1
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Qiu H, Li Y, Yuan M, Chen H, Dandekar AA, Dai W. Uncovering a hidden functional role of the XRE-cupin protein PsdR as a novel quorum-sensing regulator in Pseudomonas aeruginosa. PLoS Pathog 2024; 20:e1012078. [PMID: 38484003 DOI: 10.1371/journal.ppat.1012078] [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: 11/16/2023] [Revised: 03/26/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
XRE-cupin family proteins containing an DNA-binding domain and a cupin signal-sensing domain are widely distributed in bacteria. In Pseudomonas aeruginosa, XRE-cupin transcription factors have long been recognized as regulators exclusively controlling cellular metabolism pathways. However, their potential functional roles beyond metabolism regulation remain unknown. PsdR, a typical XRE-cupin transcriptional regulator, was previously characterized as a local repressor involved solely in dipeptide metabolism. Here, by measuring quorum-sensing (QS) activities and QS-controlled metabolites, we uncover that PsdR is a new QS regulator in P. aeruginosa. Our RNA-seq analysis showed that rather than a local regulator, PsdR controls a large regulon, including genes associated with both the QS circuit and non-QS pathways. To unveil the underlying mechanism of PsdR in modulating QS, we developed a comparative transcriptome approach named "transcriptome profile similarity analysis" (TPSA). Using this TPSA method, we revealed that PsdR expression causes a QS-null-like transcriptome profile, resulting in QS-inactive phenotypes. Based on the results of TPSA, we further demonstrate that PsdR directly binds to the promoter for the gene encoding the QS master transcription factor LasR, thereby negatively regulating its expression and influencing QS activation. Moreover, our results showed that PsdR functions as a negative virulence regulator, as inactivation of PsdR enhanced bacterial cytotoxicity on host cells. In conclusion, we report on a new QS regulation role for PsdR, providing insights into its role in manipulating QS-controlled virulence. Most importantly, our findings open the door for a further discovery of untapped functions for other XRE-Cupin family proteins.
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Affiliation(s)
- Huifang Qiu
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yuanhao Li
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Min Yuan
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Huali Chen
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Ajai A Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Weijun Dai
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
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2
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Mendoza AG, Guercio D, Smiley MK, Sharma GK, Withorn JM, Hudson-Smith NV, Ndukwe C, Dietrich LEP, Boon EM. The histidine kinase NahK regulates pyocyanin production through the PQS system. J Bacteriol 2024; 206:e0027623. [PMID: 38169296 PMCID: PMC10809955 DOI: 10.1128/jb.00276-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Many bacterial histidine kinases work in two-component systems that combine into larger multi-kinase networks. NahK is one of the kinases in the GacS Multi-Kinase Network (MKN), which is the MKN that controls biofilm regulation in the opportunistic pathogen Pseudomonas aeruginosa. This network has also been associated with regulating many virulence factors P. aeruginosa secretes to cause disease. However, the individual role of each kinase is unknown. In this study, we identify NahK as a novel regulator of the phenazine pyocyanin (PYO). Deletion of nahK leads to a fourfold increase in PYO production, almost exclusively through upregulation of phenazine operon two (phz2). We determined that this upregulation is due to mis-regulation of all P. aeruginosa quorum-sensing (QS) systems, with a large upregulation of the Pseudomonas quinolone signal system and a decrease in production of the acyl-homoserine lactone-producing system, las. In addition, we see differences in expression of quorum-sensing inhibitor proteins that align with these changes. Together, these data contribute to understanding how the GacS MKN modulates QS and virulence and suggest a mechanism for cell density-independent regulation of quorum sensing. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative bacterium that establishes biofilms as part of its pathogenicity. P. aeruginosa infections are associated with nosocomial infections. As the prevalence of multi-drug-resistant P. aeruginosa increases, it is essential to understand underlying virulence molecular mechanisms. Histidine kinase NahK is one of several kinases in P. aeruginosa implicated in biofilm formation and dispersal. Previous work has shown that the nitric oxide sensor, NosP, triggers biofilm dispersal by inhibiting NahK. The data presented here demonstrate that NahK plays additional important roles in the P. aeruginosa lifestyle, including regulating bacterial communication mechanisms such as quorum sensing. These effects have larger implications in infection as they affect toxin production and virulence.
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Affiliation(s)
- Alicia G. Mendoza
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Danielle Guercio
- Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York, USA
| | - Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Gaurav K. Sharma
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - Jason M. Withorn
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | | | - Chika Ndukwe
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Elizabeth M. Boon
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
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3
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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4
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Lin H, Ning X, Wang D, Wang Q, Bai Y, Qu J. Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae. Appl Environ Microbiol 2023; 89:e0166223. [PMID: 38047646 PMCID: PMC10734536 DOI: 10.1128/aem.01662-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Antibiotics can induce dose-dependent hormetic effects on bacterial cell proliferation, i.e., low-dose stimulation and high-dose inhibition. However, the underlying molecular basis has yet to be clarified. Here, we showed that sulfonamides play dual roles as a weapon and signal against Comamonas testosteroni that can modulate cell physiology and phenotype. Subsequently, through investigating the hormesis mechanism, we proposed a comprehensive regulatory pathway for the hormetic effects of Comamonas testosteroni low-level sulfonamides and determined the generality of the observed regulatory model in the Comamonadaceae family. Considering the prevalence of Comamonadaceae in human guts and environmental ecosystems, we provide critical insights into the health and ecological effects of antibiotics.
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Affiliation(s)
- Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Xue Ning
- MaREI Centre, Environmental Research Institute, School of Engineering, University College Cork, Cork, Ireland
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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5
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Mellini M, Letizia M, Caruso L, Guiducci A, Meneghini C, Heeb S, Williams P, Cámara M, Visca P, Imperi F, Leoni L, Rampioni G. RsaL-driven negative regulation promotes heterogeneity in Pseudomonas aeruginosa quorum sensing. mBio 2023; 14:e0203923. [PMID: 37843294 PMCID: PMC10746200 DOI: 10.1128/mbio.02039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Single-cell analyses can reveal that despite experiencing identical physico-chemical conditions, individual bacterial cells within a monoclonal population may exhibit variations in gene expression. Such phenotypic heterogeneity has been described for several aspects of bacterial physiology, including QS activation. This study demonstrates that the transition of non-quorate cells to the quorate state is a graded process that does not occur at a specific cell density and that subpopulations of non-quorate cells also persist at high cell density. Here, we provide a mechanistic explanation for this phenomenon, showing that a negative feedback regulatory loop integrated into the las system has a pivotal role in promoting cell-to-cell variation in the QS activation state and in limiting the transition of non-quorate cells to the quorate state in P. aeruginosa.
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Affiliation(s)
- Marta Mellini
- Department of Science, University Roma Tre, Rome, Italy
| | | | | | | | | | - Stephan Heeb
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Miguel Cámara
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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6
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Simanek KA, Schumacher ML, Mallery CP, Shen S, Li L, Paczkowski JE. Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis. Nat Commun 2023; 14:7986. [PMID: 38042853 PMCID: PMC10693556 DOI: 10.1038/s41467-023-43702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Quorum sensing is a mechanism of bacterial communication that controls virulence gene expression. Pseudomonas aeruginosa regulates virulence via two synthase/transcription factor receptor pairs: LasI/R and RhlI/R. LasR is considered the master transcriptional regulator of quorum sensing, as it upregulates rhlI/R. However, clinical isolates often have inactivating mutations in lasR, while maintaining Rhl-dependent signaling. We sought to understand how quorum sensing progresses in isolates with lasR mutations, specifically via activation of RhlR. We find that clinical isolates with lasR inactivating mutations often harbor concurrent mutations in rhlI. Using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry, we discover that strains lacking lasR overproduce the RhlI-synthesized autoinducer and that RhlI variants re-calibrate autoinducer concentrations to wild-type levels, restoring virulent phenotypes. These findings provide a mechanism for the plasticity of quorum sensing progression in an acute infection niche.
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Affiliation(s)
- Kayla A Simanek
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Megan L Schumacher
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Caleb P Mallery
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Stella Shen
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA
| | - Lingyun Li
- Division of Environmental Health Sciences, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA
| | - Jon E Paczkowski
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA.
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA.
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7
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Koh CMM, Ping LSY, Xuan CHH, Theng LB, San HS, Palombo EA, Wezen XC. A data-driven machine learning approach for discovering potent LasR inhibitors. Bioengineered 2023; 14:2243416. [PMID: 37552115 PMCID: PMC10411317 DOI: 10.1080/21655979.2023.2243416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
The rampant spread of multidrug-resistant Pseudomonas aeruginosa strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the las quorum sensing (QS) system remains an attractive therapeutic strategy to combat P. aeruginosa infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat P. aeruginosa-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate P. aeruginosa infections.
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Affiliation(s)
- Christabel Ming Ming Koh
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Lilian Siaw Yung Ping
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Christopher Ha Heng Xuan
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Lau Bee Theng
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Hwang Siaw San
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Xavier Chee Wezen
- Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak, Malaysia
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8
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de Oliveira Pereira T, Groleau MC, Déziel E. Surface growth of Pseudomonas aeruginosa reveals a regulatory effect of 3-oxo-C 12-homoserine lactone in the absence of its cognate receptor, LasR. mBio 2023; 14:e0092223. [PMID: 37732738 PMCID: PMC10653899 DOI: 10.1128/mbio.00922-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/26/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE The bacterium Pseudomonas aeruginosa colonizes and thrives in many environments, in which it is typically found in surface-associated polymicrobial communities known as biofilms. Adaptation to this social behavior is aided by quorum sensing (QS), an intercellular communication system pivotal in the expression of social traits. Regardless of its importance in QS regulation, the loss of function of the master regulator LasR is now considered a conserved adaptation of P. aeruginosa, irrespective of the origin of the strains. By investigating the QS circuitry in surface-grown cells, we found an accumulation of QS signal 3-oxo-C12-HSL in the absence of its cognate receptor and activator, LasR. The current understanding of the QS circuit, mostly based on planktonic growing cells, is challenged by investigating the QS circuitry of surface-grown cells. This provides a new perspective on the beneficial aspects that underline the frequency of LasR-deficient isolates.
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Affiliation(s)
- Thays de Oliveira Pereira
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
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9
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Kesthely CA, Rogers RR, El Hafi B, Jean-Pierre F, O’Toole GA. Transcriptional profiling and genetic analysis of a cystic fibrosis airway-relevant model shows asymmetric responses to growth in a polymicrobial community. Microbiol Spectr 2023; 11:e0220123. [PMID: 37772884 PMCID: PMC10580927 DOI: 10.1128/spectrum.02201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 09/30/2023] Open
Abstract
Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to date provide a picture of the transcriptional responses of individual pathogens; however, there is relatively little data describing the transcriptional landscape of clinically relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica, we performed an RNA-Seq analysis on the biofilm population to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis largely do not alter their transcriptional profiles in the presence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context. IMPORTANCE Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can help explain clinical outcomes in the lungs of persons with CF. Here, we obtained transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.
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Affiliation(s)
- Christopher A. Kesthely
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Rendi R. Rogers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Bassam El Hafi
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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10
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Koirala P, Doody C, Blackwell H, Chandler JR. Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor in Chromobacterium subtsugae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.02.556004. [PMID: 37693375 PMCID: PMC10491235 DOI: 10.1101/2023.09.02.556004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The soil bacterium Chromobacterium substugae uses a single LuxI-R-type quorum-sensing system, CviI-R, to regulate genes in a cell density-dependent manner. CviI synthesizes the signal N-hexanoyl-homoserine lactone (C6-HSL) and CviR is a C6-HSL-responsive cytoplasmic transcription regulator. C6-HSL-bound CviR activates dozens of genes, for example the cdeAB-oprM cluster coding for an efflux pump conferring antibiotic resistance. The cdeAB-oprM genes are also regulated by an antibiotic-responsive transcription factor, CdeR, which represses expression of these genes. We are interested in understanding how C. subtsugae integrates different environmental cues to regulate antibiotic resistance. In this study, we sought to delineate the mechanism of regulation of the cdeAB-oprM genes by CviR and CdeR. In recombinant E. coli, the cdeA promoter is activated by CviR and repressed by CdeR. We identify non-overlapping sequence elements in the cdeA promoter that are required for CviR activation and CdeR repression, respectively. We also examined the role of CdeR in modulating cdeA activation by C6-HSL in C. subtsugae. We show that CviR and CdeR can independently modulate transcription from the cdeA promoter in C. subtsugae, consistent with the conclusion that CviR and CdeR regulate the cdeAB-oprM genes by interacting directly with different binding sites in the cdeA promoter. These results contribute to a molecular understanding of how the cdeAB-oprM genes are regulated and provide new insight into how C. subtsugae integrates different environmental cues to regulate antibiotic resistance.
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Affiliation(s)
- Pratik Koirala
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Cassie Doody
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Helen Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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11
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Kesthely CA, Rogers RR, Hafi BE, Jean-Pierre F, O’Toole GA. Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542191. [PMID: 37293107 PMCID: PMC10245937 DOI: 10.1101/2023.05.24.542191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to-date provide a picture of the transcriptional responses of individual pathogens, however, there is relatively little data describing the transcriptional landscape of clinically-relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica , we performed an RNA-Seq analysis to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis largely do not alter their transcriptional profiles in the presence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context. Importance Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can explain clinical outcomes in the lungs of persons with CF. Here we obtain transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.
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Affiliation(s)
| | - Rendi R. Rogers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - Bassam El Hafi
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
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12
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Haas AL, Zemke AC, Melvin JA, Armbruster CR, Hendricks MR, Moore J, Nouraie SM, Thibodeau PH, Lee SE, Bomberger JM. Iron bioavailability regulates Pseudomonas aeruginosa interspecies interactions through type VI secretion expression. Cell Rep 2023; 42:112270. [PMID: 36930643 PMCID: PMC10586262 DOI: 10.1016/j.celrep.2023.112270] [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: 08/24/2022] [Revised: 12/16/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
The cystic fibrosis (CF) respiratory tract harbors pathogenic bacteria that cause life-threatening chronic infections. Of these, Pseudomonas aeruginosa becomes increasingly dominant with age and is associated with worsening lung function and declining microbial diversity. We aimed to understand why P. aeruginosa dominates over other pathogens to cause worsening disease. Here, we show that P. aeruginosa responds to dynamic changes in iron concentration, often associated with viral infection and pulmonary exacerbations, to become more competitive via expression of the TseT toxic effector. However, this behavior can be therapeutically targeted using the iron chelator deferiprone to block TseT expression and competition. Overall, we find that iron concentration and TseT expression significantly correlate with microbial diversity in the respiratory tract of people with CF. These findings improve our understanding of how P. aeruginosa becomes increasingly dominant with age in people with CF and provide a therapeutically targetable pathway to help prevent this shift.
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Affiliation(s)
- Allison L Haas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Matthew R Hendricks
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Seyed Mehdi Nouraie
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Patrick H Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Division of Otolaryngology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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13
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Schuster M, Li C, Smith P, Kuttler C. Parameters, architecture and emergent properties of the Pseudomonas aeruginosa LasI/LasR quorum-sensing circuit. J R Soc Interface 2023; 20:20220825. [PMID: 36919437 PMCID: PMC10015328 DOI: 10.1098/rsif.2022.0825] [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: 11/15/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Quorum sensing is a widespread process in bacteria that controls collective behaviours in response to cell density. Populations of cells coordinate gene expression through the perception of self-produced chemical signals. Although this process is well-characterized genetically and biochemically, quantitative information about network properties, including induction dynamics and steady-state behaviour, is scarce. Here we integrate experiments with mathematical modelling to quantitatively analyse the LasI/LasR quorum sensing pathway in the opportunistic pathogen Pseudomonas aeruginosa. We determine key kinetic parameters of the pathway and, using the parametrized model, show that quorum sensing behaves as a bistable hysteretic switch, with stable on and off states. We investigate the significance of feedback architecture and find that positive feedback on signal production is critical for induction dynamics and bistability, whereas positive feedback on receptor expression and negative feedback on signal production play a minor role. Taken together, our data-based modelling approach reveals fundamental and emergent properties of a bacterial quorum sensing circuit, and provides evidence that native quorum sensing can indeed function as the gene expression switch it is commonly perceived to be.
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Affiliation(s)
- Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Christina Li
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Christina Kuttler
- Department of Mathematics, Technische Universität München, 85748 Garching, Germany
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14
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Loo C, Koirala P, Smith NC, Evans KC, Benomar S, Parisi IR, Oller A, Chandler JR. Cross-species activation of hydrogen cyanide production by a promiscuous quorum-sensing receptor promotes Chromobacterium subtsugae competition in a dual-species model. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36790401 DOI: 10.1099/mic.0.001294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Many saprophytic bacteria have LuxR-I-type acyl-homoserine lactone (AHL) quorum-sensing systems that may be important for competing with other bacteria in complex soil communities. LuxR AHL receptors specifically interact with cognate AHLs to cause changes in expression of target genes. Some LuxR-type AHL receptors have relaxed specificity and are responsive to non-cognate AHLs. These promiscuous receptors might be used to sense and respond to AHLs produced by other bacteria by eavesdropping. We are interested in understanding the role of eavesdropping during interspecies competition. The soil saprophyte Chromobacterium subtsugae has a single AHL circuit, CviR-I, which produces and responds to N-hexanoyl-HSL (C6-HSL). The AHL receptor CviR can respond to a variety of AHLs in addition to C6-HSL. In prior studies we have utilized a coculture model with C. subtsugae and another soil saprophyte, Burkholderia thailandensis. Using this model, we previously showed that promiscuous activation of CviR by B. thailandensis AHLs provides a competitive advantage to C. subtsugae. Here, we show that B. thailandensis AHLs activate transcription of dozens of genes in C. subtsugae, including the hcnABC genes coding for production of hydrogen cyanide. We show that hydrogen cyanide production is population density-dependent and demonstrate that the cross-induction of hydrogen cyanide by B. thailandensis AHLs provides a competitive advantage to C. subtsugae. Our results provide new information on C. subtsugae quorum sensing and are the basis for future studies aimed at understanding the role of eavesdropping in interspecies competition.
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Affiliation(s)
- Cheyenne Loo
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.,Present address: Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Pratik Koirala
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Nathan C Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Kara C Evans
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.,Present address: International Flavors and Fragrances Health and Biosciences, Madison WI, 53716, USA
| | - Saida Benomar
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.,Present address: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta GA, 30322, USA
| | - Isabelle R Parisi
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Anna Oller
- Department of Biological and Clinical Sciences, University of Central Missouri, Warrensburg, MO 64093, USA
| | - Josephine R Chandler
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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15
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Gajera G, Henriksen N, Cox B, Kothari V. Identification of anti-pathogenic activity among in silico predicted small-molecule inhibitors of Pseudomonas aeruginosa LasR or nitric oxide reductase (NOR). Drug Target Insights 2023; 17:101-109. [PMID: 37811195 PMCID: PMC10551673 DOI: 10.33393/dti.2023.2638] [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: 07/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Antibiotic-resistant Pseudomonas aeruginosa strains cause considerable morbidity and mortality globally. Identification of novel targets in this notorious pathogen is urgently warranted to facilitate discovery of new anti-pathogenic agents against it. This study attempted to identify small-molecule inhibitors of two important proteins LasR and nitric oxide reductase (NOR) in P. aeruginosa. 'Las' system can be said to be the 'master' regulator of quorum sensing in P. aeruginosa, whose receptor protein is LasR. Similarly, NOR is crucial to detoxification of reactive nitrogen species. Methods In silico identification of potential LasR or NOR inhibitors was attempted through a virtual screening platform AtomNet® to obtain a final subset of <100 top scoring compounds. These compounds were evaluated for their in vivo anti-pathogenic activity by challenging the model host Caenorhabditis elegans with P. aeruginosa in the presence or absence of test compounds. Survival of the worm population in 24-well assay plates was monitored over a period of 5 days microscopically. Results Of the 96 predicted LasR inhibitors, 11 exhibited anti-Pseudomonas activity (23%-96% inhibition of bacterial virulence as per third-day end-point) at 25-50 µg/mL. Of the 85 predicted NOR inhibitors, 8 exhibited anti-Pseudomonas activity (40%-85% inhibition of bacterial virulence as per second-day end-point) at 25-50 µg/mL. Conclusion Further investigation on molecular mode of action of compounds found active in this study is warranted. Virtual screening can be said to be a useful tool in narrowing down the list of compounds requiring actual wet-lab screening, saving considerable time and efforts for drug discovery.
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Affiliation(s)
- Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad - India
| | | | - Bryan Cox
- Atomwise Inc, San Francisco, CA - USA
| | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad - India
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16
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Cai W, Lu M, Cheng X, Dai W. Improved probe detection sensitivity by flexible tandem biotin labeling. J Microbiol Methods 2023; 204:106654. [PMID: 36509134 DOI: 10.1016/j.mimet.2022.106654] [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: 10/22/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
We develop a biotin-based tandem labeling approach to improve detection sensitivity of DNA probe. Through DNA polymerase-mediated overhand filling, the 3'end of DNA probe was tandemly labeled with biotin molecules. The intensity of biotin signals could be flexibly manipulated by controlling the introduced length of poly(A) in the 5' overhang.
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Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Mingqi Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyan Cheng
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
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17
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Deng T, Lin FC, Zink JI, Yu Q. Regulation of Bacterial Behavior by Light and Magnetism Mediated by Mesoporous Silica-Coated MnFe 2O 4@CoFe 2O 4 Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:56007-56017. [PMID: 36509713 DOI: 10.1021/acsami.2c12589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Unicellular bacterial cells exhibit diverse population behaviors (i.e., aggregation, dispersion, directed assembly, biofilm formation, etc.) to facilitate communication and cooperation. Suitable bacterial behaviors are required for efficient nutrient uptake, cell recycling, and stress response for environmental and industrial application of bacterial populations. However, it remains a great challenge to artificially control bacterial behaviors because of complicated genetic and biochemical mechanisms. In this study, we designed facile mesoporous silica nanoparticle (MSN)-based assemblies to intelligently regulate bacterial behaviors with the help of light and magnetic field. This system was composed of magnetic MSNs, i.e., MnFe2O4@CoFe2O4@MSN modified by photoactive spiropyran (SP), and the chitosan-based polymers ChiPSP, i.e., chitosan grafted by triphenylphosphine and SP. The assembly strongly bound bacterial cells, inducing reversible bacterial aggregation by visible-light irradiation and dark. Moreover, the formed bacterial aggregates could be further governed by a directed magnetic field (DMF) to form microfibers and by an alternating magnetic field (AMF) to form biofilms. This study realized stimulus-triggered regulation of bacterial behaviors by MSNs and implied the great power of chemical strategies in intelligent control of diverse biological processes for environmental and industrial applications.
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Affiliation(s)
- Tian Deng
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Fang-Chu Lin
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jeffrey I Zink
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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18
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Collective decision-making in Pseudomonas aeruginosa involves transient segregation of quorum-sensing activities across cells. Curr Biol 2022; 32:5250-5261.e6. [PMID: 36417904 DOI: 10.1016/j.cub.2022.10.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022]
Abstract
A hallmark of bacterial sociality is that groups can coordinate cooperative actions through a cell-to-cell communication process called quorum sensing (QS). QS regulates key bacterial phenotypes such as virulence in infections and digestion of extracellular compounds in the environment. Although QS responses are typically studied as group-level phenotypes, it is unclear whether individuals coordinate their actions at the single-cell level or whether group phenotypes simply reflect the sum of their noisy members. Here, we studied the behavior of Pseudomonas aeruginosa individuals by tracking their temporal commitments to the two intertwined Las and Rhl-QS systems, from low to high population density. Using chromosomally integrated fluorescent gene reporters, we found that QS gene expression (signal, receptor, and cooperative exoproduct) was noisy with heterogeneity peaking during the build-up phase of QS. Moreover, we observed the formation of discrete subgroups of cells that transiently segregate into two gene expression states: low Las-receptor expressers that instantly activate exoproduct production and high Las-receptor expressers with delayed exoproduct production. Later, gene expression activities converged with all cells fully committing to QS. We developed general mathematical models to show that gene expression segregation can mechanistically be spurred by molecular resource limitations during the initiation phase of regulatory cascades such as QS. Moreover, our models indicate that gene expression segregation across cells can operate as a built-in brake enabling a temporary bet-hedging strategy in unpredictable environments. Altogether, our work reveals that studying the behavior of bacterial individuals is key to understanding emergent collective actions at the group level.
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19
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Evolution of Quorum Sensing in Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation. mSystems 2022; 7:e0035422. [PMID: 36190124 PMCID: PMC9600717 DOI: 10.1128/msystems.00354-22] [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] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa populations evolving in cystic fibrosis lungs, animal hosts, natural environments and in vitro undergo extensive genetic adaption and diversification. A common mutational target is the quorum sensing (QS) system, a three-unit regulatory system that controls the expression of virulence factors and secreted public goods. Three evolutionary scenarios have been advocated to explain selection for QS mutants: (i) disuse of the regulon, (ii) cheating through the exploitation of public goods, or (ii) modulation of the QS regulon. Here, we examine these scenarios by studying a set of 61 QS mutants from an experimental evolution study. We observed nonsynonymous mutations in all three QS systems: Las, Rhl, and Pseudomonas Quinolone Signal (PQS). The majority of the Las mutants had large deletions of the Las regulon, resulting in loss of QS function and the inability to produce QS-regulated traits, thus supporting the first or second scenarios. Conversely, phenotypic and gene expression analyses of Rhl mutants support network modulation (third scenario), as these mutants overexpressed the Las and Rhl receptors and showed an altered QS-regulated trait production profile. PQS mutants also showed patterns of regulon modulation leading to strain diversification and phenotypic tradeoffs, where the upregulation of certain QS traits is associated with the downregulation of others. Overall, our results indicate that mutations in the different QS systems lead to diverging effects on the QS trait profile in P. aeruginosa populations. These mutations might not only affect the plasticity and diversity of evolved populations but could also impact bacterial fitness and virulence in infections. IMPORTANCE Pseudomonas aeruginosa uses quorum sensing (QS), a three-unit multilayered network, to coordinate expression of traits required for growth and virulence in the context of infections. Despite its importance for bacterial fitness, the QS regulon appears to be a common mutational target during long-term adaptation of P. aeruginosa in the host, natural environments, and experimental evolutions. This raises questions of why such an important regulatory system is under selection and how mutations change the profile of QS-regulated traits. Here, we examine a set of 61 experimentally evolved QS mutants to address these questions. We found that mutations involving the master regulator, LasR, resulted in an almost complete breakdown of QS, while mutations in RhlR and PqsR resulted in modulations of the regulon, where both the regulon structure and the QS-regulated trait profile changed. Our work reveals that natural selection drives diversification in QS activity patterns in evolving populations.
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20
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Styles MJ, Boursier ME, McEwan MA, Santa EE, Mattmann ME, Slinger BL, Blackwell HE. Autoinducer-fluorophore conjugates enable FRET in LuxR proteins in vitro and in cells. Nat Chem Biol 2022; 18:1115-1124. [PMID: 35927585 PMCID: PMC9529866 DOI: 10.1038/s41589-022-01089-1] [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: 09/29/2021] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Cell-to-cell signaling, or quorum sensing (QS), in many Gram-negative bacteria is governed by small molecule signals (N-acyl-L-homoserine lactones, AHLs) and their cognate receptors (LuxR-type proteins). The mechanistic underpinnings of QS in these bacteria are severely limited due to the challenges of isolating and manipulating most LuxR-type proteins. Reports of quantitative direct-binding experiments on LuxR-type proteins are scarce, and robust and generalizable methods that provide such data are largely nonexistent. We report herein a Förster resonance energy transfer (FRET) assay that leverages (1) conserved tryptophans located in the LuxR-type protein ligand-binding site and synthetic fluorophore-AHL conjugates, and (2) isolation of the proteins bound to weak agonists. The FRET assay permits straightforward measurement of ligand-binding affinities with receptor-either in vitro or in cells-and was shown to be compatible with six LuxR-type proteins. These methods will advance fundamental investigations of LuxR-type protein mechanism and the development of small molecule QS modulators.
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Affiliation(s)
- Matthew J Styles
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Emma E Santa
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Betty L Slinger
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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21
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Abstract
Quorum sensing is described as a widespread cell density-dependent signaling mechanism in bacteria. Groups of cells coordinate gene expression by secreting and responding to diffusible signal molecules. Theory, however, predicts that individual cells may short-circuit this mechanism by directly responding to the signals they produce irrespective of cell density. In this study, we characterize this self-sensing effect in the acyl-homoserine lactone quorum sensing system of Pseudomonas aeruginosa. We show that antiactivators, a set of proteins known to affect signal sensitivity, function to prevent self-sensing. Measuring quorum-sensing gene expression in individual cells at very low densities, we find that successive deletion of antiactivator genes qteE and qslA produces a bimodal response pattern, in which increasing proportions of constitutively induced cells coexist with uninduced cells. Comparing responses of signal-proficient and -deficient cells in cocultures, we find that signal-proficient cells show a much higher response in the antiactivator mutant background but not in the wild-type background. Our results experimentally demonstrate the antiactivator-dependent transition from group- to self-sensing in the quorum-sensing circuitry of P. aeruginosa. Taken together, these findings extend our understanding of the functional capacity of quorum sensing. They highlight the functional significance of antiactivators in the maintenance of group-level signaling and experimentally prove long-standing theoretical predictions.
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22
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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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23
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Genetic and Transcriptomic Characteristics of RhlR-Dependent Quorum Sensing in Cystic Fibrosis Isolates of Pseudomonas aeruginosa. mSystems 2022; 7:e0011322. [PMID: 35471121 PMCID: PMC9040856 DOI: 10.1128/msystems.00113-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested in determining whether there were reproducible genetic characteristics of these isolates and whether there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. We did not identify a common genetic mechanism to explain the switch from Las- to Rhl-dominated QS. We describe a core RhlR regulon encompassing 20 genes encoding 7 products. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infections and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understand QS beyond what has been described in laboratory strains. IMPORTANCE The bacterial pathogen Pseudomonas aeruginosa can cause chronic infections that are resistant to treatment in immunocompromised individuals. Over the course of these infections, the original infecting organism adapts to the host environment. P. aeruginosa uses a cell-cell signaling mechanism termed quorum sensing (QS) to regulate virulence factors and cooperative behaviors. The key QS regulator in laboratory strains, LasR, is frequently mutated in infection-adapted isolates, leaving another transcription factor, RhlR, in control of QS gene regulation. Such isolates provide an opportunity to understand Rhl-QS regulation without the confounding effects of LasR, as well as the scope of QS in the context of within-host evolution. We show that a core group of virulence genes is regulated by RhlR in a variety of infection-adapted LasR-null isolates. Our results reveal commonalities in infection-adapted QS gene regulation and key QS factors that may serve as therapeutic targets in the future.
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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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25
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Wang D, Chen H, Li J, Li T, Ren L, Liu J, Shen Y. Screening and validation of quorum quenching enzyme PF2571 from Pseudomonas fluorescens strain PF08 to inhibit the spoilage of red sea bream filets. Int J Food Microbiol 2022; 362:109476. [PMID: 34798478 DOI: 10.1016/j.ijfoodmicro.2021.109476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
Bacteria are the main cause of spoilage for fish and fishery products. Through the inactivation of the quorum sensing (QS) system, quorum quenching (QQ) enzymes can block the synthesis of bacterial virulence factors and effectively inhibit bacteria-induced food spoilage. This study analyzed the changes of microbiota in red sea bream filets during refrigerated storage. The results showed a decrease in microbial diversity with storage time, with Aeromonas veronii becoming the dominant bacteria on day 4. A novel N-acyl homoserine lactones (AHL) acylase PF2571, from the screened QQ bacterium Pseudomonas fluorescens PF08, was identified and expressed in Escherichia coli to evaluate its QQ efficiency and effects on spoilage potential. Spoilage-related QS factors of A. veronii BY-8, including biofilm formation, motility, and protease, lipase, and alginate production, were inhibited by PF2571. Its inhibitory effect on red sea bream spoilage was demonstrated by the lower freshness indicators for PF2571 treated filets. Our study demonstrates the potential of the QQ enzyme for prolonging the shelf life of fish and fishery products.
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Affiliation(s)
- Dangfeng Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Haitao Chen
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jianrong Li
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresource Utilization (Dalian Minzu University), Ministry of Education, Dalian, Liaoning 116029, China
| | - Likun Ren
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin, Heilongjiang 150076, China
| | - Jingyun Liu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Yue Shen
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
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Li S, Wu S, Ren Y, Meng Q, Yin J, Yu Z. Characterization of differentiated autoregulation of LuxI/LuxR-type quorum sensing system in Pseudoalteromonas. Biochem Biophys Res Commun 2022; 590:177-183. [PMID: 34990892 DOI: 10.1016/j.bbrc.2021.12.107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022]
Abstract
Gram-negative bacteria usually use acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR-type quorum sensing (QS) systems for cell-cell cooperation and/or bacteria-environment communication. LuxI and LuxR are AHLs synthase and receptor, respectively. These two parts could form a positive regulatory feedback loop, controlling various types of group behaviors. However, the autoregulation mechanisms between them are fragmented and could be highly differentiated in different bacteria. Here, we clarified the autoregulation mechanism between LuxI and LuxR in Pseudoalteromonas sp. R3. YasI (LuxI in strain R3) synthesizes two types of AHLs, C8-HSL and 3-OH-C8-HSL. It is worth noting that YasR (LuxR in strain R3) only responds to C8-HSL rather than 3-OH-C8-HSL. YasR-C8HSL can activate the yasI transcription by recognizing "lux box" at yasI upstream. Interestingly, YasR can directly promote the yasR expression with AHL-independent manner, but AHL absence caused by the yasI-deficiency led to the significant decrease in the yasR expression. Further study demonstrated that the yasI-deficiency can result in the decrease in the yasR mRNA stability. Notably, both yasI-deficiency and yasR-deficiency led to the significant decrease in the expression of hfq encoding RNA chaperone. Therefore, it was speculated that not only YasR itself can directly regulate the yasR transcription, but YasR-C8HSL complex indirectly affects the yasR mRNA stability by regulating Hfq.
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Affiliation(s)
- Shuangjia Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shijun Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yixuan Ren
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
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Functional metagenomic analysis of quorum sensing signaling in a nitrifying community. NPJ Biofilms Microbiomes 2021; 7:79. [PMID: 34711833 PMCID: PMC8553950 DOI: 10.1038/s41522-021-00250-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/08/2021] [Indexed: 01/12/2023] Open
Abstract
Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.
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Abstract
Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities in cases of chronic infections. Biofilms are regarded as a biological condition, where a large group of microorganisms gets adhered to a biotic or abiotic surface. In this context, Pseudomonas aeruginosa, a Gram-negative nosocomial pathogen is the main causative organism responsible for life-threatening and persistent infections in individuals affected with cystic fibrosis and other lung ailments. The bacteria can form a strong biofilm structure when it adheres to a surface suitable for the development of a biofilm matrix. These bacterial biofilms pose higher natural resistance to conventional antibiotic therapy due to their multiple tolerance mechanisms. This prevailing condition has led to an increasing rate of treatment failures associated with P. aeruginosa biofilm infections. A better understanding of the effect of a diverse group of antibiotics on established biofilms would be necessary to avoid inappropriate treatment strategies. Hence, the search for other alternative strategies as effective biofilm treatment options has become a growing area of research. The current review aims to give an overview of the mechanisms governing biofilm formation and the different strategies employed so far in the control of biofilm infections caused by P. aeruginosa. Moreover, this review can also help researchers to search for new antibiofilm agents to tackle the effect of biofilm infections that are currently imprudent to conventional antibiotics.
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Xuan G, Lv C, Xu H, Li K, Liu H, Xia Y, Xun L. Sulfane Sulfur Regulates LasR-Mediated Quorum Sensing and Virulence in Pseudomonas aeruginosa PAO1. Antioxidants (Basel) 2021; 10:antiox10091498. [PMID: 34573130 PMCID: PMC8469610 DOI: 10.3390/antiox10091498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
Sulfane sulfur, such as inorganic and organic polysulfide (HSn- and RSn-, n > 2), is a common cellular component, produced either from hydrogen sulfide oxidation or cysteine metabolism. In Pseudomonas aeruginosa PAO1, LasR is a quorum sensing master regulator. After binding its autoinducer, LasR binds to its target DNA to activate the transcription of a suite of genes, including virulence factors. Herein, we report that the production of hydrogen sulfide and sulfane sulfur were positively correlated in P. aeruginosa PAO1, and sulfane sulfur was able to modify LasR, which generated Cys188 persulfide and trisulfide and produced a pentasulfur link between Cys201 and Cys203. The modifications did not affect LasR binding to its target DNA site, but made it several-fold more effective than unmodified LasR in activating transcription in both in vitro and in vivo assays. On the contrary, H2O2 inactivates LasR via producing a disulfide bond between Cys201 and Cys203. P. aeruginosa PAO1 had a high cellular sulfane sulfur and high LasR activity in the mid log phase and early stationary phase, but a low sulfane sulfur and low LasR activity in the declination phase. Thus, sulfane sulfur is a new signaling factor in the bacterium, adding another level of control over LasR-mediated quorum sensing and turning down the activity in old cells.
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Affiliation(s)
- Guanhua Xuan
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
| | - Chuanjuan Lv
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
| | - Huangwei Xu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
- Correspondence: (Y.X.); (L.X.); Tel.: +86-532-5863-1572 (Y.X.); +1-509-335-2787 (L.X.)
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (G.X.); (C.L.); (H.X.); (K.L.); (H.L.)
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Correspondence: (Y.X.); (L.X.); Tel.: +86-532-5863-1572 (Y.X.); +1-509-335-2787 (L.X.)
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Inhibitory Effects of Artificial Sweeteners on Bacterial Quorum Sensing. Int J Mol Sci 2021; 22:ijms22189863. [PMID: 34576027 PMCID: PMC8472786 DOI: 10.3390/ijms22189863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Despite having been tagged as safe and beneficial, recent evidence remains inconclusive regarding the status of artificial sweeteners and their putative effects on gut microbiota. Gut microorganisms are essential for the normal metabolic functions of their host. These microorganisms communicate within their community and regulate group behaviors via a molecular system termed quorum sensing (QS). In the present study, we aimed to study the effects of artificial sweeteners on this bacterial communication system. Using biosensor assays, biophysical protein characterization methods, microscale thermophoresis, swarming motility assays, growth assays, as well as molecular docking, we show that aspartame, sucralose, and saccharin have significant inhibitory actions on the Gram-negative bacteria N-acyl homoserine lactone-based (AHL) communication system. Our studies indicate that these three artificial sweeteners are not bactericidal. Protein-ligand docking and interaction profiling, using LasR as a representative participating receptor for AHL, suggest that the artificial sweeteners bind to the ligand-binding pocket of the protein, possibly interfering with the proper housing of the native ligand and thus impeding protein folding. Our findings suggest that these artificial sweeteners may affect the balance of the gut microbial community via QS-inhibition. We, therefore, infer an effect of these artificial sweeteners on numerous molecular events that are at the core of intestinal microbial function, and by extension on the host metabolism.
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Duddy OP, Huang X, Silpe JE, Bassler BL. Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors. PLoS Genet 2021; 17:e1009550. [PMID: 34228715 PMCID: PMC8284805 DOI: 10.1371/journal.pgen.1009550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/16/2021] [Accepted: 06/16/2021] [Indexed: 11/19/2022] Open
Abstract
Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. In the global pathogen Vibrio cholerae, one quorum-sensing receptor and transcription factor, called VqmA (VqmAVc), activates expression of the vqmR gene encoding the small regulatory RNA VqmR, which represses genes involved in virulence and biofilm formation. Vibriophage VP882 encodes a VqmA homolog called VqmAPhage that activates transcription of the phage gene qtip, and Qtip launches the phage lytic program. Curiously, VqmAPhage can activate vqmR expression but VqmAVc cannot activate expression of qtip. Here, we investigate the mechanism underlying this asymmetry. We find that promoter selectivity is driven by each VqmA DNA-binding domain and key DNA sequences in the vqmR and qtip promoters are required to maintain specificity. A protein sequence-guided mutagenesis approach revealed that the residue E194 of VqmAPhage and A192, the equivalent residue in VqmAVc, in the helix-turn-helix motifs contribute to promoter-binding specificity. A genetic screen to identify VqmAPhage mutants that are incapable of binding the qtip promoter but maintain binding to the vqmR promoter delivered additional VqmAPhage residues located immediately C-terminal to the helix-turn-helix motif as required for binding the qtip promoter. Surprisingly, these residues are conserved between VqmAPhage and VqmAVc. A second, targeted genetic screen revealed a region located in the VqmAVc DNA-binding domain that is necessary to prevent VqmAVc from binding the qtip promoter, thus restricting DNA binding to the vqmR promoter. We propose that the VqmAVc helix-turn-helix motif and the C-terminal flanking residues function together to prohibit VqmAVc from binding the qtip promoter. Bacteria use a chemical communication process called quorum sensing (QS) to orchestrate collective behaviors. Recent studies demonstrate that bacteria-infecting viruses, called phages, also employ chemical communication to regulate collective activities. Phages can encode virus-specific QS-like systems, or they can harbor genes encoding QS components resembling those of bacteria. The latter arrangement suggests the potential for chemical communication across domains, i.e., between bacteria and phages. Ramifications stemming from such cross-domain communication are not understood. Phage VP882 infects the global pathogen Vibrio cholerae, and “eavesdrops” on V. cholerae QS to optimize the timing of its transition from existing as a parasite to killing the host, and moreover, to manipulate V. cholerae biology. To accomplish these feats, phage VP882 relies on VqmAPhage, the phage-encoded homolog of the V. cholerae VqmAVc QS receptor and transcription factor. VqmAVc, by contrast, is constrained to the control of only V. cholerae genes and is incapable of regulating phage biology. Here, we discover the molecular mechanism underpinning the asymmetric transcriptional preferences of the phage-encoded and bacteria-encoded VqmA proteins. We demonstrate how VqmA transcriptional regulation is crucial to the survival and persistence of both the pathogen V. cholerae, and the phage that preys on it.
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Affiliation(s)
- Olivia P. Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Xiuliang Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Justin E. Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bonnie L. Bassler
- 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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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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Ahmed SAKS, Rudden M, Elias SM, Smyth TJ, Marchant R, Banat IM, Dooley JSG. Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing. Sci Rep 2021; 11:5729. [PMID: 33707533 PMCID: PMC7970962 DOI: 10.1038/s41598-021-85100-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Pseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.
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Affiliation(s)
- Syed A K Shifat Ahmed
- School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Michelle Rudden
- Department of Biology, University of York, Wentworth, York, YO10 5DD, UK
| | - Sabrina M Elias
- School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Thomas J Smyth
- School of Science, Institute of Technology Sligo, Sligo, Ireland
| | - Roger Marchant
- School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Ibrahim M Banat
- School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - James S G Dooley
- School of Biomedical Sciences, Ulster University, Coleraine, UK.
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34
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Zhang M, Li S, Zhao Y, Wang Y, Zhang W, Wu S, Zhang J, Hu Z, Ding M, Meng Q, Yin J, Yu Z. Stringent starvation protein A and LuxI/LuxR-type quorum sensing system constitute a mutual positive regulation loop in Pseudoalteromonas. Biochem Biophys Res Commun 2020; 534:885-890. [PMID: 33143873 DOI: 10.1016/j.bbrc.2020.10.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022]
Abstract
Bacteria commonly exhibit social activities through acyl-homoserine lactones (AHLs)-based quorum sensing (QS) systems to form their unique social network. The sigma factor RpoS is an important regulator that controls QS system in different bacteria. However, the upstream of RpoS involving regulation on QS system remains unclear. In Escherichia coli RpoS is regulated by stringent starvation protein A (SspA), which is dependent of histone-like nucleoid structuring protein (H-NS). To date, the connection between SspA and QS system is essentially unknown. Here, we characterized a typical LuxI/LuxR-type QS system in marine bacterium Pseudoalteromonas sp. T1lg65 which can produce four types of AHLs. The luxI encoding AHLs synthase and luxR encoding AHLs-responsive receptor are co-transcribed, providing advantages in rapidly amplifying QS signaling. Notably, SspA positively regulated luxI/luxR transcription by activating RpoS expression, which is mediated by H-NS. Interestingly, LuxR in turn positively regulated SspA expression. Therefore, SspA and QS system constitute a mutual positive regulation loop in T1lg65. In view of the crucial roles of SspA and QS system in environmental adaption, we believe that the improvement of bacterial tolerance to marine environments could be related to rapidly tuning SspA-involved QS programming.
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Affiliation(s)
- Mengting Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shuangjia Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yifan Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yaoyang Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wei Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shijun Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiadi Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zeyu Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mengdan Ding
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
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35
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Pip serves as an intermediate in RpoS-modulated phz2 expression and pyocyanin production in Pseudomonas aeruginosa. Microb Pathog 2020; 147:104409. [PMID: 32707314 DOI: 10.1016/j.micpath.2020.104409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022]
Abstract
Pyocyanin, a main virulence factor that is produced by Pseudomonas aeruginosa, plays an important role in pathogen-host interaction during infection. Two copies of phenazine-biosynthetic operons on genome, phz1 (phzA1B1C1D1E1F1G1) and phz2 (phzA2B2C2D2E2F2G2), contribute to phenazine biosynthesis. In our previous study, we found that RpoS positively regulates expression of the phz2 operon and pyocyanin biosynthesis in P. aeruginosa PAO1. In this work, when a TetR-family regulator gene, pip, was knocked out, we found that pyocyanin production was dramatically reduced, indicating that Pip positively regulates pyocyanin biosynthesis. With further phenazines quantification and β-galactosidase assay, we confirmed that Pip positively regulates phz2 expression, but does not regulate phz1 expression. In addition, while the rpoS gene was deleted, expression of pip was down-regulated. Expression of rpoS in the wild-type PAO1 strain, however, was similar to that in the Pip-deficient mutant PAΔpip, suggesting that expression of pip could positively be regulated by RpoS, whereas rpoS could not be regulated by Pip. Taken together, we drew a conclusion that Pip might serve as an intermediate in RpoS-modulated expression of the phz2 operon and pyocyanin biosynthesis in P. aeruginosa.
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Chatterjee P, Sass G, Swietnicki W, Stevens DA. Review of Potential Pseudomonas Weaponry, Relevant to the Pseudomonas-Aspergillus Interplay, for the Mycology Community. J Fungi (Basel) 2020; 6:jof6020081. [PMID: 32517271 PMCID: PMC7345761 DOI: 10.3390/jof6020081] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most prominent opportunistic bacteria in airways of cystic fibrosis patients and in immunocompromised patients. These bacteria share the same polymicrobial niche with other microbes, such as the opportunistic fungus Aspergillus fumigatus. Their inter-kingdom interactions and diverse exchange of secreted metabolites are responsible for how they both fare in competition for ecological niches. The outcomes of their contests likely determine persistent damage and degeneration of lung function. With a myriad of virulence factors and metabolites of promising antifungal activity, P. aeruginosa products or their derivatives may prove useful in prophylaxis and therapy against A. fumigatus. Quorum sensing underlies the primary virulence strategy of P. aeruginosa, which serves as cell–cell communication and ultimately leads to the production of multiple virulence factors. Understanding the quorum-sensing-related pathogenic mechanisms of P. aeruginosa is a first step for understanding intermicrobial competition. In this review, we provide a basic overview of some of the central virulence factors of P. aeruginosa that are regulated by quorum-sensing response pathways and briefly discuss the hitherto known antifungal properties of these virulence factors. This review also addresses the role of the bacterial secretion machinery regarding virulence factor secretion and maintenance of cell–cell communication.
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Affiliation(s)
- Paulami Chatterjee
- California Institute for Medical Research, San Jose, CA 95128, USA; (P.C.); (G.S.)
| | - Gabriele Sass
- California Institute for Medical Research, San Jose, CA 95128, USA; (P.C.); (G.S.)
| | - Wieslaw Swietnicki
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 50-114 Wroclaw, Poland;
| | - David A. Stevens
- California Institute for Medical Research, San Jose, CA 95128, USA; (P.C.); (G.S.)
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Correspondence: ; Tel.: +1-408-998-4554
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Shah N, Gislason AS, Becker M, Belmonte MF, Fernando WGD, de Kievit TR. Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23. PLoS One 2020; 15:e0226232. [PMID: 32109244 PMCID: PMC7048289 DOI: 10.1371/journal.pone.0226232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol, as well as CsaRI and AurRI, which have not yet been characterized in PA23. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. In this work, we investigated genes under the control of the main QS transcriptional regulator, PhzR, as well as those differentially expressed in an AHL-deficient strain, PA23-6863, which constitutively expresses an AiiA lactonase, rendering the strain QS defective. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism.
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Affiliation(s)
- Nidhi Shah
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - April S. Gislason
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Teresa R. de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Hernando-Amado S, Alcalde-Rico M, Gil-Gil T, Valverde JR, Martínez JL. Naringenin Inhibition of the Pseudomonas aeruginosa Quorum Sensing Response Is Based on Its Time-Dependent Competition With N-(3-Oxo-dodecanoyl)-L-homoserine Lactone for LasR Binding. Front Mol Biosci 2020; 7:25. [PMID: 32181260 PMCID: PMC7059128 DOI: 10.3389/fmolb.2020.00025] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/07/2020] [Indexed: 12/23/2022] Open
Abstract
Bacterial quorum sensing (QS) is a cell-to-cell communication system that governs the expression of a large set of genes involved in bacterial-host interactions, including the production of virulence factors. Conversely, the hosts can produce anti-QS compounds to impair virulence of bacterial pathogens. One of these inhibitors is the plant flavonoid naringenin, which impairs the production of QS-regulated Pseudomonas aeruginosa virulence factors. In the present work, we analyze the molecular basis for such inhibition. Our data indicate that naringenin produces its effect by directly binding the QS regulator LasR, hence competing with its physiological activator, N-(3-oxo-dodecanoyl)-L-homoserine lactone (3OC12-HSL). The in vitro analysis of LasR binding to its cognate target DNA showed that the capacity of naringenin to outcompete 3OC12-HSL, when the latter is previously bound to LasR, is low. By using an E. coli LasR-based biosensor strain, which does not produce 3OC12-HSL, we determined that the inhibition of LasR is more efficient when naringenin binds to nascent LasR than when this regulator is already activated through 3OC12-HSL binding. According to these findings, at early exponential growth phase, when the amount of 3OC12-HSL is low, naringenin should proficiently inhibit the P. aeruginosa QS response, whereas at later stages of growth, once 3OC12-HSL concentration reaches a threshold enough for binding LasR, naringenin would not efficiently inhibit the QS response. To test this hypothesis, we analyze the potential effect of naringenin over the QS response by adding naringenin to P. aeruginosa cultures at either time zero (early inhibition) or at stationary growth phase (late inhibition). In early inhibitory conditions, naringenin inhibited the expression of QS-regulated genes, as well as the production of the QS-regulated virulence factors, pyocyanin and elastase. Nevertheless, in late inhibitory conditions, the P. aeruginosa QS response was not inhibited by naringenin. Therefore, this time-dependent inhibition may compromise the efficiency of this flavonoid, which will be effective just when used against bacterial populations presenting low cellular densities, and highlight the importance of searching for QS inhibitors whose mechanism of action does not depend on the QS status of the population.
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Affiliation(s)
- Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance, Valparaíso, Chile
| | - Teresa Gil-Gil
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José R. Valverde
- Servicio de Computación Científica, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José L. Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Curtailing Quorum Sensing in Pseudomonas aeruginosa by Sitagliptin. Curr Microbiol 2020; 77:1051-1060. [PMID: 32020464 DOI: 10.1007/s00284-020-01909-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/29/2020] [Indexed: 12/26/2022]
Abstract
Pseudomonas aeruginosa coordinates the secretion of virulence factors through quorum sensing. Quorum sensing inhibitors can attenuate the pathogenesis of bacteria and help the immune system to eradicate them without targeting the bacterial growth. This study aimed to explore the anti-quorum sensing and anti-virulence activities of sitagliptin against P. aeruginosa PAO1 strain. Sub-inhibitory concentration of sitagliptin significantly inhibited the virulence factors pyocyanin, hemolysin, protease and elastase in addition to blocking swimming, swarming and twitching motilities and biofilm formation. In silico analysis showed that sitagliptin interacted with LasR receptors by hydrogen bonding and hydrophobic interaction, mainly with the amino acids leucine present at positions 40 and 125, tyrosine at position 56, serine at position 129, tryptophan at position 60, alanine at position 50 and phenyl alanine at position 101. qRT-PCR confirmed the anti-quorum sensing activity by reducing the expression level of QS genes lasI, lasR, rhlI, rhlR, pqsA and pqsR. In conclusion, sitagliptin is a novel anti-quorum sensing agent that can be used for treating P. aeruginosa infections.
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Prescott RD, Decho AW. Flexibility and Adaptability of Quorum Sensing in Nature. Trends Microbiol 2020; 28:436-444. [PMID: 32001099 DOI: 10.1016/j.tim.2019.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/28/2019] [Accepted: 12/09/2019] [Indexed: 02/02/2023]
Abstract
Quorum sensing (QS), a type of chemical communication, allows bacteria to sense and coordinate activities in natural biofilm communities using N-acyl homoserine lactones (AHLs) as one type of signaling molecule. For AHL-based communication to occur, bacteria must produce and recognize the same signals, which activate similar genes in different species. Our current understanding of AHL-QS suggests that signaling between species would arise randomly, which is not probable. We propose that AHL-QS signaling is a mutable and adaptable process, within limits. AHLs are highly-conserved signals, however, their corresponding receptor proteins (LuxR) are highly variable. We suggest that both flexibility and adaptation occur among receptor proteins, allowing for complex signaling networks to develop in biofilms over time.
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Affiliation(s)
- Rebecca D Prescott
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK; Microbial Interactions Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA.
| | - Alan W Decho
- Microbial Interactions Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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41
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Huang X, Duddy OP, Silpe JE, Paczkowski JE, Cong J, Henke BR, Bassler BL. Mechanism underlying autoinducer recognition in the Vibrio cholerae DPO-VqmA quorum-sensing pathway. J Biol Chem 2020; 295:2916-2931. [PMID: 31964715 DOI: 10.1074/jbc.ra119.012104] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Indexed: 11/06/2022] Open
Abstract
Quorum sensing is a bacterial communication process whereby bacteria produce, release, and detect extracellular signaling molecules called autoinducers to coordinate collective behaviors. In the pathogen Vibrio cholerae, the quorum-sensing autoinducer 3,5-dimethyl-pyrazin-2-ol (DPO) binds the receptor and transcription factor VqmA. The DPO-VqmA complex activates transcription of vqmR, encoding the VqmR small RNA, which represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA is soluble and properly folded and activates basal-level transcription of its target vqmR in the absence of DPO. VqmA transcriptional activity is increased in response to increasing concentrations of DPO, allowing VqmA to drive the V. cholerae quorum-sensing transition at high cell densities. We solved the DPO-VqmA crystal structure to 2.0 Å resolution and compared it with existing structures to understand the conformational changes VqmA undergoes upon DNA binding. Analysis of DPO analogs showed that a hydroxyl or carbonyl group at the 2'-position is critical for binding to VqmA. The proposed DPO precursor, a linear molecule, N-alanyl-aminoacetone (Ala-AA), also bound and activated VqmA. Results from site-directed mutagenesis and competitive ligand-binding analyses revealed that DPO and Ala-AA occupy the same binding site. In summary, our structure-function analysis identifies key features required for VqmA activation and DNA binding and establishes that, whereas VqmA binds two different ligands, VqmA does not require a bound ligand for folding or basal transcriptional activity. However, bound ligand is required for maximal activity.
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Affiliation(s)
- Xiuliang Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Jon E Paczkowski
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Jianping Cong
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Brad R Henke
- Opti-Mol Consulting, LLC, Cary, North Carolina 27513
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815.
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42
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Li T, Wang D, Ren L, Mei Y, Ding T, Li Q, Chen H, Li J. Involvement of Exogenous N-Acyl-Homoserine Lactones in Spoilage Potential of Pseudomonas fluorescens Isolated From Refrigerated Turbot. Front Microbiol 2019; 10:2716. [PMID: 31849873 PMCID: PMC6895499 DOI: 10.3389/fmicb.2019.02716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/08/2019] [Indexed: 01/18/2023] Open
Abstract
Some bacteria can modulate their spoilage potential by responding to environmental signaling molecules via the quorum sensing (QS) system. However, the ability of Pseudomonas fluorescens, the specific spoilage organism (SSO) of turbot, to response to environmental signaling molecules remains unclear. This study investigated the effects of six synthetic N-acyl homoserine lactones (AHLs) on typical behaviors mediated by QS in P. fluorescens, such as biofilm formation and extracellular protease activity. Total volatile basic nitrogen (TVB-N) was used as a spoilage indicator to evaluate quality changes in AHL-treated turbot filets during storage. The results confirm the enhancing effect of environmental AHLs on QS-dependent factors of P. fluorescens and quality deterioration of turbot filets, with C4-HSL and C14-HSL being the most effective. Moreover, the content decrease of exogenous AHLs was also validated by gas chromatography–mass spectrometry analysis. Further, changes in rhlR transcription levels in P. fluorescens suggest that this bacterium can sense environmental AHLs. Finally, molecular docking analysis demonstrates the potential interactions of RhlR protein with various exogenous AHLs. These findings strongly implicate environmental AHLs in turbot spoilage caused by P. fluorescens, suggesting preservation of turbot should not exclusively consider the elimination of SSO-secreted AHLs.
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Affiliation(s)
- Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Likun Ren
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Yongchao Mei
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Ting Ding
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qiuying Li
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Haitao Chen
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, Beijing, China
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
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43
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Li T, Wang D, Ren L, Mei Y, Ding T, Li Q, Chen H, Li J. Involvement of Exogenous N-Acyl-Homoserine Lactones in Spoilage Potential of Pseudomonas fluorescens Isolated From Refrigerated Turbot. Front Microbiol 2019; 10:2716. [PMID: 31849873 DOI: 10.3389/fmicb.2019.0271610.3389/fmicb.2019.02716.s001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/08/2019] [Indexed: 05/28/2023] Open
Abstract
Some bacteria can modulate their spoilage potential by responding to environmental signaling molecules via the quorum sensing (QS) system. However, the ability of Pseudomonas fluorescens, the specific spoilage organism (SSO) of turbot, to response to environmental signaling molecules remains unclear. This study investigated the effects of six synthetic N-acyl homoserine lactones (AHLs) on typical behaviors mediated by QS in P. fluorescens, such as biofilm formation and extracellular protease activity. Total volatile basic nitrogen (TVB-N) was used as a spoilage indicator to evaluate quality changes in AHL-treated turbot filets during storage. The results confirm the enhancing effect of environmental AHLs on QS-dependent factors of P. fluorescens and quality deterioration of turbot filets, with C4-HSL and C14-HSL being the most effective. Moreover, the content decrease of exogenous AHLs was also validated by gas chromatography-mass spectrometry analysis. Further, changes in rhlR transcription levels in P. fluorescens suggest that this bacterium can sense environmental AHLs. Finally, molecular docking analysis demonstrates the potential interactions of RhlR protein with various exogenous AHLs. These findings strongly implicate environmental AHLs in turbot spoilage caused by P. fluorescens, suggesting preservation of turbot should not exclusively consider the elimination of SSO-secreted AHLs.
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Affiliation(s)
- Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Likun Ren
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Yongchao Mei
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Ting Ding
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qiuying Li
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Haitao Chen
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, Beijing, China
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, National and Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
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Pseudomonas aeruginosa ExsA Regulates a Metalloprotease, ImpA, That Inhibits Phagocytosis of Macrophages. Infect Immun 2019; 87:IAI.00695-19. [PMID: 31527124 DOI: 10.1128/iai.00695-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogenic bacterium whose type III secretion system (T3SS) plays a critical role in acute infections. Translocation of the T3SS effectors into host cells induces cytotoxicity. In addition, the T3SS promotes the intracellular growth of P. aeruginosa during host infections. The T3SS regulon genes are regulated by an AraC-type regulator, ExsA. In this study, we found that an extracellular metalloprotease encoded by impA (PA0572) is under the regulation of ExsA. An ExsA consensus binding sequence was identified upstream of the impA gene, and direct binding of the site by ExsA was demonstrated via an electrophoretic mobility shift assay. We further demonstrate that secreted ImpA cleaves the macrophage surface protein CD44, which inhibits the phagocytosis of the bacterial cells by macrophages. Combined, our results reveal a novel ExsA-regulated virulence factor that cooperatively inhibits the functions of macrophages with the T3SS.
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45
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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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46
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Charlesworth JC, Watters C, Wong HL, Visscher PT, Burns BP. Isolation of novel quorum-sensing active bacteria from microbial mats in Shark Bay Australia. FEMS Microbiol Ecol 2019; 95:5382036. [PMID: 30877766 DOI: 10.1093/femsec/fiz035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/15/2019] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing is a potent system of genetic control allowing phenotypes to be coordinated across localized communities. In this study, quorum sensing systems in Shark Bay microbial mats were delineated using a targeted approach analyzing whole mat extractions as well as the creation of an isolate library. A library of 165 isolates from different mat types were screened using the AHL biosensor E. coli MT102. Based on sequence identity 30 unique isolates belonging to Proteobacteria, Actinobacteria and Firmicutes were found to activate the AHL biosensor, suggesting AHLs or analogous compounds were potentially present. Several of the isolates have not been shown previously to produce signal molecules, particularly the members of the Actinobacteria and Firmicutes phyla including Virgibacillus, Halobacillius, Microbacterium and Brevibacterium. These active isolates were further screened using thin-layer chromatography (TLC) providing putative identities of AHL molecules present within the mat communities. Nine isolates were capable of producing several spots of varying sizes after TLC separation, suggesting the presence of multiple signalling molecules. This study is the first to delineate AHL-based signalling in the microbial mats of Shark Bay, and suggests quorum sensing may play a role in the ecosphysiological coordination of complex phenotypes across microbial mat communities.
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Affiliation(s)
- James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Cara Watters
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia.,Department of Marine Sciences, University of Connecticut, Storrs, 06269, CT, USA
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
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47
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Paczkowski JE, McCready AR, Cong JP, Li Z, Jeffrey PD, Smith CD, Henke BR, Hughson FM, Bassler BL. An Autoinducer Analogue Reveals an Alternative Mode of Ligand Binding for the LasR Quorum-Sensing Receptor. ACS Chem Biol 2019; 14:378-389. [PMID: 30763066 DOI: 10.1021/acschembio.8b00971] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria use a cell-cell communication process called quorum sensing to coordinate collective behaviors. Quorum sensing relies on production and group-wide detection of extracellular signal molecules called autoinducers. Here, we probe the activity of the Pseudomonas aeruginosa LasR quorum-sensing receptor using synthetic agonists based on the structure of the native homoserine lactone autoinducer. The synthetic compounds range from low to high potency, and agonist activity tracks with the ability of the agonist to stabilize the LasR protein. Structural analyses of the LasR ligand binding domain complexed with representative synthetic agonists reveal two modes of ligand binding, one mimicking the canonical autoinducer binding arrangement, and the other with the lactone head group rotated approximately 150°. Iterative mutagenesis combined with chemical synthesis reveals the amino acid residues and the chemical moieties, respectively, that are key to enabling each mode of binding. Simultaneous alteration of LasR residues Thr75, Tyr93, and Ala127 converts low-potency compounds into high-potency compounds and converts ligands that are nearly inactive into low-potency compounds. These results show that the LasR binding pocket displays significant flexibility in accommodating different ligands. The ability of LasR to bind ligands in different conformations, and in so doing, alter their potency as agonists, could explain the difficulties that have been encountered in the development of competitive LasR inhibitors.
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Affiliation(s)
- Jon E. Paczkowski
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Amelia R. McCready
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jian-Ping Cong
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Zhijie Li
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, 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
| | - Frederick M. Hughson
- 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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48
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Structural determinants driving homoserine lactone ligand selection in the Pseudomonas aeruginosa LasR quorum-sensing receptor. Proc Natl Acad Sci U S A 2018; 116:245-254. [PMID: 30559209 DOI: 10.1073/pnas.1817239116] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quorum sensing is a cell-cell communication process that bacteria use to orchestrate group behaviors. Quorum sensing is mediated by signal molecules called autoinducers. Autoinducers are often structurally similar, raising questions concerning how bacteria distinguish among them. Here, we use the Pseudomonas aeruginosa LasR quorum-sensing receptor to explore signal discrimination. The cognate autoinducer, 3OC12 homoserine lactone (3OC12HSL), is a more potent activator of LasR than other homoserine lactones. However, other homoserine lactones can elicit LasR-dependent quorum-sensing responses, showing that LasR displays ligand promiscuity. We identify mutants that alter which homoserine lactones LasR detects. Substitution at residue S129 decreases the LasR response to 3OC12HSL, while enhancing discrimination against noncognate autoinducers. Conversely, the LasR L130F mutation increases the potency of 3OC12HSL and other homoserine lactones. We solve crystal structures of LasR ligand-binding domains complexed with noncognate autoinducers. Comparison with existing structures reveals that ligand selectivity/sensitivity is mediated by a flexible loop near the ligand-binding site. We show that LasR variants with modified ligand preferences exhibit altered quorum-sensing responses to autoinducers in vivo. We suggest that possessing some ligand promiscuity endows LasR with the ability to optimally regulate quorum-sensing traits.
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Vadakkan K, Choudhury AA, Gunasekaran R, Hemapriya J, Vijayanand S. Quorum sensing intervened bacterial signaling: Pursuit of its cognizance and repression. J Genet Eng Biotechnol 2018; 16:239-252. [PMID: 30733731 PMCID: PMC6353778 DOI: 10.1016/j.jgeb.2018.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/09/2018] [Accepted: 07/03/2018] [Indexed: 01/24/2023]
Abstract
Bacteria communicate within a system by means of a density dependent mechanism known as quorum sensing which regulate the metabolic and behavioral activities of a bacterial community. This sort of interaction occurs through a dialect of chemical signals called as autoinducers synthesized by bacteria. Bacterial quorum sensing occurs through various complex pathways depending upon specious diversity. Therefore the cognizance of quorum sensing mechanism will enable the regulation and thereby constrain bacterial communication. Inhibition strategies of quorum sensing are collectively called as quorum quenching; through which bacteria are incapacitated of its interaction with each other. Many virulence mechanism such as sporulation, biofilm formation, toxin production can be blocked by quorum quenching. Usually quorum quenching mechanisms can be broadly classified into enzymatic methods and non-enzymatic methods. Substantial understanding of bacterial communication and its inhibition enhances the development of novel antibacterial therapeutic drugs. In this review we have discussed the types and mechanisms of quorum sensing and various methods to inhibit and regulate density dependent bacterial communication.
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Affiliation(s)
- Kayeen Vadakkan
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | - Abbas Alam Choudhury
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | - Ramya Gunasekaran
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | | | - Selvaraj Vijayanand
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
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50
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Fernández M, Corral-Lugo A, Krell T. The plant compound rosmarinic acid induces a broad quorum sensing response in Pseudomonas aeruginosa PAO1. Environ Microbiol 2018; 20:4230-4244. [PMID: 30051572 DOI: 10.1111/1462-2920.14301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023]
Abstract
The interference of plant compounds with bacterial quorum sensing (QS) is a major mechanism through which plants and bacteria communicate. However, little is known about the modes of action and effects on signal integrity during this type of communication. We have recently shown that the plant compound rosmarinic acid (RA) specifically binds to the Pseudomonas aeruginosa RhlR QS receptor. To determine the effect of RA on expression patterns, we carried out global RNA-seq analysis. The results show that RA induces the expression of 128 genes, amongst which many virulence factor genes. RA triggers a broad QS response because 88% of the induced genes are known to be controlled by QS, and because RA stimulated genes were found to be involved in all four QS signalling systems within P. aeruginosa. This finding was confirmed through the analysis of transcriptional fusions transferred to wt and a rhlI/lasI double mutant. RA did not induce gene expression in the rhlI/lasI/rhlR triple mutant indicating that the effects observed are due to the RA-RhlR interaction. Furthermore, RA induced seven sRNAs that were all encoded in regions close to QS and/or RA induced genes. This work significantly enhances our understanding of plant bacteria interaction.
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Affiliation(s)
- Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Gif-Sur-Yvette, France
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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