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Hetta HF, Ramadan YN, Rashed ZI, Alharbi AA, Alsharef S, Alkindy TT, Alkhamali A, Albalawi AS, Battah B, Donadu MG. Quorum Sensing Inhibitors: An Alternative Strategy to Win the Battle against Multidrug-Resistant (MDR) Bacteria. Molecules 2024; 29:3466. [PMID: 39124871 PMCID: PMC11313800 DOI: 10.3390/molecules29153466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/29/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Antibiotic resistance is a major problem and a major global health concern. In total, there are 16 million deaths yearly from infectious diseases, and at least 65% of infectious diseases are caused by microbial communities that proliferate through the formation of biofilms. Antibiotic overuse has resulted in the evolution of multidrug-resistant (MDR) microbial strains. As a result, there is now much more interest in non-antibiotic therapies for bacterial infections. Among these revolutionary, non-traditional medications is quorum sensing inhibitors (QSIs). Bacterial cell-to-cell communication is known as quorum sensing (QS), and it is mediated by tiny diffusible signaling molecules known as autoinducers (AIs). QS is dependent on the density of the bacterial population. QS is used by Gram-negative and Gram-positive bacteria to control a wide range of processes; in both scenarios, QS entails the synthesis, identification, and reaction to signaling chemicals, also known as auto-inducers. Since the usual processes regulated by QS are the expression of virulence factors and the creation of biofilms, QS is being investigated as an alternative solution to antibiotic resistance. Consequently, the use of QS-inhibiting agents, such as QSIs and quorum quenching (QQ) enzymes, to interfere with QS seems like a good strategy to prevent bacterial infections. This review sheds light on QS inhibition strategy and mechanisms and discusses how using this approach can aid in winning the battle against resistant bacteria.
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Affiliation(s)
- Helal F. Hetta
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Yasmin N. Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Y.N.R.); (Z.I.R.)
| | - Zainab I. Rashed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Y.N.R.); (Z.I.R.)
| | - Ahmad A. Alharbi
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Shomokh Alsharef
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Tala T. Alkindy
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.A.); (S.A.); (T.T.A.)
| | - Alanoud Alkhamali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.); (A.S.A.)
| | - Abdullah S. Albalawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia; (A.A.); (A.S.A.)
| | - Basem Battah
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Antioch Syrian Private University, Maaret Siadnaya 22734, Syria
| | - Matthew G. Donadu
- Hospital Pharmacy, Giovanni Paolo II Hospital, ASL Gallura, 07026 Olbia, Italy;
- Department of Medicine, Surgery and Pharmacy, Scuola di Specializzazione in Farmacia Ospedaliera, University of Sassari, 07100 Sassari, Italy
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Gosset-Erard C, Han G, Kyrko D, Hueber A, Nay B, Eparvier V, Touboul D. Structural characterization of N-acyl-homoserine lactones from bacterial quorum sensing using LC-MS/MS analyses after Paternò-Büchi derivatization in solution. Anal Bioanal Chem 2024:10.1007/s00216-024-05355-0. [PMID: 38842688 DOI: 10.1007/s00216-024-05355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
Bacterial quorum sensing is a chemical language allowing bacteria to interact through the excretion of molecules called autoinducers, like N-acyl-homoserine lactones (AHLs) produced by Gram-negative Burkholderia and Paraburkholderia bacteria known as opportunistic pathogens. The AHLs differ in their acyl-chain length and may be modified by a 3-oxo or 3-hydroxy substituent, or C = C double bonds at different positions. As the bacterial signal specificity depends on all of these chemical features, their structural characterization is essential to have a better understanding of the population regulation and virulence phenomenon. This study aimed at enabling the localization of the C = C double bond on such specialized metabolites while using significantly lower amounts of biological material. The approach is based on LC-MS/MS analyses of bacterial extracts after in-solution derivatization by a photochemical Paternò-Büchi reaction, leading to the formation of an oxetane ring and subsequently to specific fragmentations when performing MS/MS experiments. The in-solution derivatization of AHLs was optimized on several standards, and then the matrix effect of bacterial extracts on the derivatization was assessed. As a proof of concept, the optimized conditions were applied to a bacterial extract enabling the localization of C = C bonds on unsaturated AHLs.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Guanghui Han
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Dimitra Kyrko
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Amandine Hueber
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Bastien Nay
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Véronique Eparvier
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France.
- Laboratoire de Chimie Moléculaire (LCM), CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.
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de la Fuente I, Manzano-Morales S, Sanz D, Prieto A, Barriuso J. Quorum sensing in bacteria: in silico protein analysis, ecophysiology, and reconstruction of their evolutionary history. BMC Genomics 2024; 25:441. [PMID: 38702600 PMCID: PMC11069264 DOI: 10.1186/s12864-024-10355-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Quorum sensing (QS) is a sophisticated cell-to-cell signalling mechanism that allows the coordination of important processes in microbial populations. The AI-1 and AI-2 autoinducer systems are among the best characterized bacterial QS systems at the genetic level. RESULTS In this study, we present data derived from in silico screening of QS proteins from bacterial genomes available in public databases. Sequence analyses allowed identifying candidate sequences of known QS systems that were used to build phylogenetic trees. Eight categories were established according to the number of genes from the two major QS systems present in each genome, revealing a correlation with specific taxa, lifestyles or metabolic traits. Many species had incomplete QS systems, encoding the receptor protein but not the biosynthesis of the quorum sensing molecule (QSMs). Reconstruction of the evolutionary history of the LuxR family and prediction of the 3D structure of the ancestral protein suggested their monomeric configuration in the absence of the signal molecule and the presence of a cavity for its binding. CONCLUSIONS Here we correlate the taxonomic affiliation and lifestyle of bacteria from different genera with the QS systems encoded in their genomes. Moreover, we present the first ancestral reconstruction of the LuxR QS receptors, providing further insight in their evolutionary history.
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Affiliation(s)
- Iñigo de la Fuente
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Saioa Manzano-Morales
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - David Sanz
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain.
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Corbella M, Bravo J, Demkiv AO, Calixto AR, Sompiyachoke K, Bergonzi C, Elias MH, Kamerlin SCL. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592096. [PMID: 38746346 PMCID: PMC11092605 DOI: 10.1101/2024.05.01.592096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.
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Lau MML, Kho CJY, Chung HH, Zulkharnain A. Isolation, identification and characterisation of Pseudomonas koreensis CM-01 isolated from diseased Malaysian mahseer (Tor tambroides). FISH & SHELLFISH IMMUNOLOGY 2024; 148:109518. [PMID: 38513913 DOI: 10.1016/j.fsi.2024.109518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Pseudomonas species are one of the most threatening fish pathogens which reside a wide range of environments. In this study, the dominant bacteria were isolated from diseased Malaysian mahseer (Tor tambroides) and tentatively named CM-01. It was identified as Pseudomonas koreensis based on its biochemical, morphological, genetic and physiological information. Its pathogenicity was found to be correlated with twelve virulence genes identified including iron uptake, protease, acylhomoserine lactone synthase gacS/gacA component regulation system, type IV secretion system, hydrogen cyanide production, exolysin, alginate biosynthesis, flagella and pili. The median lethal dose (LD50) for the CM-01 isolate on Malaysian mahseer was documented at 5.01 × 107 CFU/mL. The experimental infection revealed that CM-01 led to significant histological lesions in the fish, ultimately resulting in death. These lesions comprise necrosis, tissue thickening and aggregation. Drug sensitivity tests had shown its susceptibility to beta-lactam combination agents and further suggest its drug of choice. Its growing features had shown its growth at optimal temperature and pH. To the best of our knowledge, this is the first report of P. koreensis linked to diseased T. tambroides. STATEMENT OF RELEVANCE: In this research, a novel strain of Pseudomonas koreensis, CM-01 was isolated from diseased T. tambroides for the first time. The antimicrobial susceptibility, pathogenicity, virulence genes and growth characteristics of CM-01 were studied. These findings established a scientific foundation for the recognition of P. koreensis and the management of fish infections caused by this pathogen.
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Affiliation(s)
- Melinda Mei Lin Lau
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Cindy Jia Yung Kho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of system Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, 337-8570, Japan.
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Manson DE, Ananiev GE, Guo S, Ericksen SS, Santa EE, Blackwell HE. Abiotic Small Molecule Inhibitors and Activators of the LasR Quorum Sensing Receptor in Pseudomonas aeruginosa with Potencies Comparable or Surpassing N-Acyl Homoserine Lactones. ACS Infect Dis 2024; 10:1212-1221. [PMID: 38506163 PMCID: PMC11014758 DOI: 10.1021/acsinfecdis.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa controls almost 10% of its genome, including myriad virulence genes, via a cell-to-cell chemical communication system called quorum sensing (QS). Small molecules that either inhibit or activate QS in P. aeruginosa represent useful research tools to study the role of this signaling pathway in infection and interrogate its viability as an antivirulence target. However, despite active research in this area over the past 20+ years, there are relatively few synthetic compounds known to strongly inhibit or activate QS in P. aeruginosa. Most reported QS modulators in this pathogen are of low potency or have structural liabilities that limit their application in biologically relevant environments such as mimics of the native N-acyl l-homoserine lactone (AHL) signals. Here, we report the results of a high-throughput screen for abiotic small molecules that target LasR, a key QS regulator in P. aeruginosa. We screened a 25,000-compound library and discovered four new structural classes of abiotic LasR modulators. These compounds include antagonists that surpass the potency of all known AHL-type compounds and mimetics thereof, along with an agonist with potency approaching that of LasR's native ligand. The novel structures of this compound set, along with their anticipated robust physicochemical profiles, underscore their potential value as probe molecules to interrogate the roles of QS in this formidable pathogen.
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Affiliation(s)
- Daniel E Manson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Gene E Ananiev
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Song Guo
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Spencer S Ericksen
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Emma E Santa
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
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Al-Rabia MW, Asfour HZ, Alhakamy NA, Abdulaal WH, Ibrahim TS, Abbas HA, Salem IM, Hegazy WAH, Nazeih SI. Thymoquinone is a natural antibiofilm and pathogenicity attenuating agent in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 14:1382289. [PMID: 38638827 PMCID: PMC11024287 DOI: 10.3389/fcimb.2024.1382289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
Pseudomonas aeruginosa belongs to the critical pathogens that represent a global public health problem due to their high rate of resistance as listed by WHO. P. aeruginosa can result in many nosocomial infections especially in individuals with compromised immune systems. Attenuating virulence factors by interference with quorum sensing (QS) systems is a promising approach to treat P. aeruginosa-resistant infections. Thymoquinone is a natural compound isolated from Nigella sativa (black seed) essential oil. In this study, the minimum inhibitory concentration of thymoquinone was detected followed by investigating the antibiofilm and antivirulence activities of the subinhibitory concentration of thymoquinone against P. aeruginosa PAO1. The effect of thymoquinone on the expression of QS genes was assessed by quantitative real-time PCR, and the protective effect of thymoquinone against the pathogenesis of PAO1 in mice was detected by the mouse survival test. Thymoquinone significantly inhibited biofilm, pyocyanin, protease activity, and swarming motility. At the molecular level, thymoquinone markedly downregulated QS genes lasI, lasR, rhlI, and rhlR. Moreover, thymoquinone could protect mice from the pathologic effects of P. aeruginosa increasing mouse survival from 20% to 100%. In conclusion, thymoquinone is a promising natural agent that can be used as an adjunct therapeutic agent with antibiotics to attenuate the pathogenicity of P. aeruginosa.
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Affiliation(s)
- Mohammed W. Al-Rabia
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Z. Asfour
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nabil A. Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wesam H. Abdulaal
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tarek S. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hisham A. Abbas
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Ibrahim M. Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sphinx University, Assiut, Egypt
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat, Oman
| | - Shaimaa I. Nazeih
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
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Simpson CA, Celentano Z, McKinlay JB, Nadell CD, van Kessel JC. Bacterial quorum sensing controls carbon metabolism to optimize growth in changing environmental conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576522. [PMID: 38328067 PMCID: PMC10849521 DOI: 10.1101/2024.01.21.576522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Bacteria sense population density via the cell-cell communication system called quorum sensing (QS). Some QS-regulated phenotypes ( e.g. , secreted enzymes, chelators), are public goods exploitable by cells that stop producing them. We uncovered a phenomenon in which Vibrio cells optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS. Strains that are genetically 'locked' at high cell density grow slowly in minimal glucose media and suppressor mutants accumulate via inactivating-mutations in metF (methylenetetrahydrofolate reductase) and luxR (the master QS transcriptional regulator). Methionine/THF synthesis genes are repressed at low cell density when glucose is plentiful and are de-repressed by LuxR at high cell density as glucose becomes limiting. In mixed cultures, QS mutant strains initially co-exist with wild-type, but as glucose is depleted, wild-type outcompetes the QS mutants. Thus, QS regulation of methionine/THF synthesis is a fitness benefit that links private and public goods within the QS regulon, preventing accumulation of QS-defective mutants.
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Wallace M, Cummings, Jr. DA, Roberts AG, Puri AW. A widespread methylotroph acyl-homoserine lactone synthase produces a new quorum sensing signal that regulates swarming in Methylobacterium fujisawaense. mBio 2024; 15:e0199923. [PMID: 38085021 PMCID: PMC10790750 DOI: 10.1128/mbio.01999-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases promote plant growth. However, little is known about how these organisms interact with each other and their environment. In this work, we identify one of the chemical signals commonly used by these bacteria and discover that this signal controls swarming motility in the pink-pigmented facultative methylotroph Methylobacterium fujisawaense DSM5686. This work provides new molecular details about interactions between these important bacteria and will help scientists predict these interactions and the group behaviors they regulate from genomic sequencing information.
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Affiliation(s)
- Mike Wallace
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Dale A. Cummings, Jr.
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Andrew G. Roberts
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Aaron W. Puri
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
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10
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Panchal J, Prajapati J, Dabhi M, Patel A, Patel S, Rawal R, Saraf M, Goswami D. Comprehensive computational investigation for ligand recognition and binding dynamics of SdiA: a degenerate LuxR -type receptor in Klebsiella pneumoniae. Mol Divers 2024:10.1007/s11030-023-10785-6. [PMID: 38212453 DOI: 10.1007/s11030-023-10785-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/26/2023] [Indexed: 01/13/2024]
Abstract
SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum sensing signals produced by other bacterial species. However, the molecular details of how SdiA recognizes and binds to different ligands and how this affects its function and regulation in K. pneumoniae still need to be better understood. This study uses computational methods to explore the protein-ligand binding dynamics of SdiA with 11 AHLs and 2 AI-2 ligands. The 3D structure of SdiA was predicted through homology modeling, followed by molecular docking with AHLs and AI-2 ligands. Binding affinities were quantified using MM-GBSA, and complex stability was assessed via Molecular Dynamics (MD) simulations. Results demonstrated that SdiA in Klebsiella pneumoniae exhibits a degenerate binding nature, capable of interacting with multiple AHLs and AI-2. Specific ligands, namely C10-HSL, C8-HSL, 3-oxo-C8-HSL, and 3-oxo-C10-HSL, were found to have high binding affinities and formed critical hydrogen bonds with key amino acid residues of SdiA. This finding aligns with the observed preference of SdiA for AHLs having 8 to 10 carbon-length acyl chains and lacking hydroxyl groups. In contrast, THMF and HMF demonstrated poor binding properties. Furthermore, AI-2 exhibited a low affinity, corroborating the inference that SdiA is not the primary receptor for AI-2 in K. pneumoniae. These findings provide insights into the protein-ligand binding dynamics of SdiA and its role in quorum sensing and virulence of K. pneumoniae.
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Affiliation(s)
- Janki Panchal
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Jignesh Prajapati
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Milan Dabhi
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Meenu Saraf
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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Alasiri A, Soltane R, Taha MN, Abd El-Aleam RH, Alshehri F, Sayed AM. Bakuchiol inhibits Pseudomonas aeruginosa's quorum sensing-dependent biofilm formation by selectively inhibiting its transcriptional activator protein LasR. Int J Biol Macromol 2024; 255:128025. [PMID: 37979739 DOI: 10.1016/j.ijbiomac.2023.128025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
In the present study, we characterized Bakuchiol (Bak) as a new potent quorum sensing (QS) inhibitor against Pseudomonas aeruginosa biofilm formation. Upon extensive in vitro investigations, Bak was found to suppress the P. aeruginosa biofilm formation (75.5 % inhibition) and its associated virulence factor e.g., pyocyanin and rhamnolipids (% of inhibition = 71.5 % and 66.9 %, respectively). Upon LuxR-type receptors assay, Bak was found to selectively inhibit P. aeruginosa's LasR in a dose-dependent manner. Further in-depth molecular investigations (e.g., sedimentation velocity and thermal shift assays) revealed that Bak destabilized LasR upon binding and disrupted its functioning quaternary structure (i.e., the functioning dimeric form). The subsequent modeling and molecular dynamics (MD) simulations explained in more molecular detail how Bak interacts with LasR and how it can induce its dimeric form disruption. In conclusion, our study identified Bak as a potent and specific LasR antagonist that should be widely used as a chemical probe of QS in P. aeruginosa, offering new insights into LasR antagonism processes. The new findings shed light on the cryptic world of LuxR-type QS in this important opportunistic pathogen.
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Affiliation(s)
- Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Mostafa N Taha
- Microbiology and Immunology Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.
| | - Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo 11571, Egypt.
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Ahmed M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni Suef, Egypt; Department of Pharmacognosy, College of Pharmacy, Almaaqal University, 61014 Basra, Iraq.
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12
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Cho SK, Igliński B, Kumar G. Biomass based biochar production approaches and its applications in wastewater treatment, machine learning and microbial sensors. BIORESOURCE TECHNOLOGY 2024; 391:129904. [PMID: 37918492 DOI: 10.1016/j.biortech.2023.129904] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Biochar is a stable carbonaceous material derived from various biomass and can be utilized as adsorbents, catalysts and precursors in various environmental applications. This review discusses various feedstock materials and methods of biochar production via traditional as well as modern approaches. Additionally, the biochar characteristics, HTC process, and its modification by employing steam and gas purging, acidic, basic / alkaline and organo-solvent, electro- and magnetic fields have been discussed. The recent biochar applications for real water, wastewater and industrial wastewater for the abstraction of environmental contaminants also reviewed. Moreover, applications in machine learning and microbial sensors were discussed. In the meantime, analyses on commercial and environmental profit, current ecological concerns and the future directions of biochar application have been well presented.
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Affiliation(s)
- Si-Kyung Cho
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, 10326, Republic of Korea
| | - Bartłomiej Igliński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus, 4036 Stavanger, Norway; School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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13
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Anburajan P, Cayetano RD, Prohim YM, Thau NT, Kim S, Kim H, Ko JH, Oh HS. Role of quorum sensing and quorum quenching in anaerobic digestion: A scoping review. ENVIRONMENTAL RESEARCH 2023; 239:117413. [PMID: 37839533 DOI: 10.1016/j.envres.2023.117413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Anaerobic digestion (AD) is a biological process that employs anaerobic microorganisms to degrade organic material, yielding biogas and biofertilizers. Understanding quorum sensing (QS) signaling in mixed microbial systems provides valuable insights into microbial behavior and functions. This review aims to examine recent studies on the roles of QS and QQ in the AD processes. A QS signal molecule, N-acyl homoserine lactone (AHL), induce the production of extraceluller polymers, promoting biofilm formation and bacterial aggregation, thereby the efficiency of AD process. QS-assisted granule formation fosters syntrophy between acetogens and methanogens, leading to increased organic removal and methane production. Specific AHLs were shown to be correlated with the abundance of hydrolytic bacteria and acidogens, further benefiting methane production. QQ was shown to effectively control membrane fouling in anaerobic membrane bioreactors, yet its impact on methane productivity remains unclear. This review shed lights on the existing literature gaps regarding the mechanisms of QS and QQ in AD systems, which will play a vital role in advancing AD applications in the future.
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Affiliation(s)
- Parthiban Anburajan
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea; Institute of Environmental Technology, Seoul National University of Science and Technology, Seoul, South Korea
| | - Roent Dune Cayetano
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea; Institute of Environmental Technology, Seoul National University of Science and Technology, Seoul, South Korea
| | - You Mit Prohim
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea
| | - Nguyen Tang Thau
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea
| | - Sungmi Kim
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea
| | - Hyeok Kim
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea
| | - Je Hyeon Ko
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea
| | - Hyun-Suk Oh
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul, South Korea; Institute of Environmental Technology, Seoul National University of Science and Technology, Seoul, South Korea.
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14
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Simanek KA, Schumacher ML, Mallery CP, Shen S, Li L, Paczkowski JE. Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis. Nat Commun 2023; 14:7986. [PMID: 38042853 PMCID: PMC10693556 DOI: 10.1038/s41467-023-43702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Quorum sensing is a mechanism of bacterial communication that controls virulence gene expression. Pseudomonas aeruginosa regulates virulence via two synthase/transcription factor receptor pairs: LasI/R and RhlI/R. LasR is considered the master transcriptional regulator of quorum sensing, as it upregulates rhlI/R. However, clinical isolates often have inactivating mutations in lasR, while maintaining Rhl-dependent signaling. We sought to understand how quorum sensing progresses in isolates with lasR mutations, specifically via activation of RhlR. We find that clinical isolates with lasR inactivating mutations often harbor concurrent mutations in rhlI. Using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry, we discover that strains lacking lasR overproduce the RhlI-synthesized autoinducer and that RhlI variants re-calibrate autoinducer concentrations to wild-type levels, restoring virulent phenotypes. These findings provide a mechanism for the plasticity of quorum sensing progression in an acute infection niche.
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Affiliation(s)
- Kayla A Simanek
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Megan L Schumacher
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Caleb P Mallery
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA
| | - Stella Shen
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA
| | - Lingyun Li
- Division of Environmental Health Sciences, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA
| | - Jon E Paczkowski
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, 12201, USA.
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, 12208, USA.
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15
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Soltane R, Alasiri A, Taha MN, Abd El-Aleam RH, Alghamdi KS, Ghareeb MA, Keshek DEG, Cardoso SM, Sayed AM. Norlobaridone Inhibits Quorum Sensing-Dependent Biofilm Formation and Some Virulence Factors in Pseudomonas aeruginosa by Disrupting Its Transcriptional Activator Protein LasR Dimerization. Biomolecules 2023; 13:1573. [PMID: 38002255 PMCID: PMC10669572 DOI: 10.3390/biom13111573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/26/2023] Open
Abstract
In the present study, norlobaridone (NBD) was isolated from Parmotrema and then evaluated as a new potent quorum sensing (QS) inhibitor against Pseudomonas aeruginosa biofilm development. This phenolic natural product was found to reduce P. aeruginosa biofilm formation (64.6% inhibition) and its related virulence factors, such as pyocyanin and rhamnolipids (% inhibition = 61.1% and 55%, respectively). In vitro assays inhibitory effects against a number of known LuxR-type receptors revealed that NBD was able to specifically block P. aeruginosa's LasR in a dose-dependent manner. Further molecular studies (e.g., sedimentation velocity and thermal shift assays) demonstrated that NBD destabilized LasR upon binding and damaged its functional quaternary structure (i.e., the functional dimeric form). The use of modelling and molecular dynamics (MD) simulations also allowed us to further understand its interaction with LasR, and how this can disrupt its dimeric form. Finally, our findings show that NBD is a powerful and specific LasR antagonist that should be widely employed as a chemical probe in QS of P. aeruginosa, providing new insights into LasR antagonism processes. The new discoveries shed light on the mysterious world of LuxR-type QS in this key opportunistic pathogen.
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Affiliation(s)
- Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Ahlam Alasiri
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Mostafa N. Taha
- Microbiology and Immunology Department, Faculty of Pharmacy, Nahda University, Beni-Suef 62764, Egypt;
| | - Rehab H. Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo 11571, Egypt;
| | - Kawthar Saad Alghamdi
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin 39511, Saudi Arabia;
| | - Mosad A. Ghareeb
- Medicinal Chemistry Department, Theodor Bilharz Research Institute Kornaish El Nile, Warrak El-Hadar, Imbaba, P.O. Box 30, Giza 12411, Egypt;
| | - Doaa El-Ghareeb Keshek
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Center, Giza 11571, Egypt
| | - Susana M. Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Ahmed M. Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
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16
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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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17
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Grigg JC, Copp JN, Krekhno JMC, Liu J, Ibrahimova A, Eltis LD. Deciphering the biosynthesis of a novel lipid in Mycobacterium tuberculosis expands the known roles of the nitroreductase superfamily. J Biol Chem 2023; 299:104924. [PMID: 37328106 PMCID: PMC10404671 DOI: 10.1016/j.jbc.2023.104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Mycobacterium tuberculosis's (Mtb) success as a pathogen is due in part to its sophisticated lipid metabolic programs, both catabolic and biosynthetic. Several of Mtb lipids have specific roles in pathogenesis, but the identity and roles of many are unknown. Here, we demonstrated that the tyz gene cluster in Mtb, previously implicated in resistance to oxidative stress and survival in macrophages, encodes the biosynthesis of acyl-oxazolones. Heterologous expression of tyzA (Rv2336), tyzB (Rv2338c) and tyzC (Rv2337c) resulted in the biosynthesis of C12:0-tyrazolone as the predominant compound, and the C12:0-tyrazolone was identified in Mtb lipid extracts. TyzA catalyzed the N-acylation of l-amino acids, with highest specificity for l-Tyr and l-Phe and lauroyl-CoA (kcat/KM = 5.9 ± 0.8 × 103 M-1s-1). In cell extracts, TyzC, a flavin-dependent oxidase (FDO) of the nitroreductase (NTR) superfamily, catalyzed the O2-dependent desaturation of the N-acyl-L-Tyr produced by TyzA, while TyzB, a ThiF homolog, catalyzed its ATP-dependent cyclization. The substrate preference of TyzB and TyzC appear to determine the identity of the acyl-oxazolone. Phylogenetic analyses revealed that the NTR superfamily includes a large number of broadly distributed FDOs, including five in Mtb that likely catalyze the desaturation of lipid species. Finally, TCA1, a molecule with activity against drug-resistant and persistent tuberculosis, failed to inhibit the cyclization activity of TyzB, the proposed secondary target of TCA1. Overall, this study identifies a novel class of Mtb lipids, clarifies the role of a potential drug target, and expands our understanding of the NTR superfamily.
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Affiliation(s)
- Jason C Grigg
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Janine N Copp
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica M C Krekhno
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jie Liu
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aygun Ibrahimova
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada.
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18
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Naga NG, El-Badan DE, Ghanem KM, Shaaban MI. It is the time for quorum sensing inhibition as alternative strategy of antimicrobial therapy. Cell Commun Signal 2023; 21:133. [PMID: 37316831 DOI: 10.1186/s12964-023-01154-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/29/2023] [Indexed: 06/16/2023] Open
Abstract
Multiple drug resistance poses a significant threat to public health worldwide, with a substantial increase in morbidity and mortality rates. Consequently, searching for novel strategies to control microbial pathogenicity is necessary. With the aid of auto-inducers (AIs), quorum sensing (QS) regulates bacterial virulence factors through cell-to-cell signaling networks. AIs are small signaling molecules produced during the stationary phase. When bacterial cultures reach a certain level of growth, these molecules regulate the expression of the bound genes by acting as mirrors that reflect the inoculum density.Gram-positive bacteria use the peptide derivatives of these signaling molecules, whereas Gram-negative bacteria use the fatty acid derivatives, and the majority of bacteria can use both types to modulate the expression of the target gene. Numerous natural and synthetic QS inhibitors (QSIs) have been developed to reduce microbial pathogenesis. Applications of QSI are vital to human health, as well as fisheries and aquaculture, agriculture, and water treatment. Video Abstract.
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Affiliation(s)
- Nourhan G Naga
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt.
| | - Dalia E El-Badan
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Khaled M Ghanem
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mona I Shaaban
- Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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19
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Meng Q, Xu Q, Xu Y, Ren H, Ge X, Yu J, Cao X, Yin J, Yu Z. A FadR-Type Regulator Activates the Biodegradation of Polycyclic Aromatic Hydrocarbons by Mediating Quorum Sensing in Croceicoccus naphthovorans Strain PQ-2. Appl Environ Microbiol 2023; 89:e0043323. [PMID: 37098893 PMCID: PMC10231186 DOI: 10.1128/aem.00433-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 04/27/2023] Open
Abstract
Bacteria employ multiple transcriptional regulators to orchestrate cellular responses to adapt to constantly varying environments. The bacterial biodegradation of polycyclic aromatic hydrocarbons (PAHs) has been extensively described, and yet, the PAH-related transcriptional regulators remain elusive. In this report, we identified an FadR-type transcriptional regulator that controls phenanthrene biodegradation in Croceicoccus naphthovorans strain PQ-2. The expression of fadR in C. naphthovorans PQ-2 was induced by phenanthrene, and its deletion significantly impaired both the biodegradation of phenanthrene and the synthesis of acyl-homoserine lactones (AHLs). In the fadR deletion strain, the biodegradation of phenanthrene could be recovered by supplying either AHLs or fatty acids. Notably, FadR simultaneously activated the fatty acid biosynthesis pathway and repressed the fatty acid degradation pathway. As intracellular AHLs are synthesized with fatty acids as substrates, boosting the fatty acid supply could enhance AHL synthesis. Collectively, these findings demonstrate that FadR in C. naphthovorans PQ-2 positively regulates PAH biodegradation by controlling the formation of AHLs, which is mediated by the metabolism of fatty acids. IMPORTANCE Master transcriptional regulation of carbon catabolites is extremely important for the survival of bacteria that face changes in carbon sources. Polycyclic aromatic hydrocarbons (PAHs) can be utilized as carbon sources by some bacteria. FadR is a well-known transcriptional regulator involved in fatty acid metabolism; however, the connection between FadR regulation and PAH utilization in bacteria remains unknown. This study revealed that a FadR-type regulator in Croceicoccus naphthovorans PQ-2 stimulated PAH biodegradation by controlling the biosynthesis of the acyl-homoserine lactone quorum-sensing signals that belong to fatty acid-derived compounds. These results provide a unique perspective for understanding bacterial adaptation to PAH-containing environments.
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Affiliation(s)
- Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Qimiao Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Yinming Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Huiping Ren
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Xuzhe Ge
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Jianming Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Xueqiang Cao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang Province, China
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20
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Duan Y, Han M, Grimm M, Ponath J, Reichelt M, Mithöfer A, Schikora A. Combination of bacterial N-acyl homoserine lactones primes Arabidopsis defenses via jasmonate metabolism. PLANT PHYSIOLOGY 2023; 191:2027-2044. [PMID: 36649188 PMCID: PMC10022612 DOI: 10.1093/plphys/kiad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
N-acyl homoserine lactones (AHLs) are important players in plant-bacteria interactions. Different AHL-producing bacteria can improve plant growth and resistance against plant pathogens. In nature, plants may host a variety of AHL-producing bacteria and frequently experience numerous AHLs at the same time. Therefore, a coordinated response to combined AHL molecules is necessary. The purpose of this study was to explore the mechanism of AHL-priming using combined AHL molecules including N-(3-oxo-hexanoyl)-L-homoserine lactone, N-3-oxo-octanoyl-L-homoserine lactone, N-3-oxo-dodecanoyl-L-homoserine lactone, and N-3-oxo-tetradecanoyl-L-homoserine lactone and AHL-producing bacteria including Serratia plymuthica HRO-C48, Rhizobium etli CFN42, Burkholderia graminis DSM17151, and Ensifer meliloti (Sinorhizobium meliloti) Rm2011. We used transcriptome analysis, phytohormone measurements, as well as genetic and microbiological approaches to assess how the combination of structurally diverse AHL molecules influence Arabidopsis (Arabidopsis thaliana). Our findings revealed a particular response to a mixture of AHL molecules (AHL mix). Different expression patterns indicated that the reaction of plants exposed to AHL mix differs from that of plants exposed to single AHL molecules. In addition, different content of jasmonic acid (JA) and derivatives revealed that jasmonates play an important role in AHL mix-induced priming. The fast and stable decreased concentration of COOH-JA-Ile after challenge with the flagellin-derived peptide flg22 indicated that AHL mix modifies the metabolism of jasmonates. Study of various JA- and salicylic acid-related Arabidopsis mutants strengthened the notion that JA homeostasis is involved in AHL-priming. Understanding how the combination of AHLs primes plants for enhanced resistance has the potential to broaden our approaches in sustainable agriculture and will help to effectively protect plants against pathogens.
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Affiliation(s)
- Yongming Duan
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Min Han
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Maja Grimm
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Jessica Ponath
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Axel Mithöfer
- Max-Planck-Institute for Chemical Ecology, Research Group Plant Defense Physiology, Hans-Knöll-Str. 8, 07745 Jena, Germany
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21
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Patel R, Soni M, Soyantar B, Shivangi S, Sutariya S, Saraf M, Goswami D. A clash of quorum sensing vs quorum sensing inhibitors: an overview and risk of resistance. Arch Microbiol 2023; 205:107. [PMID: 36881156 DOI: 10.1007/s00203-023-03442-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as quorum sensing (QS). Such pathogens express their pathogenicity through various QS-regulated virulence factors. Interference of QS could lead to decisive results in controlling such pathogenicity. Hence, QS inhibition has become an attractive new approach for the development of novel drugs. Many quorum sensing inhibitors (QSIs) of diverse origins have been reported. It is imperative that more such anti-QS compounds be found and studied, as they have significant effect on microbial pathogenicity. This review attempts to give a brief account of QS mechanism, its inhibition and describes some compounds with anti-QS potential. Also discussed is the possibility of emergence of quorum sensing resistance.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Mansi Soni
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Bilv Soyantar
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Suruchi Shivangi
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Swati Sutariya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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22
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Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology. Catalysts 2023. [DOI: 10.3390/catal13020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven α-helices and six β sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.
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23
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The Role of Quorum Sensing Molecules in Bacterial-Plant Interactions. Metabolites 2023; 13:metabo13010114. [PMID: 36677039 PMCID: PMC9863971 DOI: 10.3390/metabo13010114] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Quorum sensing (QS) is a system of communication of bacterial cells by means of chemical signals called autoinducers, which modulate the behavior of entire populations of Gram-negative and Gram-positive bacteria. Three classes of signaling molecules have been recognized, Al-1, Al-2, Al-3, whose functions are slightly different. However, the phenomenon of quorum sensing is not only concerned with the interactions between bacteria, but the whole spectrum of interspecies interactions. A growing number of research results confirm the important role of QS molecules in the growth stimulation and defense responses in plants. Although many of the details concerning the signaling metabolites of the rhizosphere microflora and plant host are still unknown, Al-1 compounds should be considered as important components of bacterial-plant interactions, leading to the stimulation of plant growth and the biological control of phytopathogens. The use of class 1 autoinducers in plants to induce beneficial activity may be a practical solution to improve plant productivity under field conditions. In addition, researchers are also interested in tools that offer the possibility of regulating the activity of autoinducers by means of degrading enzymes or specific inhibitors (QSI). Current knowledge of QS and QSI provides an excellent foundation for the application of research to biopreparations in agriculture, containing a consortia of AHL-producing bacteria and QS inhibitors and limiting the growth of phytopathogenic organisms.
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24
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Borgert SR, Henke S, Witzgall F, Schmelz S, Zur Lage S, Hotop SK, Stephen S, Lübken D, Krüger J, Gomez NO, van Ham M, Jänsch L, Kalesse M, Pich A, Brönstrup M, Häussler S, Blankenfeldt W. Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa. Nat Commun 2022; 13:7402. [PMID: 36456567 PMCID: PMC9715718 DOI: 10.1038/s41467-022-35030-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determine crystal structures of the complex and identify residues essential for the interaction. To corroborate the chaperone-like activity of PqsE, we design stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.
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Affiliation(s)
- Sebastian Roman Borgert
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Henke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Florian Witzgall
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Sven-Kevin Hotop
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Stephen
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Dennis Lübken
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jonas Krüger
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Core Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Mark Brönstrup
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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25
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Zhang J, Das B, Verho O, Bäckvall J. Electrochemical Palladium‐Catalyzed Oxidative Carbonylation‐Cyclization of Enallenols. Angew Chem Int Ed Engl 2022; 61:e202212131. [PMID: 36222322 PMCID: PMC10098644 DOI: 10.1002/anie.202212131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Indexed: 11/06/2022]
Abstract
Herein, we report an electrochemical oxidative palladium-catalyzed carbonylation-carbocyclization of enallenols to afford γ-lactones and spirolactones, which proceeds with excellent chemoselectivity. Interestingly, electrocatalysis was found to have an accelerating effect on the rate of the tandem process, leading to a more efficient reaction than that under chemical redox conditions.
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Affiliation(s)
- Jianwei Zhang
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Biswanath Das
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Oscar Verho
- Department of Medicinal Chemistry Uppsala Biomedical Center, BMC Uppsala University 75236 Uppsala Sweden
| | - Jan‐E. Bäckvall
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University 10691 Stockholm Sweden
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26
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Molecular Mechanisms and Applications of N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Bacteria. Molecules 2022; 27:molecules27217584. [PMID: 36364411 PMCID: PMC9654057 DOI: 10.3390/molecules27217584] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial biodiversity includes biotic and abiotic components that support all life forms by adapting to environmental conditions. Climate change, pollution, human activity, and natural calamities affect microbial biodiversity. Microbes have diverse growth conditions, physiology, and metabolism. Bacteria use signaling systems such as quorum sensing (QS) to regulate cellular interactions via small chemical signaling molecules which also help with adaptation under undesirable survival conditions. Proteobacteria use acyl-homoserine lactone (AHL) molecules as autoinducers to sense population density and modulate gene expression. The LuxI-type enzymes synthesize AHL molecules, while the LuxR-type proteins (AHL transcriptional regulators) bind to AHLs to regulate QS-dependent gene expression. Diverse AHLs have been identified, and the diversity extends to AHL synthases and AHL receptors. This review comprehensively explains the molecular diversity of AHL signaling components of Pseudomonas aeruginosa, Chromobacterium violaceum, Agrobacterium tumefaciens, and Escherichia coli. The regulatory mechanism of AHL signaling is also highlighted in this review, which adds to the current understanding of AHL signaling in Gram-negative bacteria. We summarize molecular diversity among well-studied QS systems and recent advances in the role of QS proteins in bacterial cellular signaling pathways. This review describes AHL-dependent QS details in bacteria that can be employed to understand their features, improve environmental adaptation, and develop broad biomolecule-based biotechnological applications.
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27
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Illuminating the signalomics of microbial biofilm on plant surfaces. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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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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29
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Barra L, Awakawa T, Abe I. Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis. JACS AU 2022; 2:1950-1963. [PMID: 36186570 PMCID: PMC9516700 DOI: 10.1021/jacsau.2c00391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.
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Affiliation(s)
- Lena Barra
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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30
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AHL-mediated quorum sensing to regulate bacterial substance and energy metabolism: A review. Microbiol Res 2022; 262:127102. [DOI: 10.1016/j.micres.2022.127102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/08/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023]
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31
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Zhu L, Huang J, Lu X, Zhou C. Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:952397. [PMID: 36017257 PMCID: PMC9396261 DOI: 10.3389/fpls.2022.952397] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
A plant growing in nature is not an individual, but it holds an intricate community of plants and microbes with relatively stable partnerships. The microbial community has recently been demonstrated to be closely linked with plants since their earliest evolution, to help early land plants adapt to environmental threats. Mounting evidence has indicated that plants can release diverse kinds of signal molecules to attract beneficial bacteria for mediating the activities of their genetics and biochemistry. Several rhizobacterial strains can promote plant growth and enhance the ability of plants to withstand pathogenic attacks causing various diseases and loss in crop productivity. Beneficial rhizobacteria are generally called as plant growth-promoting rhizobacteria (PGPR) that induce systemic resistance (ISR) against pathogen infection. These ISR-eliciting microbes can mediate the morphological, physiological and molecular responses of plants. In the last decade, the mechanisms of microbial signals, plant receptors, and hormone signaling pathways involved in the process of PGPR-induced ISR in plants have been well investigated. In this review, plant recognition, microbial elicitors, and the related pathways during plant-microbe interactions are discussed, with highlights on the roles of root hair-specific syntaxins and small RNAs in the regulation of the PGPR-induced ISR in plants.
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Affiliation(s)
- Lin Zhu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiameng Huang
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Xiaoming Lu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Cheng Zhou
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
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32
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VfqI-VfqR quorum sensing circuit modulates type VI secretion system VflT6SS2 in Vibrio fluvialis. Biochem Biophys Rep 2022; 31:101282. [PMID: 35669988 PMCID: PMC9166416 DOI: 10.1016/j.bbrep.2022.101282] [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: 03/02/2022] [Revised: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/03/2022] Open
Abstract
V. fluvialis is an emerging foodborne pathogen and could cause cholera-like gastroenteritis syndrome and poses a potential threat to public health. VflT6SS2 is a functionally active type VI secretion system (T6SS) in V. fluvialis which confers bactericidal activity. VflT6SS2 is composed of one major cluster and three hcp-vgrG orphan clusters. Previously, we identified two quorum sensing (QS) systems CqsA/LuxS-HapR and VfqI-VfqR in V. fluvialis and demonstrated that the former regulates VflT6SS2. However, whether VfqI-VfqR QS regulates VflT6SS2 is unknown. In this study, we showed that the mRNA abundances of VflT6SS2 tssD2 (hcp), tssI2 (vgrG) and tssB2 (vipA) were all significantly decreased in VfqI or/and VfqR deletion mutant(s). Consistently, Hcp expression/secretion was reduced too in these mutants. Complementation assay with VfqR mutant further confirmed that the reduced Hcp expression/secretion and impaired antibacterial virulence are restored by introducing VfqR-expressing plasmid. Reporter fusion analyses revealed that VfqR modulates the promoter activities of VflT6SS2. Bioinformatical prediction and further reporter fusion assay in E. coli supported that VfqR acts as a transcriptional factor to bind and regulate the gene expression of the VflT6SS2 major cluster. However, VfqR seems to promote transcription of hcp (tssD2) in the orphan clusters through elevating the expression of vasH which is encoded by the VflT6SS2 major cluster. Additionally, we found that the regulation intensity of VfqR on VflT6SS2 is weaker than that of HapR. In conclusion, our current study disclosed that in V. fluvialis, VfqI-VfqR circuit upregulates the expression and function of VflT6SS2 by directly or indirectly activating its transcription. These findings will enhance our understanding of the complicated regulatory network between QS and T6SS in V. fluvialis. VfqI-VfqR quorum sensing (QS) circuit positively modulates VflT6SS2 in V. fluvialis. VfqR directly activates VflT6SS2 major cluster while indirectly activates hcp orphan clusters. VfqR functions as a secondary QS regulator manipulating VflT6SS2 comparing with HapR.
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33
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Jiang C, Wang X, Wang H, Xu S, Zhang W, Meng Q, Zhuang X. Achieving Partial Nitritation by Treating Sludge With Free Nitrous Acid: The Potential Role of Quorum Sensing. Front Microbiol 2022; 13:897566. [PMID: 35572707 PMCID: PMC9095614 DOI: 10.3389/fmicb.2022.897566] [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: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Partial nitritation is increasingly regarded as a promising biological nitrogen removal process owing to lower energy consumption and better nitrogen removal performance compared to the traditional nitrification process, especially for the treatment of low carbon wastewater. Regulating microbial community structure and function in sewage treatment systems, which are mainly determined by quorum sensing (QS), by free nitrous acid (FNA) to establish a partial nitritation process is an efficient and stable method. Plenty of research papers reported that QS systems ubiquitously existed in ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), and various novel nitrogen removal processes based on partial nitritation were successfully established using FNA. Although the probability that partial nitritation process might be achieved by the regulation of FNA on microbial community structure and function through the QS system was widely recognized and discussed, the potential role of QS in partial nitritation achievement by FNA and the regulation mechanism of FNA on QS system have not been reviewed. This article systematically reviewed the potential role of QS in the establishment of partial nitritation using FNA to regulate activated sludge flora based on the summary and analysis of the published literature for the first time, and future research directions were also proposed.
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Affiliation(s)
- Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xu Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Huacai Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Shengjun Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Qingjie Meng
- Shenzhen Shenshui Water Resources Consulting Co., Ltd., Shenzhen, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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34
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Chattopadhyay I, J RB, Usman TMM, Varjani S. Exploring the role of microbial biofilm for industrial effluents treatment. Bioengineered 2022; 13:6420-6440. [PMID: 35227160 PMCID: PMC8974063 DOI: 10.1080/21655979.2022.2044250] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Biofilm formation on biotic or abiotic surfaces is caused by microbial cells of a single or heterogeneous species. Biofilm protects microbes from stressful environmental conditions, toxic action of chemicals, and antimicrobial substances. Quorum sensing (QS) is the generation of autoinducers (AIs) by bacteria in a biofilm to communicate with one other. QS is responsible for the growth of biofilm, synthesis of exopolysaccharides (EPS), and bioremediation of environmental pollutants. EPS is used for wastewater treatment due to its three-dimensional matrix which is composed of proteins, polysaccharides, humic-like substances, and nucleic acids. Autoinducers mediate significantly the degradation of environmental pollutants. Acyl-homoserine lactone (AHL) producing bacteria as well as quorum quenching enzyme or bacteria can effectively improve the performance of wastewater treatment. Biofilms-based reactors due to their economic and ecofriendly nature are used for the treatment of industrial wastewaters. Electrodes coated with electro-active biofilm (EAB) which are obtained from sewage sludge, activated sludge, or industrial and domestic effluents are getting popularity in bioremediation. Microbial fuel cells are involved in wastewater treatment and production of energy from wastewater. Synthetic biological systems such as genome editing by CRISPR-Cas can be used for the advanced bioremediation process through modification of metabolic pathways in quorum sensing within microbial communities. This narrative review discusses the impacts of QS regulatory approaches on biofilm formation, extracellular polymeric substance synthesis, and role of microbial community in bioremediation of pollutants from industrial effluents.
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Affiliation(s)
| | - Rajesh Banu J
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - T M Mohamed Usman
- Department of Civil Engineering, PET Engineering College, Vallioor, Tirunelveli, India
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, India
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35
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Dhivya R, Rajakrishnapriya VC, Sruthi K, Chidanand DV, Sunil CK, Rawson A. Biofilm combating in the food industry: Overview, non‐thermal approaches, and mechanisms. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- R. Dhivya
- Industry Academia Cell National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
| | - V. C. Rajakrishnapriya
- Industry Academia Cell National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
| | - K. Sruthi
- Industry Academia Cell National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
| | - D. V. Chidanand
- Industry Academia Cell National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
| | - C. K. Sunil
- Department of Food Engineering National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
| | - Ashish Rawson
- Department of Food Safety and Quality Testing National Institute of Food Technology, Entrepreneurship and Management (NIFTEM) ‐ Thanjavur Thanjavur India
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36
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Ali F, Cai Q, Hu J, Zhang L, Hoare R, Monaghan SJ, Pang H. In silico analysis of AhyI protein and AI-1 inhibition using N-cis-octadec-9z-enoyl-l-homoserine lactone inhibitor in Aeromonas hydrophila. Microb Pathog 2021; 162:105356. [PMID: 34915138 DOI: 10.1016/j.micpath.2021.105356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
AhyI is homologous to the protein LuxI and is conserved throughout bacterial species including Aeromonas hydrophila. A. hydrophila causes opportunistic infections in fish and other aquatic organisms. Furthermore, this pathogennot only poses a great risk for the aquaculture industry, but also for human public health. AhyI (expressing acylhomoserine lactone) is responsible for the biosynthesis of autoinducer-1 (AI-1), commonly referred to as a quorum sensing (QS) signaling molecule, which plays an essential role in bacterial communication. Studying protein structure is essential for understanding molecular mechanisms of pathogenicity in microbes. Here, we have deduced a predicted structure of AhyI protein and characterized its function using in silico methods to aid the development of new treatments for controlling A.hydrophila infections. In addition to modeling AhyI, an appropriate inhibitor molecule was identified via high throughput virtual screening (HTVS) using mcule drug-like databases.The AhyI-inhibitor N-cis-octadec-9Z-enoyl-l-Homoserine lactone was selected withthe best drug score. In order to understand the pocket sites (ligand binding sites) and their interaction with the selected inhibitor, docking (predicted protein binding complex) servers were used and the selected ligand was docked with the predicted AhyI protein model. Remarkably, N-cis-octadec-9Z-enoyl-l-Homoserine lactone established interfaces with the protein via16 residues (V24, R27, F28, R31, W34, V36, D45, M77, F82, T101, R102, L103, 104, V143, S145, and V168), which are involved with regulating mechanisms of inhibition. These proposed predictions suggest that this inhibitor molecule may be used as a novel drug candidate for the inhibition of auto-inducer-1 (AI-1) activity.The N-cis-octadec-9Z-enoyl-l-Homoserine lactone inhibitor molecule was studied on cultured bacteria to validate its potency against AI-1 production. At a concentration of 40 μM, optimal inhibition efficiency of AI-1 was observedin bacterial culture media.These results suggest that the inhibitor molecule N-cis-octadec-9Z-enoyl-l-Homoserine lactone is a competitive inhibitor of AI-1 biosynthesis.
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Affiliation(s)
- Farman Ali
- Fujian Provincial Key Laboratory of Agro Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 35002, China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University) Fujian Province University, Fuzhou, 35002, China
| | - Qilan Cai
- Fujian Provincial Key Laboratory of Agro Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 35002, China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University) Fujian Province University, Fuzhou, 35002, China
| | - Jialing Hu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524025, China
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agro Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 35002, China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University) Fujian Province University, Fuzhou, 35002, China
| | - Rowena Hoare
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Sean J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Huanying Pang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524025, China.
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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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Wang X, Yu D, Chen G, Liu C, Xu A, Tang Z. Effects of interactions between quorum sensing and quorum quenching on microbial aggregation characteristics in wastewater treatment: A review. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:2883-2902. [PMID: 34719836 DOI: 10.1002/wer.1657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Due to the increasingly urgent demand for effective wastewater denitrification and dephosphorization systems, there is a need to improve the performance of existing biological treatment technologies. As a bacteria-level communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. On this basis, the QS-based bacterial communication mechanism and environmental factors affecting QS are discussed. This paper reviews the influence of QS on sludge granulation, biofilm formation, emerging contaminants (ECs) removal, and horizontal gene transfer in sewage treatment system. Furthermore, the QS inhibition strategies are compared. Based on the coexistence and balance of QQ and QS in the long-term operation system, QQ, as an effective tool to regulate the growth density of microorganisms, provides a promising exogenous regulation strategy for residual sludge reduction and biofilm pollution control. This paper reviews the potential of improving wastewater treatment efficiency based on QS theory and points out the feasibility and prospect of exogenous regulation strategy. PRACTITIONER POINTS: The mechanism of bacterial communication based on QS and the environmental factors affecting QS were discussed. The application of QS and QQ in improving the sludge performance of biological treatment systems was described. The significance of QS and QQ coexistence in sewage treatment process was described.
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Affiliation(s)
- Xueping Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Deshuang Yu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Guanghui Chen
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, China
| | - Chengju Liu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Ao Xu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Zhihao Tang
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
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Importance of N-Acyl-Homoserine Lactone-Based Quorum Sensing and Quorum Quenching in Pathogen Control and Plant Growth Promotion. Pathogens 2021; 10:pathogens10121561. [PMID: 34959516 PMCID: PMC8706166 DOI: 10.3390/pathogens10121561] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe–plant interactions. Different aspects of QS systems in bacteria–plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.
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Ibrahim S, Al-Saryi N, Al-Kadmy IMS, Aziz SN. Multidrug-resistant Acinetobacter baumannii as an emerging concern in hospitals. Mol Biol Rep 2021; 48:6987-6998. [PMID: 34460060 PMCID: PMC8403534 DOI: 10.1007/s11033-021-06690-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
Acinetobacter baumannii has become a major concern for scientific attention due to extensive antimicrobial resistance. This resistance causes an increase in mortality rate because strains resistant to antimicrobial agents are a major challenge for physicians and healthcare workers regarding the eradication of either hospital or community-based infections. These strains with emerging resistance are a serious issue for patients in the intensive care unit (ICU). Antibiotic resistance has increased because of the acquirement of mobile genetic elements such as transposons, plasmids, and integrons and causes the prevalence of multidrug resistance strains (MDR). In addition, an increase in carbapenem resistance, which is used as last line antibiotic treatment to eliminate infections with multidrug-resistant Gram-negative bacteria, is a major concern. Carbapenems resistant A. baumannii (CR-Ab) is a worldwide problem. Because these strains are often resistant to all other commonly used antibiotics. Therefore, pathogenic multi-drug resistance A. baumannii (MDR-Ab) associated infections become hard to eradicate. Plasmid-mediated resistance causes outbreaks of extensive drug-resistant. A. baumannii (XDR-Ab). In addition, recent outbreaks relating to livestock and community settings illustrate the existence of large MDR-Ab strain reservoirs within and outside hospital settings. The purpose of this review, proper monitoring, prevention, and treatment are required to control (XDR-Ab) infections. Attachment, the formation of biofilms and the secretion of toxins, and low activation of inflammatory responses are mechanisms used by pathogenic A. baumannii strain. This review will discuss some aspects associated with antibiotics resistance in A. baumannii as well as cover briefly phage therapy as an alternative therapeutic treatment.
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Affiliation(s)
- Susan Ibrahim
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10422, Baghdad, Iraq
| | - Nadal Al-Saryi
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10422, Baghdad, Iraq
| | - Israa M S Al-Kadmy
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10422, Baghdad, Iraq.
| | - Sarah Naji Aziz
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10422, Baghdad, Iraq
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Li J, Liu R, Chen Y, Liu S, Chen C, Liu T, Yang S, Zhuang Y, Yang R, Cui Y, Song Y, Wang T, Teng Y. Computer-Aided Rational Engineering of Signal Sensitivity of Quorum Sensing Protein LuxR in a Whole-Cell Biosensor. Front Mol Biosci 2021; 8:729350. [PMID: 34485387 PMCID: PMC8415086 DOI: 10.3389/fmolb.2021.729350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
LuxR, a bacterial quorum sensing-related transcription factor that responds to the signaling molecule 3-oxo-hexanoyl-homoserine lactone (3OC6-HSL). In this study, we employed molecular dynamics simulation and the Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) method to rationally identify residues in Vibrio fischeri LuxR that are important for its interaction with 3OC6-HSL. Isoleucine-46 was selected for engineering as the key residue for interaction with 3OC6-HSL-LuxR-I46F would have the strongest binding energy to 3OC6-HSL and LuxR-I46R the weakest binding energy. Stable wild-type (WT) LuxR, I46F and I46R variants were produced in Escherichia coli (E. coli) in the absence of 3OC6-HSL by fusion with maltose-binding protein (MBP). Dissociation constants for 3OC6-HSL from MBP-fusions of WT-, I46F- and I46R-LuxR determined by surface plasmon resonance confirmed the binding affinity. We designed and constructed a novel whole-cell biosensor on the basis of LuxR-I46F in E. coli host cells with a reporting module that expressed green fluorescent protein. The biosensor had high sensitivity in response to the signaling molecule 3OC6-HSL produced by the target bacterial pathogen Yersinia pestis. Our work demonstrates a practical, generalizable framework for the rational design and adjustment of LuxR-family proteins for use in bioengineering and bioelectronics applications.
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Affiliation(s)
- Jinyu Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruicun Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yulu Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shuxia Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Tuoyu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yingtan Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
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Joshi JR, Khazanov N, Charkowski A, Faigenboim A, Senderowitz H, Yedidia I. Interkingdom Signaling Interference: The Effect of Plant-Derived Small Molecules on Quorum Sensing in Plant-Pathogenic Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:153-190. [PMID: 33951403 DOI: 10.1146/annurev-phyto-020620-095740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the battle between bacteria and plants, bacteria often use a population density-dependent regulatory system known as quorum sensing (QS) to coordinate virulence gene expression. In response, plants use innate and induced defense mechanisms that include low-molecular-weight compounds, some of which serve as antivirulence agents by interfering with the QS machinery. The best-characterized QS system is driven by the autoinducer N-acyl-homoserine lactone (AHL), which is produced by AHL synthases (LuxI homologs) and perceived by response regulators (LuxR homologs). Several plant compounds have been shown to directly inhibit LuxI or LuxR. Gaining atomic-level insight into their mode of action and how they interfere with QS enzymes supports the identification and design of novel QS inhibitors.Such information can be gained by combining experimental work with molecular modeling and docking simulations. The summary of these findings shows that plant-derived compounds act as interkingdom cues and that these allomones specifically target bacterial communication systems.
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Affiliation(s)
- Janak Raj Joshi
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion, Israel 7528809;
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel 5290002;
| | - Amy Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Adi Faigenboim
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion, Israel 7528809;
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel 5290002;
| | - Iris Yedidia
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion, Israel 7528809;
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43
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Vetrivel A, Natchimuthu S, Subramanian V, Murugesan R. High-Throughput Virtual Screening for a New Class of Antagonist Targeting LasR of Pseudomonas aeruginosa. ACS OMEGA 2021; 6:18314-18324. [PMID: 34308062 PMCID: PMC8296597 DOI: 10.1021/acsomega.1c02191] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/16/2021] [Indexed: 05/28/2023]
Abstract
Pseudomonas aeruginosa, an opportunistic human pathogen, causes fatal effects in patients with cystic fibrosis and immunocompromised individuals and leads to around 1000 deaths annually. The quorum sensing mechanism of P. aeruginosa plays a major role in promoting biofilm formation and expression of virulent genes. Hence, quorum sensing inhibition is a promising novel approach to treat these bacterial infections as these organisms show a wide range of antibiotic resistance. Among the interconnected quorum sensing network of P. aeruginosa, targeting the las system is of increased interest as its principal receptor protein LasR is the earliest activated gene. It is also shown to be involved in the regulation of other virulence-associated genes. In this study, we have applied high-throughput virtual screening, an in silico computational method to identify a new class of LasR inhibitors that could serve as potent antagonists to treat P. aeruginosa-associated infections. Three-tire structure-based virtual screening was performed on the Schrödinger small molecule database, which resulted in 12 top hit compounds with docking scores lesser than -11.0 kcal/mol. Three of these best-scored compounds CACPD2011a-0001928786 (C1), CACPD2011a-0001927437 (C2), and CACPD2011a-0000896051 (C3) were further analyzed. The binding free energies of these compounds in complex with the target protein LasR (3IX4) were evaluated, and the pharmacokinetic properties were determined. The stability of the docked complexes was assessed by running a molecular dynamics simulation for 100 ns. Molecular dynamics simulation analysis revealed that all three compounds were found to be in stable contact with the protein over the entire simulation period. The antagonistic effect of these compounds was validated using the LasR reporter gene assay in the presence of acyl homoserine lactone. Significant reduction in the β-galactosidase enzyme activity was achieved at 100 nM concentration for all three compounds pursued. Hence, the present study provides strong evidence that these three compounds could serve as quorum sensing inhibitors of P. aeruginosa LasR protein and can be a probable candidate to treat Pseudomonas-associated infections.
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Affiliation(s)
- Aishwarya Vetrivel
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, Tamil Nadu, India
| | - Santhi Natchimuthu
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, Tamil Nadu, India
| | | | - Rajeswari Murugesan
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, Tamil Nadu, India
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Wang N, Gao J, Liu Y, Wang Q, Zhuang X, Zhuang G. Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review. CHEMOSPHERE 2021; 274:129970. [PMID: 33979914 DOI: 10.1016/j.chemosphere.2021.129970] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ya'ar Bar S, Dor S, Erov M, Afriat-Jurnou L. Identification and Characterization of a New Quorum-Quenching N-acyl Homoserine Lactonase in the Plant Pathogen Erwinia amylovora. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5652-5662. [PMID: 33974427 DOI: 10.1021/acs.jafc.1c00366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Quorum quenching (QQ) is the ability to interfere with bacterial cell to cell communication, known as quorum sensing (QS). QQ enzymes that degrade or modify acyl homoserine lactones (AHLs) have been attracting increasing interest as promising agents for inhibiting QS-mediated bacterial pathogenicity. Plant pathogens from the genus Erwinia cause diseases in several economically important crops. Fire blight is a devastating plant disease caused by Erwinia amylovora, affecting a wide range of host species within the Rosaceae and posing a major global threat for commercial apple and pear production. While QS has been described in Erwinia species, no AHL-degrading enzymes were identified and characterized. Here, phylogenetic analysis and structural modeling were applied to identify an AHL lactonase in E. amylovora (dubbed EaAiiA). Following recombinant expression and purification, the enzyme was biochemically characterized. EaAiiA lactonase activity was dependent on metal ions and effectively degraded AHLs with high catalytic efficiency. Its highest specific activity (kcat/KM value) was observed against one of the AHLs (3-oxo-C6-homoserine lactone) secreted from E. amylovora. Exogenous addition of the purified enzyme to cultures of E. amylovora reduced the formation of levan, a QS-regulated virulence factor, by 40% and the transcription level of the levansucrase-encoding gene by 55%. Furthermore, preincubation of E. amylovora cultures with EaAiiA inhibited the progress of fire blight symptoms in immature Pyrus communis fruits. These results demonstrate the ability of the identified enzyme from E. amylovora to act as a quorum-quenching lactonase.
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Affiliation(s)
- Sapir Ya'ar Bar
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
| | - Shlomit Dor
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Mayan Erov
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
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Wang Q, Zhang T, Wu G, Xu Q. Deciphering acyl-homoserine lactones-mediated quorum sensing on geotextile bio-clogging in municipal solid waste and bottom ash co-disposal landfills. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 124:136-143. [PMID: 33621757 DOI: 10.1016/j.wasman.2021.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Bottom ash co-disposed in landfills accelerates geotextile clogging and decreases landfill stability. As the main contributor to clogging, bio-clogging may be associated with quorum sensing (QS) in microbial communities. This study investigated the potential roles of acyl-homoserine lactones (AHLs)-mediated QS in geotextile bio-clogging under different landfill conditions, including municipal solid waste landfill and bottom ash co-disposal landfill. The unit area of geotextile bio-clogging mass in the municipal solid waste landfill (MSW_G) ranged from 5.2 × 10-3 to 8.2 × 10-3 g/cm2, while it was in the range of 8.4 × 10-3 to 1.2 × 10-2 g/cm2 in the bottom ash co-disposal landfill (BA_G). Two types of AHLs were detected and the total AHLs content in the MSW_G (1,616.9 ± 103.8 ng/g VSS) was half of that in the BA_G (3,233.0 ± 646.8 ng/g VSS). High contents of the AHLs could increase bio-clogging. The bio-clogging was also attributed to QS genes and extracellular polymeric substances (EPS). EPS aggregation was stimulated due to the higher Ca2+ and Mg2+ in the BA_G. These results suggested that the co-disposal of bottom ash could increase the AHLs content, resulting in accelerated bio-clogging.
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Affiliation(s)
- Qian Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tianqi Zhang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Guangxue Wu
- Civil Engineering, School of Engineering, College of Science and Engineering, National University of Ireland, Galway, Galway, Ireland
| | - Qiyong Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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Huang Y, Lu Z, Jiang T, Zeng Y, Zeng Y, Chen B. Oxygen availability affects the synthesis of quorum sensing signal in the facultative anaerobe Novosphingobium pentaromativorans US6-1. Appl Microbiol Biotechnol 2021; 105:1191-1201. [PMID: 33439275 DOI: 10.1007/s00253-021-11089-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/13/2020] [Accepted: 01/03/2021] [Indexed: 01/01/2023]
Abstract
Bacterial populations rely on quorum sensing (QS) to coordinate their behaviors and are often challenged by the fluctuation in oxygen concentrations in their habitats. Oxygen is a crucial factor that affects bacterial metabolism in multiple ways. However, little is known about whether and how oxygen availability affects QS activities. To fill this gap, we used the facultative anaerobe Novosphingobium pentaromativorans US6-1 as a model system, and observed that the QS signal acyl homoserine-lactones (AHLs) were produced only in anoxic environments, such as biofilm, or liquid medium that initially contained less than 2 mg/L dissolved oxygen, but not in highly oxic environments. Comparative transcriptome analysis revealed that oxygen availability significantly affected the physiological activities in US6-1, including fatty acid metabolism, oxidative phosphorylation, citrate cycle, QS activities, and flagellar assembly. The absence of AHLs in the oxic culture was not due to degradation, but to the very low expression of the AHL synthase gene novI. High concentration of NADH during the middle log phase under static cultivation may be a trigger for AHL synthesis. This is the first report that production of AHLs is coupled with anoxic metabolism in a facultative anaerobe, which extends our knowledge on factors affecting bacterial QS occurrence. KEY POINTS: • AHL production is anoxic cultivation related. • Oxygen availability affects AHL synthesis by influencing novI expression. • Oxygen availability changes many metabolism activities including NADH production.
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Affiliation(s)
- Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China.
| | - Zejia Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Tingting Jiang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Yonghui Zeng
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Baoliang Chen
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
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Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication. mSystems 2020; 5:5/5/e00414-20. [PMID: 33051376 PMCID: PMC7567580 DOI: 10.1128/msystems.00414-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated. The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.
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Fei C, Ochsenkühn MA, Shibl AA, Isaac A, Wang C, Amin SA. Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere. Environ Microbiol 2020; 22:4761-4778. [PMID: 32896070 PMCID: PMC7693213 DOI: 10.1111/1462-2920.15228] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
Abstract
Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell–cell signalling mechanism that uses small infochemicals to coordinate bacterial gene expression. However, the role of QS in regulating bacterial attachment in the phycosphere is not clear. Here, we isolated a Sulfitobacter pseudonitzschiae F5 and a Phaeobacter sp. F10 belonging to the marine Roseobacter group and an Alteromonas macleodii F12 belonging to Alteromonadaceae, from the microbial community of the ubiquitous diatom Asterionellopsis glacialis. We show that only the Roseobacter group isolates (diatom symbionts) can attach to diatom transparent exopolymeric particles. Despite all three bacteria possessing genes involved in motility, chemotaxis, and attachment, only S. pseudonitzschiae F5 and Phaeobacter sp. F10 possessed complete QS systems and could synthesize QS signals. Using UHPLC–MS/MS, we identified three QS molecules produced by both bacteria of which only 3‐oxo‐C16:1‐HSL strongly inhibited bacterial motility and stimulated attachment in the phycosphere. These findings suggest that QS signals enable colonization of the phycosphere by algal symbionts.
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Affiliation(s)
- Cong Fei
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,College of Resources and Environmental Science, Nanjing Agriculture University, Nanjing, China
| | - Michael A Ochsenkühn
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ahmed A Shibl
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ashley Isaac
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,International Max Planck Research School of Marine Microbiology, University of Bremen, Bremen, Germany
| | - Changhai Wang
- College of Resources and Environmental Science, Nanjing Agriculture University, Nanjing, China
| | - Shady A Amin
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Zeng YH, Cai ZH, Zhu JM, Du XP, Zhou J. Two hierarchical LuxR-LuxI type quorum sensing systems in Novosphingobium activate microcystin degradation through transcriptional regulation of the mlr pathway. WATER RESEARCH 2020; 183:116092. [PMID: 32622230 DOI: 10.1016/j.watres.2020.116092] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Microcystins (MCs) are the most common cyanotoxins produced by harmful cyanobacterial blooms and pose an increasing global threat to human health and ecosystems. Microbial degradation represents an efficient and sustainable approach for the removal of MCs. Although the enzymatic pathway for biodegradation of MCs has been characterized, the regulatory mechanisms underlying the degradation processes remain unclear. Quorum sensing (QS) is a cell-density-dependent regulatory mechanism that enables bacteria to orchestrate collective behaviors. The acyl-homoserine lactone (AHL)-mediated QS system regulates the biodegradation of many organic pollutants. However, it is not known whether this QS system is involved in the degradation of MCs. This study aimed to fill this knowledge gap. In this study, the proportion of culturable AHL-producers increased significantly after enrichment of MCs, and AHL-based QS systems were present in all genome-sequenced MC-degrading strains, supporting the hypothesis that QS participates in the degradation of MCs. Two bifunctional Novosphingobium strains (with MC-degrading and AHL-producing abilities) were isolated using a novel primer pair targeting mlrA, the marker gene of mlr degradation pathway. Biochemical and genetic analysis revealed that the MC-degrading bacterium Novosphingobium sp. ERW19 encodes two hierarchical regulatory QS systems designated novR1/novI1 and novR2/novI2. Gene knockout and complementation experiments indicated that both systems were required for efficient degradation of MCs. Transcriptomic analyses revealed that the QS systems positively regulate degradation of MCs through transcriptional activation of MC-degrading genes, especially mlrA. Given that QS may be a common trait within mlr pathway-dependent MC-degrading bacterial strains and the degradation activity is directly regulated by QS, manipulation of the QS systems may be a promising strategy to control biodegradation of MCs.
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Affiliation(s)
- Yan-Hua Zeng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Xiao-Peng Du
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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