogenic bacteria has been discussed.
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Affiliation(s)
- Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
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3
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Keegan NR, Colón Torres NJ, Stringer AM, Prager LI, Brockley MW, McManaman CL, Wade JT, Paczkowski JE. Promoter selectivity of the RhlR quorum-sensing transcription factor receptor in Pseudomonas aeruginosa is coordinated by distinct and overlapping dependencies on C4-homoserine lactone and PqsE. PLoS Genet 2023; 19:e1010900. [PMID: 38064526 PMCID: PMC10732425 DOI: 10.1371/journal.pgen.1010900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection of small molecule autoinducers, which facilitate the synchronous expression of genes involved in group behaviors, such as virulence factor production and biofilm formation. The Pseudomonas aeruginosa quorum sensing network consists of multiple interconnected transcriptional regulators, with the transcription factor, RhlR, acting as one of the main drivers of quorum sensing behaviors. RhlR is a LuxR-type transcription factor that regulates its target genes when bound to its cognate autoinducer, C4-homoserine lactone, which is synthesized by RhlI. RhlR function is also regulated by the metallo-β-hydrolase enzyme, PqsE. We recently showed that PqsE binds RhlR to alter its affinity for promoter DNA, a new mechanism of quorum-sensing receptor activation. Here, we perform ChIP-seq analyses of RhlR to map the binding of RhlR across the P. aeruginosa genome, and to determine the impact of C4-homoserine lactone and PqsE on RhlR binding to different sites across the P. aeruginosa genome. We identify 40 RhlR binding sites, all but three of which are associated with genes known to be regulated by RhlR. C4-homoserine lactone is required for maximal binding of RhlR to many of its DNA sites. Moreover, C4-homoserine lactone is required for maximal RhlR-dependent transcription activation from all sites, regardless of whether it impacts RhlR binding to DNA. PqsE is required for maximal binding of RhlR to many DNA sites, with similar effects on RhlR-dependent transcription activation from those sites. However, the effects of PqsE on RhlR specificity are distinct from those of C4-homoserine lactone, and PqsE is sufficient for RhlR binding to some DNA sites in the absence of C4-homoserine lactone. Together, C4-homoserine lactone and PqsE are required for RhlR binding at the large majority of its DNA sites. Thus, our work reveals three distinct modes of activation by RhlR: i) when RhlR is unbound by autoinducer but bound by PqsE, ii) when RhlR is bound by autoinducer but not bound by PqsE, and iii) when RhlR is bound by both autoinducer and PqsE, establishing a stepwise mechanism for the progression of the RhlR-RhlI-PqsE quorum sensing pathway in P. aeruginosa.
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Affiliation(s)
- Nicholas R. Keegan
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Nathalie J. Colón Torres
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Anne M. Stringer
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Lia I. Prager
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Matthew W. Brockley
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Charity L. McManaman
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Jon E. Paczkowski
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
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4
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Feathers JR, Richael EK, Simanek KA, Fromme JC, Paczkowski JE. Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation. Structure 2022; 30:1626-1636.e4. [PMID: 36379213 PMCID: PMC9722607 DOI: 10.1016/j.str.2022.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for thousands of deaths every year in the United States. P. aeruginosa virulence factor production is mediated by quorum sensing, a mechanism of bacterial cell-cell communication that relies on the production and detection of signal molecules called autoinducers. In P. aeruginosa, the transcription factor receptor RhlR is activated by a RhlI-synthesized autoinducer. We recently showed that RhlR-dependent transcription is enhanced by a physical interaction with the enzyme PqsE via increased affinity of RhlR for promoter DNA. However, the molecular basis for complex formation and how complex formation enhanced RhlR transcriptional activity remained unclear. Here, we report the structure of ligand-bound RhlR in complex with PqsE. Additionally, we determined the structure of the complex bound with DNA, revealing the mechanism by which RhlR-mediated transcription is enhanced by PqsE, thereby establishing the molecular basis for RhlR-dependent virulence factor production in P. aeruginosa.
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Affiliation(s)
- J Ryan Feathers
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Erica K Richael
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Kayla A Simanek
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jon E Paczkowski
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY 12201, USA.
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5
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Borgert SR, Henke S, Witzgall F, Schmelz S, Zur Lage S, Hotop SK, Stephen S, Lübken D, Krüger J, Gomez NO, van Ham M, Jänsch L, Kalesse M, Pich A, Brönstrup M, Häussler S, Blankenfeldt W. Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa. Nat Commun 2022; 13:7402. [PMID: 36456567 PMCID: PMC9715718 DOI: 10.1038/s41467-022-35030-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determine crystal structures of the complex and identify residues essential for the interaction. To corroborate the chaperone-like activity of PqsE, we design stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.
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Affiliation(s)
- Sebastian Roman Borgert
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Henke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Florian Witzgall
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Sven-Kevin Hotop
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Stephen
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Dennis Lübken
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jonas Krüger
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Core Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Mark Brönstrup
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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6
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Minetti CA, Remeta DP. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:1438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Affiliation(s)
- Conceição A. Minetti
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David P. Remeta
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
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7
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Taylor IR, Jeffrey PD, Moustafa DA, Goldberg JB, Bassler BL. The PqsE Active Site as a Target for Small Molecule Antimicrobial Agents against Pseudomonas aeruginosa. Biochemistry 2022; 61:1894-1903. [PMID: 35985643 PMCID: PMC9454246 DOI: 10.1021/acs.biochem.2c00334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The opportunistic pathogen Pseudomonas
aeruginosa causes antibiotic-resistant, nosocomial
infections in immuno-compromised
individuals and is a high priority for antimicrobial development.
Key to pathogenicity in P. aeruginosa are biofilm formation and virulence factor production. Both traits
are controlled by the cell-to-cell communication process called quorum
sensing (QS). QS involves the synthesis, release, and population-wide
detection of signal molecules called autoinducers. We previously reported
that the activity of the RhlR QS transcription factor depends on a
protein–protein interaction with the hydrolase, PqsE, and PqsE
catalytic activity is dispensable for this interaction. Nonetheless,
the PqsE–RhlR interaction could be disrupted by the substitution
of an active site glutamate residue with tryptophan [PqsE(E182W)].
Here, we show that disruption of the PqsE–RhlR interaction
via either the E182W change or alteration of PqsE surface residues
that are essential for the interaction with RhlR attenuates P. aeruginosa infection in a murine host. We use
crystallography to characterize the conformational changes induced
by the PqsE(E182W) substitution to define the mechanism underlying
disruption of the PqsE–RhlR interaction. A loop rearrangement
that repositions the E280 residue in PqsE(E182W) is responsible for
the loss of interaction. We verify the implications garnered from
the PqsE(E182W) structure using mutagenic, biochemical, and additional
structural analyses. We present the next generation of molecules targeting
the PqsE active site, including a structure of the tightest binding
of these compounds, BB584, in complex with PqsE. The findings presented
here provide insights into drug discovery against P.
aeruginosa with PqsE as the target.
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Affiliation(s)
- Isabelle R Taylor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Dina A Moustafa
- School of Medicine, Children's Healthcare of Atlanta, Inc., Department of Pediatrics, and Center for Cystic Fibrosis and Airway Diseases Research, Emory University, Atlanta, Georgia 30322, United States
| | - Joanna B Goldberg
- School of Medicine, Children's Healthcare of Atlanta, Inc., Department of Pediatrics, and Center for Cystic Fibrosis and Airway Diseases Research, Emory University, Atlanta, Georgia 30322, United States
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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8
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Letizia M, Mellini M, Fortuna A, Visca P, Imperi F, Leoni L, Rampioni G. PqsE Expands and Differentially Modulates the RhlR Quorum Sensing Regulon in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0096122. [PMID: 35604161 PMCID: PMC9241726 DOI: 10.1128/spectrum.00961-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 12/22/2022] Open
Abstract
In the opportunistic pathogen Pseudomonas aeruginosa, many virulence traits are finely regulated by quorum sensing (QS), an intercellular communication system that allows the cells of a population to coordinate gene expression in response to cell density. The key aspects underlying the functionality of the complex regulatory network governing QS in P. aeruginosa are still poorly understood, including the interplay between the effector protein PqsE and the transcriptional regulator RhlR in controlling the QS regulon. Different studies have focused on the characterization of PqsE- and RhlR-controlled genes in genetic backgrounds in which RhlR activity can be modulated by PqsE and pqsE expression is controlled by RhlR, thus hampering identification of the distinct regulons controlled by PqsE and RhlR. In this study, a P. aeruginosa PAO1 mutant strain with deletion of multiple QS elements and inducible expression of pqsE and/or rhlR was generated and validated. Transcriptomic analyses performed on this genetic background allowed us to unambiguously define the regulons controlled by PqsE and RhlR when produced alone or in combination. Transcriptomic data were validated via reverse transcription-quantitative PCR (RT-qPCR) and transcriptional fusions. Overall, our results showed that PqsE has a negligible effect on the P. aeruginosa transcriptome in the absence of RhlR, and that multiple RhlR subregulons exist with distinct dependency on PqsE. Overall, this study contributes to untangling the regulatory link between the pqs and rhl QS systems mediated by PqsE and RhlR and clarifying the impact of these QS elements on the P. aeruginosa transcriptome. IMPORTANCE The ability of Pseudomonas aeruginosa to cause difficult-to-treat infections relies on its capacity to fine-tune the expression of multiple virulence traits via the las, rhl, and pqs QS systems. Both the pqs effector protein PqsE and the rhl transcriptional regulator RhlR are required for full production of key virulence factors in vitro and pathogenicity in vivo. While it is known that PqsE can stimulate the ability of RhlR to control some virulence factors, no data are available to allow clear discrimination of the PqsE and RhlR regulons. The data produced in this study demonstrate that PqsE mainly impacts the P. aeruginosa transcriptome via an RhlR-dependent pathway and splits the RhlR regulon into PqsE-dependent and PqsE-independent subregulons. Besides contributing to untangling of the complex QS network of P. aeruginosa, our data confirm that both PqsE and RhlR are suitable targets for the development of antivirulence drugs.
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Affiliation(s)
| | - Marta Mellini
- Department of Science, Roma Tre University, Rome, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, Roma Tre University, Rome, Italy
| | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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9
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Resistance Is Not Futile: The Role of Quorum Sensing Plasticity in Pseudomonas aeruginosa Infections and Its Link to Intrinsic Mechanisms of Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10061247. [PMID: 35744765 PMCID: PMC9228389 DOI: 10.3390/microorganisms10061247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of extracellular signal molecules called autoinducers (AI). Quorum sensing is required for virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. In P. aeruginosa, LasR and RhlR are homologous LuxR-type soluble transcription factor receptors that bind their cognate AIs and activate the expression of genes encoding functions required for virulence and biofilm formation. While some bacterial signal transduction pathways follow a linear circuit, as phosphoryl groups are passed from one carrier protein to another ultimately resulting in up- or down-regulation of target genes, the QS system in P. aeruginosa is a dense network of receptors and regulators with interconnecting regulatory systems and outputs. Once activated, it is not understood how LasR and RhlR establish their signaling hierarchy, nor is it clear how these pathway connections are regulated, resulting in chronic infection. Here, we reviewed the mechanisms of QS progression as it relates to bacterial pathogenesis and antimicrobial resistance and tolerance.
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10
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Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Thioesterase enzyme families: Functions, structures, and mechanisms. Protein Sci 2022; 31:652-676. [PMID: 34921469 PMCID: PMC8862431 DOI: 10.1002/pro.4263] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.
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Affiliation(s)
- Benjamin T. Caswell
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Caio C. de Carvalho
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Hung Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Monikrishna Roy
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Tin Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - David C. Cantu
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
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11
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The PqsE-RhlR Interaction Regulates RhlR DNA Binding to Control Virulence Factor Production in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0210821. [PMID: 35019777 PMCID: PMC8754118 DOI: 10.1128/spectrum.02108-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes disease in immunocompromised individuals and individuals with underlying pulmonary disorders. P. aeruginosa virulence is controlled by quorum sensing (QS), a bacterial cell-cell communication mechanism that underpins transitions between individual and group behaviors. In P. aeruginosa, the PqsE enzyme and the QS receptor RhlR directly interact to control the expression of genes involved in virulence. Here, we show that three surface-exposed arginine residues on PqsE comprise the site required for interaction with RhlR. We show that a noninteracting PqsE variant [PqsE(NI)] possesses catalytic activity, but is incapable of promoting virulence phenotypes, indicating that interaction with RhlR, and not catalysis, drives these PqsE-dependent behaviors. Biochemical characterization of the PqsE-RhlR interaction coupled with RNA-seq analyses demonstrates that the PqsE-RhlR complex increases the affinity of RhlR for DNA, enabling enhanced expression of genes encoding key virulence factors. These findings provide the mechanism for PqsE-dependent regulation of RhlR and identify a unique regulatory feature of P. aeruginosa QS and its connection to virulence. IMPORTANCE Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of molecules called autoinducers (AI). QS is required for virulence in the human pathogen Pseudomonas aeruginosa, which can cause fatal infections in patients with underlying pulmonary disorders. In this study, we determine the molecular basis for the physical interaction between two virulence-driving QS components, PqsE and RhlR. We find that the ability of PqsE to bind RhlR correlates with virulence factor production. Since current antimicrobial therapies exacerbate the growing antibiotic resistance problem because they target bacterial growth, we suggest that the PqsE-RhlR interface discovered here represents a new candidate for targeting with small molecule inhibition. Therapeutics that disrupt the PqsE-RhlR interaction should suppress virulence. Targeting bacterial behaviors such as QS, rather than bacterial growth, represents an attractive alternative for exploration because such therapies could potentially minimize the development of resistance.
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12
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Abstract
Antimicrobial resistance is a serious medical threat, particularly given the decreasing rate of discovery of new treatments. Although attempts to find new treatments continue, it has become clear that merely discovering new antimicrobials, even if they are new classes, will be insufficient. It is essential that new strategies be aggressively pursued. Toward that end, the search for treatments that can mitigate bacterial virulence and tilt the balance of host-pathogen interactions in favor of the host has become increasingly popular. In this review, we will discuss recent progress in this field, with a special focus on synthetic small molecule antivirulents that have been identified from high-throughput screens and on treatments that are effective against the opportunistic human pathogen Pseudomonas aeruginosa.
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13
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Taylor IR, Paczkowski JE, Jeffrey PD, Henke BR, Smith CD, Bassler BL. Inhibitor Mimetic Mutations in the Pseudomonas aeruginosa PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production. ACS Chem Biol 2021; 16:740-752. [PMID: 33793200 PMCID: PMC8056388 DOI: 10.1021/acschembio.1c00049] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
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Pseudomonas
aeruginosa is an opportunistic human
pathogen that causes fatal infections. There exists an urgent need
for new antimicrobial agents to combat P. aeruginosa. We conducted a screen for molecules that bind the virulence-controlling
protein PqsE and characterized hit compounds for inhibition of PqsE
enzymatic activity. The binding conformations of two inhibitory molecules,
BB391 and BB393, were identified by crystallography, and inhibitor
binding was mimicked by the substitution of PqsE residues E182 and
S285 with tryptophan. Comparison of the inhibitor-mimetic mutations
to the catalytically inactive PqsE D73A protein demonstrated that
catalysis is not responsible for the role PqsE plays in driving virulence
factor production. Rather, the PqsE E182W protein fails to interact
with the quorum-sensing receptor, RhlR, and our results suggest that
it is this interaction that is responsible for promoting virulence
factor production in P. aeruginosa. These findings
provide a new route for drug discovery efforts targeting PqsE.
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Affiliation(s)
- Isabelle R. Taylor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jon E. Paczkowski
- Department of Health, Wadsworth Center, Albany, New York 12208, United States
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201, United States
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Brad R. Henke
- Opti-Mol Consulting, LLC, Cary, North Carolina 27518, United States
| | - Chari D. Smith
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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14
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González JM. Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis. Heliyon 2021; 7:e05867. [PMID: 33426353 PMCID: PMC7785958 DOI: 10.1016/j.heliyon.2020.e05867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/19/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-β-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
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15
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Baldelli V, D’Angelo F, Pavoncello V, Fiscarelli EV, Visca P, Rampioni G, Leoni L. Identification of FDA-approved antivirulence drugs targeting the Pseudomonas aeruginosa quorum sensing effector protein PqsE. Virulence 2020; 11:652-668. [PMID: 32423284 PMCID: PMC7549961 DOI: 10.1080/21505594.2020.1770508] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The ability of the bacterial pathogen Pseudomonas aeruginosa to cause both chronic and acute infections mainly relies on its capacity to finely modulate the expression of virulence factors through a complex network of regulatory circuits, including the pqs quorum sensing (QS) system. While in most QS systems the signal molecule/receptor complexes act as global regulators that modulate the expression of QS-controlled genes, the main effector protein of the pqs system is PqsE. This protein is involved in the synthesis of the QS signal molecules 2-alkyl-4(1H)-quinolones (AQs), but it also modulates the expression of genes involved in virulence factors production and biofilm formation via AQ-independent pathway(s). P. aeruginosa pqsE mutants disclose attenuated virulence in plant and animal infection models, hence PqsE is considered a good target for the development of antivirulence drugs against P. aeruginosa. In this study, the negative regulation exerted by PqsE on its own transcription has been exploited to develop a screening system for the identification of PqsE inhibitors in a library of FDA-approved drugs. This led to the identification of nitrofurazone and erythromycin estolate, two antibiotic compounds that reduce the expression of PqsE-dependent virulence traits and biofilm formation in the model strain P. aeruginosa PAO1 at concentrations far below those affecting the bacterial growth rate. Notably, both drugs reduce the production of the PqsE-controlled virulence factor pyocyanin also in P. aeruginosa strains isolated from cystic fibrosis patients, and do not antagonize the activity of antibiotics commonly used to treat P. aeruginosa infection.
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Affiliation(s)
| | | | | | | | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
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16
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Current Knowledge and Future Directions in Developing Strategies to Combat Pseudomonas aeruginosa Infection. J Mol Biol 2020; 432:5509-5528. [PMID: 32750389 DOI: 10.1016/j.jmb.2020.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
In the face of growing antimicrobial resistance, there is an urgent need for the development of effective strategies to target Pseudomonas aeruginosa. This metabolically versatile bacterium can cause a wide range of severe opportunistic infections in patients with serious underlying medical conditions, such as those with burns, surgical wounds or people with cystic fibrosis. Many of the key adaptations that arise in this organism during infection are centered on core metabolism and virulence factor synthesis. Interfering with these processes may provide a new strategy to combat infection which could be combined with conventional antibiotics. This review will provide an overview of the most recent work that has advanced our understanding of P. aeruginosa infection. Strategies that exploit this recent knowledge to combat infection will be highlighted alongside potential alternative therapeutic options and their limitations.
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17
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Valastyan JS, Tota MR, Taylor IR, Stergioula V, Hone GAB, Smith CD, Henke BR, Carson KG, Bassler BL. Discovery of PqsE Thioesterase Inhibitors for Pseudomonas aeruginosa Using DNA-Encoded Small Molecule Library Screening. ACS Chem Biol 2020; 15:446-456. [PMID: 31880429 DOI: 10.1021/acschembio.9b00905] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pseudomonas aeruginosa is a leading cause of hospital-acquired infections in the United States. PqsE, a thioesterase enzyme, is vital for virulence of P. aeruginosa, making PqsE an attractive target for inhibition. Neither the substrate nor the product of PqsE catalysis has been identified. A library of 550 million DNA-encoded drug-like small molecules was screened for those that bind to the purified PqsE protein. The structures of the bound molecules were identified by high throughput sequencing of the attached DNA barcodes. Putative PqsE binders with the strongest affinity features were examined for inhibition of PqsE thioesterase activity in vitro. The most potent inhibitors were resynthesized off DNA and examined for the ability to alter PqsE thermal melting and for PqsE thioesterase inhibition. Here, we report the synthesis, biological activity, mechanism of action, and early structure-activity relationships of a series of 2-(phenylcarbamoyl)benzoic acids that noncompetitively inhibit PqsE. A small set of analogs designed to probe initial structure-activity relationships showed increases in potency relative to the original hits, the best of which has an IC50 = 5 μM. Compound refinement is required to assess their in vivo activities as the current compounds do not accumulate in the P. aeruginosa cytosol. Our strategy validates DNA-encoded compound library screening as a rapid and effective method to identify catalytic inhibitors of the PqsE protein, and more generally, for discovering binders to bacterial proteins revealed by genetic screening to have crucial in vivo activities but whose biological functions have not been well-defined.
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Affiliation(s)
- Julie S. Valastyan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Michael R. Tota
- Macroceutics Incorporated, (now HotSpot Therapeutics), Monmouth Junction, New Jersey 08852, United States
| | - Isabelle R. Taylor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Vasiliki Stergioula
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Graham A. B. Hone
- Macroceutics Incorporated, (now HotSpot Therapeutics), Monmouth Junction, New Jersey 08852, United States
| | - Chari D. Smith
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Brad R. Henke
- Opti-Mol Consulting, LLC, Cary, North Carolina 27513, United States
| | - Kenneth G. Carson
- Macroceutics Incorporated, (now HotSpot Therapeutics), Monmouth Junction, New Jersey 08852, United States
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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18
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García-Reyes S, Soberón-Chávez G, Cocotl-Yanez M. The third quorum-sensing system of Pseudomonas aeruginosa: Pseudomonas quinolone signal and the enigmatic PqsE protein. J Med Microbiol 2020; 69:25-34. [PMID: 31794380 DOI: 10.1099/jmm.0.001116] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that produces several virulence factors such as lectin A, pyocyanin, elastase and rhamnolipids. These compounds are controlled transcriptionally by three quorum-sensing circuits, two based on the synthesis and detection of N-acyl-homoserine-lactone termed the Las and Rhl system and a third system named the Pseudomonas quinolone signal (PQS) system, which is responsible for generating 2-alkyl-4(1 h)-quinolones (AQs). The transcriptional regulator called PqsR binds to the promoter of pqsABCDE in the presence of PQS or HHQ creating a positive feedback-loop. PqsE, encoded in the operon for AQ synthesis, is a crucial protein for pyocyanin production, activating the Rhl system by a still not fully understood mechanism. In turn, the regulation of the PQS system is modulated by Las and Rhl systems, which act positively and negatively, respectively. This review focuses on the PQS system, from its discovery to its role in Pseudomonas pathogenesis, such as iron depletion and pyocyanin synthesis that involves the PqsE protein - an intriguing player of this system.
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Affiliation(s)
- Selene García-Reyes
- Departamento de Biología molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo Postal 70228, C.P. 04510, Ciudad de México, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo Postal 70228, C.P. 04510, Ciudad de México, Mexico
| | - Miguel Cocotl-Yanez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México. Av. Universidad 3000, Cd. Universitaria, C.P. 04510, Coyoacán, Ciudad de México, Mexico
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19
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McCready AR, Paczkowski JE, Cong JP, Bassler BL. An autoinducer-independent RhlR quorum-sensing receptor enables analysis of RhlR regulation. PLoS Pathog 2019; 15:e1007820. [PMID: 31194839 PMCID: PMC6564026 DOI: 10.1371/journal.ppat.1007820] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. Pseudomonas aeruginosa, an opportunistic pathogen, employs multiple quorum-sensing systems to control behaviors including virulence factor production and biofilm formation. One P. aeruginosa quorum-sensing receptor, called RhlR, binds the cognate autoinducer N-butryl-homoserine lactone (C4HSL), and the RhlR:C4HSL complex activates transcription of target quorum-sensing genes. Here, we use a genetic screen to identify RhlR mutants that function independently of the autoinducer. The RhlR Y64F W68F V133F triple mutant, which we call RhlR*, exhibits ligand-independent activity in vitro and in vivo. RhlR* can drive wildtype biofilm formation and infection in a nematode animal model. The ability of RhlR* to properly regulate quorum-sensing-controlled genes in vivo depends on the quorum-sensing regulator RsaL keeping RhlR* activity in check. RhlR is known to function together with PqsE to control production of the virulence factor called pyocyanin. Likewise, RhlR* requires PqsE for pyocyanin production in planktonic cultures, however, PqsE is dispensable for RhlR*-driven pyocyanin production on surfaces. Finally, wildtype RhlR protein is not sufficiently stabilized by C4HSL to allow purification. However, wildtype RhlR can be stabilized by the synthetic ligand mBTL (meta-bromo-thiolactone) and RhlR* is stable without a ligand. These features enabled purification of the RhlR:mBTL complex and of RhlR* for in vitro examination of their biochemical activities. To our knowledge, this work reports the first RhlR protein purification.
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Affiliation(s)
- Amelia R. McCready
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jon E. Paczkowski
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jian-Ping Cong
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Bonnie L. Bassler
- The Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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20
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Quorum Sensing as Antivirulence Target in Cystic Fibrosis Pathogens. Int J Mol Sci 2019; 20:ijms20081838. [PMID: 31013936 PMCID: PMC6515091 DOI: 10.3390/ijms20081838] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder which leads to the secretion of a viscous mucus layer on the respiratory epithelium that facilitates colonization by various bacterial pathogens. The problem of drug resistance has been reported for all the species able to colonize the lung of CF patients, so alternative treatments are urgently needed. In this context, a valid approach is to investigate new natural and synthetic molecules for their ability to counteract alternative pathways, such as virulence regulating quorum sensing (QS). In this review we describe the pathogens most commonly associated with CF lung infections: Staphylococcus aureus, Pseudomonas aeruginosa, species of the Burkholderia cepacia complex and the emerging pathogens Stenotrophomonas maltophilia, Haemophilus influenzae and non-tuberculous Mycobacteria. For each bacterium, the QS system(s) and the molecules targeting the different components of this pathway are described. The amount of investigations published in the last five years clearly indicate the interest and the expectations on antivirulence therapy as an alternative to classical antibiotics.
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21
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Wellington S, Greenberg EP. Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk. mBio 2019; 10:e00146-19. [PMID: 30837333 PMCID: PMC6401477 DOI: 10.1128/mbio.00146-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 01/03/2023] Open
Abstract
Many species of proteobacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). Most AHL receptors are thought to be specific for their cognate signal, ensuring that bacteria cooperate and share resources only with closely related kin cells. Although specificity is considered fundamental to QS, there are reports of "promiscuous" receptors that respond broadly to nonself signals. These promiscuous responses expand the function of QS systems to include interspecies interactions and have been implicated in both interspecies competition and cooperation. Because bacteria are frequently members of polymicrobial communities, AHL cross talk between species could have profound impacts. To better understand the prevalence of QS promiscuity, we measured the activity of seven QS receptors in their native host organisms. To facilitate comparison of our results to previous studies, we also measured receptor activity using heterologous expression in Escherichia coli We found that the standard E. coli methods consistently overestimate receptor promiscuity and sensitivity and that overexpression of the receptors is sufficient to account for the discrepancy between native and E. coli reporters. Additionally, receptor overexpression resulted in AHL-independent activity in Pseudomonas aeruginosa Using our activation data, we developed a quantitative score of receptor selectivity. We find that the receptors display a wide range of selectivity and that most receptors respond sensitively and strongly to at least one nonself signal, suggesting a broad potential for cross talk between QS systems.IMPORTANCE Specific recognition of cognate signals is considered fundamental to cell signaling circuits as it creates fidelity in the communication system. In bacterial quorum sensing (QS), receptor specificity ensures that bacteria cooperate only with kin. There are examples, however, of QS receptors that respond promiscuously to multiple signals. "Eavesdropping" by these promiscuous receptors can be beneficial in both interspecies competition and cooperation. Despite their potential significance, we know little about the prevalence of promiscuous QS receptors. Further, many studies rely on methods requiring receptor overexpression, which is known to increase apparent promiscuity. By systematically studying QS receptors in their natural parent strains, we find that the receptors display a wide range of selectivity and that there is potential for significant cross talk between QS systems. Our results provide a basis for hypotheses about the evolution and function of promiscuous signal receptors and for predictions about interspecies interactions in complex microbial communities.
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Affiliation(s)
- Samantha Wellington
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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22
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Prothiwa M, Englmaier F, Böttcher T. Competitive Live-Cell Profiling Strategy for Discovering Inhibitors of the Quinolone Biosynthesis of Pseudomonas aeruginosa. J Am Chem Soc 2018; 140:14019-14023. [DOI: 10.1021/jacs.8b07629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michaela Prothiwa
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Felix Englmaier
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
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23
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Synthetic small molecules as anti-biofilm agents in the struggle against antibiotic resistance. Eur J Med Chem 2018; 161:154-178. [PMID: 30347328 DOI: 10.1016/j.ejmech.2018.10.036] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 01/24/2023]
Abstract
Biofilm formation significantly contributes to microbial survival in hostile environments and it is currently considered a key virulence factor for pathogens responsible for serious chronic infections. In the last decade many efforts have been made to identify new agents able to modulate bacterial biofilm life cycle, and many compounds have shown interesting activities in inhibiting biofilm formation or in dispersing pre-formed biofilms. However, only a few of these compounds were tested using in vivo models for their clinical significance. Contrary to conventional antibiotics, most of the anti-biofilm compounds act as anti-virulence agents as they do not affect bacterial growth. In this review we selected the most relevant literature of the last decade, focusing on the development of synthetic small molecules able to prevent bacterial biofilm formation or to eradicate pre-existing biofilms of clinically relevant Gram-positive and Gram-negative pathogens. In addition, we provide a comprehensive list of the possible targets to counteract biofilm formation and development, as well as a detailed discussion the advantages and disadvantages of the different current biofilm-targeting strategies.
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24
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Schütz C, Empting M. Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers. Beilstein J Org Chem 2018; 14:2627-2645. [PMID: 30410625 PMCID: PMC6204780 DOI: 10.3762/bjoc.14.241] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
The Gram-negative opportunistic pathogen Pseudomonas aeruginosa causes severe nosocomial infections. It uses quorum sensing (QS) to regulate and coordinate population-wide group behaviours in the infection process like concerted secretion of virulence factors. One very important signalling network is the Pseudomonas quinolone signal (PQS) QS. With the aim to devise novel and innovative anti-infectives, inhibitors have been designed to address the various potential drug targets present within pqs QS. These range from enzymes within the biosynthesis cascade of the signal molecules PqsABCDE to the receptor of these autoinducers PqsR (MvfR). This review shortly introduces P. aeruginosa and its pathogenicity traits regulated by the pqs system and highlights the published drug discovery efforts providing insights into the compound binding modes if available. Furthermore, suitability of the individual targets for pathoblocker design is discussed.
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Affiliation(s)
- Christian Schütz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Saarbrücken, Germany
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25
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The PqsE and RhlR proteins are an autoinducer synthase-receptor pair that control virulence and biofilm development in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2018; 115:E9411-E9418. [PMID: 30224496 PMCID: PMC6176596 DOI: 10.1073/pnas.1814023115] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The human pathogen Pseudomonas aeruginosa is the leading cause of hospital-acquired infections and, moreover, is resistant to commonly used antibiotics. P. aeruginosa uses the cell-to-cell communication process called quorum sensing (QS) to control virulence. QS relies on production and response to extracellular signaling molecules called autoinducers. Here, we identify the PqsE enzyme as the synthase of an autoinducer that activates the QS receptor RhlR. We show that the PqsE-derived autoinducer is the key molecule driving P. aeruginosa biofilm formation and virulence in animal models of infection. We propose that PqsE and RhlR constitute a QS synthase–receptor pair, and that this system can be targeted for antimicrobial development. Pseudomonas aeruginosa is a leading cause of life-threatening nosocomial infections. Many virulence factors produced by P. aeruginosa are controlled by the cell-to-cell communication process called quorum sensing (QS). QS depends on the synthesis, release, and groupwide response to extracellular signaling molecules called autoinducers. P. aeruginosa possesses two canonical LuxI/R-type QS systems, LasI/R and RhlI/R, that produce and detect 3OC12-homoserine lactone and C4-homoserine lactone, respectively. Previously, we discovered that RhlR regulates both RhlI-dependent and RhlI-independent regulons, and we proposed that an alternative ligand functions together with RhlR to control the target genes in the absence of RhlI. Here, we report the identification of an enzyme, PqsE, which is the alternative-ligand synthase. Using biofilm analyses, reporter assays, site-directed mutagenesis, protein biochemistry, and animal infection studies, we show that the PqsE-produced alternative ligand is the key autoinducer that promotes virulence gene expression. Thus, PqsE can be targeted for therapeutic intervention. Furthermore, this work shows that PqsE and RhlR function as a QS-autoinducer synthase–receptor pair that drives group behaviors in P. aeruginosa.
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Soukarieh F, Williams P, Stocks MJ, Cámara M. Pseudomonas aeruginosa Quorum Sensing Systems as Drug Discovery Targets: Current Position and Future Perspectives. J Med Chem 2018; 61:10385-10402. [PMID: 29999316 DOI: 10.1021/acs.jmedchem.8b00540] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is a serious threat to public health globally, manifested by the frequent emergence of multidrug resistant pathogens that render current chemotherapy inadequate. Health organizations worldwide have recognized the severity of this crisis and implemented action plans to contain its adverse consequences and prolong the utility of conventional antibiotics. Hence, there is a pressing need for new classes of antibacterial agents with novel modes of action. Quorum sensing (QS), a communication system employed by bacterial populations to coordinate virulence gene expression, is a potential target that has been intensively investigated over the past decade. This Perspective will focus on recent advances in targeting the three main quorum sensing systems ( las, rhl, and pqs) of a major opportunistic human pathogen, Pseudomonas aeruginosa, and will specifically evaluate the medicinal chemistry strategies devised to develop QS inhibitors from a drug discovery perspective.
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Affiliation(s)
- Fadi Soukarieh
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Michael J Stocks
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences , University of Nottingham , Nottingham , NG7 2RD , U.K
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Lin J, Cheng J, Wang Y, Shen X. The Pseudomonas Quinolone Signal (PQS): Not Just for Quorum Sensing Anymore. Front Cell Infect Microbiol 2018; 8:230. [PMID: 30023354 PMCID: PMC6039570 DOI: 10.3389/fcimb.2018.00230] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022] Open
Abstract
The Pseudomonas quinolone signal (PQS) has been studied primarily in the context of its role as a quorum-sensing signaling molecule. Recent data suggest, however, that this molecule may also function to mediate iron acquisition, cytotoxicity, outer-membrane vesicle biogenesis, or to exert host immune modulatory activities.
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Affiliation(s)
- Jinshui Lin
- Shaanxi Engineering and Technological Research Center for Conservation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, China.,College of Life Sciences, Yan'an University, Yan'an, China
| | - Juanli Cheng
- Shaanxi Engineering and Technological Research Center for Conservation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, China.,College of Life Sciences, Yan'an University, Yan'an, China
| | - Yao Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
| | - Xihui Shen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
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Kamal AAM, Petrera L, Eberhard J, Hartmann RW. Structure-functionality relationship and pharmacological profiles of Pseudomonas aeruginosa alkylquinolone quorum sensing modulators. Org Biomol Chem 2018; 15:4620-4630. [PMID: 28513746 DOI: 10.1039/c7ob00263g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An important paradigm in anti-infective research is the antivirulence concept. Pathoblockers are compounds which disarm bacteria of their arsenal of virulence factors. PqsR is a transcriptional regulator controlling the production of such factors in Pseudomonas aeruginosa, most prominently pyocyanin. In this work, a series of tool compounds based on the structure of the natural ligand 2-heptyl-4-quinolone (HHQ) were used for probing the structure-functionality relationship. Four different profiles are identified namely agonists, antagonists, inverse agonists and biphasic modulators. Molecular docking studies revealed that each class of the PqsR modulators showed distinctive interactions in the PqsR binding domain. It was found that the substituents in position 3 of the quinolone core act as a switch between the different profiles, according to their ability to donate or accept a hydrogen bond, or form a hydrophobic interaction. Finally, it was shown that only inverse agonists were able to strongly inhibit pyocyanin production.
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Affiliation(s)
- Ahmed A M Kamal
- Helmholtz-Institute for Pharmaceutical Research Saarland, Department of Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
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Witzgall F, Ewert W, Blankenfeldt W. Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis. Chembiochem 2017; 18:2045-2055. [PMID: 28834007 DOI: 10.1002/cbic.201700374] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 12/16/2022]
Abstract
Pseudomonas aeruginosa, a prevalent pathogen in nosocomial infections and a major burden in cystic fibrosis, uses three interconnected quorum-sensing systems to coordinate virulence processes. At variance with other Gram-negative bacteria, one of these systems relies on 2-alkyl-4(1H)-quinolones (Pseudomonas quinolone signal, PQS) and might hence be an attractive target for new anti-infective agents. Here we report crystal structures of the N-terminal domain of anthranilate-CoA ligase PqsA, the first enzyme of PQS biosynthesis, in complex with anthraniloyl-AMP and with 6-fluoroanthraniloyl-AMP (6FABA-AMP) at 1.4 and 1.7 Å resolution. We find that PqsA belongs to an unrecognized subfamily of anthranilate-CoA ligases that recognize the amino group of anthranilate through a water-mediated hydrogen bond. The complex with 6FABA-AMP explains why 6FABA, an inhibitor of PQS biosynthesis, is a good substrate of PqsA. Together, our data might pave a way to new pathoblockers in P. aeruginosa infections.
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Affiliation(s)
- Florian Witzgall
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Wiebke Ewert
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
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Kamal AAM, Maurer CK, Allegretta G, Haupenthal J, Empting M, Hartmann RW. Quorum Sensing Inhibitors as Pathoblockers for Pseudomonas aeruginosa Infections: A New Concept in Anti-Infective Drug Discovery. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Ji C, Sharma I, Pratihar D, Hudson LL, Maura D, Guney T, Rahme LG, Pesci EC, Coleman JP, Tan DS. Designed Small-Molecule Inhibitors of the Anthranilyl-CoA Synthetase PqsA Block Quinolone Biosynthesis in Pseudomonas aeruginosa. ACS Chem Biol 2016; 11:3061-3067. [PMID: 27658001 PMCID: PMC5117135 DOI: 10.1021/acschembio.6b00575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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The Gram-negative bacterial pathogen Pseudomonas aeruginosa uses three interconnected intercellular
signaling systems regulated
by the transcription factors LasR, RhlR, and MvfR (PqsR), which mediate
bacterial cell–cell communication via small-molecule natural
products and control the production of a variety of virulence factors.
The MvfR system is activated by and controls the biosynthesis of the
quinolone quorum sensing factors HHQ and PQS. A key step in the biosynthesis
of these quinolones is catalyzed by the anthranilyl-CoA synthetase
PqsA. To develop inhibitors of PqsA as novel potential antivirulence
antibiotics, we report herein the design and synthesis of sulfonyladeonsine-based
mimics of the anthranilyl-AMP reaction intermediate that is bound
tightly by PqsA. Biochemical, microbiological, and pharmacological
studies identified two potent PqsA inhibitors, anthranilyl-AMS (1) and anthranilyl-AMSN (2), that decreased HHQ
and PQS production in P. aeruginosa strain
PA14. However, these compounds did not inhibit
production of the virulence factor pyocyanin. Moreover, they exhibited
limited bacterial penetration in compound accumulation studies. This
work provides the most potent PqsA inhibitors reported to date and
sets the stage for future efforts to develop analogues with improved
cellular activity to investigate further the complex relationships
between quinolone biosynthesis and virulence factor production in P. aeruginosa and the therapeutic potential of targeting
PqsA.
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Affiliation(s)
| | | | | | - L. Lynn Hudson
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - Damien Maura
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
| | | | - Laurence G. Rahme
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Shriners Hospitals for
Children Boston, Boston, Massachusetts 02114, United States
| | - Everett C. Pesci
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - James P. Coleman
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
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