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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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2
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Ruiz CH, Osorio-Llanes E, Trespalacios MH, Mendoza-Torres E, Rosales W, Gómez CMM. Quorum Sensing Regulation as a Target for Antimicrobial Therapy. Mini Rev Med Chem 2021; 22:848-864. [PMID: 34856897 DOI: 10.2174/1389557521666211202115259] [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: 10/04/2020] [Revised: 05/20/2021] [Accepted: 09/04/2021] [Indexed: 11/22/2022]
Abstract
Some bacterial species use a cell-to-cell communication mechanism called Quorum Sensing (QS). Bacteria release small diffusible molecules, usually termed signals which allow the activation of beneficial phenotypes that guarantee bacterial survival and the expression of a diversity of virulence genes in response to an increase in population density. The study of the molecular mechanisms that relate signal molecules with bacterial pathogenesis is an area of growing interest due to its use as a possible therapeutic alternative through the development of synthetic analogues of autoinducers as a strategy to regulate bacterial communication as well as the study of bacterial resistance phenomena, the study of these relationships is based on the structural diversity of natural or synthetic autoinducers and their ability to inhibit bacterial QS, which can be approached with a molecular perspective from the following topics: i) Molecular signals and their role in QS regulation; ii) Strategies in the modulation of Quorum Sensing; iii) Analysis of Bacterial QS circuit regulation strategies; iv) Structural evolution of natural and synthetic autoinducers as QS regulators. This mini-review allows a molecular view of the QS systems, showing a perspective on the importance of the molecular diversity of autoinducer analogs as a strategy for the design of new antimicrobial agents.
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Affiliation(s)
- Caterine Henríquez Ruiz
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Estefanie Osorio-Llanes
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Mayra Hernández Trespalacios
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Evelyn Mendoza-Torres
- Faculty of Health Sciences. Grupo de Investigación Avanzada en Biomedicina-Universidad Libre. Barranquilla. Colombia
| | - Wendy Rosales
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Carlos Mario Meléndez Gómez
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
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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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4
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Ziegler EW, Brown AB, Nesnas N, Chouinard CD, Mehta AK, Palmer AG. β-Cyclodextrin Encapsulation of Synthetic AHLs: Drug Delivery Implications and Quorum-Quenching Exploits. Chembiochem 2020; 22:1292-1301. [PMID: 33238068 DOI: 10.1002/cbic.202000773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/23/2020] [Indexed: 12/22/2022]
Abstract
Many bacteria, such as Pseudomonas aeruginosa, regulate phenotypic switching in a population density-dependent manner through a phenomenon known as quorum sensing (QS). For Gram-negative bacteria, QS relies on the synthesis, transmission, and perception of low-molecular-weight signal molecules that are predominantly N-acyl-l-homoserine lactones (AHLs). Efforts to disrupt AHL-mediated QS have largely focused on the development of synthetic AHL analogues (SAHLAs) that are structurally similar to native AHLs. However, like AHLs, these molecules tend to be hydrophobic and are poorly soluble under aqueous conditions. Water-soluble macrocycles, such as cyclodextrins (CDs), that encapsulate hydrophobic guests have long been used by both the agricultural and pharmaceutical industries to overcome the solubility issues associated with hydrophobic compounds of interest. Conveniently, CDs have also demonstrated anti-AHL-mediated QS effects. Here, using fluorescence spectroscopy, NMR spectrometry, and mass spectrometry, we evaluate the affinity of SAHLAs, as well as their hydrolysis products, for β-CD inclusion. We also evaluated the ability of these complexes to inhibit wild-type P. aeruginosa virulence in a Caenorhabditis elegans host infection study, for the first time. Our efforts confirm the potential of β-CDs for the improved delivery of SAHLAs at the host/microbial interface, expanding the utility of this approach as a strategy for probing and controlling QS.
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Affiliation(s)
- Eric W Ziegler
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA
| | - Alan B Brown
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA
| | - Nasri Nesnas
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA
| | - Christopher D Chouinard
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA
| | - Anil K Mehta
- National High Magnetic Field Laboratory, McKnight Brain Institute, University of Florida, 1149 Newell Drive, Gainesville, FL 32610, USA
| | - Andrew G Palmer
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA.,Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, 150W. University Boulevard, Melbourne, FL 32901, USA
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5
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Ge C, Sheng H, Chen X, Shen X, Sun X, Yan Y, Wang J, Yuan Q. Quorum Sensing System Used as a Tool in Metabolic Engineering. Biotechnol J 2020; 15:e1900360. [DOI: 10.1002/biot.201900360] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/07/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Chang Ge
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Huakang Sheng
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Xin Chen
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Yajun Yan
- College of EngineeringThe University of Georgia Athens GA 30605 USA
| | - Jia Wang
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical Technology Beijing Chaoyang 100029 China
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Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. mSystems 2020; 5:5/1/e00650-19. [PMID: 31992632 PMCID: PMC6989131 DOI: 10.1128/msystems.00650-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study a phytopathosystem comprised of potato tubers and the soft-rot pathogen Pectobacterium brasiliense 1692 (Pb1692). Genome simulations and statistical analyses uncovered the tendency of PhoP and SlyA networks to mobilize lineage-specific traits predicted as horizontal gene transfer at late infection, highlighting the prominence of regulatory network rearrangements in this stage of infection. The evidence further supports the circumscription of two horizontally acquired quorum-sensing regulators (carR and expR1) by the PhoP network. By recruiting carR and expR1, the PhoP network also impacts certain host adaptation- and bacterial competition-related systems, seemingly in a quorum sensing-dependent manner, such as the type VI secretion system, carbapenem biosynthesis, and plant cell wall-degrading enzymes (PCWDE) like cellulases and pectate lyases. Conversely, polygalacturonases and the type III secretion system (T3SS) exhibit a transcriptional pattern that suggests quorum-sensing-independent regulation by the PhoP network. This includes an uncharacterized novel phage-related gene family within the T3SS gene cluster that has been recently acquired by two Pectobacterium species. The evidence further suggests a PhoP-dependent regulation of carbapenem- and PCWDE-encoding genes based on the synthesized products' optimum pH. The PhoP network also controls slyA expression in planta, which seems to impact carbohydrate metabolism regulation, especially at early infection, when 76.2% of the SlyA-regulated genes from that category also require PhoP to achieve normal expression levels.IMPORTANCE Exchanging genetic material through horizontal transfer is a critical mechanism that drives bacteria to efficiently adapt to host defenses. In this report, we demonstrate that a specific plant-pathogenic species (from the Pectobacterium genus) successfully integrated a population density-based behavior system (quorum sensing) acquired through horizontal transfer into a resident stress-response gene regulatory network controlled by the PhoP protein. Evidence found here underscores that subsets of bacterial weaponry critical for colonization, typically known to respond to quorum sensing, are also controlled by PhoP. Some of these traits include different types of enzymes that can efficiently break down plant cell walls depending on the environmental acidity level. Thus, we hypothesize that PhoP's ability to elicit regulatory responses based on acidity and nutrient availability fluctuations has strongly impacted the fixation of its regulatory connection with quorum sensing. In addition, another global gene regulator, known as SlyA, was found under the PhoP regulatory network. The SlyA regulator controls a series of carbohydrate metabolism-related traits, which also seem to be regulated by PhoP. By centralizing quorum sensing and slyA under PhoP scrutiny, Pectobacterium cells added an advantageous layer of control over those two networks that potentially enhances colonization efficiency.
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Proctor CR, McCarron PA, Ternan NG. Furanone quorum-sensing inhibitors with potential as novel therapeutics against Pseudomonas aeruginosa. J Med Microbiol 2020; 69:195-206. [PMID: 31971503 DOI: 10.1099/jmm.0.001144] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Micro-organisms use quorum sensing (QS), a cell density-dependent process, to communicate. This QS mode of interchange leads to the production of a variety of virulence factors, co-ordination of complex bacterial behaviours, such as swarming motility, degradation of host tissue and biofilm formation. QS is implicated in numerous human infections and consequently researchers have sought ways of effectively inhibiting the process in pathogenic bacteria. Two decades ago, furanones were the first class of chemical compounds identified as Pseudomonas aeruginosa QS inhibitors (QSIs). P. aeruginosa is a ubiquitous organism, capable of causing a wide range of infections in humans, including eye and ear infections, wound infections and potentially fatal bacteraemia and thus novel treatments against this organism are greatly needed. This review provides a brief background on QS and the use of furanones as QSIs. Based on the effectiveness of action, both in vivo and in vitro, we will explore the use of furanones as potential antimicrobial therapeutics and conclude with open questions.
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Affiliation(s)
- Chris R Proctor
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Northern Ireland, UK.,School of Pharmacy and Pharmaceutical Sciences, Ulster University, Northern Ireland, UK
| | - Paul A McCarron
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, Northern Ireland, UK
| | - Nigel G Ternan
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Northern Ireland, UK
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Shastry RP, Dolan SK, Abdelhamid Y, Vittal RR, Welch M. Purification and characterisation of a quorum quenching AHL-lactonase from the endophytic bacterium Enterobacter sp. CS66. FEMS Microbiol Lett 2018; 365:4923023. [PMID: 29518220 PMCID: PMC5905603 DOI: 10.1093/femsle/fny054] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
The quorum quenching (QQ) activity of endophytic bacteria associated with medicinal plants was explored. Extracts of the Gram-negative Enterobacter sp. CS66 possessed potent N-acylhomoserine lactone (AHL) hydrolytic activity in vitro. Using degenerate primers, we PCR-amplified an open reading frame (denoted aiiE) from CS66 that was 96% identical to the well-characterised AHL-lactonase AiiA from Bacillus thuringiensis, but only 30% was identical to AHL-lactonases from other Gram-negative species. This confirms that close AiiA homologs can be found in both Gram-positive and Gram-negative bacteria. Purified AiiE exhibited potent AHL-lactonase activity against a broad range of AHLs. Furthermore, aiiE was able to reduce the production of secreted plant cell wall-degrading hydrolytic enzymes when expressed in trans in the economically important plant pathogen, Pectobacterium atrosepticum. Our results indicate the presence of a novel AHL-lactonase in Enterobacter sp. CS66 with significant potential as a biocontrol agent.
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Affiliation(s)
- Rajesh Padumane Shastry
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore 570006, India
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Stephen K Dolan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Yassmin Abdelhamid
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ravishankar Rai Vittal
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore 570006, India
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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9
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How fast is a collective bacterial state established? PLoS One 2017. [PMID: 28644896 PMCID: PMC5482491 DOI: 10.1371/journal.pone.0180199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules. Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence. The reaction-diffusion system describing a basal quorum sensing loop involves production of signal molecules, diffusion of signal molecules, and detection of signal molecules. We study the ignition process in a numerical solution for a basal quorum sensor and demonstrate that even in a large colony the ignition travels through the whole colony in a less than a minute. The ignition of the positive feedback loop was examined in different approximations. As expected, in the exact calculation the ignition was found to be delayed compared to a calculation where the binding of signal molecules was quasistatic. The buffering of signal molecules is found to have little effect on the ignition process. Contrary to expectation, we find that the ignition does not start when the threshold is reached at the center—instead it allows for the threshold to be approached in the whole colony followed by an almost simultaneous ignition of the whole biofilm aggregate.
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Pulse Generation in the Quorum Machinery of Pseudomonas aeruginosa. Bull Math Biol 2017; 79:1360-1389. [PMID: 28527130 PMCID: PMC5486814 DOI: 10.1007/s11538-017-0288-z] [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: 09/28/2016] [Accepted: 05/03/2017] [Indexed: 12/03/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is responsible for a wide range of infections in humans. Colonies employ quorum sensing (QS) to coordinate gene expression, including for virulence factors, swarming motility and complex social traits. The QS signalling system of P. aeruginosa is known to involve multiple control components, notably the las, rhl and pqs systems. In this paper, we examine the las system and, in particular, the repressive interaction of rsaL, an embedded small regulative protein, employing recent biochemical information to aid model construction. Using analytic methods, we show how this feature can give rise to excitable pulse generation in this subsystem with important downstream consequences for rhamnolipid production. We adopt a symmetric competitive inhibition to capture the binding in the lasI–rsaL intergenic region and show our results are not dependent on the exact choice of this functional form. Furthermore, we examine the coupling of lasR to the rhl system, the impact of the predicted capacity for pulse generation and the biophysical consequences of this behaviour. We hypothesize that the interaction between the las and rhl systems may provide a quorum memory to enable cells to trigger rhamnolipid production only when they are at the edge of an established aggregation.
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11
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Corral Lugo A, Daddaoua A, Ortega A, Morel B, Díez Peña AI, Espinosa-Urgel M, Krell T. Purification and characterization of Pseudomonas aeruginosa LasR expressed in acyl-homoserine lactone free Escherichia coli cultures. Protein Expr Purif 2016; 130:107-114. [PMID: 27756565 DOI: 10.1016/j.pep.2016.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/06/2016] [Accepted: 10/14/2016] [Indexed: 11/25/2022]
Abstract
Quorum sensing systems are essential for bacterial communication. We report here the purification and characterization of the Pseudomonas aeruginosa LasR quorum sensing regulator purified from lysates of E. coli cultures grown in the absence of added acyl-homoserine lactones (AHL). We show by isothermal titration calorimetry that LasR recognizes different AHLs with an affinity of approximately 1 μM. The affinity of LasR for its cognate 3-Oxo-C12-AHL was similar to that of other AHLs, indicating that this regulator has not evolved to preferentially recognize its cognate AHL. The α-helical content as determined by CD spectroscopy was found to be in agreement with the corresponding value derived from the homology model. Analytical ultracentrifugation studies show that LasR is a mixture of monomers and dimers and that AHL binding does not alter its oligomeric state. Thermal unfolding studies indicate that LasR has a significant thermal stability and that AHL binding does not significantly alter the unfolding temperature. Two LasR-DNA complexes were observed in electrophoretic mobility shift assays using the hcnABC promoter that has two lux boxes. Taken together, data indicate that the presence of AHLs is not a requisite for correct LasR protein folding. The protein is able to bind AHL ligands in a reversible manner, revising initial concepts of this regulator. The availability of AHL-free protein will permit further studies to determine more precisely its mode of action.
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Affiliation(s)
- Andrés Corral Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Alvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Ana Isabel Díez Peña
- Department of Physical Chemistry, Faculty of Chemistry, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30071 Murcia, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain.
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12
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Vaughn VL, Gross DC. Characterization of salA, syrF, and syrG Genes and Attendant Regulatory Networks Involved in Plant Pathogenesis by Pseudomonas syringae pv. syringae B728a. PLoS One 2016; 11:e0150234. [PMID: 26954255 PMCID: PMC4783005 DOI: 10.1371/journal.pone.0150234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/10/2016] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas syringae pv. syringae B728a, causal agent of brown spot on bean, is an economically important plant pathogen that utilizes extracellular signaling to initiate a lifestyle change from an epiphyte to a pathogen. LuxR regulatory proteins play an important role in the transcriptional regulation of a variety of biological processes involving two-component signaling, quorum sensing, and secondary metabolism. Analysis of the B728a genome identified 24 LuxR-like proteins, three of which are encoded by salA, syrF, and syrG located adjacent to the syringomycin gene cluster. The LuxR-like proteins encoded by these three genes exhibit a domain architecture that places them in a subfamily of LuxR-like proteins associated with regulation of secondary metabolism in B728a. Deletion mutants of salA, syrF, and syrG failed to produce syringomycin and displayed reduction of virulence on bean. The transcriptional start sites of salA, syrG, and syrF were located 63, 235, and 498 bp upstream of the start codons, respectively, using primer extension analysis. The predicted -10/-35 promoter regions of syrF and syrG were confirmed using site-directed mutagenesis and GFP reporters that showed conserved promoter sequences around the -35 promoter region. Overexpression analysis and GFP reporters identified SyrG as an upstream transcriptional activator of syrF, where both SyrG and SyrF activate promoters of syringomycin biosynthesis genes. This study shows that syrG and syrF encode important transcriptional regulators of syringomycin biosynthesis genes.
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Affiliation(s)
- Vanessa L Vaughn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Dennis C Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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13
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Costas C, López-Puente V, Bodelón G, González-Bello C, Pérez-Juste J, Pastoriza-Santos I, Liz-Marzán LM. Using surface enhanced Raman scattering to analyze the interactions of protein receptors with bacterial quorum sensing modulators. ACS NANO 2015; 9:5567-76. [PMID: 25927541 PMCID: PMC4446724 DOI: 10.1021/acsnano.5b01800] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins.
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Affiliation(s)
- Celina Costas
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
| | | | - Gustavo Bodelón
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
- Address correspondence to ,
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jorge Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
| | | | - Luis M. Liz-Marzán
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Address correspondence to ,
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14
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Brameyer S, Heermann R. Specificity of Signal-Binding via Non-AHL LuxR-Type Receptors. PLoS One 2015; 10:e0124093. [PMID: 25923884 PMCID: PMC4414361 DOI: 10.1371/journal.pone.0124093] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/25/2015] [Indexed: 12/02/2022] Open
Abstract
Quorum sensing is a typical communication system among Gram-negative bacteria used to control group-coordinated behavior via small diffusible molecules dependent on cell number. The key components of a quorum sensing system are a LuxI-type synthase, producing acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor that detects AHLs to control expression of specific target genes. Six conserved amino acids are present in the signal-binding domain of AHL-sensing LuxR-type proteins, which are important for ligand-binding and -specificity as well as shaping the ligand-binding pocket. However, many proteobacteria possess LuxR-type regulators without a cognate LuxI synthase, referred to as LuxR solos. The two LuxR solos PluR and PauR from Photorhabdus luminescens and Photorhabdus asymbiotica, respectively, do not sense AHLs. Instead PluR and PauR sense alpha-pyrones and dialkylresorcinols, respectively, and are part of cell-cell communication systems contributing to the overall virulence of these Photorhabdus species. However, PluR and PauR both harbor substitutions in the conserved amino acid motif compared to that in AHL sensors, which appeared to be important for binding the corresponding signaling molecules. Here we analyze the role of the conserved amino acids in the signal-binding domain of these two non-AHL LuxR-type receptors for their role in signal perception. Our studies reveal that the conserved amino acid motif alone is essential but not solely responsible for ligand-binding.
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Affiliation(s)
- Sophie Brameyer
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Martinsried/München, Germany
| | - Ralf Heermann
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Martinsried/München, Germany
- * E-mail:
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15
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Microbial biofilm as a smart material. SENSORS 2015; 15:4229-41. [PMID: 25686310 PMCID: PMC4367407 DOI: 10.3390/s150204229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 11/16/2022]
Abstract
Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa.
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Brameyer S, Kresovic D, Bode HB, Heermann R. LuxR solos in Photorhabdus species. Front Cell Infect Microbiol 2014; 4:166. [PMID: 25478328 PMCID: PMC4235431 DOI: 10.3389/fcimb.2014.00166] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/24/2014] [Indexed: 01/18/2023] Open
Abstract
Bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. The basic molecular quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase producing acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor detecting the AHLs to control expression of specific genes. However, many proteobacteria possess one or more unpaired LuxR-type receptors that lack a cognate LuxI-like synthase, referred to as LuxR solos. The enteric and insect pathogenic bacteria of the genus Photorhabdus harbor an extraordinarily high number of LuxR solos, more than any other known bacteria, and all lack a LuxI-like synthase. Here, we focus on the presence and the different types of LuxR solos in the three known Photorhabdus species using bioinformatics analyses. Generally, the N-terminal signal-binding domain (SBD) of LuxR-type receptors sensing AHLs have a motif of six conserved amino acids that is important for binding and specificity of the signaling molecule. However, this motif is altered in the majority of the Photorhabdus-specific LuxR solos, suggesting the use of other signaling molecules than AHLs. Furthermore, all Photorhabdus species contain at least one LuxR solo with an intact AHL-binding motif, which might allow the ability to sense AHLs of other bacteria. Moreover, all three species have high AHL-degrading activity caused by the presence of different AHL-lactonases and AHL-acylases, revealing a high quorum quenching activity against other bacteria. However, the majority of the other LuxR solos in Photorhabdus have a N-terminal so-called PAS4-domain instead of an AHL-binding domain, containing different amino acid motifs than the AHL-sensors, which potentially allows the recognition of a highly variable range of signaling molecules that can be sensed apart from AHLs. These PAS4-LuxR solos are proposed to be involved in host sensing, and therefore in inter-kingdom signaling. Overall, Photorhabdus species are perfect model organisms to study bacterial communication via LuxR solos and their role for a symbiotic and pathogenic life style.
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Affiliation(s)
- Sophie Brameyer
- Bereich Mikrobiologie, Biozentrum, Ludwig-Maximilians-Universität München München, Germany
| | - Darko Kresovic
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt Frankfurt am Main, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt Frankfurt am Main, Germany
| | - Ralf Heermann
- Bereich Mikrobiologie, Biozentrum, Ludwig-Maximilians-Universität München München, Germany
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17
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Carbonell-Ballestero M, Duran-Nebreda S, Montañez R, Solé R, Macía J, Rodríguez-Caso C. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology. Nucleic Acids Res 2014; 42:14060-9. [PMID: 25404136 PMCID: PMC4267673 DOI: 10.1093/nar/gku964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.
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Affiliation(s)
- Max Carbonell-Ballestero
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain
| | - Salva Duran-Nebreda
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain
| | - Raúl Montañez
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Javier Macía
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain
| | - Carlos Rodríguez-Caso
- ICREA-Complex Systems Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Psg. de la Barceloneta 37, 08003 Barcelona, Spain
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18
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Kong W, Celik V, Liao C, Hua Q, Lu T. Programming the group behaviors of bacterial communities with synthetic cellular communication. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0024-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Synthetic biology is a newly emerged research discipline that focuses on the engineering of novel cellular behaviors and functionalities through the creation of artificial gene circuits. One important class of synthetic circuits currently under active development concerns the programming of bacterial cellular communication and collective population-scale behaviors. Because of the ubiquity of cell-cell interactions within bacterial communities, having an ability of engineering these circuits is vital to programming robust cellular behaviors. Here, we highlight recent advances in communication-based synthetic gene circuits by first discussing natural communication systems and then surveying various functional engineered circuits, including those for population density control, temporal synchronization, spatial organization, and ecosystem formation. We conclude by summarizing recent advances, outlining existing challenges, and discussing potential applications and future opportunities.
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19
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Ferkinghoff-Borg J, Sams T. Size of quorum sensing communities. MOLECULAR BIOSYSTEMS 2014; 10:103-9. [PMID: 24162891 DOI: 10.1039/c3mb70230h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ensembles of bacteria are able to coordinate their phenotypic behavior in accordance with the size, density, and growth state of the ensemble. This is achieved through production and exchange of diffusible signal molecules in a cell-cell regulatory system termed quorum sensing. In the generic quorum sensor a positive feedback in the production of signal molecules defines the conditions at which the collective behavior switches on. In spite of its conceptual simplicity, a proper measure of biofilm colony "size" appears to be lacking. We establish that the cell density multiplied by a geometric factor which incorporates the boundary conditions constitutes an appropriate size measure. The geometric factor is the square of the radius for a spherical colony or a hemisphere attached to a reflecting surface. If surrounded by a rapidly exchanged medium, the geometric factor is divided by three. For a disk-shaped biofilm the geometric factor is the horizontal dimension multiplied by the height, and the square of the height of the biofilm if there is significant flow above the biofilm. A remarkably simple factorized expression for the size is obtained, which separates the all-or-none ignition caused by the positive feedback from the smoother activation outside the switching region.
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Affiliation(s)
- Jesper Ferkinghoff-Borg
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, DK-2800, Denmark.
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20
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Zaitseva YV, Popova AA, Khmel IA. Quorum sensing regulation in bacteria of the family enterobacteriaceae. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414030120] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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21
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Garg N, Manchanda G, Kumar A. Bacterial quorum sensing: circuits and applications. Antonie Van Leeuwenhoek 2013; 105:289-305. [DOI: 10.1007/s10482-013-0082-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/16/2013] [Indexed: 11/28/2022]
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22
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Covaceuszach S, Degrassi G, Venturi V, Lamba D. Structural insights into a novel interkingdom signaling circuit by cartography of the ligand-binding sites of the homologous quorum sensing LuxR-family. Int J Mol Sci 2013; 14:20578-96. [PMID: 24132148 PMCID: PMC3821632 DOI: 10.3390/ijms141020578] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/13/2013] [Accepted: 10/01/2013] [Indexed: 01/06/2023] Open
Abstract
Recent studies have identified a novel interkingdom signaling circuit, via plant signaling molecules, and a bacterial sub-family of LuxR proteins, bridging eukaryotes and prokaryotes. Indeed pivotal plant-bacteria interactions are regulated by the so called Plant Associated Bacteria (PAB) LuxR solo regulators that, although closely related to the quorum sensing (QS) LuxR family, do not bind or respond to canonical quorum sensing N-acyl homoserine lactones (AHLs), but only to specific host plant signal molecules. The large body of structural data available for several members of the QS LuxR family complexed with different classes of ligands (AHLs and other compounds), has been exploited to dissect the cartography of their regulatory domains through structure-based multiple sequence alignments, structural superimposition and a comparative analysis of the contact residues involved in ligand binding. In the absence of experimentally determined structures of members of the PAB LuxR solos subfamily, an homology model of its prototype OryR is presented, aiming to elucidate the architecture of its ligand-binding site. The obtained model, in combination with the cartography of the regulatory domains of the homologous QS LuxRs, provides novel insights into the 3D structure of its ligand-binding site and unveils the probable molecular determinants responsible for differences in selectivity towards specific host plant signal molecules, rather than to canonical QS compounds.
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Affiliation(s)
- Sonia Covaceuszach
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park-Basovizza, S.S. n° 14 Km 163.5, I-34149 Trieste, Italy; E-Mail:
| | - Giuliano Degrassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy; E-Mail:
- IBIOBA-CONICET-ICGEB, International Centre for Genetic Engineering and Biotechnology, Scientific and Technological Center, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (V.V.); (D.L.); Tel.: +39-40-3757319 (V.V.); +39-40-3758514 (D.L.); Fax: +39-40-226555 (V.V.); +39-40-9221126 (D.L.)
| | - Doriano Lamba
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park-Basovizza, S.S. n° 14 Km 163.5, I-34149 Trieste, Italy; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (V.V.); (D.L.); Tel.: +39-40-3757319 (V.V.); +39-40-3758514 (D.L.); Fax: +39-40-226555 (V.V.); +39-40-9221126 (D.L.)
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23
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Chen JW, Chin S, Tee KK, Yin WF, Choo YM, Chan KG. N-acyl homoserine lactone-producing Pseudomonas putida strain T2-2 from human tongue surface. SENSORS 2013; 13:13192-203. [PMID: 24084113 PMCID: PMC3859058 DOI: 10.3390/s131013192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 08/28/2013] [Accepted: 09/22/2013] [Indexed: 01/30/2023]
Abstract
Bacterial cell-to-cell communication (quorum sensing) refers to the regulation of bacterial gene expression in response to changes in microbial population density. Quorum sensing bacteria produce, release and respond to chemical signal molecules called autoinducers. Bacteria use two types of autoinducers, namely autoinducer-1 (AI-1) and autoinducer-2 (AI-2) where the former are N-acylhomoserine lactones and the latter is a product of the luxS gene. Most of the reported literatures show that the majority of oral bacteria use AI-2 for quorum sensing but rarely the AI-1 system. Here we report the isolation of Pseudomonas putida strain T2-2 from the oral cavity. Using high resolution mass spectrometry, it is shown that this isolate produced N-octanoylhomoserine lactone (C8-HSL) and N-dodecanoylhomoserine lactone (C12-HSL) molecules. This is the first report of the finding of quorum sensing of P. putida strain T2-2 isolated from the human tongue surface and their quorum sensing molecules were identified.
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Affiliation(s)
- Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (J.-W.C.); (S.C.); (W.-F.Y.)
| | - Shenyang Chin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (J.-W.C.); (S.C.); (W.-F.Y.)
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mail:
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (J.-W.C.); (S.C.); (W.-F.Y.)
| | - Yeun Mun Choo
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mail:
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (J.-W.C.); (S.C.); (W.-F.Y.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +603-7967-5162; Fax: +603-7967-4509
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24
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Claussen A, Jakobsen TH, Bjarnsholt T, Givskov M, Welch M, Ferkinghoff-Borg J, Sams T. Kinetic model for signal binding to the Quorum sensing regulator LasR. Int J Mol Sci 2013; 14:13360-76. [PMID: 23807499 PMCID: PMC3742191 DOI: 10.3390/ijms140713360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 11/27/2022] Open
Abstract
We propose a kinetic model for the activation of the las regulon in the opportunistic pathogen Pseudomonas aeruginosa. The model is based on in vitro data and accounts for the LasR dimerization and consecutive activation by binding of two OdDHL signal molecules. Experimentally, the production of the active LasR quorum-sensing regulator was studied in an Escherichia coli background as a function of signal molecule concentration. The functional activity of the regulator was monitored via a GFP reporter fusion to lasB expressed from the native lasB promoter. The new data shows that the active form of the LasR dimer binds two signal molecules cooperatively and that the timescale for reaching saturation is independent of the signal molecule concentration. This favors a picture where the dimerized regulator is protected against proteases and remains protected as it is activated through binding of two successive signal molecules. In absence of signal molecules, the dimerized regulator can dissociate and degrade through proteolytic turnover of the monomer. This resolves the apparent contradiction between our data and recent reports that the fully protected dimer is able to “degrade” when the induction of LasR ceases.
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Affiliation(s)
- Anetta Claussen
- Biomedical Engineering, Department of Electrical Engineering, Ørsteds Plads 349, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark; E-Mail:
- Costerton Biofilm Center, Department of International Health, Immunology, and Microbiology, Panum Institute, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark; E-Mails: (T.H.J.); (T.B.); (M.G.)
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of International Health, Immunology, and Microbiology, Panum Institute, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark; E-Mails: (T.H.J.); (T.B.); (M.G.)
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of International Health, Immunology, and Microbiology, Panum Institute, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark; E-Mails: (T.H.J.); (T.B.); (M.G.)
| | - Michael Givskov
- Costerton Biofilm Center, Department of International Health, Immunology, and Microbiology, Panum Institute, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark; E-Mails: (T.H.J.); (T.B.); (M.G.)
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge CB2 1QW, UK; E-Mail:
| | - Jesper Ferkinghoff-Borg
- Center for Biological Sequence Analysis, Department of Systems Biology, Building 301, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark; E-Mail:
| | - Thomas Sams
- Biomedical Engineering, Department of Electrical Engineering, Ørsteds Plads 349, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +45-4525-5725; Fax: +45-4588-0117
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25
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Fujimoto K, Sawai S. A design principle of group-level decision making in cell populations. PLoS Comput Biol 2013; 9:e1003110. [PMID: 23825937 PMCID: PMC3694814 DOI: 10.1371/journal.pcbi.1003110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
Populations of cells often switch states as a group to cope with environmental changes such as nutrient availability and cell density. Although the gene circuits that underlie the switches are well understood at the level of single cells, the ways in which such circuits work in concert among many cells to support group-level switches are not fully explored. Experimental studies of microbial quorum sensing show that group-level changes in cellular states occur in either a graded or an all-or-none fashion. Here, we show through numerical simulations and mathematical analysis that these behaviors generally originate from two distinct forms of bistability. The choice of bistability is uniquely determined by a dimensionless parameter that compares the synthesis and the transport of the inducing molecules. The role of the parameter is universal, such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling. Furthermore, in gene circuits with negative feedback, the same dimensionless parameter determines the coherence of group-level transitions from quiescence to a rhythmic state. The set of biochemical parameters in bacterial quorum-sensing circuits appear to be tuned so that the cells can use either type of transition. The design principle identified here serves as the basis for the analysis and control of cellular collective decision making. Although the genetic circuits underlying state switching at the single-cell level are well understood, how such circuits work in concert among many cells to support the population-level switching of cellular behaviors is not fully explored. Experiments using microbial signaling systems show that group-level changes in cellular state occur in either a graded or an all-or-none fashion. We show that the type of group-level decision making used by populations is uniquely determined by a single dimensionless parameter that compares the quorum-signaling molecules accumulated within the cells with those secreted by the population. Bacterial quorum-sensing circuits appear to be tuned so that the cells can convert between the two types of decision-making in response to slight biochemical variations. Furthermore, the role of the parameter is universal such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling and negative feedback. The design principle that we describe thus serves as the basis for the analysis and control of collective cellular decision making in general.
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Affiliation(s)
- Koichi Fujimoto
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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26
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Welch M, Hodgkinson JT, Gross J, Spring DR, Sams T. Ligand binding kinetics of the quorum sensing regulator PqsR. Biochemistry 2013; 52:4433-8. [PMID: 23713667 DOI: 10.1021/bi400315s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Pseudomonas aeruginosa quinolone signal (PQS) is a quorum sensing molecule that plays an important role in regulating the virulence of this organism. We have purified the ligand binding domain of the receptor PqsRLBD for PQS and have used Förster resonance energy transfer fluorimetry and kinetic modeling to characterize the ligand binding in vitro. The dissociation constant for binding of PQS to a ligand binding site in (PqsRLBD)2 dimers was determined to be 1.2 ± 0.3 μM. We found no cooperativity in the consecutive binding of two ligand molecules to the dimer.
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Affiliation(s)
- Martin Welch
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, United Kingdom.
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27
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González JF, Venturi V. A novel widespread interkingdom signaling circuit. TRENDS IN PLANT SCIENCE 2013; 18:167-74. [PMID: 23089307 DOI: 10.1016/j.tplants.2012.09.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/14/2012] [Accepted: 09/21/2012] [Indexed: 05/08/2023]
Abstract
Extensive communication is believed to occur between eukaryotes and prokaryotes via signaling molecules; this field of research is now called interkingdom signaling. Recently, it has been discovered that many different plant-associated bacteria possess a protein closely related to the quorum-sensing (QS) LuxR-family protein that binds and responds to plant compounds. This LuxR protein does not have a cognate N-acyl homoserine lactone (AHL) signal synthase and therefore is regarded as a 'solo' or 'orphan'. The protein is involved in interkingdom signaling in rhizobia, xanthomonads, and pseudomonads, regulating processes important for plant-bacteria interaction. In this review, we focus on this new interkingdom signaling circuit, which is widespread among pathogenic and beneficial plant-associated bacteria.
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Affiliation(s)
- Juan F González
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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28
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González A, Bellenberg S, Mamani S, Ruiz L, Echeverría A, Soulère L, Doutheau A, Demergasso C, Sand W, Queneau Y, Vera M, Guiliani N. AHL signaling molecules with a large acyl chain enhance biofilm formation on sulfur and metal sulfides by the bioleaching bacterium Acidithiobacillus ferrooxidans. Appl Microbiol Biotechnol 2012; 97:3729-37. [PMID: 22752316 DOI: 10.1007/s00253-012-4229-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/29/2012] [Accepted: 06/05/2012] [Indexed: 01/22/2023]
Abstract
Biofilm formation plays a pivotal role in bioleaching activities of bacteria in both industrial and natural environments. Here, by visualizing attached bacterial cells on energetic substrates with different microscopy techniques, we obtained the first direct evidence that it is possible to positively modulate biofilm formation of the extremophilic bacterium Acidithiobacillus ferrooxidans on sulfur and pyrite surfaces by using Quorum Sensing molecules of the N-acylhomoserine lactone type (AHLs). Our results revealed that AHL-signaling molecules with a long acyl chain (12 or 14 carbons) increased the adhesion of A. ferrooxidans cells to these substrates. In addition, Card-Fish experiments demonstrated that C14-AHL improved the adhesion of indigenous A. ferrooxidans cells from a mixed bioleaching community to pyrite. Finally, we demonstrated that this improvement of cell adhesion is correlated with an increased production of extracellular polymeric substances. Our results open up a promising means to develop new strategies for the improvement of bioleaching efficiency and metal recovery, which could also be used to control environmental damage caused by acid mine/rock drainage.
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Affiliation(s)
- Alex González
- Laboratory of Bacterial Communication, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes. SENSORS 2012; 12:5432-44. [PMID: 22778593 PMCID: PMC3386692 DOI: 10.3390/s120505432] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 03/24/2012] [Accepted: 04/26/2012] [Indexed: 12/04/2022]
Abstract
Virulence and adaptability of many Gram-negative bacterial species are associated with an N-acylhomoserine lactone (AHL) gene regulation mechanism called quorum sensing (QS). The arrangement of quorum sensing genes is variable throughout bacterial genomes, although there are unifying themes that are common among the various topological arrangements. A bioinformatics survey of 1,403 complete bacterial genomes revealed characteristic gene topologies in 152 genomes that could be classified into 16 topological groups. We developed a concise notation for the patterns and show that the sequences of LuxR regulators and LuxI autoinducer synthase proteins cluster according to the topological patterns. The annotated topologies are deposited online with links to sequences and genome annotations at http://bacteria.itk.ppke.hu/QStopologies/.
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The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J Bacteriol 2012; 194:3098-108. [PMID: 22505688 DOI: 10.1128/jb.06679-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa has at least three quorum-sensing (QS) systems, including the acyl-homoserine lactone (acyl-HSL)-mediated las and rhl systems, as well as the 2-alkyl-4(1H)-quinolone (AHQ) signal-based system. A group of key regulators of these QS systems have been identified, such as qteE, vqsM, vqsR, and vfr. However, the underlying regulatory mechanisms of these QS systems are not yet fully understood. Here, using electrophoretic mobility shift assays, we demonstrated that VqsR indirectly regulates acyl-HSL systems but specifically binds to the qscR promoter region, which indicates that VqsR influences QS-controlled pathways through QscR. Through a dye-based DNase I footprint assay, we showed that VqsR interacts with an inverted repeat (IR) motif (TCGCCN(8)GGCGA, where N is any nucleotide) in the promoter region of qscR. A genome-wide search identified 50 other promoter regions carrying the same putative IR motif. The recombinant VqsR protein exists as a homodimer in solution. In addition, using a qscR-lux reporter assay and Northern blot hybridization, we found that the transcription level of qscR increased 4-fold in the vqsR deletion strain compared to the wild-type PAO1 strain, indicating vqsR as a negative regulator of qscR. Taken together, these findings provide new insights into the complex regulation network of QS systems in P. aeruginosa.
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31
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Quorum sensing and expression of virulence in pectobacteria. SENSORS 2012; 12:3327-49. [PMID: 22737011 PMCID: PMC3376562 DOI: 10.3390/s120303327] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/21/2012] [Accepted: 03/02/2012] [Indexed: 01/23/2023]
Abstract
Quorum sensing (QS) is a population density-dependent regulatory mechanism in which gene expression is coupled to the accumulation of a chemical signaling molecule. QS systems are widespread among the plant soft-rotting bacteria. In Pectobacterium carotovorum, at least two QS systems exist being specified by the nature of chemical signals involved. QS in Pectobacterium carotovorum uses N-acylhomoserine lactone (AHL) based, as well as autoinducer-2 (AI-2) dependent signaling systems. This review will address the importance of the QS in production of virulence factors and interaction of QS with other regulatory systems in Pectobacterium carotovorum.
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Zhao Y, Qian G, Fan J, Yin F, Zhou Y, Liu C, Shen Q, Hu B, Liu F. Identification and characterization of a novel gene, hshB, in Xanthomonas oryzae pv. oryzicola co-regulated by quorum sensing and clp. PHYTOPATHOLOGY 2012; 102:252-259. [PMID: 22106829 DOI: 10.1094/phyto-06-11-0169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Virulence factors of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak in rice, are regulated by a diffusible signal factor (DSF)-dependent quorum-sensing (QS) system. In this study, a novel pathogenicity-related gene, Xoryp_010100018570 (named hshB), of X. oryzae pv. oryzicola was characterized. hshB encodes a hydrolase with a putative signal peptide, which is a homolog of imidazolonepropionase. Bioinformatic analysis showed that hshB is relatively conserved in the genus Xanthomonas but the homologous gene of hshB was not found in X. oryzae pv. oryzae. Reverse-transcription polymerase chain reaction (PCR) analysis showed that hshB and its upstream gene, Xoryp_010100018565 (named hshA), are co-transcribed in X. oryzae pv. oryzicola. Subsequent experimental results indicated that mutation of hshB remarkably impaired the virulence, extracellular protease activity, extracellular polysaccharide production, growth in minimal medium, and resistance to oxidative stress and bismerthiazol of X. oryzae pv. oryzicola. Mutation of clp, encoding a global regulator, resulted in similar phenotypes. Real-time PCR assays showed that hshB transcription is positively regulated by clp and DSF, and induced by poor nutrition. Our study not only found a novel gene hshB regulated by DSF-dependent QS system and clp but also showed that hshB was required for virulence of X. oryzae pv. oryzicola.
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Affiliation(s)
- Yancun Zhao
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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Leung MM, Brimacombe CA, Spiegelman GB, Beatty JT. The GtaR protein negatively regulates transcription of the gtaRI operon and modulates gene transfer agent (RcGTA) expression in Rhodobacter capsulatus. Mol Microbiol 2012; 83:759-74. [PMID: 22211723 PMCID: PMC3641048 DOI: 10.1111/j.1365-2958.2011.07963.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gtaI gene of Rhodobacter capsulatus encodes an N-acyl-homoserine lactone (acyl-HSL) synthase. Immediately 5' of the gtaI gene is ORF rcc00328 that encodes a potential acyl-HSL receptor protein. A combination of genetic and biochemical approaches showed that rcc00328 (renamed gtaR) modulates the production of a genetic exchange element called the gene transfer agent (RcGTA), and regulates the transcription of gtaI. Although gtaI mutants exhibited decreased levels of RcGTA production, mutagenesis of gtaR did not, whereas a gtaR/gtaI double mutant produced wild-type levels of RcGTA. Because mutagenesis of gtaR suppressed the effect of the gtaI mutation, we suggest that the GtaR protein is a negative transcriptional regulator of RcGTA gene expression. We discovered that the gtaR and gtaI genes are co-transcribed, and also negatively regulated by the GtaR protein in the absence of acyl-HSL. A His-tagged GtaR protein was purified, and DNA-binding experiments revealed a binding site in the promoter region of the gtaRI operon. This GtaR protein did not bind to the RcGTA promoter region, and therefore modulation of RcGTA production appears to require at least one additional factor. We found that RcGTA production was stimulated by spent media from other species, and identified exogenous acyl-HSLs that induce RcGTA.
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Affiliation(s)
| | | | - G. B. Spiegelman
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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Yong YC, Zhong JJ. Impacts of quorum sensing on microbial metabolism and human health. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 131:25-61. [PMID: 22767136 DOI: 10.1007/10_2012_138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacteria were considered to be lonely 'mutes' for hundreds of years. However, recently it was found that bacteria usually coordinate their behaviors at the population level by producing (speaking), sensing (listening), and responding to small signal molecules. This so-called quorum sensing (QS) regulation enables bacteria to live in a 'society' with cell-cell communication and controls many important bacterial behaviors. In this chapter, QS systems and their signal molecules for Gram-negative and Gram-positive bacteria are introduced. Most interestingly, QS regulates the important bacterial behaviors such as metabolism and pathogenesis. QS-regulated microbial metabolism includes antibiotic synthesis, pollutant biodegradation, and bioenergy production, which are very relevant to human health. QS is also well-known for its involvement in bacterial pathogenesis, such as iin nfections by Pseudomonas aeruginosa and Staphylococcus aureus. Novel disease diagnosis strategies and antimicrobial agents have also been developed based on QS regulation on bacterial infections. In addition, to meet the requirements for the detection/quantification of QS signaling molecules for research and application, different biosensors have been constructed, which will also be reviewed here. QS regulation is essential to bacterial survival and important to human health. A better understanding of QS could lead better control/manipulation of bacteria, thus making them more helpful to people.
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Affiliation(s)
- Yang-Chun Yong
- Biofuels Institute, School of the Environment, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu Province, China
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35
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Abstract
Many bacteria use 'quorum sensing' (QS) as a mechanism to regulate gene induction in a population-dependent manner. In its simplest sense this involves the accumulation of a signaling metabolite during growth; the binding of this metabolite to a regulator or multiple regulators activates induction or repression of gene expression. However QS regulation is seldom this simple, because other inputs are usually involved. In this review we have focussed on how those other inputs influence QS regulation and as implied by the title, this often occurs by environmental or physiological effects regulating the expression or activity of the QS regulators. The rationale of this review is to briefly introduce the main QS signals used in Gram-negative bacteria and then introduce one of the earliest understood mechanisms of regulation of the regulator, namely the plant-mediated control of expression of the TraR QS regulator in Agrobacterium tumefaciens. We then describe how in several species, multiple QS regulatory systems can act as integrated hierarchical regulatory networks and usually this involves the regulation of QS regulators. Such networks can be influenced by many different physiological and environmental inputs and we describe diverse examples of these. In the final section, we describe different examples of how eukaryotes can influence QS regulation in Gram-negative bacteria.
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Affiliation(s)
- Marijke Frederix
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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36
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Probing the impact of ligand binding on the acyl-homoserine lactone-hindered transcription factor EsaR of Pantoea stewartii subsp. stewartii. J Bacteriol 2011; 193:6315-22. [PMID: 21949066 DOI: 10.1128/jb.05956-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The quorum-sensing regulator EsaR from Pantoea stewartii subsp. stewartii is a LuxR homologue that is inactivated by acyl-homoserine lactone (AHL). In the corn pathogen P. stewartii, production of exopolysaccharide (EPS) is repressed by EsaR at low cell densities. However, at high cell densities when high concentrations of its cognate AHL signal are present, EsaR is inactivated and derepression of EPS production occurs. Thus, EsaR responds to AHL in a manner opposite to that of most LuxR family members. Depending on the position of its binding site within target promoters, EsaR serves as either a repressor or activator in the absence rather than in the presence of its AHL ligand. The effect of AHL on LuxR homologues has been difficult to study in vitro because AHL is required for purification and stability. EsaR, however, can be purified without AHL enabling an in vitro analysis of the response of the protein to ligand. Western immunoblots and pulse-chase experiments demonstrated that EsaR is stable in vivo in the absence or presence of AHL. Limited in vitro proteolytic digestions of a biologically active His-MBP tagged version of EsaR highlighted intradomain and interdomain conformational changes that occur in the protein in response to AHL. Gel filtration chromatography of the full-length fusion protein and cross-linking of the N-terminal domain both suggest that this conformational change does not impact the multimeric state of the protein. These findings provide greater insight into the diverse mechanisms for AHL responsiveness found within the LuxR family.
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37
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Crystal structure of QscR, a Pseudomonas aeruginosa quorum sensing signal receptor. Proc Natl Acad Sci U S A 2011; 108:15763-8. [PMID: 21911405 DOI: 10.1073/pnas.1112398108] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acyl-homoserine lactone (AHL) quorum sensing controls gene expression in hundreds of Proteobacteria including a number of plant and animal pathogens. Generally, the AHL receptors are members of a family of related transcription factors, and although they have been targets for development of antivirulence therapeutics there is very little structural information about this class of bacterial receptors. We have determined the structure of the transcription factor, QscR, bound to N-3-oxo-dodecanoyl-homoserine lactone from the opportunistic human pathogen Pseudomonas aeruginosa at a resolution of 2.55 Å. The ligand-bound QscR is a dimer with a unique symmetric "cross-subunit" arrangement containing multiple dimerization interfaces involving both domains of each subunit. The QscR dimer appears poised to bind DNA. Predictions about signal binding and dimerization contacts were supported by studies of mutant QscR proteins in vivo. The acyl chain of the AHL is in close proximity to the dimerization interfaces. Our data are consistent with an allosteric mechanism of signal transmission in the regulation of DNA binding and thus virulence gene expression.
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38
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Poulter S, Carlton TM, Spring DR, Salmond GPC. The Serratia LuxR family regulator CarR 39006 activates transcription independently of cognate quorum sensing signals. Mol Microbiol 2011; 80:1120-31. [PMID: 21435033 DOI: 10.1111/j.1365-2958.2011.07634.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In Gram-negative bacteria, quorum sensing control of gene expression is mediated by transcription factors of the LuxR family, whose DNA-binding affinity is modulated by diffusible N-acyl homoserine lactone (AHL) signalling molecules. In Serratia sp. ATCC 39006 and the plant pathogen Erwinia carotovora ssp. carotovora (Ecc), the biosynthesis of the β-lactam antibiotic 1-carbapen-2-em-3-carboxylic acid (Car) is under quorum sensing control. This study has revealed that, uniquely, the LuxR family transcriptional activator CarR(39006) from Serratia 39006 has no detectable affinity for cognate AHL molecules. Furthermore, CarR(39006) was shown to be naturally competent to bind to its target promoter with high affinity, activate transcription and resist cellular proteolysis, and was unaffected by AHL signals. Experiments with chimeric proteins suggest that the C-terminal DNA-binding domain of CarR(39006) may be responsible for conferring AHL independence. In contrast, we show that the homologous CarR(Ecc) protein binds to its 3O-C6-HSL ligand with high affinity, and that the highly conserved Trp-44 residue is critical for this interaction. Unlike TraR from Agrobacterium tumefaciens, CarR(Ecc) is not directly protected from cellular proteolysis by AHL binding, but via AHL-induced DNA binding. At physiological protein concentrations, AHL binding induces CarR(Ecc) to bind to its target promoter with higher affinity and activate transcription.
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Affiliation(s)
- Simon Poulter
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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39
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Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR. J Bacteriol 2011; 193:2598-607. [PMID: 21378182 DOI: 10.1128/jb.01479-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rhodopseudomonas palustris transcriptional regulator RpaR responds to the RpaI-synthesized quorum-sensing signal p-coumaroyl-homoserine lactone (pC-HSL). Other characterized RpaR homologs respond to fatty acyl-HSLs. We show here that RpaR functions as a transcriptional activator, which binds directly to the rpaI promoter. We developed an RNAseq method that does not require a ribosome depletion step to define a set of transcripts regulated by pC-HSL and RpaR. The transcripts include several noncoding RNAs. A footprint analysis showed that purified His-tagged RpaR (His(6)-RpaR) binds to an inverted repeat element centered 48.5 bp upstream of the rpaI transcript start site, which we mapped by S1 nuclease protection and primer extension analyses. Although pC-HSL-RpaR bound to rpaI promoter DNA, it did not bind to the promoter regions of a number of RpaR-regulated genes not in the rpaI operon. This indicates that RpaR control of these other genes is indirect. Because the RNAseq analysis allowed us to track transcript strand specificity, we discovered that there is pC-HSL-RpaR-activated antisense transcription of rpaR. These data raise the possibility that this antisense RNA or other RpaR-activated noncoding RNAs mediate the indirect activation of genes in the RpaR-controlled regulon.
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40
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Goryachev AB. Design principles of the bacterial quorum sensing gene networks. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 1:45-60. [PMID: 20835981 DOI: 10.1002/wsbm.27] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bacterial quorum sensing (QS) has attracted much interest as the manifestation of collective behavior in prokaryotic organisms once considered strictly solitary. Significant amount of genetic, biochemical, and structural data which, has been accumulated in studies on QS in many species allows us to map properties of specific molecules and their interactions on the observed population-wide bacterial behavior. The present review attempts to give a systems biology perspective on the structure of genetic regulatory networks that control QS and considers functional implications of a variety of design principles that recur in the organization of these networks across species.
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Affiliation(s)
- Andrew B Goryachev
- Centre for Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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41
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Acyl-homoserine lactone binding to and stability of the orphan Pseudomonas aeruginosa quorum-sensing signal receptor QscR. J Bacteriol 2010; 193:421-8. [PMID: 21097632 DOI: 10.1128/jb.01041-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Pseudomonas aeruginosa transcription factor QscR responds to a variety of fatty acyl-homoserine lactones (HSLs), including N-3-oxododecanoyl-HSL (3OC12-HSL), which is produced and detected by the P. aeruginosa quorum-sensing circuit LasI and LasR. As is true for LasR and many other acyl-HSL-dependent transcription factors, production of soluble QscR in sufficient amounts for purification requires growth of recombinant bacteria in the presence of an appropriate acyl-HSL. QscR is thought to bind 3OC12-HSL relatively weakly compared to LasR, and unlike LasR, binding of purified QscR to target DNA was shown to strongly depend on exogenously added 3OC12-HSL. We show that purified QscR is dimeric at sufficiently high concentrations and monomeric at lower concentrations. Furthermore, QscR bound 3OC12-HSL more tightly than previously believed. Purified QscR retained 3OC12-HSL, and at sufficiently high concentrations, it bound target DNA in the absence of added 3OC12-HSL. We also obtained soluble QscR from recombinant Escherichia coli grown in the presence of N-3-oxohexanoyl-HSL (3OC6-HSL) instead of 3OC12-HSL, and because 3OC6-HSL bound much more loosely to QscR than other acyl-HSLs tested, we were able to exchange 3OC6-HSL with other acyl-HSLs in vitro and then estimate binding affinities of QscR for different acyl-HSLs and for target DNA. Our data support a model whereby QscR polypeptides fold properly in the absence of an acyl-HSL, but soluble, acyl-HSL-free QscR does not accumulate because it is subject to rapid aggregation or proteolysis.
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42
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Marsden DM, Nicholson RL, Skindersoe ME, Galloway WRJD, Sore HF, Givskov M, Salmond GPC, Ladlow M, Welch M, Spring DR. Discovery of a quorum sensing modulator pharmacophore by 3D small-molecule microarray screening. Org Biomol Chem 2010; 8:5313-23. [PMID: 20886127 DOI: 10.1039/c0ob00300j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The screening of large arrays of drug-like small-molecules was traditionally a time consuming and resource intensive task. New methodology developed within our laboratories provides an attractive low cost, 3D microarray-assisted screening platform that could be used to rapidly assay thousands of compounds. As a proof-of-principle the platform was exploited to screen a number of quorum sensing analogs. Quorum sensing is used by bacterium to initiate and spread infection; in this context its modulation may have significant clinical value. 3D microarray slides were probed with fluorescently labeled ligand-binding domains of the LuxR homolog CarR from Erwinia carotovora subsp. carotovora. The 3D microarray platform was used to discover the biologically active chloro-pyridine pharmacophore, which was validated using a fluorometric ligand binding assay and ITC. Analogs containing the chloro-pyridine pharmacophore were found to be potent inhibitors of N-acyl-homoserine-lactone (AHL) mediated quorum sensing phenotypes in Serratia (IC(50) = ∼5 μM) and Pseudomonas aeruginosa (IC(50) = 10-20 μM).
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Affiliation(s)
- David M Marsden
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW
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43
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Mandrich L, Merone L, Manco G. Hyperthermophilic phosphotriesterases/lactonases for the environment and human health. ENVIRONMENTAL TECHNOLOGY 2010; 31:1115-1127. [PMID: 20718294 DOI: 10.1080/09593331003789529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the last decades the idea to use enzymes for environmental bioremediation has been more and more proposed and, in the light of this, new solutions have been suggested and detailed studies on some classes of enzymes have been performed. In particular, our attention in the last few years has been focused on the enzymes belonging to the amidohydrolase superfamily. Several members of this superfamily are endowed with promiscuous activities. The term 'catalytic promiscuity' describes the capability of an enzyme to catalyse different chemical reactions, called secondary activities, at the active site responsible for the main activity. Recently, a new family of microbial lactonases with promiscuous phosphotriesterase activity, dubbed PTE-Like Lactonase (PLL), has been ascribed to the amidohydrolase superfamily. Among members of this family are enzymes found in the archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, which show high thermophilicity and thermal resistance. Enzymes showing phosphotriesterase activity are attractive from a biotechnological point of view because they are capable of hydrolysing the organophosphate phosphotriesters (OPs), a class of synthetic compounds employed worldwide both as insecticides and chemical warfare agents. Furthermore, from a basic point of view, studies of catalytic promiscuity offer clues to understand natural evolution of enzymes and to translate this into in vitro adaptation of enzymes to specific human needs. Thermostable enzymes able to hydrolyse OPs are considered good candidates for the set-up of efficient detoxification tools.
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Affiliation(s)
- Luigi Mandrich
- Institute of Protein Biochemistry (IBP), National Research Council (CNR), Naples, Italy
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44
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Leung MM, Florizone SM, Taylor TA, Lang AS, Beatty JT. The gene transfer agent of Rhodobacter capsulatus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 675:253-64. [PMID: 20532745 DOI: 10.1007/978-1-4419-1528-3_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
When Rhodobacter capsulatus cultures enter the stationary phase of growth, particles of the gene transfer agent (RcGTA) are released from cells. The morphology of RcGTA resembles that of a small, tailed bacteriophage, with a protein capsid surrounding a ~4 kb linear, double-stranded fragment of DNA. However, the DNA present consists of random segments of the R. capsulatus genome, which may be transferred to another strain of R. capsulatus. The recipient in RcGTA-mediated gene transduction may acquire new alleles and thus express a new phenotype. The genes encoding the structural proteins of the RcGTA are clustered on the R. capsulatus chromosome, whereas genes that encode proteins that regulate the production of RcGTA are scattered around the chromosome. These regulatory proteins include a homoserine lactone synthase (GtaI) that produces a quorum-sensing signal, a two-component sensor-kinase protein (CckA), and a two-component response regulator protein (CtrA). We review the proposed evolutionary origin of RcGTA, as well as environmental and cellular factors involved in the induction of this unusual process of genetic exchange.
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Affiliation(s)
- Molly M Leung
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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45
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Fekete A, Kuttler C, Rothballer M, Hense BA, Fischer D, Buddrus-Schiemann K, Lucio M, Müller J, Schmitt-Kopplin P, Hartmann A. Dynamic regulation ofN-acyl-homoserine lactone production and degradation inPseudomonas putidaIsoF. FEMS Microbiol Ecol 2010; 72:22-34. [DOI: 10.1111/j.1574-6941.2009.00828.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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46
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McIntosh M, Meyer S, Becker A. NovelSinorhizobium melilotiquorum sensing positive and negative regulatory feedback mechanisms respond to phosphate availability. Mol Microbiol 2009; 74:1238-56. [DOI: 10.1111/j.1365-2958.2009.06930.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Liao RZ, Yu JG, Himo F. Reaction Mechanism of the Dinuclear Zinc Enzyme N-Acyl-l-homoserine Lactone Hydrolase: A Quantum Chemical Study. Inorg Chem 2009; 48:1442-8. [PMID: 19159270 DOI: 10.1021/ic801531n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rong-Zhen Liao
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Jian-Guo Yu
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
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48
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Ni N, Li M, Wang J, Wang B. Inhibitors and antagonists of bacterial quorum sensing. Med Res Rev 2009; 29:65-124. [DOI: 10.1002/med.20145] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Tanouchi Y, Tu D, Kim J, You L. Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Comput Biol 2008; 4:e1000167. [PMID: 18769706 PMCID: PMC2507755 DOI: 10.1371/journal.pcbi.1000167] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 07/23/2008] [Indexed: 11/18/2022] Open
Abstract
Cellular interactions are subject to random fluctuations (noise) in quantities of interacting molecules. Noise presents a major challenge for the robust function of natural and engineered cellular networks. Past studies have analyzed how noise is regulated at the intracellular level. Cell-cell communication, however, may provide a complementary strategy to achieve robust gene expression by enabling the coupling of a cell with its environment and other cells. To gain insight into this issue, we have examined noise regulation by quorum sensing (QS), a mechanism by which many bacteria communicate through production and sensing of small diffusible signals. Using a stochastic model, we analyze a minimal QS motif in Gram-negative bacteria. Our analysis shows that diffusion of the QS signal, together with fast turnover of its transcriptional regulator, attenuates low-frequency components of extrinsic noise. We term this unique mechanism "diffusional dissipation" to emphasize the importance of fast signal turnover (or dissipation) by diffusion. We further show that this noise attenuation is a property of a more generic regulatory motif, of which QS is an implementation. Our results suggest that, in a QS system, an unstable transcriptional regulator may be favored for regulating expression of costly proteins that generate public goods.
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Affiliation(s)
- Yu Tanouchi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Dennis Tu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Jungsang Kim
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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50
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Smith C, Song H, You L. Signal discrimination by differential regulation of protein stability in quorum sensing. J Mol Biol 2008; 382:1290-7. [PMID: 18721812 DOI: 10.1016/j.jmb.2008.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/30/2008] [Accepted: 08/02/2008] [Indexed: 11/29/2022]
Abstract
Quorum sensing (QS) is a communication mechanism exploited by a large variety of bacteria to coordinate gene expression at the population level. In Gram-negative bacteria, QS occurs via synthesis and detection of small chemical signals, most of which belong to the acyl-homoserine lactone class. In such a system, binding of an acyl-homoserine lactone signal to its cognate transcriptional regulator (R-protein) often induces stabilization and subsequent dimerization of the R-protein, which results in the regulation of downstream gene expression. Existence of diverse QS systems within and among species of bacteria indicates that each bacterium needs to distinguish among a myriad of structurally similar chemical signals. We show, using a mathematical model, that fast degradation of an R-protein monomer can facilitate discrimination of signals that differentially stabilize it. Furthermore, our results suggest an inverse correlation between the stability of an R-protein and the achievable limits of fidelity in signal discrimination. In particular, an unstable R-protein tends to be more specific to its cognate signal, whereas a stable R-protein tends to be more promiscuous. These predictions are consistent with experimental data on well-studied natural and engineered R-proteins and thus have implications for understanding the functional design of QS systems.
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Affiliation(s)
- Cameron Smith
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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