201
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Amir Y, Abu-Horowitz A, Werfel J, Bachelet I. Nanoscale Robots Exhibiting Quorum Sensing. ARTIFICIAL LIFE 2019; 25:227-231. [PMID: 31397602 DOI: 10.1162/artl_a_00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Multi-agent systems demonstrate the ability to collectively perform complex tasks (e.g., construction, search, and locomotion) with greater speed, efficiency, or effectiveness than could a single agent alone. Direct and indirect coordination methods allow agents to collaborate to share information and adapt their activity to fit dynamic situations. A well-studied example is quorum sensing (QS), a mechanism allowing bacterial communities to coordinate and optimize various phenotypes in response to population density. Here we implement, for the first time, bio-inspired QS in robots fabricated from DNA origami, which communicate by transmitting and receiving diffusing signals. The mechanism we describe includes features such as programmable response thresholds and quorum quenching, and is capable of being triggered by proximity of a specific target cell. Nanoscale robots with swarm intelligence could carry out tasks that have been so far unachievable in diverse fields such as industry, manufacturing, and medicine.
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Affiliation(s)
| | | | - Justin Werfel
- Harvard University, Wyss Institute for Biologically Inspired Engineering
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202
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Arraiano CM. Stories of the future: manipulating RNA and Intra/Interkingdom communication. Microb Biotechnol 2019; 12:48-50. [PMID: 30485669 PMCID: PMC6302701 DOI: 10.1111/1751-7915.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022] Open
Affiliation(s)
- Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República2780‐157OeirasPortugal
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203
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Abstract
Investigating the multidimensional integration between different microbiological kingdoms possesses potential toward engineering next-generation bionic architectures. Bacterial and fungal kingdom exhibits mutual symbiosis that can offer advanced functionalities to these bionic architectures. Moreover, functional nanomaterials can serve as probing agents for accessing newer information from microbial organisms due to their dimensional similarities. In this article, a bionic mushroom was created by intertwining cyanobacterial cells with graphene nanoribbons (GNRs) onto the umbrella-shaped pileus of mushroom for photosynthetic bioelectricity generation. These seamlessly merged GNRs function as agents for mediating extracellular electron transport from cyanobacteria resulting in photocurrent generation. Additionally, three-dimensional (3D) printing technique was used to assemble cyanobacterial cells in anisotropic, densely packed geometry resulting in adequate cell-population density for efficient collective behavior. These 3D printed cyanobacterial colonies resulted in comparatively higher photocurrent (almost 8-fold increase) than isotropically casted cyanobacteria of similar seeding density. An insight of the proposed integration between cyanobacteria and mushroom derives remarkable advantage that arises from symbiotic relationship, termed here as engineered bionic symbiosis. Existence of this engineered bionic symbiosis was confirmed by UV-visible spectroscopy and standard plate counting method. Taken together, the present study augments scientific understanding of multidimensional integration between the living biological microworld and functional abiotic nanomaterials to establish newer dimensionalities toward advancement of bacterial nanobionics.
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Affiliation(s)
- Sudeep Joshi
- Neuro-Bionics and Neuro-Electric Medicine Laboratory, Department of Mechanical Engineering , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Ellexis Cook
- Neuro-Bionics and Neuro-Electric Medicine Laboratory, Department of Mechanical Engineering , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Manu S Mannoor
- Neuro-Bionics and Neuro-Electric Medicine Laboratory, Department of Mechanical Engineering , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
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204
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Bushin LB, Clark KA, Pelczer I, Seyedsayamdost MR. Charting an Unexplored Streptococcal Biosynthetic Landscape Reveals a Unique Peptide Cyclization Motif. J Am Chem Soc 2018; 140:17674-17684. [PMID: 30398325 DOI: 10.1021/jacs.8b10266] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Peptide natural products are often used as signals or antibiotics and contain unusual structural modifications, thus providing opportunities for expanding our understanding of Nature's therapeutic and biosynthetic repertoires. Herein, we have investigated the under-explored biosynthetic potential of Streptococci, prevalent bacteria in mammalian microbiomes that include mutualistic, commensal, and pathogenic members. Using a new bioinformatic search strategy, in which we linked the versatile radical S-adenosylmethionine (RaS) enzyme superfamily to an emerging class of natural products in the context of quorum sensing control, we identified numerous, uncharted biosynthetic loci. Focusing on one such locus, we identified an unprecedented post-translational modification, consisting of a tetrahydro[5,6]benzindole cyclization motif in which four unactivated positions are linked by two C-C bonds in a regio- and stereospecific manner by a single RaS enzyme. Our results expand the scope of reactions that microbes have at their disposal in concocting complex ribosomal peptides.
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Affiliation(s)
- Leah B Bushin
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Kenzie A Clark
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - István Pelczer
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States.,Department of Molecular Biology , Princeton University , Princeton , New Jersey 08544 , United States
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205
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Martín-Rodríguez AJ, Álvarez-Méndez SJ, Overå C, Baruah K, Lourenço TM, Norouzitallab P, Bossier P, Martín VS, Fernández JJ. The 9 H-Fluoren Vinyl Ether Derivative SAM461 Inhibits Bacterial Luciferase Activity and Protects Artemia franciscana From Luminescent Vibriosis. Front Cell Infect Microbiol 2018; 8:368. [PMID: 30467537 PMCID: PMC6236115 DOI: 10.3389/fcimb.2018.00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/03/2018] [Indexed: 11/13/2022] Open
Abstract
Vibrio campbellii is a major pathogen in aquaculture. It is a causative agent of the so-called “luminescent vibriosis,” a life-threatening condition caused by bioluminescent Vibrio spp. that often involves mass mortality of farmed shrimps. The emergence of multidrug resistant Vibrio strains raises a concern and poses a challenge for the treatment of this infection in the coming years. Inhibition of bacterial cell-to-cell communication or quorum sensing (QS) has been proposed as an alternative to antibiotic therapies. Aiming to identify novel QS disruptors, the 9H-fluroen-9yl vinyl ether derivative SAM461 was found to thwart V. campbellii bioluminescence, a QS-regulated phenotype. Phenotypic and gene expression analyses revealed, however, that the mode of action of SAM461 was unrelated to QS inhibition. Further evaluation with purified Vibrio fischeri and NanoLuc luciferases revealed enzymatic inhibition at micromolar concentrations. In silico analysis by molecular docking suggested binding of SAM461 in the active site cavities of both luciferase enzymes. Subsequent in vivo testing of SAM461 with gnotobiotic Artemia franciscana nauplii demonstrated naupliar protection against V. campbellii infection at low micromolar concentrations. Taken together, these findings suggest that suppression of luciferase activity could constitute a novel paradigm in the development of alternative anti-infective chemotherapies against luminescent vibriosis, and pave the ground for the chemical synthesis and biological characterization of derivatives with promising antimicrobial prospects.
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Affiliation(s)
- Alberto J Martín-Rodríguez
- Instituto Universitario de Bio-Orgánica "Antonio González", Centro de Investigaciones Biomédicas de Canarias, Universidad de La Laguna, Tenerife, Spain.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sergio J Álvarez-Méndez
- Instituto Universitario de Bio-Orgánica "Antonio González", Centro de Investigaciones Biomédicas de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Caroline Overå
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Kartik Baruah
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tânia Margarida Lourenço
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Parisa Norouzitallab
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Laboratory of Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Víctor S Martín
- Instituto Universitario de Bio-Orgánica "Antonio González", Centro de Investigaciones Biomédicas de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - José J Fernández
- Instituto Universitario de Bio-Orgánica "Antonio González", Centro de Investigaciones Biomédicas de Canarias, Universidad de La Laguna, Tenerife, Spain
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206
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Celik Ozgen V, Kong W, Blanchard AE, Liu F, Lu T. Spatial interference scale as a determinant of microbial range expansion. SCIENCE ADVANCES 2018; 4:eaau0695. [PMID: 30474057 PMCID: PMC6248950 DOI: 10.1126/sciadv.aau0695] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
In microbial communities, social interactions such as competition occur ubiquitously across multiple spatial scales from local proximity to remote distance. However, it remains unclear how such a spatial variation of interaction contributes to the structural development of microbial populations. Here, we developed synthetic consortia, biophysical theory, and simulations to elucidate the role of spatial interference scale in governing ecosystem organization during range expansion. For consortia with unidirectional interference, we discovered that, at growing fronts, the extinction time of toxin-sensitive species is reciprocal to the spatial interference scale. In contrast, for communities with bidirectional interference, their structures diverge into distinct monoculture colonies under different initial conditions, with the corresponding separatrix set by the spatial scale of interference. Near the separatrix, ecosystem development becomes noise-driven and yields opposite structures. Our results establish spatial interaction scale as a key determinant for microbial range expansion, providing insights into microbial spatial organization and synthetic ecosystem engineering.
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Affiliation(s)
- Venhar Celik Ozgen
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, Faculty of Engineering, University of Firat, 23119 Elazig, Turkey
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew E. Blanchard
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Feng Liu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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207
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Calvert MB, Jumde VR, Titz A. Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections. Beilstein J Org Chem 2018; 14:2607-2617. [PMID: 30410623 PMCID: PMC6204809 DOI: 10.3762/bjoc.14.239] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/20/2018] [Indexed: 12/19/2022] Open
Abstract
The rapid development of antimicrobial resistance is threatening mankind to such an extent that the World Health Organization expects more deaths from infections than from cancer in 2050 if current trends continue. To avoid this scenario, new classes of anti-infectives must urgently be developed. Antibiotics with new modes of action are needed, but other concepts are also currently being pursued. Targeting bacterial virulence as a means of blocking pathogenicity is a promising new strategy for disarming pathogens. Furthermore, it is believed that this new approach is less susceptible towards resistance development. In this review, recent examples of anti-infective compounds acting on several types of bacterial targets, e.g., adhesins, toxins and bacterial communication, are described.
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Affiliation(s)
- Matthew B Calvert
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Varsha R Jumde
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Germany
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208
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A Versatile Strategy for the Synthesis of 4,5-Dihydroxy-2,3-Pentanedione (DPD) and Related Compounds as Potential Modulators of Bacterial Quorum Sensing. Molecules 2018; 23:molecules23102545. [PMID: 30301207 PMCID: PMC6222300 DOI: 10.3390/molecules23102545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 01/08/2023] Open
Abstract
Resistance to antibiotics is an increasingly serious threat to global public health and its management translates to significant health care costs. The validation of new Gram-negative antibacterial targets as sources for potential new antibiotics remains a challenge for all the scientists working in this field. The interference with bacterial Quorum Sensing (QS) mechanisms represents a potentially interesting approach to control bacterial growth and pursue the next generation of antimicrobials. In this context, our research is focused on the discovery of novel compounds structurally related to (S)-4,5-dihydroxy-2,3-pentanedione, commonly known as (S)-DPD, a small signaling molecule able to modulate bacterial QS in both Gram-negative and Gram-positive bacteria. In this study, a practical and versatile synthesis of racemic DPD is presented. Compared to previously reported syntheses, the proposed strategy is short and robust: it requires only one purification step and avoids the use of expensive or hazardous starting materials as well as the use of specific equipment. It is therefore well suited to the synthesis of derivatives for pharmaceutical research, as demonstrated by four series of novel DPD-related compounds described herein.
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209
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Bettenworth V, McIntosh M, Becker A, Eckhardt B. Front-propagation in bacterial inter-colony communication. CHAOS (WOODBURY, N.Y.) 2018; 28:106316. [PMID: 30384658 DOI: 10.1063/1.5040068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
Many bacterial species exchange signaling molecules to coordinate population-wide responses. For this process, known as quorum sensing, the concentration of the respective molecules is crucial. Here, we consider the interaction between spatially distributed bacterial colonies so that the spreading of the signaling molecules in space becomes important. The exponential growth of the signal-producing populations and the corresponding increase in signaling molecule production result in an exponential concentration profile that spreads with uniform speed. The theoretical predictions are supported by experiments with different strains of the soil bacterium Sinorhizobium meliloti that display fluorescence when either producing or responding to the signaling molecules.
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Affiliation(s)
- Vera Bettenworth
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Matthew McIntosh
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Anke Becker
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Bruno Eckhardt
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
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210
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Structural basis of the arbitrium peptide–AimR communication system in the phage lysis–lysogeny decision. Nat Microbiol 2018; 3:1266-1273. [DOI: 10.1038/s41564-018-0239-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 08/06/2018] [Indexed: 11/08/2022]
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211
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Mairink SZ, Barbosa LCA, Boukouvalas J, Pedroso SHSP, Santos SG, Magalhães PP, Farias LM. Synthesis and evaluation of cadiolide analogues as inhibitors of bacterial biofilm formation. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2246-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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212
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McGrath PT, Ruvinsky I. A primer on pheromone signaling in Caenorhabditis elegans for systems biologists. ACTA ACUST UNITED AC 2018; 13:23-30. [PMID: 30984890 DOI: 10.1016/j.coisb.2018.08.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Individuals communicate information about their age, sex, social status, and recent life history with other members of their species through the release of pheromones, chemical signals that elicit behavioral or physiological changes in the recipients. Pheromones provide a fascinating example of information exchange: animals have evolved intraspecific languages in the presence of eavesdroppers and cheaters. In this review, we discuss the recent work using the nematode C. elegans to decipher its chemical language through the analysis of ascaroside pheromones. Genetic dissection has started to identify the enzymes that produce pheromones and the neural circuits that process these signals. Ecological experiments have characterized the biotic environment of C. elegans and its relatives, including ecological relationships with a variety of species that sense or release similar blends of ascarosides. Systems biology approaches should be fruitful in understanding the organization and function of communication systems in C. elegans.
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Affiliation(s)
- Patrick T McGrath
- Department of Biological Sciences, Department of Physics; Georgia Institute of Technology, Atlanta, GA 30332.
| | - Ilya Ruvinsky
- Department of Molecular Biosciences; Northwestern University, Evanston, IL 60208.
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213
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Seo Y, Hwang J, Lee E, Kim YJ, Lee K, Park C, Choi Y, Jeon H, Choi J. Engineering copper nanoparticles synthesized on the surface of carbon nanotubes for anti-microbial and anti-biofilm applications. NANOSCALE 2018; 10:15529-15544. [PMID: 29985503 DOI: 10.1039/c8nr02768d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biofilms adhere to surfaces to produce extracellular polymeric substances (EPSs). EPSs grow and protect themselves from external stresses. Their formation causes a foul odor and may lead to chronic infectious diseases in animals and people. Biofilms also inhibit the contact between bacteria and antibiotics, thereby reducing their antibacterial activity. Thus, we describe novel nanostructures, a fusion of copper and multi-walled carbon nanotubes (MWCNTs), which increase antimicrobial activity against biofilms without being toxic to human cells. Simulations based on the stochastic response were performed to predict the efficiency of synthesizing nanostructures. The synthesized Cu/MWCNTs inhibit the growth of Methylobacterium spp., which forms biofilms; antimicrobial testing and cytotoxicity assessments showed that the Cu/MWCNTs were not cytotoxic to human cells. The Cu/MWCNTs come in direct contact with the bacterial cell surface, damage the cell wall, and cause secondary oxidation of reactive oxygen species. Furthermore, the Cu/MWCNTs release copper ions, which inhibit the quorum sensing in Methylobacterium spp., thereby inhibiting the expression of the genes that form biofilms. Additionally, we confirmed excellent electrical and thermal conductivity of Cu/MWCNTs as well as biofilm removal efficiency in the microfluidic channel.
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Affiliation(s)
- Youngmin Seo
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
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214
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Hossain S, Heckler I, Boon EM. Discovery of a Nitric Oxide Responsive Quorum Sensing Circuit in Vibrio cholerae. ACS Chem Biol 2018; 13:1964-1969. [PMID: 30060647 DOI: 10.1021/acschembio.8b00360] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Group behavior of the human pathogen Vibrio cholerae, including biofilm formation and virulence factor secretion, is mediated by a process known as quorum sensing. Quorum sensing is a way by which bacteria coordinate gene expression in response to population density through the production, secretion, and detection of small molecules called autoinducers. Four autoinducer-mediated receptor histidine kinases have been implicated in quorum sensing through the phosphotransfer protein LuxU: CqsS, LuxP/Q, CqsR, and VpsS (Vc1445). Of these receptor kinases, VpsS is predicted to be cytosolic, and its cognate autoinducer is currently unknown. In this study, we demonstrate that the nitric oxide-bound complex of a member of the recently discovered family of nitric oxide-responsive hemoproteins called NosP (VcNosP is encoded by Vc1444; this gene product is also known as VpsV) inhibits the autophosphorylation activity of VpsS and thus phosphate flow to LuxU. Therefore, we propose that VpsS contributes to the regulation of quorum sensing in a nitric-oxide-dependent manner through its interaction with NosP.
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Affiliation(s)
- Sajjad Hossain
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ilana Heckler
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794, United States
| | - Elizabeth M. Boon
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794, United States
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215
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Okamoto AS, Filho RLA, Milbradt EL, Moraes ACI, Vellano IHB, Guimarães-Okamoto PTC. Bacterial communication between Lactobacillus spp. isolated from poultry in the inhibition of Salmonella Heidelberg—proof of concept. Poult Sci 2018; 97:2708-2712. [DOI: 10.3382/ps/pey141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/21/2018] [Indexed: 01/01/2023] Open
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216
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Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat Microbiol 2018; 3:909-919. [PMID: 30038309 DOI: 10.1038/s41564-018-0200-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/18/2018] [Indexed: 02/06/2023]
Abstract
Plants are colonized by phylogenetically diverse microorganisms that affect plant growth and health. Representative genome-sequenced culture collections of bacterial isolates from model plants, including Arabidopsis thaliana, have recently been established. These resources provide opportunities for systematic interaction screens combined with genome mining to discover uncharacterized natural products. Here, we report on the biosynthetic potential of 224 strains isolated from the A. thaliana phyllosphere. Genome mining identified more than 1,000 predicted natural product biosynthetic gene clusters (BGCs), hundreds of which are unknown compared to the MIBiG database of characterized BGCs. For functional validation, we used a high-throughput screening approach to monitor over 50,000 binary strain combinations. We observed 725 inhibitory interactions, with 26 strains contributing to the majority of these. A combination of imaging mass spectrometry and bioactivity-guided fractionation of the most potent inhibitor, the BGC-rich Brevibacillus sp. Leaf182, revealed three distinct natural product scaffolds that contribute to the observed antibiotic activity. Moreover, a genome mining-based strategy led to the isolation of a trans-acyltransferase polyketide synthase-derived antibiotic, macrobrevin, which displays an unprecedented natural product structure. Our findings demonstrate that the phyllosphere is a valuable environment for the identification of antibiotics and natural products with unusual scaffolds.
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217
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Arora D, Chashoo G, Singamaneni V, Sharma N, Gupta P, Jaglan S. Bacillus amyloliquefaciens induces production of a novel blennolide K in coculture of Setophoma terrestris. J Appl Microbiol 2018; 124:730-739. [PMID: 29288594 DOI: 10.1111/jam.13683] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 01/29/2023]
Abstract
AIMS The discovery of known bioactive chemical leads from microbial monocultures hinders the efficiency of drug discovery programmes. Therefore, in recent years, the use of fungal-bacterial coculture experiments has gained considerable attention due to their ability to generate new bioactive leads. In this work, fungal strain Setophoma terrestris was cocultured with Bacillus amyloliquifaciens to discover novel bioactive compounds. MATERIALS AND METHODS The bioactive methanolic coculture extract was chosen for the isolation of compounds by chromatographic methods. The isolated compounds were characterized by NMR and mass spectrometric techniques. CONCLUSION Coculture extract has resulted in the production of five blennolides. The novel compound, blennolide K was found active against PC-3 (prostate) and MCF-7 (breast) cell lines with an IC50 value of 3·7 ± 0·6 and 4·8 ± 0·4 μmol l-1 respectively. Furthermore, the nuclear morphology study in PC-3 cells after treatment with blennolide K, demonstrated chromatin condensation, formation of apoptotic bodies and shrinkage of cells. SIGNIFICANCE AND IMPACT OF THE STUDY To our knowledge, only few studies have reported the induction of bioactive compounds by coculture having long-distance inhibition morphology. This is principally due to the low occurrences of such morphology. Our study demonstrates the impact of coculture on production of new chemical leads in drug discovery programmes.
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Affiliation(s)
- D Arora
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Jammu, India
| | - G Chashoo
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - V Singamaneni
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - N Sharma
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Jammu, India
| | - P Gupta
- Academy of Scientific & Innovative Research (AcSIR), Jammu, India.,Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - S Jaglan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Jammu, India
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218
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Koirala B, Hillman RA, Tiwold EK, Bertucci MA, Tal-Gan Y. Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae. Beilstein J Org Chem 2018; 14:1769-1777. [PMID: 30112082 PMCID: PMC6071684 DOI: 10.3762/bjoc.14.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
Quorum sensing (QS) is a cell–cell communication mechanism that enables bacteria to assess their population density and alter their behavior upon reaching high cell number. Many bacterial pathogens utilize QS to initiate an attack on their host, thus QS has attracted significant attention as a potential antivirulence alternative to traditional antibiotics. Streptococcus pneumoniae, a notorious human pathogen responsible for a variety of acute and chronic infections, utilizes the competence regulon and its associated signaling peptide, the competence stimulating peptide (CSP), to acquire antibiotic resistance and establish an infection. In this work, we sought to define the binding pockets within the ComD1 receptor used for binding the hydrophobic side-chain residues in CSP1 through the introduction of highly-conservative point mutations within the peptide. Optimization of these binding interactions could lead to the development of highly potent CSP-based QS modulators while the inclusion of non-natural amino acids within the CSP sequence would confer resistance to protease degradation, a requirement for drug candidates.
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Affiliation(s)
- Bimal Koirala
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada, 89557, United States
| | - Robert A Hillman
- Department of Chemistry, Moravian College, 1200 Main Street, Bethlehem, Pennsylvania, 18018, United States
| | - Erin K Tiwold
- Department of Chemistry, Moravian College, 1200 Main Street, Bethlehem, Pennsylvania, 18018, United States
| | - Michael A Bertucci
- Department of Chemistry, Moravian College, 1200 Main Street, Bethlehem, Pennsylvania, 18018, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada, 89557, United States
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219
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Righi V, Constantinou C, Kesarwani M, Rahme LG, Tzika AA. Effects of a small, volatile bacterial molecule on Pseudomonas aeruginosa bacteria using whole cell high-resolution magic angle spinning nuclear magnetic resonance spectroscopy and genomics. Int J Mol Med 2018; 42:2129-2136. [PMID: 30015850 PMCID: PMC6108874 DOI: 10.3892/ijmm.2018.3760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/19/2015] [Indexed: 01/07/2023] Open
Abstract
In the present study, high-resolution magic-angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy was applied to live Pseudomonas aeruginosa (PA) bacterial cells to determine the metabolome of this opportunistic Gram-negative human pathogen, and in particular, its response to the volatile aromatic low molecular weight signaling molecule, 2-aminoacetophenone (2-AA). Multi-dimensional HRMAS NMR is a promising method which may be used to determine the in vivo metabolome of live intact bacterial cells; 2-AA is produced by PA and triggers the emergence of phenotypes that promote chronic infection phenotypes in in vitro and in vivo (animal) models. In the present study, we applied one-dimensional and two-dimensional proton (1H) HRMAS NMR to PA cells which were grown with or without 2-AA in order to examine the associations between metabolites and cellular processes in response to 2-AA. We also compared whole-genome transcriptome profiles of PA cells grown with or without 2-AA and found that 2-AA promoted profound metabolic changes in the PA cells. By comparing the whole-genome transcriptome profiles and metabolomic analysis, we demonstrated that 2-AA profoundly reprogramed the gene expression and metabolic profiles of the cells. Our in vivo1H HRMAS NMR spectroscopy may prove to be a helpful tool in the validation of gene functions, the study of pathogenic mechanisms, the classification of microbial strains into functional/clinical groups and the testing of anti-bacterial agents.
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Affiliation(s)
- Valeria Righi
- NMR Surgical Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Harvard Medical School, Boston, MA 02114, USA
| | - Caterina Constantinou
- NMR Surgical Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Harvard Medical School, Boston, MA 02114, USA
| | - Meenu Kesarwani
- Molecular Surgery Laboratory, Department of Surgery, Microbiology and Immunobiology, Harvard Medical School and Molecular Surgery Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Boston, MA 02114, USA
| | - Laurence G Rahme
- Molecular Surgery Laboratory, Department of Surgery, Microbiology and Immunobiology, Harvard Medical School and Molecular Surgery Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Boston, MA 02114, USA
| | - A Aria Tzika
- NMR Surgical Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Harvard Medical School, Boston, MA 02114, USA
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220
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Examining c-di-GMP and possible quorum sensing regulation in Pseudomonas fluorescens SBW25: links between intra- and inter-cellular regulation benefits community cooperative activities such as biofilm formation. UKRAINIAN BIOCHEMICAL JOURNAL 2018. [DOI: 10.15407/ubj90.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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221
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Characterization of a Two-Component System Transcriptional Regulator, LtdR, That Impacts Group B Streptococcal Colonization and Disease. Infect Immun 2018; 86:IAI.00822-17. [PMID: 29685987 DOI: 10.1128/iai.00822-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/18/2018] [Indexed: 12/29/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) is often a commensal bacterium that colonizes healthy adults asymptomatically and is a frequent inhabitant of the vaginal tract in women. However, in immunocompromised individuals, particularly the newborn, GBS may transition to an invasive pathogen and cause serious disease. Despite the use of the currently recommended intrapartum antibiotic prophylaxis for GBS-positive mothers, GBS remains a leading cause of neonatal septicemia and meningitis. To adapt to the various host environments encountered during its disease cycle, GBS possesses multiple two-component regulatory systems (TCSs). Here we investigated the contribution of a transcriptional regulator containing a LytTR domain, LtdR, to GBS pathogenesis. Disruption of the ltdR gene in the GBS chromosome resulted in a significant increase in bacterial invasion into human cerebral microvascular endothelial cells (hCMEC) in vitro as well as the greater penetration of the blood-brain barrier (BBB) and the development of meningitis in vivo Correspondingly, infection of hCMEC with the ΔltdR mutant resulted in increased secretion of the proinflammatory cytokines interleukin-8 (IL-8), CXCL-1, and IL-6. Further, using a mouse model of GBS vaginal colonization, we observed that the ΔltdR mutant was cleared more readily from the vaginal tract and also that infection with the ΔltdR mutant resulted in increased cytokine production from human vaginal epithelial cells. RNA sequencing revealed global transcriptional differences between the ΔltdR mutant and the parental wild-type GBS strain. These results suggest that LtdR regulates many bacterial processes that can influence GBS-host interactions to promote both bacterial persistence and disease progression.
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222
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Mukkayyan N, Sharan D, Ajitkumar P. A Symmetric Molecule Produced by Mycobacteria Generates Cell-Length Asymmetry during Cell-Division and Thereby Cell-Length Heterogeneity. ACS Chem Biol 2018; 13:1447-1454. [PMID: 29757604 DOI: 10.1021/acschembio.8b00080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Diadenosine polyphosphates, Ap(2-7)A, which contain two adenosines in a 5',5' linkage through phosphodiester bonds involving 2-7 phosphates, regulate diverse cellular functions in all organisms, from bacteria to humans, under normal and stress conditions. We had earlier reported consistent occurrence of asymmetric constriction during division (ACD) in 20-30% of dividing mycobacterial cells in culture, irrespective of different growth media, implying exogenous action of some factor of mycobacterial origin. Consistent with this premise, concentrated culture supernatant (CCS), but not the equivalent volume-wise concentrated unused medium, dramatically enhanced the ACD proportion to 70-90%. Mass spectrometry and biochemical analyses of the bioactive fraction from CCS revealed the ACD-effecting factor to be Ap6A. Synthetic Ap6A showed a mass spectrometry profile, biochemical characteristics, and bioactivity identical to native Ap6A in the CCS. Thus, the present work reveals a novel role for Ap6A in generating cell-length asymmetry during mycobacterial cell-division and thereby cell-length heterogeneity in the population.
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Affiliation(s)
- Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
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223
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Sugita T, Okada M, Nakashima Y, Tian T, Abe I. A Tryptophan Prenyltransferase with Broad Substrate Tolerance from Bacillus subtilis
subsp. natto. Chembiochem 2018; 19:1396-1399. [DOI: 10.1002/cbic.201800174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Tomotoshi Sugita
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Present address: Department of Material and Life Chemistry; Kanagawa University; Yokohama 221-8686 Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tian Tian
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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224
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Culler HF, Couto SCF, Higa JS, Ruiz RM, Yang MJ, Bueris V, Franzolin MR, Sircili MP. Role of SdiA on Biofilm Formation by Atypical Enteropathogenic Escherichia coli. Genes (Basel) 2018; 9:genes9050253. [PMID: 29762495 PMCID: PMC5977193 DOI: 10.3390/genes9050253] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 01/11/2023] Open
Abstract
Atypical enteropathogenic Escherichia coli are capable to form biofilm on biotic and abiotic surfaces, regardless of the adherence pattern displayed. Several E. coli mechanisms are regulated by Quorum sensing (QS), including virulence factors and biofilm formation. Quorum sensing is a signaling system that confers bacteria with the ability to respond to chemical molecules known as autoinducers. Suppressor of division inhibitor (SdiA) is a QS receptor present in atypical enteropathogenic E.coli (aEPEC) that detects acyl homoserine lactone (AHL) type autoinducers. However, these bacteria do not encode an AHL synthase, but they are capable of sensing AHL molecules produced by other species, establishing an inter-species bacterial communication. In this study, we performed experiments to evaluate pellicle, ring-like structure and biofilm formation on wild type, sdiA mutants and complemented strains. We also evaluated the transcription of genes involved in different stages of biofilm formation, such as bcsA, csgA, csgD, fliC and fimA. The sdiA mutants were capable of forming thicker biofilm structures and showed increased motility when compared to wild type and complemented strains. Moreover, they also showed denser pellicles and ring-like structures. Quantitative real-time PCR (qRT-PCR) analysis demonstrated increased csgA, csgD and fliC transcription on mutant strains. Biofilm formation, as well as csgD, csgA and fimA transcription decreased on wild type strains by the addition of AHL. These results indicate that SdiA participates on the regulation of these phenotypes in aEPEC and that AHL addition enhances the repressor effect of this receptor on the transcription of biofilm and motility related genes.
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Affiliation(s)
- Hebert F Culler
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Samuel C F Couto
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Juliana S Higa
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Renato M Ruiz
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Min J Yang
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Vanessa Bueris
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Marcia R Franzolin
- Laboratory of Bacteriology, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Marcelo P Sircili
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
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225
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Steinberg N, Rosenberg G, Keren-Paz A, Kolodkin-Gal I. Collective Vortex-Like Movement of Bacillus subtilis Facilitates the Generation of Floating Biofilms. Front Microbiol 2018; 9:590. [PMID: 29651280 PMCID: PMC5884953 DOI: 10.3389/fmicb.2018.00590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/14/2018] [Indexed: 12/29/2022] Open
Abstract
Bacteria in nature are usually found in complex multicellular structures, called biofilms. One common form of a biofilm is pellicle—a floating mat of bacteria formed in the water-air interphase. So far, our knowledge on the basic mechanisms underlying the formation of biofilms at air-liquid interfaces is not complete. In particular, the co-occurrence of motile cells and extracellular matrix producers has not been studied. In addition, the potential involvement of chemical communication in pellicle formation remained largely undefined. Our results indicate that vortex-like collective motility by aggregates of motile cells and EPS producers accelerate the formation of floating biofilms. Successful aggregation and migration to the water-air interphase depend on the chemical communication signal autoinducer 2 (AI-2). This ability of bacteria to form a biofilm in a preferable niche ahead of their potential rivals would provide a fitness advantage in the context of inter-species competition.
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Affiliation(s)
- Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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226
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van Vliet S, Dal Co A, Winkler AR, Spriewald S, Stecher B, Ackermann M. Spatially Correlated Gene Expression in Bacterial Groups: The Role of Lineage History, Spatial Gradients, and Cell-Cell Interactions. Cell Syst 2018; 6:496-507.e6. [PMID: 29655705 DOI: 10.1016/j.cels.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/24/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Gene expression levels in clonal bacterial groups have been found to be spatially correlated. These correlations can partly be explained by the shared lineage history of nearby cells, although they could also arise from local cell-cell interactions. Here, we present a quantitative framework that allows us to disentangle the contributions of lineage history, long-range spatial gradients, and local cell-cell interactions to spatial correlations in gene expression. We study pathways involved in toxin production, SOS stress response, and metabolism in Escherichia coli microcolonies and find for all pathways that shared lineage history is the main cause of spatial correlations in gene expression levels. However, long-range spatial gradients and local cell-cell interactions also contributed to spatial correlations in SOS response, amino acid biosynthesis, and overall metabolic activity. Together, our data show that the phenotype of a cell is influenced by its lineage history and population context, raising the question of whether bacteria can arrange their activities in space to perform functions they cannot achieve alone.
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Affiliation(s)
- Simon van Vliet
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Dübendorf, Switzerland.
| | - Alma Dal Co
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Dübendorf, Switzerland
| | - Annina R Winkler
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Dübendorf, Switzerland
| | | | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Dübendorf, Switzerland
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227
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Horvath V, Epstein IR. Pulse-coupled Belousov-Zhabotinsky oscillators with frequency modulation. CHAOS (WOODBURY, N.Y.) 2018; 28:045108. [PMID: 31906644 DOI: 10.1063/1.5021585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inhibitory perturbations to the ferroin-catalyzed Belousov-Zhabotinsky (BZ) chemical oscillator operated in a continuously fed stirred tank reactor cause long term changes to the limit cycle: the lengths of the cycles subsequent to the perturbation are longer than that of the unperturbed cycle, and the unperturbed limit cycle is recovered only after several cycles. The frequency of the BZ reaction strongly depends on the acid concentration of the medium. By adding strong acid or base to the perturbing solutions, the magnitude and the direction of the frequency changes concomitant to excitatory or inhibitory perturbations can be controlled independently of the coupling strength. The dynamics of two BZ oscillators coupled through perturbations carrying a coupling agent (activator or inhibitor) and a frequency modulator (strong acid or base) was explored using a numerical model of the system. Here, we report new complex temporal patterns: higher order, partially synchronized modes that develop when inhibitory coupling is combined with positive frequency modulation (FM), and complex bursting patterns when excitatory coupling is combined with negative FM. The role of time delay between the peak and perturbation (the analog of synaptic delays in networks of neurons) has also been studied. The complex patterns found under inhibitory coupling and positive FM vanish when the delay is significant, whereas a sufficiently long time delay is required for the complex temporal dynamics to occur when coupling is excitatory and FM is negative.
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Affiliation(s)
- Viktor Horvath
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Irving R Epstein
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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228
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Baquero F. Transmission as a basic process in microbial biology. Lwoff Award Prize Lecture. FEMS Microbiol Rev 2018; 41:816-827. [PMID: 29136422 DOI: 10.1093/femsre/fux042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/24/2017] [Indexed: 12/12/2022] Open
Abstract
Transmission is a basic process in biology and evolution, as it communicates different biological entities within and across hierarchical levels (from genes to holobionts) both in time and space. Vertical descent, replication, is transmission of information across generations (in the time dimension), and horizontal descent is transmission of information across compartments (in the space dimension). Transmission is essentially a communication process that can be studied by analogy of the classic information theory, based on 'emitters', 'messages' and 'receivers'. The analogy can be easily extended to the triad 'emigration', 'migration' and 'immigration'. A number of causes (forces) determine the emission, and another set of causes (energies) assures the reception. The message in fact is essentially constituted by 'meaningful' biological entities. A DNA sequence, a cell and a population have a semiotic dimension, are 'signs' that are eventually recognized (decoded) and integrated by receiver biological entities. In cis-acting or unenclosed transmission, the emitters and receivers correspond to separated entities of the same hierarchical level; in trans-acting or embedded transmission, the information flows between different, but frequently nested, hierarchical levels. The result (as in introgressive events) is constantly producing innovation and feeding natural selection, influencing also the evolution of transmission processes. This review is based on the concepts presented at the André Lwoff Award Lecture in the FEMS Microbiology Congress in Maastricht in 2015.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Division of Biology and Evolution of Microorganisms, Ramón y Cajal Institute for Health Research (IRYCIS), Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, de Colmenar km 9,100, 28034 Madrid, Spain
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229
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Reynoso Lara JE, Salgado-Zamora H, Bazin MA, Campos-Aldrete ME, Marchand P. Design and Synthesis of Imidazo[1,2-a
]pyridines with Carboxamide Group Substitution and In silico
Evaluation of their Interaction with a LuxR-type Quorum Sensing Receptor. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Juan Emmanuel Reynoso Lara
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; CDMX Mexico
| | - Héctor Salgado-Zamora
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; CDMX Mexico
| | - Marc-Antoine Bazin
- Département de Chimie Thérapeutique; EA1155 - IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités; Nantes France
| | - María Elena Campos-Aldrete
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; CDMX Mexico
| | - Pascal Marchand
- Département de Chimie Thérapeutique; EA1155 - IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités; Nantes France
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230
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Abstract
Surface-attached colonies of bacteria known as biofilms play a major role in the pathogenesis of device-related infections. Biofilm colonies are notorious for their resistance to suprainhibitory concentrations of antibiotics. Numerous studies have shown that subminimal inhibitory concentrations of some antibiotics can act as agonists of bacterial biofilm formation in vitro, a process that may have clinical relevance. This article reviews studies demonstrating that low-dose antibiotics induce bacterial biofilm formation. These studies have provided important information about the regulation of biofilm formation and the signaling pathways involved in global gene regulation in response to cell stressors. It is still unclear whether antibiotic-induced biofilm formation contributes to the inconsistent success of antimicrobial therapy for device infections.
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231
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Abstract
Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.
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232
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Spacapan M, Danevčič T, Mandic-Mulec I. ComX-Induced Exoproteases Degrade ComX in Bacillus subtilis PS-216. Front Microbiol 2018; 9:105. [PMID: 29449835 PMCID: PMC5799266 DOI: 10.3389/fmicb.2018.00105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Gram-positive bacteria use peptides as auto-inducing (AI) signals to regulate the production of extracellular enzymes (e.g., proteases). ComX is an AI peptide, mostly known for its role in the regulation of bacterial competence and surfactant production in Bacillus subtilis. These two traits are regulated accordingly to the bacterial population size, thus classifying ComX as a quorum sensing signal. ComX also indirectly regulates exoprotease production through the intermediate transcriptional regulator DegQ. We here use this peptide-based AI system (the ComQXPA system) as a model to address exoprotease regulation by ComX in biofilms. We also investigate the potential of ComX regulated proteases to degrade the ComX AI peptide. Results indicate that ComX indeed induces the expression of aprE, the gene for the major serine protease subtilisin, and stimulates overall exoprotease production in biofilms of B. subtilis PS-216 and several other B. subtilis soil isolates. We also provide evidence that these exoproteases can degrade ComX. The ComX biological activity decay is reduced in the spent media of floating biofilms with low proteolytic activity found in the comP and degQ mutants. ComX biological activity decay can be restored by the addition of subtilisin to such media. In contrast, inhibition of metalloproteases by EDTA reduces ComX biological activity decay. This suggests that both serine and metalloproteases, which are induced by ComX, are ultimately capable of degrading this signaling peptide. This work brings novel information on regulation of exoproteases in B. subtilis floating biofilms and reveals that these proteolytic enzymes degrade the AI signaling peptide ComX, which is also a major determinant of their expression in biofilms.
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Affiliation(s)
- Mihael Spacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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233
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Zheng Q, Wang Y, Xie R, Lang AS, Liu Y, Lu J, Zhang X, Sun J, Suttle CA, Jiao N. Dynamics of Heterotrophic Bacterial Assemblages within Synechococcus Cultures. Appl Environ Microbiol 2018; 84:e01517-17. [PMID: 29150500 PMCID: PMC5772231 DOI: 10.1128/aem.01517-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023] Open
Abstract
Interactions between photoautotrophic and heterotrophic microorganisms are central to the marine microbial ecosystem. Lab cultures of one of the dominant marine photoautotrophs, Synechococcus, have historically been difficult to render axenic, presumably because these bacteria depend upon other organisms to grow under these conditions. These tight associations between Synechococcus and heterotrophic bacteria represent a good relevant system to study interspecies interactions. Ten individual Synechococcus strains, isolated from eutrophic and oligotrophic waters, were chosen for investigation. Four to six dominant associated heterotrophic bacteria were detected in the liquid cultures of each Synechococcus isolate, comprising members of the Cytophaga-Flavobacteria-Bacteroides (CFB) group (mainly from Flavobacteriales and Cytophagales), Alphaproteobacteria (mainly from the Roseobacter clade), Gammaproteobacteria (mainly from the Alteromonadales and Pseudomonadales), and Actinobacteria The presence of the CFB group, Gammaproteobacteria, and Actinobacteria showed clear geographic patterns related to the isolation environments of the Synechococcus bacteria. An investigation of the population dynamics within a growing culture (XM-24) of one of the isolates, including an evaluation of the proportions of cells that were free-living versus aggregated/attached, revealed interesting patterns for different bacterial groups. In Synechococcus sp. strain XM-24 culture, flavobacteria, which was the most abundant group throughout the culture period, tended to be aggregated or attached to the Synechococcus cells, whereas the actinobacteria demonstrated a free-living lifestyle, and roseobacters displayed different patterns depending on the culture growth phase. Factors contributing to these succession patterns for the heterotrophs likely include interactions among the culture community members, their relative abilities to utilize different compounds produced by Synechococcus cells and changes in the compounds released as culture growth proceeds, and their responses to other changes in the environmental conditions throughout the culture period.IMPORTANCE Marine microbes exist within an interactive ecological network, and studying their interactions is an important part of understanding their roles in global biogeochemical cycling and the determinants of microbial diversity. In this study, the dynamic relationships between Synechococcus spp. and their associated heterotrophic bacteria were investigated. Synechococcus-associated heterotrophic bacteria had similar geographic distribution patterns as their "host" and displayed different lifestyles (free-living versus attached/aggregated) according to the Synechococcus culture growth phases. Combined organic carbon composition and bacterial lifestyle data indicated a potential for succession in carbon utilization patterns by the dominant associated heterotrophic bacteria. Comprehending the interactions between photoautotrophs and heterotrophs and the patterns of organic carbon excretion and utilization is critical to understanding their roles in oceanic biogeochemical cycling.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Jiayao Lu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
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234
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Hazan O, Silverman J, Sisma-Ventura G, Ozer T, Gertman I, Shoham-Frider E, Kress N, Rahav E. Mesopelagic Prokaryotes Alter Surface Phytoplankton Production during Simulated Deep Mixing Experiments in Eastern Mediterranean Sea Waters. FRONTIERS IN MARINE SCIENCE 2018. [PMID: 0 DOI: 10.3389/fmars.2018.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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235
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David S, Mandabi A, Uzi S, Aharoni A, Meijler MM. Mining Plants for Bacterial Quorum Sensing Modulators. ACS Chem Biol 2018; 13:247-252. [PMID: 29215859 DOI: 10.1021/acschembio.7b00859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The bacterial plant pathogen Agrobacterium tumefaciens uses quorum sensing (QS) in order to regulate the transfer of DNA into the host plant genome, and this results in the induction of crown gall tumors. The deleterious results of these infections are widespread and affect many species of fruit and crops. In order to further our understanding of this process and to provide potential solutions, we evaluated a library of 3800 natural products from plant sources and identified potent compounds that are able to strongly modulate plant-bacterial interactions.
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Affiliation(s)
- Shimrit David
- Department
of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva, Israel
| | - Aviad Mandabi
- Department
of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva, Israel
| | - Shaked Uzi
- Department
of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva, Israel
| | - Asaph Aharoni
- Department
of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michael M. Meijler
- Department
of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva, Israel
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236
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Song XD, Liu CJ, Huang SH, Li XR, Yang E, Luo YY. Cloning, expression and characterization of two S-ribosylhomocysteine lyases from Lactobacillus plantarum YM-4-3: Implication of conserved and divergent roles in quorum sensing. Protein Expr Purif 2018; 145:32-38. [PMID: 29305177 DOI: 10.1016/j.pep.2017.12.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 11/03/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
Abstract
Quorum sensing (QS) is a means of cell-to-cell communication that regulates, via small signalling molecules, expression of a series of genes and controls multicellular behaviour in many bacterial species. The enzyme S-ribosylhomocysteine lyase (LuxS) transforms S-ribosylhomocysteine (SRH) into 4, 5-dihydroxy-2, 3-pentanedione (DPD), the precursor of the interspecies QS signalling molecule autoinducer-2 (AI-2). In this study, two LuxS-coding genes, luxS1 and luxS2, with 70% sequence identity were isolated from Lactobacillus plantarum YM-4-3, and overexpressed in Escherichia coli BL21 (DE3), and the protein products were purified successfully. After incubation of LuxS1 or LuxS2 with SRH, the reaction products were able to induce Vibrio harveyi BB170 bioluminescence, clearly demonstrating that both LuxS1 and LuxS2 synthesize AI-2 from SRH in vitro. Ellman's assay results revealed optimal temperatures for LuxS1 and LuxS2 of 45 and 37 °C, respectively, and their activities were stimulated or inhibited by several metal ions and chemical reagents. In addition, enzyme kinetics data showed that Km, Vmax and Kcat value of LuxS1 for the substrate (SRH) were higher than that of LuxS2. These results suggest that LuxS1 and LuxS2 mediate QS in a temperature-dependent manner and may play conserved roles in AI-2 synthesis but exhibit different activities in response to external environmental stress. To our knowledge, this paper is the first report of two luxS genes present in one bacterial genome and the subsequent comparative elucidation of their functions in AI-2 production. Collectively, our study provides a solid basis for future research concerning the AI-2/LuxS QS system in L. plantarum YM-4-3.
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Affiliation(s)
- Xiao-Dong Song
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Chen-Jian Liu
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Shi-Hao Huang
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Xiao-Ran Li
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - En Yang
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Yi-Yong Luo
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China.
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237
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Sheng H, Wang F, Gu C, Stedtfeld R, Bian Y, Liu G, Wu W, Jiang X. Sorption characteristics of N-acyl homserine lactones as signal molecules in natural soils based on the analysis of kinetics and isotherms. RSC Adv 2018; 8:9364-9374. [PMID: 35541870 PMCID: PMC9078661 DOI: 10.1039/c7ra10421a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/19/2018] [Indexed: 11/21/2022] Open
Abstract
Quorum sensing, the communication between microorganisms, is mediated by specific diffusible signal molecules. Adsorption is an important process that influences the transport, transformation and bioavailability of N-acyl homoserine lactone (AHL) in complex natural environments such as soil. To examine the adsorption characteristics of N-hexanoyl, N-octanoyl, N-decanoyl and N-dodecanoyl homoserine lactones in soil, equilibrium and kinetic experiments were conducted in two types of soils (oxisol and alfisol) and monitored using Fourier-transform infrared spectroscopy (FTIR). A pseudo-second-order equation accurately described the sorption kinetics of AHLs in the two soils (R2 ≥ 0.97, NSD ≤ 21.25%). The AHL sorption reached equilibrium within 24 h and 12 h for oxisol and alfisol, respectively. The sorption kinetics of AHLs adsorbed on the soils were fitted to the Boyd model, suggesting that film diffusion was the rate-limiting process. Partition played a more vital role than surface adsorption in the AHL adsorption process. The adsorption isotherms of AHLs could be described by the Langmuir and Freundlich equation (R2 ≥ 0.98), indicating that the sorption process involved monolayer sorption and heterogeneous energetic distribution of active sites on the surfaces of the soils. The thermodynamic parameter, Gibbs free energy (ΔG), and a dimensionless parameter showed that the sorption of AHLs was mainly dominated by physical adsorption. Additionally, according to the FTIR data, the electrostatic forces and hydrogen bonding possibly influenced the adsorption of AHLs on the above mentioned two soils. The sorption characteristics of AHLs in soils correlated well with the molecular structure, solubility speciation and log P (n-octanol/water partition coefficient) of AHLs. Sorption characteristics of N-acyl homoserine lactones (signal molecules) in natural soils.![]()
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Affiliation(s)
- Hongjie Sheng
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Robert Stedtfeld
- Department of Civil and Environmental Engineering
- Michigan State University
- East Lansing
- USA
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Guangxia Liu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Wei Wu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
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238
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Mariam J, Anand R. Fluorescence Quenching Studies of γ-Butyrolactone-Binding Protein (CprB) from Streptomyces coelicolor A3(2). Methods Mol Biol 2018; 1673:131-143. [PMID: 29130170 DOI: 10.1007/978-1-4939-7309-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence spectroscopy is an important analytical tool which is widely employed to study biological systems. This technique can be applied to qualitatively and quantitatively probe protein-ligand interactions primarily because of its sensitivity, selectivity, nondestructive and rapid form of analysis. In this chapter we describe the utility of this technique to establish a label-free, universal screening protocol for putative γ-butyrolactone (GBL) receptors by exploiting the intrinsic fluorescence of a highly conserved tryptophan residue that constitutes the hydrophobic pocket for GBL binding, a unique feature possessed by this family of receptors. Here we demonstrate this technique using a combination of steady-state fluorescence quenching methods and fluorescence lifetime decay kinetics using CprB protein from Streptomyces coelicolor A3(2) as a model system. Interaction data between CprB and two chemically synthesized GBLs involved in quorum sensing, Cp1 and Cp2, have been used as example.
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Affiliation(s)
- Jessy Mariam
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India.
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239
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Shin D, Nagarajan R. Enzymatic Assays to Investigate Acyl-Homoserine Lactone Autoinducer Synthases. Methods Mol Biol 2018; 1673:161-176. [PMID: 29130172 PMCID: PMC5766357 DOI: 10.1007/978-1-4939-7309-5_13] [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: 06/07/2023]
Abstract
Bacteria use chemical molecules called autoinducers as votes to poll their numerical strength in a colony. This polling mechanism, commonly referred to as quorum sensing, enables bacteria to build a social network and provide a collective response for fighting off common threats. In Gram-negative bacteria, AHL synthases synthesize acyl-homoserine lactone (AHL) autoinducers to turn on the expression of several virulent genes including biofilm formation, protease secretion, and toxin production. Therefore, inhibiting AHL signal synthase would limit quorum sensing and virulence. In this chapter, we describe four enzymatic methods that could be adopted to investigate a broad array of AHL synthases. The enzymatic assays described here should accelerate our mechanistic understanding of quorum-sensing signal synthesis that could pave the way for discovery of potent antivirulence compounds.
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Affiliation(s)
- Daniel Shin
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Rajesh Nagarajan
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA.
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240
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John M, Trzcinski AP, Zhou Y, Ng WJ. Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose. Sci Rep 2017; 7:18006. [PMID: 29269771 PMCID: PMC5740137 DOI: 10.1038/s41598-017-18198-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/05/2017] [Indexed: 01/15/2023] Open
Abstract
The anaerobic digestion process is a multi - step reaction dependent on concerted activities such as exchange of metabolites among physiologically different microbial communities. This study investigated the impact of iron oxide nanoparticles on the anaerobic sludge microbiota. It was shown there were three distinct microbial phases following addition of the nanoparticles: microbial stress and cell death of approximately one log order of magnitude, followed by microbial rewiring, and recovery. Furthermore, it was noted that cellular stress led to the establishment of intercellular nanotubes within the microbial biomass. Intercellular nanotube - mediated communication among genetically engineered microorganisms and ad hoc assembled co - cultures have been previously reported. This study presents evidence of intercellular nanotube formation within an environmental sample - i.e., anaerobic sludge microbiota subjected to stress. Our observations suggested a mode of microbial communication in the anaerobic digestion process not previously explored and which may have implications on bioreactor design and microbial functions.
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Affiliation(s)
- Martina John
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, #06-08, Singapore, 637141, Singapore.
- Division of Environmental and Water Resources, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Antoine Prandota Trzcinski
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, #06-08, Singapore, 637141, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, #06-08, Singapore, 637141, Singapore
| | - Wun Jern Ng
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, #06-08, Singapore, 637141, Singapore.
- Division of Environmental and Water Resources, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
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241
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Chiu L, Bazin T, Truchetet ME, Schaeverbeke T, Delhaes L, Pradeu T. Protective Microbiota: From Localized to Long-Reaching Co-Immunity. Front Immunol 2017; 8:1678. [PMID: 29270167 PMCID: PMC5725472 DOI: 10.3389/fimmu.2017.01678] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota.
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Affiliation(s)
- Lynn Chiu
- University of Bordeaux, CNRS, ImmunoConcept, UMR 5164, Bordeaux, France
| | - Thomas Bazin
- University of Bordeaux, INRA, Mycoplasmal and Chlamydial Infections in Humans, EA 3671, Bordeaux, France.,Department of Hepato-Gastroenterology, Bordeaux Hospital University Center, Pessac, France
| | | | - Thierry Schaeverbeke
- University of Bordeaux, INRA, Mycoplasmal and Chlamydial Infections in Humans, EA 3671, Bordeaux, France.,Department of Rheumatology, Bordeaux Hospital University Center, Bordeaux, France
| | - Laurence Delhaes
- Department of Parasitology and Mycology, Bordeaux Hospital University Center, Bordeaux, France.,University of Bordeaux, INSERM, Cardio-Thoracic Research Centre of Bordeaux, U1045, Bordeaux, France
| | - Thomas Pradeu
- University of Bordeaux, CNRS, ImmunoConcept, UMR 5164, Bordeaux, France
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242
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Quorum Sensing in Burkholderia pseudomallei and Other Burkholderia species. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0127-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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243
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Thanh Nguyen H, Goycoolea FM. Chitosan/Cyclodextrin/TPP Nanoparticles Loaded with Quercetin as Novel Bacterial Quorum Sensing Inhibitors. Molecules 2017; 22:E1975. [PMID: 29140285 PMCID: PMC6150374 DOI: 10.3390/molecules22111975] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
The widespread emergence of antibiotic-resistant bacteria has highlighted the urgent need of alternative therapeutic approaches for human and animal health. Targeting virulence factors that are controlled by bacterial quorum sensing (QS), seems a promising approach. The aims of this study were to generate novel nanoparticles (NPs) composed of chitosan (CS), sulfo-butyl-ether-β-cyclodextrin (Captisol®) and/or pentasodium tripolyphosphate using ionotropic gelation technique, and to evaluate their potential capacity to arrest QS in bacteria. The resulting NPs were in the size range of 250-400 nm with CS70/5 and 330-600 nm with CS70/20, had low polydispersity index (<0.25) and highly positive zeta potential ranging from ζ ~+31 to +40 mV. Quercetin, a hydrophobic model flavonoid, could be incorporated proportionally with increasing amounts of Captisol® in the NPs formualtion, without altering significantly its physicochemical properties. Elemental analysis and FTIR studies revealed that Captisol® and quercetin were effectively integrated into the NPs. These NPs were stable in M9 bacterial medium for 7 h at 37 °C. Further, NPs containing Captisol® seem to prolong the release of associated drug. Bioassays against an E. coli Top 10 QS biosensor revealed that CS70/5 NPs could inhibit QS up to 61.12%, while CS70/20 NPs exhibited high antibacterial effects up to 88.32%. These results suggested that the interaction between NPs and the bacterial membrane could enhance either anti-QS or anti-bacterial activities.
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Affiliation(s)
- Hao Thanh Nguyen
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossgarten 3, 48149 Münster, Germany.
- Department of Biology, Faculty of Biotechnology, Vietnam National University of Agriculture, Ngo Xuan Quang Street, Hanoi 100000, Vietnam.
| | - Francisco M Goycoolea
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossgarten 3, 48149 Münster, Germany.
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK.
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244
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Rosenthal K, Oehling V, Dusny C, Schmid A. Beyond the bulk: disclosing the life of single microbial cells. FEMS Microbiol Rev 2017; 41:751-780. [PMID: 29029257 PMCID: PMC5812503 DOI: 10.1093/femsre/fux044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 09/08/2017] [Indexed: 01/08/2023] Open
Abstract
Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.
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Affiliation(s)
- Katrin Rosenthal
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Verena Oehling
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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245
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Abstract
Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. However, the increasing frequency of antibiotic-resistant infections clearly demonstrates that new antibiotics are critical for modern medicine. Because combinatorial approaches have not yielded effective drugs, we propose that the development of new antibiotics around proven natural scaffolds is the best short-term solution to the rising crisis of antibiotic resistance. We analyze herein synthetic approaches aiming to reengineer natural products into potent antibiotics. Furthermore, we discuss approaches in modulating quorum sensing and biofilm formation as a nonlethal method, as well as narrow-spectrum pathogen-specific antibiotics, which are of interest given new insights into the implications of disrupting the microbiome.
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Affiliation(s)
- Sean E. Rossiter
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Madison H. Fletcher
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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246
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Chromatography of Quorum Sensing Peptides: An Important Functional Class of the Bacterial Peptidome. Chromatographia 2017. [DOI: 10.1007/s10337-017-3411-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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247
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Heidari A, Noshiranzadeh N, Haghi F, Bikas R. Inhibition of quorum sensing related virulence factors of Pseudomonas aeruginosa by pyridoxal lactohydrazone. Microb Pathog 2017; 112:103-110. [PMID: 28939255 DOI: 10.1016/j.micpath.2017.09.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 01/03/2023]
Abstract
Pseudomonas aeruginosa quorum sensing (QS) system is a cell to cell signaling mechanism that regulates virulence factors and pathogenicity. Therefore, the QS system in P. aeruginosa may be an important target for pharmacological intervention. The present study aimed to investigate the effects of sub-MIC concentrations of (S,E)-2-hydroxy-N-(3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propane hydrazide (pyridoxal lactohydrazone) against P. aeruginosa QS related virulence factors. We investigated the effect of sub-MIC concentrations of chiral pyridoxal lactohydrazone, which formed by the reaction of chiral lactic acid hydrazide and pyridoxal (one form of Vitamin B6) as bioactive reagents, on virulence factors. Treated PAO1 cultures in the presence of tested compound at 1/4 and 1/16 MIC (32 and 8 μg/mL respectively) showed significant inhibition of virulence factors including motility, alginate and pyocyanin production and susceptibility to H2O2 (P < 0.001). Also, the pyridoxal lactohydrazone showed anti-QS activity in Chromobacterium violaceum CV026 biosensor bioassay. Because of quorum sensing is a promising target for anti-virulence therapy and also important role of LasR regulatory protein in the initiation of P. aeruginosa QS system, we carried out molecular docking for understanding the interactions of pyridoxal lactohydrazone with the LasR receptor. The results of docking study suggested that the pyridoxal lactohydrazone has potential to inhibit the LasR protein. The results indicated that sub-MIC concentrations of this compound exhibited inhibitory effect on P. aeruginosa QS related virulence factors.
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Affiliation(s)
- Azam Heidari
- Department of Chemistry, Faculty of Sciences, University of Zanjan, 45371-38791, Zanjan, IR, Iran
| | - Nader Noshiranzadeh
- Department of Chemistry, Faculty of Sciences, University of Zanjan, 45371-38791, Zanjan, IR, Iran.
| | - Fakhri Haghi
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, 45139-56111, Zanjan, IR, Iran.
| | - Rahman Bikas
- Department of Chemistry, Faculty of Sciences, University of Zanjan, 45371-38791, Zanjan, IR, Iran
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248
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Affiliation(s)
- Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Birte Abt
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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249
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Saccharomonopyrones A-C, New α-Pyrones from a Marine Sediment-Derived Bacterium Saccharomonospora sp. CNQ-490. Mar Drugs 2017; 15:md15080239. [PMID: 28771166 PMCID: PMC5577594 DOI: 10.3390/md15080239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022] Open
Abstract
Intensive study of the organic extract of the marine-derived bacterium Saccharomonospora sp. CNQ-490 has yielded three new α-pyrones, saccharomonopyrones A-C (1-3). The chemical structures of these compounds were assigned from the interpretation of 1D, 2D NMR and mass spectrometry data. Saccharomonopyrone A (1) is the first α-pyrone microbial natural product bearing the ethyl-butyl ether chain in the molecule, while saccharomonopyrones B and C possess unusual 3-methyl and a 6-alkyl side-chain within a 3,4,5,6-tetrasubstituted α-pyrone moiety. Saccharomonopyrone A exhibited weak antioxidant activity using a cation radical scavenging activity assay with an IC50 value of 140 μM.
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250
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The living organism: Strengthening the basis. Biosystems 2017; 158:10-16. [DOI: 10.1016/j.biosystems.2017.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 01/07/2023]
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